Entries |
Document | Title | Date |
20080220977 | Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles - Embodiments of this invention include application of new inferential methods to analysis of complex biological information, including gene networks. New methods include modifications of Bayesian inferential methods and application of those methods to determining cause and effect relationships between expressed genes, and in some embodiments, for determining upstream effectors of regulated genes. Additional modifications of Bayesian methods include use of time course data and use of gene disruption data to infer causal relationships between expressed genes. Other embodiments include the use of bootstrapping methods and determination of edge effects to more accurately provide network information between expressed genes. Information about gene networks can be stored in a memory device and can be transmitted to an output device, or can be transmitted to remote location. | 09-11-2008 |
20080220978 | Method of Identifying Agents that Inhibit Quorum Sensing Activity of Gamma-Proteobacteria - Screening assays that allow for the identification of agents that increase acyl homoserine lactone (AHL) acylase expression and/or AHL acylase activity in γ-proteobacteria such as | 09-11-2008 |
20080234135 | LIGAND IDENTIFICATION AND MATCHING SOFTWARE TOOLS - Using annotated structural descriptions and binding data for two, four or more input ligand molecules known to bind to a given protein target, a profile of the ligand molecules can be created by identifying patches of ligand molecules which have similar chemical and/or stereochemical descriptions, scored with the use of a weight dataset (e.g., substitution matrix). A database containing annotated molecular descriptions can be searched according to the profile to identify, for example, additional ligands that can bind to the protein target. Information such as the input ligands, the additional ligands, and literature related to these molecules, and modeling tools can be displayed in a user interface. | 09-25-2008 |
20080280768 | Reagents and Methods for Predicting Drug Resistance - The invention provides methods for prognosis, diagnosis, staging and determining disease progression in human cancer patients related to amplification levels of one or a plurality of genetic loci that are differentially amplified in chemotherapeutic drug resistant tumor cells. | 11-13-2008 |
20080280769 | SELECTIVE AND DUAL-ACTION P53/MDM2/MDM4 ANTAGONISTS - A fragment-based strategy, involving “multicomponent reaction chemistry” (MCR), can identify novel chemotypes that disrupt the p53/MDM2 or p53/MDM4 complex employs. This approach uses high resolution structural information to delineate the region of a first protein or a ligand that is nestled within the binding pocket of a second target protein. The identified region is imported into a database containing MCR scaffolds to generate a virtual library of compounds, which subsequently are docked into the binding pocket of the target protein. Results from docking then are used to select compounds for synthesis and screening. A complementary, NMR-based methodology allows for screening the ability of compounds, selected using MCR, to disrupt the p53/MDM2 or p53/MDM4 complex. | 11-13-2008 |
20080280770 | METHOD OF ISOLATING BIOLOGICALLY ACTIVE CHEMICAL COMPOUNDS FROM A CHEMICAL COMPOUND LIBRARY - A method of producing a chemical compound library comprises extracting at least one extract from at least one species of plant; processing at least one of the extract(s) to remove at least one type of chemical interference to produce a processed extract; chromatographically separating the processed extract into a plurality of chromatographic fractions, each containing an amount of chemical compounds; determining the amount of chemical compounds in at least one of the chromatographic fractions; and normalizing the chromatographic fractions in which the amounts were determined to produce normalized chromatographic fractions, each such fraction comprising from about 1 microgram to about 500 micrograms of each of from one to seven chemical compounds that were present in lower concentrations in the extract and that each have a log P of from about −1 to about 5 and a molecular weight less than about 1000 Daltons; thereby to produce a chemical compound library from at least one species of plant. | 11-13-2008 |
20090018024 | NANOGRID ROLLING CIRCLE DNA SEQUENCING - The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer. | 01-15-2009 |
20090054244 | Nucleic acid molecule encoding a novel estrogen receptor beta variant - This invention relates to an isolated nucleotide fragment of a novel estrogen receptor, in particular, a novel ERβ variant protein and isolated nucleic acid fragment comprising the coding regions of the genes encoding such variant proteins. Also provided are vectors, host cells, and methods for producing the novel ERβ variant protein. The invention further relates to method of obtaining such nucleotide fragment and the method of determining the presence of such ERβ variant protein in a sample. | 02-26-2009 |
20090118127 | Methods for Use in Human-Adapting Monoclonal Antibodies - Methods useful for human adapting non-human monoclonal antibodies are disclosed. The methods select candidate human antibody framework sequences from a database of human germline genes or human sequences with somatic mutations. | 05-07-2009 |
20090118128 | Preparation of templates for nucleic acid sequencing - The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise:
| 05-07-2009 |
20090137402 | Ditag genome scanning technology - The present invention provides for a method for analyzing large genomes using a process by where the genomic DNA is digested by a small base pair restriction enzyme. The fragments are then cloned and a unique ta-vector-tag is created. The tag-vector-tag fragments are purified and re-ligated to create a “ditag” library, which are then sequenced. In the final step, the sequenced ditags can be mapped back to the genome using software containing mapping algorithms and a unique ditag reference database to provide a method for scanning large portions of the genome in a reduced amount of time and cost. | 05-28-2009 |
20090137403 | METHODS FOR USE IN HUMAN-ADAPTING MONOCLONAL ANTIBODIES - Methods useful for human adapting non-human monoclonal antibodies are disclosed. The methods select candidate human antibody framework sequences from a human germline framework database. | 05-28-2009 |
20090253581 | High Throughput Detection of Molecular Markers Based on AFLP and High Throughput Sequencing - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers. | 10-08-2009 |
20090280992 | MULTI-WELL SYSTEM - A multi-well system is described which is comprised of a tray comprising a plurality of wells which may include thousands, tens of thousands or even hundreds of thousands of wells or more. Each of the wells has a unique address. The system includes a tray top comprised of a plurality of areas wherein each of the areas corresponds uniquely to each of the wells and includes a unique address. The system may include a second tray top also comprised of a plurality of areas with unique addresses which uniquely correspond to each of the wells. The areas on the tops have compounds bound to those areas which compounds bind to components present in the wells and are used to obtain specific material in each well for analysis. | 11-12-2009 |
20090286687 | Method and Compositions for Detection and Enumeration of Genetic Variations - Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently-labeled particles via flow cytometry. Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and employed for further experimentation. This approach can be used for the identification and quantification of rare mutations as well as to study variations in gene sequences or transcripts in specific populations or tissues. | 11-19-2009 |
20090305898 | Methods and Compositions for Identifying a Peptide Having an Intermolecular Interaction With a Target of Interest - This invention provides, in one embodiment, a recombinant virus or a recombinant virus library wherein each virus comprises a protein involved in viral attachment or infection, a polypeptide which differs by at least a single amino acid from another peptide or polypeptide in the library, and a modified cleavage site that is proximal to the peptide and the protein, wherein the cleavage site is modified such that a compound mediating cleavage has a reduced binding affinity for it as compared to a non-modified cleavage site. The invention further provides a target of interest complex comprising a protease, a target of interest involved in an intermolecular interaction, and a flexible linker that attaches the protease and target of interest. The invention further provides uses thereof, including a method for identifying a peptide which has an intermolecular interaction with a target of interest or identifying the agonistic or antagonistic feature of a peptide that has an intermolecular reaction with a target of interest. | 12-10-2009 |
20090305899 | Compositions and methods for determining immune status - The present invention provides compositions and methods for identifying molecules in samples that bind to molecules associated with pathogenic agents (e.g., infectious agents). In certain aspects, the invention may be used to identify individuals that have been exposed to one or more pathogenic agent or have generated antibodies in response to one or more pathogenic agent. In other aspects, the invention is directed to the identification of molecules of one or more pathogenic agent that may be used to generate immune responses in other individuals. | 12-10-2009 |
20090318298 | Methods for Sequencing DNA - The invention is directed to methods for using sequence by ligation to sequence DNA immobilized on miniaturized, high density bead-based arrays. Methods are provided to fabricate an array of beads where the beads are coupled directly to a solid support. Methods are also provided to improve signal and reduce background in ligation-mediated DNA sequencing. In addition, methods are provided to improve the accuracy of reported tag counts when performing DNA sequencing by fluorescent nonamer ligation. | 12-24-2009 |
20100004134 | Combinatorial libraries of conformationally constrained polypeptide sequences - The present invention concerns combinatorial libraries of conformationally constrained polypeptide sequences and their uses. In particular, the present invention concerns combinatorial libraries of conformational epitopes and their uses. | 01-07-2010 |
20100029489 | SUCROSE TRANSPORT PROTEINS - This invention relates to an isolated nucleic acid fragment encoding a sucrose transport protein. The invention also relates to the construction of a chimeric gene encoding all or a portion of the sucrose transport protein, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the sucrose transport protein in a transformed host cell. | 02-04-2010 |
20100041561 | Preparation of Nucleic Acid Templates for Solid Phase Amplification - The invention relates to a method of preparing template constructs for solid-phase nucleic acid amplification and to use of the templates in methods of solid-phase nucleic acid amplification. The method involves carrying out two ligation reactions: (a) a ligation reaction in which the first end of one or more target polynucleotide molecules are ligated to surface-bound adaptor polynucleotide molecules, and (b) a ligation reaction in which solution-phase adaptor polynucleotide molecules are ligated to the second end of said target polynucleotide molecules, in order to produce one or more template constructs attached to a solid support. | 02-18-2010 |
20100093549 | POLYNUCLEOTIDE ASSOCIATED WITH A COLON CANCER COMPRISING SINGLE NUCLEOTIDE POLYMORPHISM, MICROARRAY AND DIAGNOSTIC KIT COMPRISING THE SAME AND METHOD FOR DIAGNOSING A COLON CANCER USING THE POLYNUCLEOTIDE - Provided is a polynucleotide including at least 10 contiguous nucleotides of a nucleotide sequence selected from the group consisting of nucleotide sequences of SEQ ID NOS: 1-12 and including a nucleotide at position 101 of the nucleotide sequence, or a complementary polynucleotide thereof. | 04-15-2010 |
20100120623 | Selection of Well-Expressed Synthetic Genes - The invention relates to a method of indirectly identifying a polynucleotide comprising an open reading frame having an improved expression level from a library of polynucleotides encoding the same polypeptide of interest, or variants or homologues thereof, in a host cell expression library, the method comprising the steps of: a) providing an expression library in a host cell, said library comprising at least two different open reading frames encoding the same polypeptide of interest, or variants or homologues thereof, each open reading frame being translationally coupled to a downstream gene encoding a screenable or selectable reporter; b) culturing the host cell under conditions conducive to the expression of the polypeptide of interest, or variant or homologue thereof; and c) screening and/or selecting for a host cell having an improved expression level of the translationally coupled reporter when compared to one or more other host cells of the library, thus indirectly identifying a polynucleotide comprising an open reading frame having an improved expression level in the host cell; as well as the expression libraries and host cells comprising said libraries. | 05-13-2010 |
20100137143 | METHODS AND APPARATUS FOR MEASURING ANALYTES - Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions. | 06-03-2010 |
20100144538 | GENEMAP OF THE HUMAN GENES ASSOCIATED WITH SCHIZOPHRENIA - The present invention relates to the selection of a set of polymorphism markers for use in genome wide association studies based on linkage disequilibrium mapping. In particular, the invention relates to the fields of pharmacogenomics, diagnostics, patient therapy and the use of genetic haplotype information to predict an individual's susceptibility to SCHIZOPHRENIA disease and/or their response to a particular drug or drugs. | 06-10-2010 |
20100179065 | Clinical monitor systems for botanics and herbal medicine - The present invention provides a biological finger-print system for botanics and/or herbal medicine by using the overall gene expression profiling in peripheral white blood cells. Besides, the present invention further provides clinical application in humans for monitoring the potential adverse or side effects of botanics and/or herbal medicine. | 07-15-2010 |
20100184605 | PLANT FARNESYLTRANSFERASES - This invention relates to an isolated nucleic acid fragment encoding a farnesyltransferase subunit. The invention also relates to the construction of a chimeric gene encoding all or a portion of the farnesyltransferase subunit, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the farnesyltransferase subunit in a transformed host cell. | 07-22-2010 |
20100184606 | Methods For Selective Targeting - A selective targeting method is disclosed which comprises contacting a peptide library with an anti-target to allow the peptides to bind; separating non-binding peptides from the anti-target bound peptides, contacting the non-binding anti-target peptides with a target allowing the unbound peptides to bind with the target to form a target-bound peptide complex; separating the target-bound peptide complex from peptides which do not bind to the target, and identifying the target-bound peptides. In one embodiment the target is skin or hair. In another embodiment the anti-target is hair when the target is skin, and the anti-target is skin when the target is hair. | 07-22-2010 |
20100197507 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 08-05-2010 |
20100273658 | Methods for Assaying Gene Imprinting and Methylated CpG Islands - Genomic imprinting is a parent of origin-dependent gene silencing that involves marking of alleles in the germline and differential expression in somatic cells of the offspring. Imprinted genes and abnormal imprinting have been implicated in development, human disease, and embryonic stem cell transplantation. We have established a model system for genomic imprinting using pluripotent 8.5 d.p.c. mouse embryonic germ (EG) cell lines derived from an interspecific cross. We find that allele-specific imprinted gene expression has been lost in these cells. However, partial restoration of allele-specific silencing can occur for some imprinted genes after in vitro differentiation of EG cells into somatic cell lineages, indicating the presence of a gametic memory that is separable from allele-specific gene silencing. We have also generated a library containing most methylated CpG islands. A subset of these clones was analyzed and revealed a subdivision of methylated CpG islands into 4 distinct subtypes: CpG islands belonging to high copy number repeat families; unique CpG islands methylated in all tissues; unique methylated CpG islands that are unmethylated in the paternal germline; and unique CpG islands methylated in tumors. This approach identifies a methylome of methylated CpG islands throughout the genome. | 10-28-2010 |
20100273659 | Nitrilases, Nucleic Acids Encoding Them and Methods for Making and Using Them - The invention relates to nitrilases and to nucleic acids encoding the nitrilases. In addition methods of designing new nitrilases and method of use thereof are also provided. The nitrilases have increased activity and stability at increased pH and temperature. | 10-28-2010 |
20100285970 | METHODS OF SEQUENCING NUCLEIC ACIDS - Disclosed are high-throughput methods for sequencing nucleic acid, which entail identifying the complete set of SNPs in a genome of interest in comparison to a wild type or reference DNA whose sequence is known or substantially known. The methods may also entail use of solid supports containing colonies of amplified nucleic acid fragments e.g., prepared by digesting genomic nucleic acid having substantially known sequence, wherein the sequence of the fragments at each coordinate is known. The supports, per se, and apparati containing them, are also provided. | 11-11-2010 |
20100292084 | NOVEL DIARYLPHOSPHINE- AND DIALKYLPHOSPHINE-CONTAINING COMPOUNDS, PROCESSES OF PREPARING SAME AND USES THEREOF AS TRIDENTATE LIGANDS - A novel process of preparing tridentate ligands containing one or more of a diarylphosphine and/or dialkylphosphine electron donating groups are disclosed. Use of this process for preparing a combinatorial library of such tridentate ligands and of organometallic complexes containing same is also disclosed. Further disclosed are novel diarylphosphine-containing and dialkylphosphine-containing compounds that can serve as tridentate ligands (e.g., pincer ligands), combinatorial libraries of such tridentate ligands, organometallic complexes containing these ligands (e.g., pincer complexes), and combinatorial libraries of such complexes. Methods utilizing these libraries for screening for candidate organometallic catalysts are also disclosed. Novel precursor molecules useful for preparing the tridentate ligands and processes of preparing same are also disclosed. | 11-18-2010 |
20100298151 | EXOSOME-ASSOCIATED MICRORNA AS A DIAGNOSTIC MARKER - The presently disclosed subject matter provides methods of diagnosis of cancer or adverse pregnancy outcomes in a subject by measuring amounts of one or more microRNAs present in cancer-derived exosomes isolated from a biological sample from the subject. | 11-25-2010 |
20100311597 | METHODS FOR SEQUENCE A POLYNUCLEOTIDE TEMPLATE - The invention relates to methods for pairwise sequencing of a polynucleotide template which result in the sequential determination of nucleotide sequence in two distinct and separate regions of the polynucleotide template. | 12-09-2010 |
20100331193 | Methods for generating polynucleotides having desired characteristics by iterative selection and recombination - Methods are provided for the evolution of proteins of industrial and pharmaceutical interest, including methods for effecting recombination and selection. Compositions produced by these methods are also disclosed. | 12-30-2010 |
20100331194 | NANOPORE SEQUENCING DEVICES AND METHODS - The invention relates to devices and methods for nanopore sequencing. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS. In some cases, the arrays of nanopores comprise resistive openings for isolating the electronic signals for improved sequencing. Methods for controlling translocation of through the nanopore are disclosed. | 12-30-2010 |
20110009275 | Methods of amplifying and sequencing nucleic acids - An apparatus and method for performing rapid DNA sequencing, such as genomic sequencing, is provided herein. The method includes the steps of preparing a sample DNA for genomic sequencing, amplifying the prepared DNA in a representative manner, and performing multiple sequencing reaction on the amplified DNA with only one primer hybridization step. | 01-13-2011 |
20110015080 | Solution-based methods for RNA expression profiling - The present invention is directed to novel high-throughput, low-cost, and flexible solution-based methods for RNA expression profiling, including expression of microRNAs and mRNAs. | 01-20-2011 |
20110028330 | COMPOUNDS AND METHODS FOR THE LABELLING AND AFFINITY-SELECTION OF PROTEINS - The present invention relates to kits and methods for the isotopic/isobaric labeling and the subsequent affinity selection and analysis of proteinaceous molecules. In particular, the invention relates to a kit-of-parts comprising a combinatorial plurality of labeling reagent for the labeling of proteinaceous molecules, each labeling reagent comprising an isobaric label component, an isotopic label component, and a reactive group capable of reacting with a proteinaceous molecule, wherein the isotopic label component concomitantly is an affinity tag. The invention is also directed to a corresponding method for the analysis of proteinaceous molecules, comprising labeling at least one subset of the proteinaceous molecules present by employing a kit-of-parts as defined herein and subsequently separating the labeled molecules by affinity purification via the affinity tag comprised in the label. Finally, the invention relates to the uses of such methods for protein expression profiling or proteomic analyses. | 02-03-2011 |
20110053782 | NOVEL DNA CAPABLE OF BEING AMPLIFIED BY PCR WITH HIGH SELECTIVITY AND HIGH EFFICIENCY - The present invention relates to unnatural base pairs of Ds (a 5-amino-7-(2-thienyl)-3H-imidazo[4,5-b]pyridine-3-yl group) and a Pa derivative (a 2-nitro-1H-pyrrole-1-yl group bearing a substituent having a π-electron system attached at position 4) that can be replicated with high selectivity/high efficiency, and methods for replicating nucleic acids containing the unnatural base pairs. The present invention also relates to methods for incorporating an unnatural base bearing a functional substituent attached thereto into DNA by a nucleic acid replication reaction. The present invention also relates to methods for replicating and selectively collecting a nucleic acid containing an unnatural base pair from a nucleic acid pool. The present invention also relates to methods for determining a sequence of natural bases in the proximity of an unnatural base in DNA for achieving highly efficient and highly selective replication of a nucleic acid containing the unnatural base. | 03-03-2011 |
20110065588 | SENSOR ARRAYS AND NUCLEIC ACID SEQUENCING APPLICATIONS - Embodiments of the present invention provide devices methods for sequencing DNA using arrays of reaction regions containing electronic sensors to monitor changes in solutions contained in the reaction regions. Test and fill reaction schemes are disclosed that allow DNA to be sequenced. By sequencing DNA using parallel reactions contained in large arrays, DNA can be rapidly sequenced. | 03-17-2011 |
20110092373 | SYSTEM FOR TRANSPORTING EMULSIONS FROM AN ARRAY TO A DETECTOR - System, including apparatus and methods, for performing droplet-based assays. The system may comprise a droplet transporter configured to pick up droplets from each emulsion of an array of reacted emulsions and to drive flow of the droplets through a detection region. The system also may comprise a detector configured to collect data related to one or more analytes from individual droplets of the reacted emulsions as such individual droplets travel through the detection region. The system further may comprise a controller programmed to determine, based on the data collected, an aspect of the one or more analytes in one or more samples included in droplets of the emulsions. | 04-21-2011 |
20110105337 | METHOD OF DISCOVERING AND ANALYZING SECRETED BIOMARKERS OF DISEASE FROM SOLID TISSUE - The current invention provides a method for discovering protein biomarkers of disease for use in diagnostic assays of bodily fluids by determining differential expression patterns of proteins secreted or released directly by normal and diseased epithelial cells into glandular lumens. Determining those secreted or released proteins directly from the glandular lumen of diseased and normal solid tissue would lead to a catalogue of proteins that have a high degree of probability to be present in various bodily fluids in persons with specific diseases. This would prove useful as a means to diagnose specific conditions and diseases by simply assaying easily acquired bodily fluids. Past efforts to discover such diagnostic/screening markers in bodily fluids have proven difficult at best due to overriding complexity of the proteins within bodily fluids. This invention is a method of discovering those biomarkers in a more focused and less complex protein subpopulation, namely the secreted or released proteins present in glandular lumens. | 05-05-2011 |
20110105338 | EXPRESSION-LINKED GENE DISCOVERY - The invention relates to a method for analyzing a genomic region of an organism, comprising four major parts. The first part involves the isolation of mRNA from a selected organism that is used for the preparation of small single stranded DNA fragments with one adaptor containing an affinity label. These DNA fragments are used in part three. In the second part, genomic DNA from the same or a related organism is isolated. This genomic DNA is fragmented and ligated to adaptor molecules. In the third part, these genomic fragments are hybridized with single stranded DNA fragments from part one, and the hybrids formed in this process are used for synthesis of DNA fragments. These fragments will be used in part four which involves sequencing of these fragments using one of the available high throughput sequencing methods. | 05-05-2011 |
20110136675 | IDENTIFICATION AND CHARACTERIZATION OF PROTEINS USING NEW DATABASE SEARCH MODES - A method of selecting a set of candidate polypeptides for a sample polypeptide that includes a first refining of a collection of candidate polypeptides from differences in mass of fragments of the sample polypeptide produced by mass spectrometry and a second refining of the collection of candidate polypeptides from the absolute mass of the sample polypeptide and the absolute mass of the fragments. | 06-09-2011 |
20110172105 | GREPSEQ: An Almost Inexhaustible, Cost-Effective, High-Throughput Protocol for the Generation of Selector Sequences - Provided are compositions, libraries, and methods for the synthesis of transcripts that can be processed to produce nucleic acid capture probes. Also provided methods for using such nucleic acid capture probes in a variety of downstream applications, including, e.g., determining the sequence of an exon-exon junction. | 07-14-2011 |
20110195847 | METHODS TO TREAT SOLID TUMORS - A high throughput method for identifying promoters differentially activated in solid tumors as compared to normal tissues is described. The promoters so identified may be used to drive production of RNA's or proteins useful in treating solid tumors including toxic RNA's or proteins and other therapeutic RNA's or proteins. | 08-11-2011 |
20110207612 | COPY NUMBER VARIATIONS DETECTING APPARATUS AND METHOD - A copy number variations detecting apparatus and method according to at least one embodiment of the present invention compare column vectors adjacent to each other on array comparative genomic hybridization data (aCGH data) and compartmentalize the aCGH data into a plurality of segments according to the comparison results, compare row vectors within the segments for each segment and reconfigure the segments into a predetermined number of clusters according to the comparison results, selectively determine the segments as a candidate copy number variation zone corresponding to a distribution form of the clusters for each segment, detect the CNVs within the candidate CNVZ for each sample, and perform merging and pruning on the candidate CNVZ(s) to obtain a final CNVZ(s). | 08-25-2011 |
20110224086 | Methods and Algorithms for Selecting Polynucleotides For Synthetic Assembly - The present invention relates to methods and algorithms for identifying, synthesizing and co-assembling combinatorial libraries of polynucleotide variants. | 09-15-2011 |
20110245085 | METHODS FOR DETERMINING COPY NUMBER VARIATIONS - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. | 10-06-2011 |
20110251073 | Compositions And Methods Comprising Variant Microbial Proteases - The present invention provides methods for protein engineering. Specifically, the invention provides methods utilizing site evaluation libraries to design libraries that optimize two or more properties of a protein. The present invention also provides variant subtilisins suitable for various uses. | 10-13-2011 |
20110257018 | NUCLEIC ACID SEQUENCING - A method for determining a target nucleic acid sequence is disclosed, wherein a preparation having a first region of common sequence upstream of a first region of dissimilar sequence upstream of a second region of dissimilar sequence, is contacted with a blocking oligonucleotide complementary to at least a portion of the first region of dissimilar sequence of the non-target nucleic acid sequence, under conditions to hybridise the blocking oligonucleotide thereto and hybridized to the target nucleic acid sequence; and then sequenced, such that the sequencing reaction proceeds into the second region of dissimilar sequence of the target nucleic acid sequence, whereby at least the second region of dissimilar sequence of the target nucleic acid sequence is determined; and wherein the sequencing reaction is blocked at least from proceeding into the second region of dissimilar sequence of the non-target nucleic acid sequence. | 10-20-2011 |
20110257019 | Directed Enrichment of Genomic DNA for High-Throughput Sequencing - The present invention provides microarrays of oligonucleotide primer pairs, and in particular, microarrays of primers that comprise at least one cleavable linkage. Also provided are methods to capture oligonucleotide primer pairs from one or more microarrays, and methods to use the captured oligonucleotide primer pairs, such as for amplification of a target polynucleotide sequence. In addition, methods of using a microarray to isolate, purify and/or amplify a target polynucleotide are provided. | 10-20-2011 |
20110263435 | GENETIC MARKERS FOR BOAR TAINT - Genetic markers are disclosed with a useful association with boar taint that can be used for screening and selection of pigs for those with more favorable boar taint characteristics associated with androstenone/skatole metabolism. Specific polymorphic alleles of the 3αHSD, 3βHSD, CYP17A1, CYP2A, CYP2E1, CYTB5, BAC-CT and/or SULT1A1 genes are disclosed for tests to screen pigs to determine those more likely to produce desired boar taint traits. | 10-27-2011 |
20110263436 | RECOMBINANT ANTIBODIES AGAINST HEPATITIS C VIRUS AND METHODS OF OBTAINING AND USING SAME - Recombinant antibodies, including chimeric antibodies, specific for hepatitis C (HCV) antigenic proteins are provided. The recombinant antibodies specifically bind to diagnostically relevant regions of HCV proteins and are thus suitable for use, for example, as diagnostic reagents for the detection of HCV, and/or as standardization reagents or positive control reagents in assays for the detection of HCV. The recombinant antibodies can also be used in the treatment or prevention of a HCV infection. | 10-27-2011 |
20110269631 | Amplification and Analysis of Selected Targets on Solid Supports - Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. Targets are circularized by hybridization to probes followed by ligation of the ends of the target to form a closed circle. The targets are then used as template for extension of an array bound probe resulting in extended probes having multiple copies of the target. The extended probes can then be analyzed. The methods may be used for genotyping, sequencing and analysis of copy number. | 11-03-2011 |
20110275522 | Method and Apparatus for Rapid Nucleic Acid Sequencing - Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions. | 11-10-2011 |
20110275523 | METHODS AND KITS FOR ANALYZING POLYNUCLEOTIDE SEQUENCES - The present invention features methods for analyzing a sequence of a target polynucleotide by detecting incorporation of a nucleotide into its complementary strand, where the polynucleotides may be bound at high density and at single molecule resolution. The invention also features labeling moieties and blocking moieties, which facilitate chain termination or choking. Certain aspects provide for temporal detection of the incorporations; some allow for asynchronous analysis of a plurality of target polynucleotides and the use of short sequencing cycles. Surface chemistry aspects of the sequencing methods are also provided. The method may also be used in kits, said kits designed to carry out and facilitate the methods provided herein. | 11-10-2011 |
20110281736 | Nucleic Acid Sequencing and Process - The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods. | 11-17-2011 |
20110281737 | Method and Apparatus for Rapid Nucleic Acid Sequencing - Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions. | 11-17-2011 |
20110281738 | SELF-ASSEMBLED SINGLE MOLECULE ARRAYS AND USES THEREOF - The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences. | 11-17-2011 |
20110281739 | Charge Perturbation Detection System for DNA and Other Molecules - Methods and apparatus for direct detection of chemical reactions are provided. In a preferred embodiment, electric charge perturbations of the local environment during enzyme-catalyzed reactions are sensed by an electrode system with an immobilized target molecule. The target molecule is preferably DNA. The charge perturbation caused by the polymerase reaction can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a voltage clamp amplifier. Detection of single nucleotides in a sequence can be determined by dispensing individual dNTPs to the electrode solution and detecting the charge perturbations. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal. The initial enzyme attachment to the DNA molecule can be detected prior to polymerization, with electrode capacitance measurement using the same voltage-clamp amplifier. This technique and device may be adapted to other reaction determinations, such as enzymatic reactions, other electrode configurations, and other amplifying circuits. | 11-17-2011 |
20110287945 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 11-24-2011 |
20110287946 | Genetic Variants Useful for Risk Assessment of Thyroid Cancer - The invention discloses genetic variants that have been determined to be susceptibility variants of thyroid cancer. Methods of disease management, including methods of determining susceptibility to thyroid cancer, methods of predicting response to therapy and methods of predicting prognosis of thyroid cancer using such variants are described. The invention further relates to kits useful in the methods of the invention. | 11-24-2011 |
20110301041 | Modified Proteins and Methods of Making and Using Same - Methods, compositions, systems, apparatuses and kits comprising modified proteins, particularly modified nucleic acid-binding proteins with altered buffering properties are provided. For example, in some embodiments, methods of forming modified proteins including one or more amino acid modifications to achieve desired pKa values are described. Furthermore, the invention provides methods for using such modified proteins in ion-producing reactions, such as ion-based nucleic acid sequencing reactions. | 12-08-2011 |
20110312503 | METHODS OF FETAL ABNORMALITY DETECTION - Methods and kits for selectively enriching non-random polynucleotide sequences are provided. Methods and kits for generating libraries of sequences are provided. Methods of using selectively enriched non-random polynucleotide sequences for detection of fetal aneuploidy are provided. | 12-22-2011 |
20110312504 | METHODS, KITS, AND COMPOSITIONS FOR DETECTION OF MRSA - The present invention provides multiplex assays, methods and kits that may be used to detect and confirm the presence of MRSA in a sample. The methods include real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes. The present invention further comprises assays useful to identify and differentiate MRSA, MSSA, MRSE, MSSE, MRCNS and MSCNS in a sample. | 12-22-2011 |
20110312505 | Rapid Isolation of Monoclonal Antibodies from Animals - Methods and compositions for identification of candidate antigen-specific variable regions as well as generation of antibodies or antigen-binding fragments that could have desired antigen specificity are provided. For example, in certain aspects methods for determining amino acid sequences of serum antibody CDR and abundancy level are described. In some aspects, methods for determining nucleic acid sequences of antibody variable region sequences and frequency are provided. Furthermore, the invention provides methods for identification and generation of antibody or antigen-binding fragments that comprise highly-represented CDR. | 12-22-2011 |
20110312506 | METHODS AND KITS FOR SCREENING PROTEIN SOLUBILITY - Methods and kits useful for identifying conditions which solubilize proteins and/or reduce or eliminate protein aggregation are provided. The disclosed methods and kits find utility in any number of applications requiring solubilization, formulation or storage of protein samples. | 12-22-2011 |
20110319272 | Noninvasive Diagnosis of Fetal Aneuploidy by Sequencing - Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes. | 12-29-2011 |
20110319273 | Methods of analysis of allelic imbalance - Methods are provided for identification of genes that are imprinted. In another embodiment methods are provided for identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles. Genes whose transcription products are present in amounts that vary from expected are candidates for allelic imbalance, imprinting and imprinting errors. | 12-29-2011 |
20120004111 | DIRECT IDENTIFICATION AND MEASUREMENT OF RELATIVE POPULATIONS OF MICROORGANISMS WITH DIRECT DNA SEQUENCING AND PROBABILISTIC METHODS - The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases). | 01-05-2012 |
20120004112 | METHODS FOR DETERMINING A BREEDING VALUE BASED ON A PLURALITY OF GENETIC MARKERS - The present invention provides a method for determining the individual effect of a plurality of genetic marker alleles on udder health, fertility and/or other health of a plurality of reference bovine subjects. The marker effects are employed in another aspect of the invention for determining a genomic estimated breeding value of a bovine subject based on the genotype of said bovine subject by correlating its genotype with the effect of each individual genetic marker allele on udder health, fertility, other health and/or estimated breeding value of the reference bovine subjects. Further provided are methods and computer program products and computer readable media for executing the methods of the invention. | 01-05-2012 |
20120010085 | METHODS FOR DETERMINING FRACTION OF FETAL NUCLEIC ACIDS IN MATERNAL SAMPLES - The invention provides compositions and methods for determining the fraction of fetal nucleic acids in a maternal sample comprising a mixture of fetal and maternal nucleic acids. The fraction of fetal nucleic acids can be used in determining the presence or absence of fetal aneuploidy. | 01-12-2012 |
20120010086 | CLONAL PRE-AMPLIFICATION IN EMULSION - Disclosed is a process for clonal pre-amplification of a nucleic acid involving the steps of (i) providing a plurality of different nucleic acid molecules (b) attaching adaptor sequences to the 3′ ends and 5′ ends of the nucleic acid molecules (c) preparing a water in oil emulsion wherein the majority of water droplets comprises one or none member of the plurality of different nucleic acid molecules (d) clonally amplifying the plurality of different nucleic acid molecules. In particular, the different nucleic acid molecules are mRNA molecules. | 01-12-2012 |
20120010087 | Methods for Genotyping - Novel methods and kits are disclosed for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences, for example, to discriminating between alleles at polymorphic positions in a genome. Complexity reduction can be accomplished by extension of a capture probes followed by amplification of the extended capture probe using common primers. The capture probes may be locus specific and allele-specific. The amplified sample may be hybridized to an array designed to interrogate the desired fragments for the presence or absence of a polymorphism. In some aspects the methods employ allele-specific extension of oligonucleotides that are complementary to one of the alleles at the 3′ end of the oligonucleotide. The allele-specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele-specific manner by a DNA polymerase with a functional 3′ to 5′ exonuclease activity. | 01-12-2012 |
20120015821 | Methods of Generating Gene Specific Libraries - The invention provides compositions and methods for generating a target enriched, sequencing ready library for resequencing at least one target region of interest from a nucleic acid containing sample. | 01-19-2012 |
20120015822 | PARTICLE-ASSISTED NUCLEIC ACID SEQUENCING - This invention generally relates to particle-assisted nucleic acid sequencing. In some embodiments, sequencing may be performed in a microfluidic device, which can offer desirable properties, for example, minimal use of reagents, facile scale-up, and/or high throughput. In one embodiment, a target nucleic acid may be exposed to particles having nucleic acid probes. By determining the binding of the particles to the target nucleic acid, the sequence of the target nucleic acid (or at least a portion of the target nucleic acid) can be determined. The target nucleic acid may be encapsulated within a fluidic droplet with the particles having nucleic acid probes, in certain instances. In some cases, the sequence of the target nucleic acid may be determined, based on binding of the particles, using sequencing by hybridization (SBH) algorithms or other known techniques. | 01-19-2012 |
20120015823 | Methods for indexing samples and sequencing multiple polynucleotide templates - The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like. | 01-19-2012 |
20120021918 | DNA Sequencing and Amplification Systems Using Nanoscale Field Effect Sensor Arrays - In one aspect, described herein are field effect chemical sensor devices useful for chemical and/or biochemical sensing. Also provided herein are methods for single molecule detection. In another aspect, described herein are methods useful for amplification of target molecules by PCR. | 01-26-2012 |
20120021919 | Identification of Differentially Represented Fetal or Maternal Genomic Regions and Uses Thereof - The present invention provides a novel approach for identification and characterization of differentially represented fetal or maternal genomic regions in maternal circulation. Identification of overrepresented fetal genomic regions in the maternal circulation according to the present invention permit accurate analysis of fetal DNA without the need for enrichment or purification, which provides a simpler, more accurate and efficient prenatal diagnosis in early pregnancy. The present invention is particularly useful for noninvasive prenatal diagnosis during early pregnancy (e.g., during the first trimester). | 01-26-2012 |
20120021920 | RADIATION THERAPY BIOMARKERS - Materials and methods related to using biomarkers for prediction of response to radiation therapy. | 01-26-2012 |
20120028813 | Selecting Reference Libraries For Monitoring Of Multiple Zones On A Substrate - A method of configuring a polishing monitoring system includes receiving user input selecting a plurality of libraries, each library of the plurality of libraries comprising a plurality of reference spectra for use in matching to measured spectra during polishing, each reference spectrum of the plurality of reference spectra having an associated index value, for a first zone of a substrate, receiving user input selecting a first subset of the plurality of libraries, and for a second zone of the substrate, receiving user input selecting a second subset of the plurality of libraries. | 02-02-2012 |
20120028814 | OLIGONUCLEOTIDE LIGATION, BARCODING AND METHODS AND COMPOSITIONS FOR IMPROVING DATA QUALITY AND THROUGHPUT USING MASSIVELY PARALLEL SEQUENCING - Described herein is a buffer concentration for highly efficient ligation of two oligonucleotides. The embodiments herein have led to the development of an optimized ligation step used in the sample preparation for sequencing reactions. Further, embodiments herein describe a high-throughput method for sequencing using barcodes or the purpose of multiplexing several samples simultaneously and novel methods for making targeted DNA libraries for re-sequencing on massively parallel next-generation sequencing platforms and for alternatives to gel-purification for recovering the desired templates from small RNA libraries for next generation sequencing. | 02-02-2012 |
20120028815 | NUCLEIC ACID SEQUENCING USING MICROSPHERE ARRAYS - The invention relates to DNA sequencing by synthesis techniques, including those utilizing the detection of pyrophosphate (PPi) generated during the DNA synthesis reaction (pyrosequencing). The methods and compositions utilize biosensor arrays comprising microspheres distributed on a surface. | 02-02-2012 |
20120028816 | METHODS AND SYSTEMS FOR SCREENING FOR AND DIAGNOSING DNA METHYLATION ASSOCIATED WITH AUTISM SPECTRUM DISORDERS - Methods and systems for population screening and diagnostics are provided. In particular methods and systems for population screening of individuals for genetic disorders due to alterations in DNA methylation and for the diagnostic testing for such disorders are provided. | 02-02-2012 |
20120035060 | HIGHLY MULTIPLEXED GENOTYPING USING LEUKOREDUCED BLOOD SAMPLES - Described herein are methods and kits useful for the extraction and analysis of genomic DNA from leukoreduced blood or plasma samples. | 02-09-2012 |
20120040842 | Gene Expression Markers for Prediction of Patient Response to Chemotherapy - The present invention relates to gene sets useful in assessing prognosis and/or predicting the response of cancer, e.g. colorectal cancer to chemotherapy. In addition, the invention relates to a clinically validated cancer test, e.g. colorectal test, for assessment of prognosis and/or prediction of patient response to chemotherapy, using expression analysis. The present invention accommodates the use of archived paraffin embedded biopsy material for assay of all markers in the relevant gene sets and therefore is compatible with the most widely available type of biopsy material. | 02-16-2012 |
20120046176 | NUCLEIC ACID SEQUENCING - Nucleic acid sequencing using concatemers of DNA is provided. Optionally, amplified reaction products from the repeated incorporation and excision of a nucleoside complementary to a nucleoside of the DNA to be sequenced onto primer molecules hybridized to the concatemers of DNA are detected. Nucleic acid sequencing using concatemers of DNA and non-natural oligonucleotides is also provided. Nucleic acid sequencing reactions are detected electronically and or optically using arrays of detectors. | 02-23-2012 |
20120046177 | Mostly Natural DNA Sequencing by Synthesis - The invention provides a new method for DNA sequencing called “natural sequencing by synthesis” (nSBS). According to the method, DNA that includes a desired sequence is synthesized using a dNTP mix with a small percentage of fluorescently-labeled nucleotides. The fluorescent label is cleavable. In contrast to previous methods that utilize 100% labeled nucleic acids, use of a small percentage of labeled nucleic acids minimizes the distortion of the natural structure of the extending DNA strand and the DNA polymerase. Using the disclosed methods with less than 10,000 copies of template DNA and 10% of the nucleotides labeled, long homopolymer stretches up to 20 bases can be sequenced with high accuracy and Q20 (with 99% accuracy) read lengths of up to 1,000 bases can be achieved. A Q20 read length of greater than 100 bases can potentially be achieved, even if the sequencing is performed with 1,000 copies of a template and 10% of the nucleotides labeled. | 02-23-2012 |
20120065075 | METHOD OF DETERMINING A PREDISPOSITION TO ATRIAL FIBRILLATION (AF) IN A SUBJECT - The present invention concerns a method of determining a predisposition to atrial fibrillation (AF) in a subject comprising: determining the presence of at least one copy of a risk allele from at least one polymorphic marker in a sample from the subject, wherein the presence of at least one copy of the risk allele is indicative of a predisposition to AF, and wherein said at least one polymorphic marker is: a) rs4674485; b) rs1466560; c) rs1880039; d) rs3849387; e) rs7039; f) rs2952860; g) rs9312515; h) rs1897527; i) rs2299277; j) rs2418828; k) rs2385833; l) rs6717960; m) rs10510266; or n) a substitute polymorphic marker in linkage disequilibrium with any one of the polymorphic markers of a) to m). Also described are kits for determining a predisposition to atrial fibrillation (AF). | 03-15-2012 |
20120065076 | METHODS FOR THE DIAGNOSIS OF FETAL DISEASE - Methods are provided for detecting an aneuploidy in a fetus. These methods can be used to detect trisomy 13, 8 or 21, amongst other aneupoloidies. In some embodiments, the methods include selectively purifying fetal DNA from a maternal biological sample using the methylation status of a CpG containing genomic sequence and genotyping the fetus using the purified fetal DNA, thereby detecting aneuploidy in the fetus. | 03-15-2012 |
20120065077 | GENETIC FACTORS ASSOCIATED WITH INHIBITOR DEVELOPMENT IN HEMOPHILIA A - The present invention provides methods for predicting the risk of an individual developing antibodies to factor VIII by identifying a single nucleotide polymorphism of an immune response or immune modifier gene. The invention further provides oligonucleotides, diagnostic kits, microarrays, and isolated nucleic acids comprising single nucleotide polymorphisms of immune response or immune modifier genes. | 03-15-2012 |
20120065078 | METHOD FOR THE DIAGNOSIS AND TREATMENT OF CARDIOVASCULAR DISEASES - The present invention refers to a method for the in vitro or in vivo diagnosis of cardiovascular diseases, in particular high blood pressure, stenosis, vessel occlusion and/or other thrombotic events, wherein the nucleotide at position 950 of a nucleic acid coding for the human ARK2 protein or the amino acid at position 298 of the human ARK2 protein of a sample of a person is determined as well as to the use of ARK2 for the development and/or production of a medicament for treating a cardiovascular disease. | 03-15-2012 |
20120065079 | METHOD FOR THE DETERMINATION OF P BLOOD GROUPS - The invention relates to a method to discriminate between the P | 03-15-2012 |
20120065080 | ACID CERAMIDASE POLYMORPHISMS AND METHODS OF PREDICTING TRAITS USING THE ACID CERAMIDASE POLYMORPHISMS - Provided are methods of predicting a trait in a subject including obtaining information about at least a portion of a polynucleotide sequence of the subject, the polynucleotide sequence encoding the acid ceramidase polypeptide, and using the information to predict the expression of the trait in the subject. Further provided are methods of developing a treatment plan for a subject with a disease or condition responsive to exercise. The methods may include obtaining information about at least a portion of a polynucleotide sequence of the subject, the polynucleotide sequence encoding the acid ceramidase polypeptide, using the information to predict a trait selected from maintaining an exercise program and physiological responsiveness to an exercise program, and developing a treatment plan for the subject to treat the disease or condition. | 03-15-2012 |
20120071327 | INDEXING OF NUCLEIC ACID POPULATIONS - The invention relates to a method for acquisition of genetic information, in particular for personalized medicine. | 03-22-2012 |
20120071328 | Complexity management of Genomic DNA - The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms. | 03-22-2012 |
20120077681 | MIXED LIBRARY PARALLEL GENE MAPPING QUANTITATIVE MICRO-ARRAY TECHNIQUE FOR GENOME-WIDE IDENTIFICATION OF TRAIT CONFERRING GENES - The present disclosure concerns methods and compositions relating to mixed-library parallel gene trait mapping. In particular embodiments, the methods concern quantitative microarray hybridization techniques for genome-wide identification of trait conferring genes. In other embodiments, the compositions concern genetic elements that confer or are associated with a trait. In an exemplary embodiment, the trait is enhanced growth rate. In another exemplary embodiment, genetic elements that confer enhanced bacterial growth rate comprise part or all of the sequences of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:5. In other embodiments, the genetic elements that confer enhanced bacterial growth rate correspond to the YliF, adrA, yeaP, yddV or ydeH genes of | 03-29-2012 |
20120077682 | COMPOSITIONS AND METHODS FOR DETECTING CANCER METASTASIS - The present invention encompasses compositions and methods for detecting cancer metastasis. | 03-29-2012 |
20120077683 | KIT AND METHOD FOR PREDICTING CYTARABINE SENSITIVY OF PATIENT HAVING ACUTE MYELOID LEUKEMIA - A kit and method for predicting cytarabine sensitivity of patients having acute myeloid leukemia are disclosed. | 03-29-2012 |
20120083417 | NATIVE-EXTENSION PARALLEL SEQUENCING - The present invention provides methods for native extension parallel sequencing of polynucleotide. | 04-05-2012 |
20120088676 | MOLECULAR TYPING AND SUBTYPING OF SALMONELLA BY IDENTIFICATION OF THE VARIABLE NUCLEOTIDE SEQUENCES OF THE CRISPR LOCI - The present invention relates to a method for detecting and identifying bacteria of the | 04-12-2012 |
20120088677 | METHODS AND COMPOSITIONS FOR ANALYSIS OF REGULATORY SEQUENCES - Methods for constructing arrays of regulatory sequences, and the arrays so obtained, are provided. Regulatory sequences for use on the arrays are isolated based on their accessibility in cellular chromatin. A number of methods for using the arrays are disclosed, including regulatory DNA profiling, epigenome profiling, toxicological profiling and identification of in vivo binding sites of DNA binding proteins in complex genomes. | 04-12-2012 |
20120094842 | METHODS OF ASSESSING AND TREATING PULMONARY DISEASE - Methods of diagnosing risk of pulmonary disease in a mammal with cystic fibrosis are provided comprising screening a biological sample obtained from the mammal for MBL2 or SP-A1 deficiency, and TGFB1 over-expression. | 04-19-2012 |
20120094843 | DETECTING AND TREATING BREAST CANCER RESISTANCE TO EGFR INHIBITORS - The application describes therapeutic compositions and methods for treating cancer. For example, therapeutic compositions and methods related to inhibition of FAM83A (family with sequence similarity 83) are provided. The application also describes methods for diagnosing cancer resistance to EGFR inhibitors. For example, a method of diagnosing cancer resistance to EGFR inhibitors by detecting increased FAM83A levels is described. | 04-19-2012 |
20120094844 | GENETIC VARIANTS IN IL-6, P53, MMP-9 AND CXCR PREDICT CLINICAL OUTCOME IN PATIENTS WITH CANCER - The invention provides compositions and methods for determining the likelihood of response or survival of cancer patients treated with anti-VEGF therapy. After determining if a patient is likely to be successfully treated, the invention also provides methods for treating the patients. | 04-19-2012 |
20120094845 | METHODS AND DEVICES FOR ASSESSING INFERTILITY AND/OR EGG QUALITY - The invention generally relates to methods and devices for assessing infertility. In certain embodiments, methods of the invention involve conducting an assay to determine presence or absence of a mutation in a plurality of genes selected from Table 1, and assessing infertility based on results of the assay, wherein presence of a mutation in at least two of the genes from Table 1 is indicative of infertility. | 04-19-2012 |
20120094846 | METHOD FOR DETECTING CYSTIC FIBROSIS - The present invention relates to methods for amplifying various regions of the cystic fibrosis transmembrane regulator (CFTR) gene. Methods are provided for amplifying one or all 27 exons of the CFTR gene and a portion of the CFTR promoter region in a single tube. The method can identify the presence or absence of CF deletions or insertions in a sample and assist in the diagnosis of a genetic predisposition to cystic fibrosis. | 04-19-2012 |
20120094847 | THE USE OF CLASS IIB RESTRICTION ENDONUCLEASES IN 2ND GENERATION SEQUENCING APPLICATIONS - The present invention relates to a method for genotyping DNA molecules contained in at least one DNA sample comprising: (a) digesting the DNA molecules contained in at least one DNA sample with a class IIB restriction endonuclease to generate DNA fragments; (b) optionally separating DNA fragments comprising the recognition site for said class IIB restriction endonuclease from the remaining DNA fragments; (c) attaching at least one adaptor DNA to the 5′ and/or 3′ end of one or both strands of the DNA fragments comprising the recognition site for said class IIB restriction endonuclease obtained in a) or separated in b) to form adaptor-fragment constructs; (d) determining the sequence of at least a fraction of the DNA fragments obtained in c); and (e) assigning genotypes to said at least one DNA sample analysed based on the sequence data obtained in d). The present invention further relates to method for determining the position of DNA molecules comprised in a DNA library within the DNA sequence represented by said DNA library or within a known DNA sequence and for establishing a cross-reference between individual DNA molecules and their location in an at least three dimensional matrix. | 04-19-2012 |
20120094848 | Method for pairwise sequencing of target polynucleotides - The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template. Using the methods of the invention it is possible to obtain two linked or paired reads of sequence information from each double-stranded template on a clustered array, rather than just a single sequencing read from one strand of the template. | 04-19-2012 |
20120094849 | METHOD FOR DETERMINING COPY NUMBER VARIATIONS - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. | 04-19-2012 |
20120100995 | Biomarkers for Autism Spectrum Disorders - Methods of determining the risk of ASD or ID in an individual are provided which comprise identifying the presence of one or more specific genomic mutations in, upstream of, or comprising the PTCHD1 gene. Additionally provided are methods of determining the risk of ASD or ID in an individual comprising analyzing genomic mutations in PTCHD1AS1 and/or PTCHD1AS2 and/or PTCHD1AS3. | 04-26-2012 |
20120100996 | GENETIC MARKER IDENTIFICATION IN ATLANTIC COD - The present application describes SNPs useful for the genetic analysis of Atlantic cod. Also described are QTLs and SNP marker associations for commercially important traits such as weight, nodavirus resistance, resistance to stress and for determining geographic origin. The application also provides methods and uses of the SNPs for identifying family members and/or estimating relatedness, marker assisted selection, breeding programs, population management, identification of geographic origin and trait-association studies. A SNP-based linkage map for Atlantic cod is also provided. | 04-26-2012 |
20120100997 | CD133 POLYMORPHISMS AND EXPRESSION PREDICT CLINICAL OUTCOME IN PATIENTS WITH CANCER - The invention provides compositions and methods for aiding in the determination of or determining whether or not a cancer patient is likely to be responsive to a therapy comprising the administration of an anti-VEGF therapy. After determining if a patient is likely to be successfully treated, the invention also provides methods for treating the patients. | 04-26-2012 |
20120108440 | REDUCING ADAPTER DIMER FORMATION - Provided herein is a method of reducing adapter dimer formation comprising contacting a sample comprising target nucleic acid sequences with 5′ and 3′ adapters in the presence of one or more hairpin oligonucleotides. Also provided is a method of preparing a library of nucleic acid sequences comprising contacting first adapter oligonucleotides with a sample comprising target nucleic acid sequences under conditions to form first ligation products, contacting the sample with one or more hairpin oligonucleotides that binds to the first adapter oligonucleotides, and contacting the sample with second adapter oligonucleotides under conditions to bind to the first ligation products and form second ligation products, wherein the second ligation products form the library of nucleic acid sequences. | 05-03-2012 |
20120108441 | POLYMORPHISMS IN ANGIOGENESIS PATHWAY GENES ASSOCIATED WITH TUMOR RECURRENCE IN SURGERY TREATED CANCER PATIENTS - This invention provides compositions and methods for determining the likely tumor recurrence of cancer patients after surgical resection. Said methods are based on determining the patient's genotype for the polymorphisms PAR-1-506 ins/del C and/or EGF+61A>G. | 05-03-2012 |
20120108442 | METHOD FOR THE IDENTIFICATION OF THE CLONAL SOURCE OF A RESTRICTION FRAGMENT - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers. | 05-03-2012 |
20120115735 | Pathways Underlying Pancreatic Tumorigenesis and an Hereditary Pancreatic Cancer Gene - There are currently few therapeutic options for patients with pancreatic cancers and new insights into the pathogenesis of this lethal disease are urgently needed. To this end, we performed a comprehensive analysis of the genes altered in 24 pancreatic tumors. First, we determined the sequences of 23,781 transcripts, representing 20,583 protein-encoding genes, in DNA from these tumors. Second, we searched for homozygous deletions and amplifications using microarrays querying ˜one million single nucleotide polymorphisms in each sample. Third, we analyzed the transcriptomes of the same samples using SAGE and next-generation sequencing-by-synthesis technologies. We found that pancreatic cancers contain an average of 63 genetic alterations, of which 49 are point mutations, 8 are homozygous deletions, and 6 are amplifications. Further analyses revealed a core set of 12 regulatory processes or pathways that were each genetically altered in 70% to 100% of the samples. The data suggest that dysregulation of this core set of pathways is responsible for the major features of pancreatic tumorigenesis. | 05-10-2012 |
20120115736 | NUCLEIC ACID SEQUENCE ANALYSIS - Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions. | 05-10-2012 |
20120122698 | Genetic Variants Predictive of Cancer Risk in Humans - The present invention discloses genetic variants that have been found to be predictive of risk of particular forms of cancer, in particular basal cell carcinoma and cutaneous melanoma. The invention provides methods of predicting risk of developing such cancers, and other methods pertaining to risk management of cancer utilizing such risk variants. The invention furthermore provides kits and computer systems for use in such methods. | 05-17-2012 |
20120122699 | Methods and Oligonucleotide Designs for Insertion of Multiple Adaptors Employing Selective Methylation - Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques. | 05-17-2012 |
20120122700 | MATERIALS AND METHODS FOR DETERMINING SUBTELOMERE DNA SEQUENCE - The subject invention pertains to methods for rapid and accurate determination of subtelomere DNA sequences. Also provided are kits for determination of subtelomere sequences and uses of chromosomal terminal sequences for studying pathogenesis and treatment of diseases. | 05-17-2012 |
20120122701 | Methods for Non-Invasive Prenatal Paternity Testing - Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father. | 05-17-2012 |
20120122702 | RNA LABELING METHOD - A method of sample analysis is provided. In certain embodiments, the method involves: a) obtaining a fragmented RNA sample comprising fragments of long RNA molecules and short RNA molecules; b) ligating an adaptor to an end of the RNA of the fragmented RNA sample to produce an adaptor-ligated sample; c) hybridizing said adaptor-ligated sample to an array of nucleic acid probes; and d) reading said array to obtain an estimate of the abundance of a long RNA in the RNA sample and an estimate of the abundance a small RNA in the RNA sample. | 05-17-2012 |
20120129703 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 05-24-2012 |
20120129704 | GENERATION OF UNIFORM FRAGMENTS OF NUCLEIC ACIDS USING PATTERNED SUBSTRATES - Methods of generating nucleic acid fragments of substantially uniform length from sample nucleic acids comprising linearly stretching the sample nucleic acids over a substrate having a plurality of cleavage regions separated by relatively consistent distances, cleaving the linearly stretched sample nucleic acids at the cleavage regions, and collecting the resulting nucleic acid fragments. The method may further include collecting and concentrating the resultant nucleic acid fragments of substantially uniform length. | 05-24-2012 |
20120135870 | Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 05-31-2012 |
20120135871 | HIGH THROUGHPUT DETECTION OF MOLECULAR MARKERS BASED ON AFLP AND HIGH THROUGH-PUT SEQUENCING - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker. | 05-31-2012 |
20120149582 | METHOD FOR DETERMINING COPY NUMBER VARIATIONS - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the present method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample. | 06-14-2012 |
20120149583 | METHOD FOR DETERMINING COPY NUMBER VARIATIONS - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the present method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample. | 06-14-2012 |
20120149584 | METHODS OF DIAGNOSING AND TREATING MICROBIOME-ASSOCIATED DISEASE USING INTERACTION NETWORK PARAMETERS - Methods of diagnosing and treating microbiome-associated disease or improving health using interaction network parameters are provided. Methods are provided to analyze interaction networks between microbes, and between microbes and the host, to determine important (e.g. “highly-connected”) organisms or molecules as determined by various network parameters. Methods are provided including and beyond correlation to use these “highly-connected” organisms or molecules as targets for modulation or as therapeutic agents to improve health. | 06-14-2012 |
20120157322 | Direct Capture, Amplification and Sequencing of Target DNA Using Immobilized Primers - Certain embodiments provide a method for capturing a genomic fragment. The method may comprise: obtaining a substrate comprising a first population of surface-bound oligonucleotides and a second population of surface-bound oligonucleotides; hybridizing a first member of the first population of surface-bound oligonucleotides to a selection oligonucleotide comprising a region that hybridizes with the first member and a region that contains a genomic sequence; extending the first member of the first population of surface-bound oligonucleotides to produce a support-bound selection primer that comprises a sequence that is complementary to the genomic sequence; hybridizing the support-bound selection primer to a nucleic acid fragment comprising the genomic sequence; extending the support-bound selection primer to produce an extension product that contains a sequence that flanks the genomic sequence, e.g., in a genome; and amplifying the extension product on the substrate. | 06-21-2012 |
20120157323 | TWO-HYBRID BASED SCREEN TO IDENTIFY DISRUPTIVE RESIDUES AT MULTIPLE PROTEIN INTERFACES - The present invention is based, at least in part, on the development of a mating-based yeast two-hybrid screen that allows simultaneous screening for mutations that disrupt yeast two-hybrid interactions between a protein and multiple interacting partners. By coupling PCR mutagenesis and homologous recombination/gapped plasmid repair with a mating-based assay, the present invention allows screening for unique mutations that disrupt interaction with one partner, but not others. It also allows identification of specific mutations that may lie at protein-protein interfaces common to two or more partners, without employing multiple rounds of screening. In addition to screening against multiple interacting partners, the present invention removes the need for a two-step selection because truncations, frameshifts, or any mutations that affect folding are eliminated as disruptions that affect all protein partners. The methods of the present invention are named “Hotspot” because of its ability to identify “hotspot residues” in protein-protein interfaces. | 06-21-2012 |
20120157324 | METHYLATION BIOMARKERS AND METHODS OF USE - Disclosed are methods and compositions of assessing one or more statuses of a subject. Also disclosed are methods and compositions of identifying status biomarkers associated with a status of a subject. Also disclosed are sets of one or more status biomarkers. Also disclosed are methods and compositions of producing status biomarker capture probes. | 06-21-2012 |
20120157325 | Combinatorial Affinity Selection - In one aspect of the invention, methods for analyzing nucleic acid sample are provided. In a preferred embodiment, nucleic acids are selected using affinity matrices prior hybridization with a microarray. | 06-21-2012 |
20120165202 | METHODS AND COMPOSITIONS FOR EVALUATING GENETIC MARKERS - Aspects of the invention relates to methods and compositions that are useful to reduce bias and increase the reproducibility of multiplex analysis of genetic loci. In some configurations, predetermined preparative steps and/or nucleic acid sequence analysis techniques are used in multiplex analyses for a plurality of genetic loci in a plurality of samples. | 06-28-2012 |
20120165203 | SIMULTANEOUS DETERMINATION OF ANEUPLOIDY AND FETAL FRACTION - The invention provides compositions and methods for simultaneously determining the presence or absence of fetal aneuploidy and the relative amount of fetal nucleic acids in a sample obtained form a pregnant female. The method encompasses the use of sequencing technologies and exploits the occurrence of polymorphisms to provide a streamlined noninvasive process applicable to the practice of prenatal diagnostics. | 06-28-2012 |
20120165204 | Genetically Encoded Photomanipulation of Protein and Peptide Activity - The present invention relates to fusion proteins comprising protein light switches and methods of photomanipulating the activity of the proteins. The invention further relates to polynucleotides and vectors encoding the fusion proteins, cells comprising the fusion proteins, and methods of using the fusion proteins to study protein function and analyze subcellular activity, as well as diagnostic and therapeutic methods. | 06-28-2012 |
20120172237 | VIRUS DISCOVERY BY SEQUENCING AND ASSEMBLY OF VIRUS-DERIVED SIRNAS, MIRNAS, PIRNAS - In one embodiment, the disclosure provides methods and systems for identifying viral nucleic acids in a sample. In another embodiment the invention provides methods for viral genome assembly and viral discovery using small inhibitory RNAs, or “small silencing,” RNAs (siRNAS), micro-RNAs (miRNAs) and/or PIWI-interacting RNAs (piRNAs), including siRNAS, miRNAs and/or piRNAs isolated or sequenced from invertebrate organisms such as insects ( | 07-05-2012 |
20120172238 | METHOD AND COMPOSITIONS FOR ASSISTING IN DIAGNOSING AND/OR MONITORING BREAST CANCER PROGRESSION - The present invention relates to a method for assisting in diagnosing breast cancer and/or monitoring breast cancer progression in a given sample based on the analysis of differential DNA methylation patterns. More particularly, the method is directed to the identification of one or more epigenetic markers that derive from the application of a variety of statistical methods in order to point out the prognostic significance of the difference in methylation states at one or more genomic loci and predict whether the sample analyzed has a good or bad prognosis following treatment. | 07-05-2012 |
20120178632 | BIOMARKERS FOR IDENTIFYING PATIENT CLASSES - Disclosed are methods for classifying a patient with cancer as a candidate for therapy with a Bcl-2 family inhibitor comprising determining the level of at least one biomarker in a sample and comparing the biomarker level to a threshold level. Also described are methods for identifying classes of patients having a refractory cancer for second-line therapy comprising a Bcl-2 family inhibitor, where the method comprises determining the level of at least one biomarker in a sample and comparing the biomarker level to a threshold level. | 07-12-2012 |
20120178633 | DIAGNOSTIC COMPOSITION FOR AUTOIMMUNE DISEASES COMPRISING AGENT MEASURING CD3Z GENE METHYLATION LEVEL AND A METHOD FOR DIAGNOSING AUTOIMMUNE DISEASES USING THE SAME - The present invention relates to a diagnostic composition for autoimmune diseases, comprising agent measuring a methylation level of CD3Z gene, a diagnostic method and a kit using the same. More particularly, the present invention relates to a composition for diagnosing autoimmune diseases according to the methylation level of CD3Z gene, or additionally ADA or VHL gene, and a method for diagnosing autoimmune diseases by measuring the methylation level. The methylation of any one or more of the ADA, VHL, and CD3Z genes of the present invention is specific to autoimmune diseases, and thus the composition comprising an agent measuring a methylation level of the present invention can be used for the diagnosis of autoimmune diseases. | 07-12-2012 |
20120178634 | METHOD FOR DETERMINATION OF PRESENCE OF CANCER CELL, AND METHOD FOR DETERMINATION OF PROGNOSIS OF CANCER PATIENT - The present invention relates to a method for determination of the presence or absence of cancer cells in a biological sample or a method for determination of the progonsis of a colorectal cancer patient based on a result obtained by extracting DNA from a biological sample and analyzing methylation status of a marker gene in the DNA. | 07-12-2012 |
20120184447 | Methods and Nucleic Acids for Analysis of Bladder Cell Proliferative Disorders - The invention provides methods, nucleic acids and kits for detecting bladder carcinoma. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of said disorder, thereby enabling the improved diagnosis and treatment of patients. | 07-19-2012 |
20120190557 | RISK CALCULATION FOR EVALUATION OF FETAL ANEUPLOIDY - The present invention provides processes for determining accurate risk probabilities for chromosome dosage abnormalities. Specifically, the invention provides non-invasive evaluation of genomic variations through chromosome-selective sequencing and non-host fraction data analysis of maternal samples. | 07-26-2012 |
20120190558 | SCHIZOPHRENIA-RELATED ISOFORM OF KCNH2 AND DEVELOPMENT OF ANTIPSYCHOTIC DRUGS - The invention is related to a novel primate specific brain isoform of the potassium channel KCNH2 and genetic association with risk for schizophrenia and response to therapy. | 07-26-2012 |
20120190559 | DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING PAIRED END - Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes. | 07-26-2012 |
20120196754 | NON-INVASIVE DETERMINATION OF FETAL INHERITANCE OF PARENTAL HAPLOTYPES AT THE GENOME-WIDE SCALE - The present invention provides a method, device and a computer program for haplotyping single cells, such that a sample taken from a pregnant female, without directly sampling the fetus, provides the ability to non-invasively determine the fetal genome. The method can be performed by determining the parental and inherited haplotypes, or can be performed merely on the basis of the mother's genetic information, obtained preferably in a blood or serum sample. The novel device allows for sequence analysis of single chromosomes from a single cell, preferably by partitioning single chromosomes from a metaphase cell into long, thin channels where a sequence analysis can be performed. | 08-02-2012 |
20120196755 | COMPOSITIONS AND METHODS FOR GENOME-WIDE MAPPING OF CHROMOSOME BREAKAGE AND OTHER METHODS FOR MANIPULATION OF CELLS EMBEDDED IN MATRIX - The embodiments described herein provide for compositions and methods for genome-wide mapping of chromosome fragile sites in cellular chromosomal material. More specifically, a method of genome-wide detection of regions of single-stranded DNA and double stranded breaks in DNA, the hallmarks of chromosome fragility, comprises embedding a plurality of cells in a matrix and subsequently directly labeling the single-stranded DNA and/or double stranded DNA breaks; eluting or isolating the labeled chromosomal material from the matrix; and performing analysis to detect the location of the chromosome fragility sites. | 08-02-2012 |
20120196756 | DIGITAL SEQUENCE ANALYSIS OF DNA METHYLATION - The present invention relates to methods and compositions for determination of and uses of specific methylation patterns indicative of adenoma and carcinoma. In particular, the invention relates to analysis of defined CpG loci that are coordinately methylated in DNAs from cancer and adenoma samples, methods for identifying coordinately methylated loci, and methods of using analysis of coordinately methylated loci in one or more marker regions in the design of assays for adenoma and cancer. | 08-02-2012 |
20120196757 | PROGRAMMABLE OLIGONUCLEOTIDE SYNTHESIS - The invention relates to methods and devices for preparing synthetic nucleic acids. | 08-02-2012 |
20120202698 | HIGH THROUGHPUT DETECTION OF MOLECULAR MARKERS BASED ON AFLP AND HIGH THROUGH-PUT SEQUENCING - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker. | 08-09-2012 |
20120208705 | LINKING SEQUENCE READS USING PAIRED CODE TAGS - Artificial transposon sequences having code tags and target nucleic acids containing such sequences. Methods for making artificial transposons and for using their properties to analyze target nucleic acids. | 08-16-2012 |
20120208706 | OPTIMIZATION OF MULTIGENE ANALYSIS OF TUMOR SAMPLES - A method of analyzing a tumor sample comprising:
| 08-16-2012 |
20120208707 | LIGATION METHOD EMPLOYING RTCB - A method of processing an RNA sample is provided. In certain embodiments, the method may comprise: a) obtaining a fragmented RNA sample comprising: i. RNA fragments of long RNA molecules; and ii. unfragmented short RNA; and b) contacting said fragmented RNA sample with a first adaptor in the presence of a RtcB ligase, thereby producing a ligated RNA sample comprising adaptor-ligated fragments of long RNA. A kit for performing the method is also provided. | 08-16-2012 |
20120208708 | DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING MASSIVELY PARALLEL GENOMIC SEQUENCING - Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes. | 08-16-2012 |
20120208709 | GENETIC SUSCEPTIBILITY VARIANTS ASSOCIATED WITH CARDIOVASCULAR DISEASE - The invention relates to methods of diagnosing susceptibility to cardiovascular disease, including coronary artery disease, MI, abdominal aorta aneurysm, intracranial aneurysm restenosis and peripheral arterial disease, by assessing the presence or absence of alleles of certain polymorphic markers found to be associated with cardiovascular disease. The invention further relates to kits encompassing reagents for assessing such markers, and methods for assessing the probability of response to therapeutic agents and methods using such markers. | 08-16-2012 |
20120208710 | Noninvasive Diagnosis of Fetal Aneuoploidy by Sequencing - Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes. | 08-16-2012 |
20120208711 | Method for Analysis of DNA Methylation Profiles of Cell-Free Circulating DNA in Bodily Fluids - The invention can be summarized as follows. There is provided a method for analyzing DNA methylation profiles of cell-free DNA in body fluids by enriching a methylated or unmethylated fraction of DNA from cell-free DNA and subjecting the enriched DNA to microarray based methylome profiling and bioinformatics data analysis. | 08-16-2012 |
20120214677 | LUCIFERASE BIOSENSOR - A modified beetle luciferase protein which is an environmentally sensitive reporter protein is provided. | 08-23-2012 |
20120214678 | METHODS FOR DETERMINING FRACTION OF FETAL NUCLEIC ACIDS IN MATERNAL SAMPLES - The invention provides compositions and methods for determining the fraction of fetal nucleic acids in a maternal sample comprising a mixture of fetal and maternal nucleic acids. The fraction of fetal nucleic acids can be used in determining the presence or absence of fetal aneuploidy. | 08-23-2012 |
20120220466 | Measurement and Monitoring of Cell Clonality - Methods are provided for the detection and analysis of clonality in a cell population, where parallel sequencing is applied to a nucleic acid sample obtained from the cell population, optionally a population of lymphocytes. Replicate samples are amplified, and sequenced, where identification of coincident sequences in two or more replicates is indicative of clonal expansion. | 08-30-2012 |
20120220467 | Genetic Determinants of Prostate Cancer Risk - Described are methods of determining if a subject has a genetic predisposition to developing prostate cancer (PCa). | 08-30-2012 |
20120225785 | Automated Storage of a Discrete Sample Among Multiple Samples And Automated Selection of Such Discrete Sample for Processing - Automation of sample storage with a pipetting and nucleic acid adsorption system, which stores a patient nucleic acid sample in an identified location. In the event of system failure or interruption, software included as part of the system notes throughout the process, the stage and the sample(s) position through a tracking process. The software then generates a new set of commands for the system, based on the system's stage and the samples' position, so that the process resumes from the interruption point forward. | 09-06-2012 |
20120225786 | RISK VARIANTS FOR CANCER - It has been found that variants on chromosome 17q23.2 in the BRIP1 gene are associated with risk of cancer in humans. The invention provides diagnostic applications using such variants, including methods of determining susceptibility of cancer. | 09-06-2012 |
20120225787 | UNIFORM FRAGMENTATION OF DNA USING BINDING PROTEINS - The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least one protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments. | 09-06-2012 |
20120231959 | PERSONALIZED MEDICAL MANAGEMENT SYSTEM, NETWORKS, AND METHODS - Disclosed herein are systems and methods for the assignment of therapeutic pathways to members of a network of oncology. The systems and methods allow for storage of disparate information in a database and determine a uniform semantics for all of the stored information. In addition, the systems and methods allow for the calculation of treatment pathways based on patient information as well as publicly-available information relating to particular diseases, and for the refinement of those treatment pathways as new information is added. Robot-assisted genomic labs permit automated genetic testing, which is integrated with the system. | 09-13-2012 |
20120238455 | METHOD FOR DIAGNOSING DRUG ERUPTION RISK INDUCED BY ANTIEPILEPTIC DRUG BASED ON SINGLE NUCLEOTIDE POLYMORPHISM IN 21.33 REGION OF SHORT ARM OF CHROMOSOME 6 - The genotype of a single nucleotide polymorphism (SNP) existing in the 21.33 region of the short arm of chromosome 6, such as an SNP at the HLA-A locus, is analyzed, and, based on the results, drug eruption risk induced by an antiepileptic drug is diagnosed. | 09-20-2012 |
20120245037 | RESTRICTION ENZYME BASED WHOLE GENOME SEQUENCING - Method for de novo whole genome sequencing based on a (sequence-based) physical map of a DNA sample clone bank based on end-sequencing tagged adapter-ligated restriction fragments, in combination with sequencing adapter-ligated restriction fragments of the DNA sample wherein the recognition sequence of the restriction enzyme used in the generation of the physical map is identical to at least part of the recognition sequence of the restriction enzyme used in the generation of the DNA sample. | 09-27-2012 |
20120245038 | THERMAL CYCLING APPARATUS AND METHOD - A system for holding at least one of sample and reagent for analysis. The system includes a pair of parallel covers, at least one of which is light transmissive, of which pair a light transmissive cover forms a top, and of which pair the other forms a bottom. A frame is disposed between the covers to define, in relation to the covers, an interior volume. The frame and the covers are associated with one another to form a case, the case being substantially tight to liquids. A microfluidic array is disposed in the interior volume. The array includes a sheet of material having a pair of opposed surfaces, a thickness, and a plurality of through-holes running through the thickness between the surfaces, the through-holes containing at least one of sample and reagent. | 09-27-2012 |
20120245039 | Entangled Mate Sequencing - Methods and compositions are provided for performing a set of N DNA sequencing reaction cycles whereby sequence information is obtained for approximately 2*N nucleotide bases. | 09-27-2012 |
20120258866 | MULTI-DIMENSIONAL SELECTION OF PROTEIN MUTANTS USING HIGH THROUGHPUT SEQUENCE ANALYSIS - The invention is directed to methods for simultaneously improving a plurality of characteristics of a protein binding compound. In accordance with one aspect of the invention, a focused library of nucleic acid-encoded variants is produced and separately exposed to a plurality of reaction conditions each designed to segregate the library variants according to a different characteristic of interest, such as affinity, stability, cross-reactivity, or the like. In various embodiments, such reactions may be conducted pair-wise to simultaneously obtain improvements in two characteristics or they may be conducted three-at-a-time to simultaneously obtain improvements in three characteristics. In each case, nucleotide sequences encoding library variants segregated into improved subsets are determined, after which sequences occurring in two or more subsets are identified to obtain library variants with two or more improved characteristics. | 10-11-2012 |
20120258867 | HIGH THROUGH-PUT ANALYSIS OF TRANSGENE BORDERS - The present invention is a method to identify unknown DNA sequences which flank known DNA sequences. The invention improves the accuracy, sensitivity, and reproducibility for determining unknown DNA sequences which flank a known DNA sequence. This claimed method can be deployed as a high throughput method to quickly and efficiently identify plant genomic chromosomal sequences which flank a transgene. Further analysis of these unknown sequences can be used to characterize the transgene insertion site for the identification of rearrangements, insertions and deletions which result from the integration of the transgene. In addition, analysis of the chromosomal flanking sequences can be used to identify the location of the transgene on the chromosome. | 10-11-2012 |
20120264617 | DNA SEQUENCING EMPLOYING NANOMATERIALS - Charge transfer doped nanomaterials such as hydrogen terminated diamond, nanotubes, nanowires or similar nanostructures are used to create a highly sensitive pH sensor, or ion sensitive sensor to directly detect the addition of a newly incorporated nucleotide when performing DNA sequencing by synthesis. A single highly integrated chip can be made to sequence many strands of DNA in a massively parallel fashion in a short amount of time with a direct electronic readout that will bring the cost, size, power consumption of sequencing DNA to very attractive and useful levels. | 10-18-2012 |
20120264618 | QUANTIFICATION OF A MINORITY NUCLEIC ACID SPECIES - The technology relates in part to quantification of a minority nucleic acid species from a nucleic acid sample. In some embodiments, methods for determining the amount of fetal nucleic acid (e.g. absolute amount, relative amount) in a maternal sample are provided. | 10-18-2012 |
20120264619 | MICRORNA AFFINITY ASSAY AND USES THEREOF - The present invention provides methods and kits for determining which microRNAs bind to a target mRNA where the methods comprise the steps of (a) creating a bait sequence from the target mRNA, where the bait sequence comprises a label that binds to a binding agent; (b) adding a mixture of microRNAs to the bait sequence; (c) separating the microRNAs that bind to the bait sequence from those microRNAs that do not bind; and (d) identifying the microRNAs that bind to the bait sequence, wherein the microRNAs identified are those that bind to the target mRNA. | 10-18-2012 |
20120270739 | METHOD FOR SAMPLE ANALYSIS OF ANEUPLOIDIES IN MATERNAL SAMPLES - The invention provides methods for determining aneuploidy and/or fetal fraction in maternal samples comprising fetal and maternal cfDNA by massively parallel sequencing. The method comprises a novel protocol for preparing sequencing libraries that unexpectedly improves the quality of library DNA while expediting the process of analysis of samples for prenatal diagnoses. The novel protocol can be performed in solution or on a solid surface. | 10-25-2012 |
20120270740 | POLONY SEQUENCING METHODS - We describe ultra-high throughput polony genome sequencing that can permit, for example, generating raw data to re-sequencing the human genome in about one week (including library prep and sequencing) at a reasonable cost. The methods described herein include one or more of the following: (1) increasing polony sequencing read length, (2) improving library construction and emulsions protocols, (3) increasing bead density and/or moving to alternative clonal amplication strategies (other than emulsion PCR or ePCR), (4) extending software capabilities to allow SNP calls from our new sequencing raw data, (5) Dual Primer Emulsion PCR, and (6) diagnostic method exploiting one or more of the foregoing. | 10-25-2012 |
20120283106 | METHODS TO DETECT AND QUANTIFY RNA - Improved methods to quantitate RNA in biological or other analytical samples employ extended RNAs containing adaptors at the 5′ end and polyA sequences coupled to a tag at the 3′ end. The invention method is particularly useful in quantitating microRNAs as primers can be used that need not complement the non-conserved 3′ ends of these molecules. | 11-08-2012 |
20120283107 | Charge Perturbation Detection Method for DNA and Other Molecules - Methods for direct detection of chemical reactions are provided. Electric charge perturbations of the local environment during enzyme-catalyzed reactions are sensed by an electrode system with an immobilized target molecule. The charge perturbation caused by the polymerase reaction can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a voltage clamp amplifier. Detection of single nucleotides in a sequence can be determined by dispensing individual dNTPs to the electrode solution and detecting the charge perturbations. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal. This technique may be adapted to other reaction determinations, such as enzymatic reactions, other electrode configurations, and other amplifying circuits. | 11-08-2012 |
20120283108 | METHOD FOR PHASED GENOTYPING OF A DIPLOID GENOME - A method of sample analysis is provided. In certain embodiments the method comprises: a) obtaining from a diploid individual a chromosomal sample that comprises maternally-derived chromosomes and homologous paternally-derived chromosomes; b) determining the parent of origin of a first chromosome of the sample by detecting a parent-specific copy number variation relative to a second chromosome that is homologous to the first chromosome; c) isolating the first chromosome; and d) genotyping the first chromosome. | 11-08-2012 |
20120289408 | COMPOSITIONS AND METHODS FOR NUCLEIC ACID SEQUENCING - Compositions and methods for nucleic acid sequencing include template constructs that comprise double stranded portions in a partially or completely contiguous constructs, to provide for redundant sequence determination through one or both of sequencing sense and antisense strands, and iteratively sequencing the entire construct multiple times. Additional sequence components are also optionally included within such template constructs. Methods are also provided for the use and preparation of these constructs as well as sequencing compositions for their application. | 11-15-2012 |
20120289409 | Species Specific Nucleotide (SSN) Sequences as a Rapid Diagnostic - A data base of species specific nucleotide sequences (SSN) is created. The chemically synthesized sequences are used as DNA sequencing primers. Different mixes of DNA primers allow for the rapid and unique identification of any pathogen previously identified in the species specific data base. | 11-15-2012 |
20120289410 | GENETIC VARIANT IN FORMYL PEPTIDE RECEPTOR 2 (FPR2) PREDICTS CLINICAL OUTCOME IN CANCER PATIENTS - The disclosure provides compositions and methods for determining the likely tumor recurrence in cancer patients by screening formyl peptide receptor 2 (FPR2) polymorphism in samples isolated from the patient. | 11-15-2012 |
20120289411 | METHOD FOR SCREENING NUCLEIC ACID LIGAND - Provided is a method for screening a library of candidate for a nucleic acid ligand. The method includes the steps of: (a) preparing a library of candidate of nucleic acid ligands; (b) contacting, under the absence of a target substance, the library with a supporting member binding to at least one of conserved sequence domains included in the ligand, and then separating and removing a ligand which does not form an intermolecular duplex; and (c) dissociating the intermolecular duplex by contacting, under the presence of the target substance, the target substance with the remaining ligand forming the intermolecular duplex obtained in step (b), and then separating and collecting a ligand having a specific secondary structure formed by the binding to the target substance, wherein the method includes at least one time of step (b) and at least one time of step (c). | 11-15-2012 |
20120289412 | COMPLEXITY REDUCTION METHOD - The present invention relates to a method for the reduction of the complexity of nucleic acid pool(s), comprising
| 11-15-2012 |
20120295794 | COMPOSITIONS, METHODS, AND KITS FOR DETECTING RIBONUCLEIC ACID - Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined. | 11-22-2012 |
20120302447 | MOCK COMMUNITY FOR MEASURING PYROSEQUENCING ACCURACY AND METHOD OF MEASURING PYROSEQUENCING ACCURACY USING THE SAME - The present invention describes a method of measurement of pyrosequencing accuracy by directly calculating sequence errors from FLX Titanium pyrosequencing using mock community, according to the present invention, sequencing errors from FLX Titanium pyrosequencing in terms of microbial diversity and classification can be measured, resulting in possible effects of filtering. | 11-29-2012 |
20120302448 | DIGITAL ANALYTE ANALYSIS - The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, a method for determining the nucleic acid make-up of a sample is provided. | 11-29-2012 |
20120302449 | Chromosome Conformation Analysis - Disclosed herein are compositions, methods and kits for analyzing three-dimensional chromatin and/or chromosome conformation. Method are also disclosed for using the methods disclosed herein for diagnosing diseases such as cancer. | 11-29-2012 |
20120302450 | Bacterial Metastructure and Methods of Use - The present invention provides a method of determining bacterial metastructure by integrating multiple genome-scale information yielded by high-throughput technologies. The metastructure constructs a universal metabolic engineering platform enabling a rational design of bacterial strains through optimization of gene and protein expression. | 11-29-2012 |
20120302451 | COMPOSITIONS AND METHODS FOR GENE SIGNATURE-BASED CHEMICAL SCREENING - The invention provides products of manufacture for screening for compositions that can modify a cell's gene expression profile, and methods for making and using them. In one embodiment, the invention provides products of manufacture and methods comprising a high content, high throughput screening for a composition (e.g., chemicals, small molecules) that can modify a cell's physiology based on the composition's ability to modify the cell's gene expression signature. | 11-29-2012 |
20120309633 | HIGH THROUGHPUT SCREENING OF MUTAGENIZED POPULATIONS - Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation. | 12-06-2012 |
20120309634 | METHOD FOR PAIRWISE SEQUENCING OF TARGET POLYNUCLEOTIDES - The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template. Using the methods of the invention it is possible to obtain two linked or paired reads of sequence information from each double-stranded template on a clustered array, rather than just a single sequencing read from one strand of the template. | 12-06-2012 |
20120316072 | Methods for indexing samples and sequencing multiple polynucleotide templates - The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like. | 12-13-2012 |
20120316073 | STRATEGIES FOR HIGH THROUGHPUT IDENTIFICATION AND DETECTION OF POLYMORPHISMS - The invention relates to a method for the high throughput identification of single nucleotide polymorphisms by performing a complexity reduction on two or more samples to yield two or more libraries, sequencing at least part of the libraries, aligning the identified sequences and determining any putative single nucleotide polymorphisms, confirming any putative single nucleotide polymorphism, generating detection probes for the confirmed single nucleotide polymorphisms, subjection a test sample to the same complexity reduction to provide a test library and screen the test library for the presence or absence of the single nucleotide polymorphisms using the detection probe. | 12-13-2012 |
20120316074 | METHODS AND COMPOSITIONS FOR NUCLEIC ACID ANALYSIS - Provided herein are methods, compositions, and kits for assays, many of which involve amplification reactions such as digital PCR or droplet digital PCR. The assays may be used for such applications as sequencing, copy number variation analysis, and others. In some cases, the assays involve subdividing a sample into multiple partitions (e.g., droplets) and merging the partitions with other partitions that comprise adaptors with barcodes. | 12-13-2012 |
20120322665 | SYSTEM AND METHOD FOR DETECTION OF HIV-1 CLADES AND RECOMBINANTS OF THE REVERSE TRANSCRIPTASE AND PROTEASE REGIONS - A method for detecting low frequency occurrence of one or more HIV sequence variants associated with reverse transcriptase and/or protease is described that comprises the steps of: (a) generating a cDNA species from a plurality of RNA molecules in an HIV sample population; (b) amplifying a plurality of first amplicons from the cDNA species, wherein each first amplicon is amplified with a pair of nucleic acid primers capable of generating amplicons from an HIV clade comprising clade A, clade B, clade C, clade D, clade F, and clade G; (c) clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons; (d) determining a nucleic acid sequence composition of the second amplicons; and (e) detecting one or more sequence variants in the nucleic acid sequence composition of the second amplicons. | 12-20-2012 |
20120322666 | ISOLATION OF POLYMERASE-NUCLEIC ACID COMPLEXES - Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Active complexes can be isolated from mixtures having both active and inactive complexes by initiating nucleic acid synthesis so as to open up a portion of a double stranded region rendering that region single stranded. Hook molecules are targeted to bind the sequences that are thus exposed. The hook molecules bound to active polymerase-nucleic acid complex are isolated, and the active polymerase-nucleic acid complexes released. | 12-20-2012 |
20120322667 | METHODS OF IDENTIFYING INDIVIDUALS AT RISK OF PERIOPERATIVE BLEEDING, RENAL DYSFUNCTION OR STROKE - The present invention relates, in general, to perioperative bleeding and, in particular, to methods of identifying individuals at risk of perioperative bleeding. | 12-20-2012 |
20120322668 | ASSESSMENT OF SOLID TUMOR BURDEN - The present disclosure is directed toward measurement of expression of one or both of an activating Natural Killer (NK) cell receptor and its ligand(s) on peripheral blood cells as a means to assess solid tumor burden. In particular, the present disclosure provides tools for assessing cancer recurrence or risk thereof following reduction of a solid tumor, and for developing a treatment regime for a cancer patient. | 12-20-2012 |
20130005583 | NUCLEIC ACID SEQUENCING TECHNIQUE USING A PH-SENSING AGENT - The invention relates to a composition, method and apparatus for determining the sequence of a nucleic acid strand utilizing a pH-sensing agent. | 01-03-2013 |
20130005584 | METHODS OF MONITORING CONDITIONS BY SEQUENCE ANALYSIS - There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition. | 01-03-2013 |
20130005585 | NUCLEIC ACID ENCODING REACTIONS - Described herein are methods useful for incorporating one or more adaptors and/or nucleotide tag(s) and/or barcode nucleotide sequence(s) one, or typically more, target nucleotide sequences. In particular embodiments, nucleic acid fragments having adaptors, e.g., suitable for use in high-throughput DNA sequencing are generated. In other embodiments, information about a reaction mixture is encoded into a reaction product. Also described herein are methods and kits useful for amplifying one or more target nucleic acids in preparation for applications such as bidirectional nucleic acid sequencing. In particular embodiments, methods of the invention entail additionally carrying out bidirectional DNA sequencing. Also described herein are methods for encoding and detecting and/or quantifying alleles by primer extension. | 01-03-2013 |
20130005586 | METHOD OF DIAGNOSTIC OF OBESITY - A new method for diagnosing obesity is herein described, based on the determination of the absence of at least one gene from the human' gut microbiome. | 01-03-2013 |
20130005587 | AUTOMATED HIGH-THROUGHPUT FLOW-THROUGH REAL-TIME DIAGNOSTIC SYSTEM - An automated real-time flow-through system capable of processing multiple samples in an asynchronous, simultaneous, and parallel fashion for nucleic acid extraction and purification, followed by assay assembly, genetic amplification, multiplex detection, analysis, and decontamination. The system is able to hold and access an unlimited number of fluorescent reagents that may be used to screen samples for the presence of specific sequences. The apparatus works by associating extracted and purified sample with a series of reagent plugs that have been formed in a flow channel and delivered to a flow-through real-time amplification detector that has a multiplicity of optical windows, to which the sample-reagent plugs are placed in an operative position. The diagnostic apparatus includes sample multi-position valves, a master sample multi-position valve, a master reagent multi-position valve, reagent multi-position valves, and an optical amplification/detection system. | 01-03-2013 |
20130005588 | METHOD FOR DETERMINING SUBSTANCE NON-TOXICITY - Described herein are methods for establishing the non-toxicity of a substance. For example, described herein are methods for the construction of a comprehensive database of toxicity associated pathways and methods of using such a database. | 01-03-2013 |
20130012398 | Methods for small RNA sequencing - Next generation sequencing technologies are becoming a preferred method for sequencing nucleic acids and profiling miRNAs. Experimental results disclosed herein show that the most common platform for preparing nucleic acids such as miRNAs for sequencing introduces serious biases. Provided herein are compositions and methods for improved sequencing and miRNA profiling using a set of customized ligation adaptors. | 01-10-2013 |
20130012399 | SEQUENCING METHODS AND COMPOSITIONS - Provided herein are compositions, systems, methods and kits useful for obtaining sequence information from a nucleic acid molecule. In some embodiments, the compositions, systems, methods and kits are useful for sequencing of natural or modified nucleic acids. In some embodiments, the compositions, systems, methods and kits relate to bi-directional sequencing of nucleic acids. In some embodiments, the compositions, systems, methods and kits relate to sequencing of nucleic acids linked to a solid support. In some embodiments, the methods useful for obtaining sequence information from a nucleic acid molecule include label-free or ion-based sequencing methods. | 01-10-2013 |
20130017957 | METHODS OF MONITORING CONDITIONS BY SEQUENCE ANALYSIS - There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition. | 01-17-2013 |
20130017958 | MEANS AND METHODS FOR NON-INVASIVE DIAGNOSIS OF CHROMOSOMAL ANEUPLOIDY - The invention relates to a prenatal diagnostic method for the determination of a fetal chromosomal aneuploidy in a biological sample obtained from a pregnant woman, which method comprises enrichment and quantification of selected cell-free deoxyribonucleic acid sequences showing consensus nucleosome binding regions. | 01-17-2013 |
20130017959 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 01-17-2013 |
20130023420 | SUSCEPTIBILITY TO HSP90-INHIBITORS - The present invention relates to a combination of cell lines as well as a method of selecting (a) cell(s), (a) tissue(s) or (a) cell culture(s) with susceptibility to an HSP90 inhibitor anti-tumor agent. Also a method for determining the responsiveness of a mammalian tumor cell or cancer cell or collection of cells or cell lines to treatment with a drug such as an HSP90 inhibitor anti-tumor agent is described herein. | 01-24-2013 |
20130023421 | PROTEIN DISPLAY - The present invention relates to methods for screening a polypeptide for desired activity against a target molecule In particular, the present invention relates to methods for screening a polypeptide for desired activity against a target molecule by expressing the polypeptide in a bacterial cell and permeabilising the cell. | 01-24-2013 |
20130029851 | CALORIMETER SENSOR - A calorimeter device includes various components located on a common substrate. A first (calorimeter) integrated chip device is located on the substrate. This first device has a first microfluidic channel that has first side and a second side. A first heat sensing circuit is located on the first side of the first channel and a second heat sensing circuit is located on the second side of the channel, opposite the first side and facing the first heat sensing circuit. A second integrated chip device is located on the substrate and proximal to the first device. The second device includes a second microfluidic channel having a fourth side and fifth side. A third heat sensing circuit is located on the third side of the second channel. A fourth heat sensing circuit is located on the fourth side of the channel, opposite the third side and facing the third heat sensing circuit. | 01-31-2013 |
20130029852 | DETECTING AND CLASSIFYING COPY NUMBER VARIATION - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample. | 01-31-2013 |
20130029853 | CLASSIFICATION OF NUCLEIC ACID TEMPLATES - Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid. | 01-31-2013 |
20130035237 | Nucleotides and Nucleosides and Methods for their Use in DNA Sequencing - The present invention relates generally to labeled and unlabled cleavable terminating groups and methods for DNA sequencing and other types of DNA analysis. More particularly, the invention relates in part to nucleotides and nucleosides with chemically cleavable, photocleavable, enzymatically cleavable, or non-photocleavable groups and methods for their use in DNA sequencing and its application in biomedical research. | 02-07-2013 |
20130035238 | METHOD FOR GENOME COMPLEXITY REDUCTION AND POLYMORPHISM DETECTION - The present invention provides methods to produce a reduced representation of a genome for sequencing and DNA polymorphism detection. In particular, the invention provides PCR-based methods, with normalization of the amplified products using a duplex-specific nuclease, in order to reduce over-representation of PCR products. Oligonucleotides for use in the disclosed method are also provided. | 02-07-2013 |
20130035239 | FILTERING SMALL NUCLEIC ACIDS USING PERMEABILIZED CELLS - Filtering small nucleic acids using permeabilized cells and methods for using the filtering to detect genomic DNA accessibility are described. | 02-07-2013 |
20130035240 | Markers for Obesity and Methods of Use Thereof - Markers for obesity, particularly childhood obesity, are provided along with methods of use thereof. | 02-07-2013 |
20130035241 | KEY GENES, MICRORNAS, OTHER NON-CODING RNAS AND COMBINATION THEREOF FOR IDENTIFYING AND REGULATING THE PLURIPOTENT STATUS OF CELLS - Key genes, microRNAs, other non-coding RNAs and a combination thereof for identifying and regulating pluripotency of cells are provided. The key genes, microRNAs, other non-coding RNAs and a combination thereof are highly expressed in full pluripotent stem cells but are significantly suppressed or silenced in partially pluripotent stem cells. The genes, microRNAs and other non-coding RNAs are those of a chromosome imprinted Dlk1-Dio3 region located on the long arm of mouse chromosome 12, and are homologous genes, microRNAs and other non-coding RNAs having 70-100% homology with them in genomic syntenic regions of other mammals. Also provided are uses of the genes, microRNAs, other non-coding RNAs and combination thereof in identifying the pluripotent status of stem cells and regulating pluripotency of cells; in typing stem cells; regulating pluripotency of cells, pluripotent states and levels of cells; treating diseases; and developing drug targets for tumor treatment and antitumor drugs. | 02-07-2013 |
20130035242 | HIGH THROUGHPUT SAMPLE ANALYZER - A sample processing system ( | 02-07-2013 |
20130040824 | DETECTION OF GENETIC OR MOLECULAR ABERRATIONS ASSOCIATED WITH CANCER - Biological samples including cell-free DNA fragments are analyzed to identify imbalances in chromosomal regions, e.g., due to deletions and/or amplifications in a tumor. Multiple loci are used for each chromosomal region. Such imbalances can then be used to diagnose (screen) a patient for cancer, as well as prognosticate a patient with cancer, or to detect the presence or to monitor the progress of a premalignant condition in a patient. The severity of an imbalance as well as the number of regions exhibiting an imbalance can be used. A systematic analysis of non-overlapping segments of a genome can provide a general screening tool for a sample. Additionally, a patient can be tested over time to track severity of each of one or more chromosomal regions and a number of chromosomal regions to enable screening and prognosticating, as well as monitoring of progress (e.g. after treatment). | 02-14-2013 |
20130040825 | DNA DAMAGE DETECTION ASSAY AND METHOD - A novel assay for determining in vivo or in vitro strand-specific endogenous and/or induced damage in a DNA sample. The method is rapid, reliable, and highly sensitive, and comprises a primer-anchored DNA damage detection assay (“PADDA”). The method can be used for, but is not limited to, quantification and/or mapping of overall or site-specific damage in the template DNA sample. By quantification or mapping of DNA damage, this assay can be used to assess individual or a tumor's susceptibility to specific genotoxics (e.g., tobacco and chemotherapeutic agents) and therefore determine cancer risk and therapeutic response. Additionally, by quantification or mapping of DNA damage, this assay can be used to determine multiple responses of certain genes to a variety of DNA lesions in a research oriented setting. | 02-14-2013 |
20130040826 | METHODS FOR TRAIT MAPPING IN PLANTS - The present invention provides methods for identifying the nucleic acid sequences responsible for phenotypic traits in plants. | 02-14-2013 |
20130040827 | METHOD AND COMPOSITIONS FOR DETECTING AND SEQUENCING NUCLEIC ACIDS - The invention is directed to methods of nucleic acid sequencing that use nanopores to detect and/or measure amounts of compounds, such as products or byproducts of nucleic acid sequencing reactions, and to the determination of a nucleotide sequence using such detection and/or measurement. The detection or measurements may employ products or byproducts having resistive-pulse labels, optical labels, or labels that are capable of generating both optical and resistive-pulse signals. Resistive-pulse labels are molecular labels bound or attached to an analyte which allows detection of the labeled analyte by a change in the electrical properties of a nanopore, such as trans-nanopore resistance. Labels for nanopore detection may also be optical labels, particularly acceptors of acceptor-donor pairs capable of undergoing fluorescent resonance energy transfer (FRET), where the donors are associated with, or label, a nanopore. | 02-14-2013 |
20130040828 | METHOD FOR DETECTING GENE REGION FEATURES BASED ON INTER-ALU POLYMERASE CHAIN REACTION - The present invention provides a method for detecting features of genic region based on inter-Alu polymerase chain reaction using segments of the consensus sequences of Alu element family, especially the AluY subfamily, as the main oligonucleotide primers to amplify genomic DNA, followed by massively-parallel DNA sequencing of the amplicons. The features of genomic regions detected comprise single nucleotide polymorphisms (SNP), point mutations, sequence insertion/deletions (indel) and the level of DNA CpG loci methylation. | 02-14-2013 |
20130045872 | METHODS OF TARGETED SEQUENCING - The present invention provides methods for targeted sequencing of polynucleotide. In one aspect, the present invention provides a method of sequencing a target polynucleotide with fewer probes. In another aspect, the present invention provides a method of sequencing a target polynucleotide with longer reads. Locus-specific, ligation-assisted sequencing/genotyping method and ligation-captured sequencing method are also provided in the present invention. The methods of the present invention allow low-cost, high-throughput and accurate sequencing of nucleic acids. | 02-21-2013 |
20130045873 | METHODS FOR IDENTIFYING AND USING ORGAN-SPECIFIC PROTEINS IN BLOOD - The present invention relates generally to methods for identifying organ-specific secreted proteins and for identifying organ-specific molecular blood fingerprints therefrom. As such, the present invention provides compositions comprising such proteins, detection reagents for detecting such proteins, and panels, and arrays for determining organ-specific molecular blood fingerprints. | 02-21-2013 |
20130045874 | Method of Diagnostic of Inflammatory Bowel Diseases - A new method for diagnosing an inflammatory bowel disease is herein described, based on the determination of the absence of at least one gene from the human' gut microbiome. | 02-21-2013 |
20130053252 | NUCLEIC ACID AMPLIFICATION AND SEQUENCING BY SYNTHESIS WITH FLUOROGENIC NUCLEOTIDES - In general, the invention features methods and systems for sequencing of nucleic acids based on the measurement of the incorporation of fluorogenic nucleotides in microreactors. The invention provides numerous advantages over previous systems such as unambiguous determination of sequence, fast cycle time, long read lengths, low overall cost of reagents, low instrument cost, and high throughput. The invention also features methods and kits for nucleic acid amplification. The amplification and sequencing aspects of the invention may or may not be employed in conjunction with one another. The invention also features fluorogenic nucleotides that may be used in the sequencing methods of the invention. | 02-28-2013 |
20130059733 | MOLECULAR TESTING OF MULTIPLE PREGNANCIES - Methods, systems, and apparatus are provided for determining zygosity of a multiple-fetus pregnancy using a biological sample taken from the mother. The fetal and maternal DNA in the sample (e.g. plasma) can be analyzed for a particular chromosomal region to identify genetic differences in the fetuses. For example, a normalized parameter for the measure of a primary or secondary allele can show variances for different chromosomal regions when fetuses are dizygotic. Such a variance can be determined relative to an expected value if the fetuses were genetically identical. Statistical methods are provided for analyzing the variation of the normalized parameters to determine fetal DNA concentration and the maternal-fetal mixed genotype at various loci. Parental genotype and haplotype information can also be used to identify inheritance of different parental haplotypes to indicate genetic differences among the fetuses. | 03-07-2013 |
20130059734 | Epigenetic analysis - Provided herein are methods for the analysis of methylation in nucleic acid molecules, comprising bisulfite conversion and subsequent copying or amplification in the presence of a ligand-labelled dCTP or a ligand-labelled dGTP incorporated at the site of a cytosine or complementary guanine, respectively, at positions corresponding to methylated cytosines in the bisulfite-treated nucleic acid or after the copying or amplification, subjecting the resulting nucleic acid molecules to restriction endonuclease digestion with an enzyme which comprises a cytosine nucleotide in its target recognition sequence to generate nucleic acid fragments with termini proximal or adjacent to one or more cytosines and attaching a ligand or oligonucleotide adaptor and subsequently amplifying the nucleic acid molecules. | 03-07-2013 |
20130059735 | METHODS FOR MULTIPLEX AMPLIFICATION - Methods for multiplex amplification of target nucleic acid sequences are provided. | 03-07-2013 |
20130059736 | METHODS AND COMPOSITIONS FOR PROFILING RNA MOLECULES - Disclosed are compositions and methods for detecting target RNA molecules. A specialized DNA probe can be used to form RNA/DNA hybrids with target RNA molecules. Separation of the RNA/DNA hybrids increases the ease and sensitivity of detection and quantitation of the target RNA molecules. | 03-07-2013 |
20130059737 | EFFICIENT SHOTGUN SEQUENCING METHODS - Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes). By designing an efficient (simple to implement, speedy, high specificity, low cost) selection procedure, a more complete sequence is achieved with less effort than by using highly redundant shotgun sequencing in an initial sequencing procedure | 03-07-2013 |
20130059738 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for determining copy number variation of one or more nucleic acids present in a sample. In some aspects, the method includes various target-specific primers that allow for the selective amplification of one or more target nucleic acids in the sample. In yet another aspect, the invention relates to determining copy number variation with respect to gene or chromosome representation of a nucleic acid in the sample. In some aspects, the method for determining copy number variation of different target nucleic acids in a sample using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including diagnosis, predictive therapeutic regimes or other therapeutic purposes. | 03-07-2013 |
20130059739 | METHOD FOR HIGH-THROUGHPUT AFLP-BASED POLYMORPHISM DETECTION - The invention relates to a method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of restriction endonuclease digest of DNA, adaptor-ligation, optional pre-amplification, selective amplification, pooling of the amplified products, sequencing the libraries with sufficient redundancy, clustering followed by identification of the genetic markers within the library and/or between libraries and determination of (co-)dominant genotypes of the genetic markers. | 03-07-2013 |
20130065768 | RANDOM ARRAY SEQUENCING OF LOW-COMPLEXITY LIBRARIES - The invention is directed to a method of sequencing low-complexity amplicons randomly arrayed at high density on a surface. Methods of the invention include preparing amplicons for sequencing by a sets of primers that ensure initial signals front different amplicons on the surface will be evenly distributed among the different nucleotides being added in a sequencing by synthesis operation. | 03-14-2013 |
20130065769 | SALIVARY BIOMARKERS FOR GASTRIC CANCER DETECTION - Disclosed herein are biomarkers related to gastric cancer. The presently identified salivary biomarkers create the basis for a gastric cancer detection bioassay with sensitivity and specificity. Means and methods for evaluating the data generated using multiple biomarkers in order to validate findings and further use of the multiplexed gastric cancer assay in clinical, diagnostic and therapeutic uses is also included. | 03-14-2013 |
20130072386 | PHYSICAL MAP CONSTRUCTION OF WHOLE GENOME AND POOLED CLONE MAPPING IN NANOCHANNEL ARRAY - Methods for generating physical maps for polynucleotides, such as genomic DNA, are disclosed herein. Also disclosed are methods for identifying the source of polynucleotides. The methods can, for example, be used in physical map construction of whole genome. In addition, methods and systems capable of performing high throughput characterization of macromolecules using nanofludic devices are enclosed. | 03-21-2013 |
20130072387 | Method of Pooling and/or Concentrating Biological Specimens for Analysis - The present invention provides methods for concentrating and pooling liquid suspensions of biological specimens containing analytes of interest in a dry state. The dried biological specimens containing analytes of interest are reconstituted and released from the matrix for subsequent analysis in concentrated form. | 03-21-2013 |
20130079231 | METHODS FOR OBTAINING A SEQUENCE - The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads. | 03-28-2013 |
20130079232 | METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING - The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected. | 03-28-2013 |
20130085073 | CONTINUOUS EXTENSION AND DEBLOCKING IN REACTIONS FOR NUCLLEIC ACIDS SYNTHESIS AND SEQUENCING - A reaction mixture including (a) a nucleic acid having a primer hybridized to a template, (b) nucleotide analogs, wherein the nucleotide analogs have a blocking moiety; (c) a polymerase that is capable of forming an extended primer by adding the nucleotide analogs to the primer, and (d) a deblocking agent that is capable of removing the blocking moiety from the extended primer. Also provided is a method of synthesizing a polynucleotide including sequentially adding a plurality of the different nucleotides analogs to the nucleic acid via several reaction cycles in the reaction mixture, wherein each reaction cycle includes (i) the polymerase adding a nucleotide analog to the nucleic acid to form a transient nucleic acid species comprising a blocking moiety, and (ii) the deblocking agent modifying the transient nucleic acid species to remove the blocking moiety. | 04-04-2013 |
20130090247 | METHODS AND SYSTEMS FOR IDENTIFICATION OF BINDING PHARMACOPHORES - The invention provides systems and methods for generating 3D binding consensus pharmacophores. Initially, peptide screening sequence data is aligned. For one or more positions of the alignment: an observed distance matrix describing a distance between the relative binding activity of pairwise comparisons of each amino acid at the selected position is constructed, the observed distance matrix is compared to a plurality of field-based amino acid substitution matrices having the same shape as the observed distance matrix, preferred amino acid substitution matrices are identified from the plurality of amino acid substitution matrices based on the comparison, and a plurality of characteristics for the selected position are identified using the preferred amino acid substitution matrices. Characteristics for a plurality of positions of the alignment are used to generate three-dimensional peptide structures that represent predicted binding conformations. Molecular field information for these structures is clustered to determine a consensus field pharmacophore. | 04-11-2013 |
20130090248 | SELECTION OF COMPARTMENTALISED SCREENING - The present invention provides novel microfluidic substrates and methods that are useful for performing biological, chemical and diagnostic assays. The substrates can include a plurality of electrically addressable, channel bearing fluidic modules integrally arranged such that a continuous channel is provided for flow of immiscible fluids. | 04-11-2013 |
20130090249 | TOOLS FOR THE IDENTIFICATION OF LINGO-1, LINGO-2, LINGO-3 AND LINGO-4 LIGANDS, AND USES THEREOF - The present invention relates to a system comprising coupling products formed by a monomer of a protein chosen from Lingo-1, Lingo-2, Lingo-3 and Lingo-4 and by a probe emitting a signal when said monomer undergoes conformational changes, and to a screening method using said system, enabling ligands of a protein chosen from Lingo-1, Lingo-2, Lingo-3 and Lingo-4 to be identified. The present invention is industrially applicable in the field of methods for detecting molecules, for detecting interaction between molecules and for molecular screening, and also in the medical field. | 04-11-2013 |
20130090250 | ASSAY SYSTEMS FOR GENETIC ANALYSIS - The present invention provides assays systems and methods for detection of chromosomal abnormalities and status of single loci associated with monogenic or polygenic traits in a sample containing nucleic acids from a maternal and a fetal source. | 04-11-2013 |
20130096009 | METHODS OF IDENTIFYING INTERACTIONS BETWEEN GENOMIC LOCI - The disclosed Hi-C protocol can identify genomic loci that are spatially co-located in vivo. These spatial co-locations may include, but are not limited to, intrachromosomal interactions and/or interchromosomal interactions. Hi-C techniques may be applied to many different scales of interest. For example, on a large scale, Hi-C techniques can be used to identify long-range interactions between distant genomic loci. | 04-18-2013 |
20130096010 | HtSNPs FOR DETERMINING A GENOTYPE OF CYTOCHROME P450 1A2, 2A6 AND 2D6, PXR AND UDP-GLUCURONOSYLTRANSFERASE 1A GENE AND MULTIPLEX GENOTYPING METHODS USING THEREOF - The present invention relates to htSNPs for determining a genotype of cytochrome P450 1A2 (CYP1A2), 2A6 (CYP2A6) and 2D6 (CYP2D6), PXR and UDP-glucuronosyltransferase 1a (UGT1A) genes and a gene chip using the same, and more particularly, to a selection method of htSNPs for determining a haplotype of human CYP1A2, CYP2A6, CYP2D6, PXR and UGT1A genes, a method of determining a genotype of the genes by using the htSNPs and a gene chip therefor. | 04-18-2013 |
20130096011 | DETECTING AND CLASSIFYING COPY NUMBER VARIATION - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample. | 04-18-2013 |
20130096012 | METHOD AND KIT FOR IDENTIFYING A TRANSLATION INITIATION SITE ON AN MRNA - The present invention relates to a method and kit for identifying a translation initiation site on an mRNA. The method involves contacting a first mRNA with a first translation inhibitor to preferentially stabilize one or more initiation ribosomes at translation initiation sites on the first mRNA. A second mRNA is contacted with a second translation inhibitor different from the first translation inhibitor to stabilize one or more initiation ribosomes and one or more elongation ribosomes on the second mRNA. The location of ribosomes stabilized on the first mRNA is compared to the location of ribosomes stabilized on the second mRNA. | 04-18-2013 |
20130096013 | METHODS AND SYSTEMS FOR ELECTRONIC SEQUENCING - The present invention provides for methods and systems for Electronic DNA sequencing, single molecule DNA sequencing, and combinations of the above, providing low cost and convenient sequencing. | 04-18-2013 |
20130096014 | MULTIPLEX AMPLIFICATION OF POLYNUCLEOTIDES - The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis. | 04-18-2013 |
20130102476 | COMBINED CGH & ALLELE SPECIFIC HYBRIDISATION METHOD - The invention combines the fields of comparative genomic hybridisation (CGH) analysis and SNP array analysis. It relates to methods for detecting and mapping genetic abnormalities associated with various diseases. In particular the invention provides a method for simultaneously performing array CGH and SNP array analysis on a genomic DNA sample comprising contacting a nucleic acid array which comprises a first probe set and a second probe set with a genomic DNA sample, comprising a test and reference sample, under hybridisation conditions, comparing the amount of test sample and reference sample hybridised to the hybridisation probes of the first probe set, comparing the amount of test sample and reference sample hybridised to the hybridisation probes of the second probe set; and using the data obtained to determine the copy number of at least one locus; and at least one SNP in the genomic DNA sample. | 04-25-2013 |
20130102477 | BIOMARKERS FOR NON-HODGKIN LYMPHOMAS AND USES THEREOF - The disclosure provides a method of identifying a subject as having B-cell non-Hodgkin lymphoma (NHL) such as testing a sample from a subject for a mutation in one or more biomarkers. Also described are methods for classifying or monitoring a subject having, or suspected of having, B-cell non-Hodgkin lymphoma comprising testing the sample for a mutation in one or more biomarkers. | 04-25-2013 |
20130109575 | MICROFLUIDIC SYSTEMS AND METHODS FOR REDUCING THE EXCHANGE OF MOLECULES BETWEEN DROPLETS | 05-02-2013 |
20130109576 | METHODS FOR DETECTING MUTATIONS | 05-02-2013 |
20130116126 | COMPOSITIONS AND METHODS FOR IDENTIFYING AND MODIFYING CARBONACEOUS COMPOSITIONS - This invention generally relates to natural gas and methylotrophic energy generation, bio-generated fuels and microbiology. In alternative embodiments, the invention provides nutrient amendments and microbial compositions, e.g., consortia, that are both specifically optimized to stimulate methanogenesis, or for “methylotrophic” or other conversions. In alternative embodiments, the invention provides methods to develop nutrient amendments and microbial compositions that are both specifically optimized to stimulate methanogenesis in a given reservoir. The invention also provides methods for the evaluation of potentially damaging biomass formation and scale precipitation resulting from the addition of nutrient amendments. In other embodiments, the invention provides methods for simulating biogas in sub-surface conditions using a computational model. | 05-09-2013 |
20130116127 | BREAST CANCER ASSOCIATED CIRCULATING NUCLEIC ACID BIOMARKERS - The invention provides methods and reagents for diagnosing breast cancer that are based on the detection of biomarkers in the circulating nucleic acids from a patient to be evaluated. | 05-09-2013 |
20130116128 | INTEGRATED SEQUENCING APPARATUSES AND METHODS OF USE - Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing. | 05-09-2013 |
20130116129 | METHOD FOR DETECTING TARGET MOLECULES - The present invention provides a method for detecting a target molecule using the sequence information of a collection (pool) of aptamers capable of specifically binding to a target molecule, comprising the following steps of: (a) bringing a target molecule into contact with a collection of oligonucleotides which comprise multiple nucleic acid aptamers having different randomized sequences; (b) selecting a subcollection of oligonucleotides that bind to the target molecule; (c) examining the sequence of each oligonucleotide of the selected subcollection; (d) extracting sequence information which is characteristic to the oligonucleotides having affinity for the target molecule, from the sequences of the selected oligonucleotides; and (e) identifying the target molecule based on the sequence information. | 05-09-2013 |
20130123113 | METHODS FOR SEQUENCE-DIRECTED MOLECULAR BREEDING - The present invention provides breeding methods and compositions to enhance the germplasm of a plant by the use of direct nucleic acid sequence information. The methods describe the identification and accumulation of preferred nucleic acid sequences in the germplasm of a breeding population of plants. | 05-16-2013 |
20130123114 | METHOD FOR DETECTING HUMAN PAPILLOMA VIRUS BASED ON SOLEXA SEQUENCING METHOD - The present invention relates to a method for detecting Human Papilloma Virus (HPV), in particular, to a method for detecting HPV based on Solexa sequencing method. | 05-16-2013 |
20130123115 | OPTIMIZED CELLULASE ENZYMES - The invention discloses cellulase enzymes with optimized properties for processing of cellulose- and lignocellulose-containing substrates. In particular, cellobiohydrolase enzymes with preferred characteristics are disclosed. The present invention provides fusion, insertion, deletion and/or substitution variants of such enzymes. Enzyme variants have enhanced thermostability, proteolytic stability, specific activity and/or stability at extreme pH. Nucleic acid molecules encoding said enzymes, a composition comprising said enzymes, a method for preparation, and the use for cellulose processing and/or for the production of biofuels are disclosed. | 05-16-2013 |
20130123116 | DIAGNOSIS KIT AND CHIP FOR BLADDER CANCER USING BLADDER CANCER SPECIFIC METHYLATION MARKER GENE - The present invention relates to a kit and nucleic acid chip for diagnosing bladder cancer using a bladder cancer-specific marker gene. More particularly, the invention relates to a kit and nucleic acid chip for diagnosing bladder cancer, which can detect the promoter methylation of a bladder cancer-specific gene, the promoter or exon region of which is methylated specifically in transformed cells of bladder cancer. The use of the diagnostic kit or nucleic acid chip of the invention enables diagnosis of bladder cancer at an early stage of transformation, thus enabling early diagnosis of bladder cancer, and can diagnose bladder cancer in a more accurate and rapid manner compared to a conventional method. | 05-16-2013 |
20130123117 | CAPTURE PROBE AND ASSAY FOR ANALYSIS OF FRAGMENTED NUCLEIC ACIDS - Disclosed is an efficient and scalable method for targeted resequencing and variant identification of nucleic acids such as genomic DNA found in single stranded, fragmented form, such as in a clinical sample of formalin-fixed, paraffin-embedded (FFPE) tissue. The method uses a large number of capture probes mixed with the sample in the presence of a 5′ to 3′ exonuclease, a 3′ to 5′ exonuclease, a ligase, and a universal amplification oligonucleotide that hybridizes to the various capture probes. The nucleases act on ssDNA, not dsDNA. A single stranded circle is formed by the ligase, and is then amplified to produce a population (library) of double stranded linear DNA molecules that are suitable for sequencing. It is shown that the library produces a high degree of fidelity to the original sample, and predictable base changes are shown. | 05-16-2013 |
20130130917 | METHOD FOR SPECIFIC ENRICHMENT OF NUCLEIC ACID SEQUENCES - The invention discloses a method for immobilizing nucleic acid probes to solid substrates. Also disclosed is a micro column format for specific sequence capture which enables efficient and convenient enrichment of target sequences from a complex source. The capture probes are immobilized onto microspheres or fibrous filter as the active component inside the column. The column format allows hybridization, post-hybridization wash and recovery of captured sequences all to take place in a simple device without sophisticated equipment. | 05-23-2013 |
20130130918 | EXERCISE GENOTYPING - The invention relates to a method for identifying a genetic predisposition of a subject to increased exercise endurance, increased muscular power, muscle damage and/or injury risk, a method for formulating an exercise program for improving physical performance, a kit suitable for use in the methods and use of the method for improving physical performance. | 05-23-2013 |
20130130919 | Long-Range Barcode Labeling-Sequencing - Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes. | 05-23-2013 |
20130130920 | HIGH THROUGH-PUT ANALYSIS OF TRANSGENE BORDERS - A method of analyzing, in chromosomal DNA having a transgene incorporated therein, a DNA flanking region derived from the chromosome which is adjacent to the transgene. Wherein, the DNA flanking region is characterized by isolation and digestion of genomic DNA with a restriction enzyme, ligation of a double stranded adapter to the isolated and digested genomic DNA, a primer extension reaction of the adapter ligated genomic DNA, and the isolation of the primer extension reaction product via a streptavidin-biotin interaction. The DNA flanking region is further characterized via subsequent PCR amplification reactions and DNA sequencing. | 05-23-2013 |
20130130921 | Kit, a Device and a Method for Detecting Copy Number of Fetal Chromosomes or Tumor Cell Chromosomes - The invention relates to a kit, a device and a method for detecting the copy number of fetal chromosomes and tumor cell chromosomes. The method for detecting the copy number of fetal chromosomes or tumor cell chromosomes of the invention includes the following steps: collecting maternal plasma or plasma of tumor patient; separating the plasma from blood cells in blood; preparing Deoxyribonucleic Acids (DNA) in the plasma into a sequencing library; sequencing the DNA sequencing library; comparing a sequencing result with a genomic sequence map to determine which chromosome the DNA sequence comes from and the length of each DNA sequence; and calculating the ratio of the DNA segments from the chromosomes to be detected to all DNA segments in the same sample by a sequencing and comparison result of DNA, correcting the ratio according to a GC content of the DNA segments from the chromosomes to be detected, and calculating the variation of the corrected ratio of the DNA segments from the chromosomes to be detected in a sample to be detected, and determining the copy number of the chromosomes to be detected according to degree of variation. | 05-23-2013 |
20130137583 | Complexity Management of Genomic DNA - The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms. | 05-30-2013 |
20130137584 | NOVEL DIAGNOSTIC AND THERAPEUTIC TARGETS ASSOCIATED WITH OR REGULATED BY N-CADHERIN EXPRESSION AND/OR EPITHELIAL TO MESENCHYMAL TRANSITION (EMT) IN PROSTATE CANCER AND OTHER MALIGNANCIES - The present invention provides methods of diagnosing a cancer or providing a prognosis for a cancer by analyzing the level of expression of a marker that is a downstream target of N-cadherin. | 05-30-2013 |
20130137585 | NEW COMBINATION OF EIGHT RISK ALLELES ASSOCIATED WITH AUTISM - The invention relates to a method of detecting the presence of or predisposition to autism, or to an autism spectrum disorder in a subject, the method comprising detecting the combined presence of an alteration in the gene loci of at least PITX1, ATP2B2, EN2, JARID2, MARK1, ITGB3, CNTNAP2, and HOXA1 in a sample from said subject. | 05-30-2013 |
20130137586 | STABILIZATION OF NUCLEIC ACIDS IN CELL MATERIAL-CONTAINING BIOLOGICAL SAMPLES - The present invention relates to the use of an aqueous system for stabilizing cell material-containing biological samples while preserving the cell morphology of the cell material and to a method for stabilizing nucleic acids in cell material-containing biological samples while preserving the cell morphology of the cell material. | 05-30-2013 |
20130137587 | COMBINATORIAL SEQUENCE BARCODES FOR HIGH THROUGHPUT SCREENING - The invention involves methods and uses of a combination of at least two nucleotide sequence identifiers in the preparation of a sample DNA for high throughput sequencing. Accordingly, in the high throughput sequencing a plurality of prepared sample DNAs, each preparation of a sample DNA comprises a unique combination of the at least two nucleotide sequence identifiers wherein a first nucleotide sequence identifier is selected from a group of nucleotide sequence identifiers and a second nucleotide sequence identifier is selected from the group of nucleotide sequence identifiers. | 05-30-2013 |
20130137588 | SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS - The invention provides compositions and methods for preparing DNA sequencing libraries. In particular, the method relates to preparing DNA sequencing libraries from kilobase scale nucleic acids. The invention also provides methods for assembling short read sequencing data into longer contiguous sequences. The method is useful for various applications in genomics, including genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes. | 05-30-2013 |
20130143745 | COMPOSITIONS AND METHODS FOR IDENTIFYING THE ESSENTIAL GENOME OF AN ORGANISM - Compositions and methods are provided for the rapid and highly accurate identification of the entire essential genome of any organism under a given selection condition at a resolution of a few base pairs. An engineered transposon bearing an adapter sequence for ultra high throughput adaptor-based sequencing is employed for hyper-saturated transposon mutagenesis. Transposon junctions are subsequently isolated and collectively amplified through a shared parallel PCR strategy such that a second adaptor sequence is further incorporated into template DNA so that the first adaptor sequence and the second adaptor sequence flank the 5′ and 3′ regions of the sample DNA, respectively. Sample DNA is then sequenced in an ultra high-throughput adaptor-based DNA sequencer using adaptor primers. Transposon insertion sites are mapped onto the organism's genome, allowing for the algorithmic identification of essential genetic elements based on genomic transposition frequency. | 06-06-2013 |
20130143746 | METHOD FOR DETECTING GENE REGION FEATURES BASED ON INTER-ALU POLYMERASE CHAIN REACTION - An array of inter-Alu gene-enriched amplicons produced by a polymerase chain reaction (“PCR”) process. The PCR process comprises combining one or a plurality of Head-type/Tail-type Alu- or AluY- or any other Alu-subfamily-consensus sequence-based primer; a genomic DNA template isolated from cells; and a PCR-extension mix. The combination of primers, DNA template; and PCR extension mix comprises an inter-Alu-PCR-mixture. After making the inter-Alu-PCR mixture, an inter-Alu PCR cycle program is used in connection with a PCR machine for a period of time to produce the array of inter-Alu gene-enriched amplicons that are sequenced by massively parallel sequencing to allow genome wide scanning of sequence and structure variations in the human genome. | 06-06-2013 |
20130150248 | Arrays of Nucleic Acid Probes for Analyzing Biotransformation Genes - The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set. The probes in the second, third and fourth probe sets are identical to a sequence comprising the corresponding probe from the first probe set or a subsequence of at least three nucleotides thereof that includes the at least one interrogation position, except that the at least one interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the four probe sets. | 06-13-2013 |
20130150249 | PROCESSES AND COMPOSITIONS FOR METHYLATION-BASED ENRICHMENT OF FETAL NUCLEIC ACID FROM A MATERNAL SAMPLE USEFUL FOR NON-INVASIVE PRENATAL DIAGNOSES - Provided are compositions and processes that utilize genomic regions differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuplodies. | 06-13-2013 |
20130150250 | RISK FACTORS OF CIGARETTE SMOKE-INDUCED SPIROMETRIC PHENOTYPES - The technology provided herein relates to the SNPs identified as described herein, both singly and in combination, as well as to the use of these SNPs, and others in linkage disequilibrium with these SNPs, for diagnosis, prediction of clinical course, and/or treatment response for pulmonary disease such as COPD, development of new treatments for pulmonary disease such as COPD based upon comparison of the variant and normal versions of the gene or gene product, and development of cell-culture based and animal models for research and treatment of pulmonary disease such as COPD. The technology provided herein further relates to novel compounds, pharmaceutical compositions, and kits for use in the diagnosis, treatment, and evaluation of such disorders. | 06-13-2013 |
20130150251 | METHODS FOR ANALYZING LARIAT RNA - The present invention relates to compositions and methods useful for analyzing lariat RNA, which plays a role in the regulation of gene expression. A sample of RNA is specifically treated to remove linear mRNA and enrich for lariat RNA. The enriched lariat RNA sample may be analyzed further to identify introns, branch point sequences, alternative splicing patters, and gene transcription levels. The enriched lariat RNA sample may also be exploited as a detection or compound screening tool, as well as other uses. | 06-13-2013 |
20130150252 | DETECTION AND MEASUREMENT OF TISSUE-INFILTRATING LYMPHOCYTES - The present invention is drawn to methods for measuring numbers, levels, and/or ratios of cells, such as lymphocytes, infiltrated into a solid tissue, such as a tumor or a tissue affected by an autoimmune disease, and to methods for making patient prognoses based on such measurements. In one aspect, methods of the invention comprise sorting lymphocytes from an accessible tissue, such as peripheral blood, into functional subsets, such as cytotoxic T cells and regulatory T cells, and generating clonotype profiles of each subset. An inaccessible disease-affected tissue is sampled and one or more clonotype profiles are generated. From the latter clonotype profiles, levels lymphocytes in each of the functional subsets are determined in the disease-affected tissue by their clonotypes, which are identified from lymphocytes sorted into subsets from the accessible tissue. | 06-13-2013 |
20130150253 | DIAGNOSTIC PROCESSES THAT FACTOR EXPERIMENTAL CONDITIONS - Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations. | 06-13-2013 |
20130157869 | Method for Reducing Adapter-Dimer Formation - Methods are provided for ligating a 3′ adapter and a 5′ adapter to a target polynucleotide so as to avoid adapter dimer formation. Embodiments of the methods include adding a blocking oligonucleotide after the first ligation in which a 3′ adapter is ligated to the target polynucleotide so that the blocking oligonucleotide is capable of hybridizing to excess 3′ adapter and the ligated 3′ adapter. Subsequently, a 5′ adapter is ligated to the target polynucleotide thus avoiding adapter dimer formation. | 06-20-2013 |
20130157870 | METHODS FOR OBTAINING A SEQUENCE - The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads. | 06-20-2013 |
20130157871 | METHODS FOR MULTIPLEXED SELECTION OF FUNCTIONAL LIGANDS - The present invention relates to methods for generating functional biomolecules. In one exemplary aspect of the invention, generation of functional biomolecules may be performed against multiple targets simultaneously within a single system. In general, a plurality of targets may be disposed within in a single reaction volume and a library of biomolecules, such as a nucleic acid library, may be applied to the reaction volume. The members of the library that do not bind to any of the plurality of targets under given conditions may then be partitioned. The remaining members of the library may then be marked and/or tagged, such as to identify the particular target or targets to which the member of the library binds. The binding members of the library may then be isolated and, by virtue of the marking or tagging, be matched to a particular target or targets. | 06-20-2013 |
20130157872 | IN VITRO EVOLUTION IN MICROFLUIDIC SYSTEMS - The invention describes a method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising the steps of: (a) compartmentalising genetic elements into microcapsules; and (b) sorting the genetic elements which express the gene product having the desired activity; wherein at least one step is under microfluidic control. The invention enables the in vitro evolution of nucleic acids and proteins by repeated mutagenesis and iterative applications of the method of the invention. | 06-20-2013 |
20130157873 | METHODS OF ASSESSING A RISK OF DEVELOPING NECROTIZING MENINGOENCEPHALITIS - Methods of using single nucleotide polymorphisms (SNPs), SNP haplotype block, and haplotype to predict whether or not a subject will develop necrotizing meningoencephalitis (NME) and probe sets that facilitate those methods are disclosed. In particular, the subject is a canine species. | 06-20-2013 |
20130157874 | UNIVERSAL OR BROAD RANGE ASSAYS AND MULTI-TAG SAMPLE SPECIFIC DIAGNOSTIC PROCESS USING NON-OPTICAL SEQUENCING - The present invention includes a method for determining the identify of an organism or virus in a sample comprising the steps of: isolating DNA or RNA from the sample; combining the DNA or RNA directly or with one or more universal or target specific amplification primers, wherein the one or more primers are specific for one or more group of target microorganisms or virus; and amplifying the DNA, or the RNA following reverse transcription with a reverse transcriptase; and contacting the amplification product with one or more species-, organism- or virus-specific detectable marker. | 06-20-2013 |
20130157875 | METHODS FOR ASSESSING GENOMIC INSTABILITIES - The invention generally relates to methods for assessing a fetal abnormality. | 06-20-2013 |
20130157876 | Systems and Methods for Detecting Antibiotic Resistance - A robust, automated computational pipeline was used to design a system comprising a microarray for the identification of microorganisms and their antibiotic resistance profiles. This system and methods will facilitate the study of the epidemiology and microbial ecology of antibiotic resistance and be an invaluable tool to rapidly and simultaneously identify organisms and their antimicrobial resistance elements in environmental, food and clinical samples. | 06-20-2013 |
20130165327 | Method for Sequencing a Polynucelotide Template - The invention provides methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template. | 06-27-2013 |
20130165328 | APPARATUS AND METHODS FOR KINETIC ANALYSIS AND DETERMINATION OF NUCLEIC ACID SEQUENCES - A method of distinguishing nucleotide sequences for different nucleic acid molecules including the steps of (a) mixing a plurality of different nucleic acid molecules with polymerase molecules and nucleotide molecules, wherein the different nucleic acid molecules are attached to a surface in the form of an array of nucleic acid features; (b) determining a transient state of the polymerase molecules at the nucleic acid features; and (c) identifying a subset of nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules at the nucleic acid features, thereby distinguishing the nucleotide sequences for the different nucleic acid molecules. | 06-27-2013 |
20130172197 | HIGH THROUGHPUT NUCLEIC ACID SEQUENCING BY EXPANSION - Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected. Corresponding products, including Xpandomers and oligomeric and monomeric substrate constructs are also disclosed. | 07-04-2013 |
20130172198 | CELLS FOR CHROMATIN IMMUNOPRECIPITATION AND METHODS FOR MAKING - The present invention provides isolated, non-viable bacterial cells comprising a plurality of nucleic acid crosslinks, methods for making said cells, and methods for using said cells to isolate DNA-protein complexes. In particular, the nucleic acids of the cells are crosslinked by contacting the cells with a furocoumarin compound and ultraviolet light. | 07-04-2013 |
20130178369 | TREATMENT FOR STABILIZING NUCLEIC ACID ARRAYS - The present invention is directed to treatment of nucleic acid molecules that are attached or associated with solid supports for biochemical analysis, including nucleic acid sequencing. After loading on the solid support, the nucleic acid molecules are treated with a composition comprising a condensing agent, a volume excluding agent, or both, then treated with a composition comprising a protein. | 07-11-2013 |
20130178370 | PROTEOMIC IDENTIFICATION OF ANTIBODIES - Methods and compositions for identification of candidate antigen-specific variable regions as well as generation of antibodies or antigen-binding fragments that could have desired antigen specificity are provided. For example, in certain aspects, methods for determining amino acid sequences of serum antibody CDR3 and abundancy levels are described. In some aspects, methods for determining nucleic acid sequences of antibody variable region sequences and the frequency thereof in biological samples are provided. Furthermore, the invention provides methods for identification and generation of antibodies or antigen-binding fragments that comprise highly-represented CDR domains. | 07-11-2013 |
20130178371 | NONINVASIVE DETECTION OF FETAL ANEUPLOIDY IN EGG DONOR PREGNANCIES - The present invention provides assay systems and methods for determining the percent fetal contribution of cell-free DNA in a maternal sample from a pregnant female with an egg donor pregnancy. Further provided, are assay systems and methods for determining a statistical likelihood of the presence or absence of a fetal aneuploidy in a maternal sample using a determined percent fetal cell-free DNA in the sample. | 07-11-2013 |
20130178372 | Methods And Computer Systems For Identifying Target-Specific Sequences For Use In Nanoreporters - The present invention relates to compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to coded, labeled probes that are capable of binding to and identifying target molecules based on the probes' label codes. Methods, computers, and computer program products for identifying target-specific sequences for inclusion in the probes are also provided, as are methods of making and using such probes. The probes can be used in diagnostic, prognostic, quality control and screening applications. | 07-11-2013 |
20130178373 | METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING - The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR. | 07-11-2013 |
20130184161 | Methods and Systems for Medical Sequencing Analysis - Disclosed are methods of identifying elements associated with a trait, such as a disease. The methods can comprise, for example, identifying the association of a relevant element (such as a genetic variant) with a relevant component phenotype (such as a disease symptom) of the trait, wherein the association of the relevant element with the relevant component phenotype identifies the relevant element as an element associated with the trait, wherein the relevant component phenotype is a component phenotype having a threshold value of severity, age of onset, specificity to the trait or disease, or a combination, wherein the relevant element is an element having a threshold value of importance of the element to homeostasis relevant to the trait, intensity of the perturbation of the element, duration of the effect of the element, or a combination. The disclosed methods are based on a model of how elements affect complex diseases. The disclosed model is based on the existence of significant genetic and environmental heterogeneity in complex diseases. Thus, the specific combinations of genetic and environmental elements that cause disease vary widely among the affected individuals in a cohort. The disclosed model is an effective, general experimental design and analysis approach for the identification of causal variants in common, complex diseases by medical sequencing. Also disclosed herein are methods of identifying an inherited trait in a subject. The disclosed methods compare a reference sequence from a subject to a library of sequences that contain each mutation. For a given mutation, a normal sequence read aligns best to the normal library sequence. A read having the mutation aligns best to the mutant library sequence. The disclosed model and the disclosed methods based on the model can be used to generate valuable and useful information. | 07-18-2013 |
20130184162 | SYSTEM AND APPARATUS FOR SEQUENTIAL PROCESSING OF ANALYTES - An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array. A key feature of the invention is the correlation of the sequence of optical signals generated by each microparticle in the planar array during the analytical process. | 07-18-2013 |
20130184163 | METHOD FOR IDENTIFYING COMPOUNDS - The present invention relates to a method for identifying compounds comprising the steps of: (a) providing a set of compounds; (b) optionally selecting a sub-set from the set of compounds based on one or more specific compound properties; (c) generating a 3D structure of each of the compounds provided and/or selected in step (a) or (b); (d) encoding each 3D structure; (e) providing at least one known compound having at least one desired property and/or providing a target molecule; (f) encoding the 3D structure of (each of) the known compound(s) provided in step (e) and/or the active site of the target molecule provided in step (e); (g) comparing said encoded 3D structure(s) of step (d) with the encoded 3D structure(s) of step (f); and (h) selecting all compounds falling within a specified similarity range. | 07-18-2013 |
20130184164 | DNA Chip for Genotyping of Human Papilloma Virus, Kit Having Same, and Method for Genotyping - Disclosed is a DNA chip (or DNA microarray) on which probes complementarily binding to the nucleic acids of 44 types of HPV, which is the main cause of cervical cancer and the most common cause of sexually transmitted diseases, are spotted, a genotyping kit including same and a genotyping method using same. In accordance with the present disclosure, all the 44 types of HPV invading the genitalia can be detected and coinfection by more than one type of HPV can be diagnosed accurately. The sensitivity and specificity of HPV genotyping is close to 100% and a number of samples can be tested quickly. The present disclosure is very useful in predicting cervical cancer and precancerous lesions. | 07-18-2013 |
20130184165 | GENOTYPING BY NEXT-GENERATION SEQUENCING - Provided herein is technology relating to genotyping and particularly, but not exclusively, to methods for genotyping one or more organisms by genome sequencing. | 07-18-2013 |
20130184166 | METHOD FOR THE IDENTIFICATION OF THE CLONAL SOURCE OF A RESTRICTION FRAGMENT - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers. | 07-18-2013 |
20130190190 | MOLECULAR TARGETS FOR MODULATING INTRAOCCULAR PRESSURE AND DIFFERENTIATION OF STEROID RESPONSES VERSUS NON-RESPONDERS - Molecular biomarkers as indicators of responses to steroids, drug targets, predictors of steroid responses and identification of drugs for modulating intraocular pressure. Kits and methods of identifying and distinguishing between steroid responders and non-responders. | 07-25-2013 |
20130190191 | MINIATURIZED, HIGH-THROUGHPUT NUCLEIC ACID ANALYSIS - The present invention is directed to method for analyzing multiple nucleic acid molecules of interest comprising in the steps of (i) providing a plurality of beads, characterized in that each bead comprises at least two sequence specific amplification primers, further characterized in that at least one of the primers is bound to the bead via a cleavable linker, (ii) capturing the nucleic acid molecules of interest from a sample, (iii) clonally isolating the plurality of beads, (iv) cleaving the at least one primer, (v) clonally amplifying the nucleic acid thereby creating multiple amplification products, and (vi) analyzing the amplification products. | 07-25-2013 |
20130196859 | NOVEL GENOME SEQUENCING STRATEGIES - The invention relates to a method for the determination of a genome sequence comprising the steps of providing a physical map of a sample genome by sequencing fragment ends of pooled BAC clones; providing a set of sequence reads from a sample genome generating a contig of the physical map and the sequence reads. | 08-01-2013 |
20130196860 | TRANSPOSON END COMPOSITIONS AND METHODS FOR MODIFYING NUCLEIC ACIDS - Compositions of transposome complexes for generating DNA fragments with specific 5′- and 3′-tags. Kits for generating libraries for sequencing, with transposome complexes, enzymes, oligonucleotides or other components. | 08-01-2013 |
20130196861 | MEASUREMENT AND COMPARISON OF IMMUNE DIVERSITY BY HIGH-THROUGHPUT SEQUENCING - A precise measurement of the immunological receptor diversity present in a sample is obtained by sequence analysis. Samples of interest are generally complex, comprising more than 10 | 08-01-2013 |
20130196862 | Informatics Enhanced Analysis of Fetal Samples Subject to Maternal Contamination - The invention provides methods for chromosome copy number calling on genetic samples, such as fetal samples subject to contamination from maternal DNA. The present disclosure provides methods for determining the ploidy status of a chromosome in a fetus (such as a gestating fetus or a POC sample) from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. In some embodiments, the ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR. | 08-01-2013 |
20130196863 | METHOD OF DETERMINING CHROMATIN STRUCTURE - A method of determining chromatin structure is described. The method comprises the steps of (i) fragmenting a nucleotide sequence at multiple HSs; and (ii) analysing fragments formed in step (i) from a plurality of sequences. In a preferred aspect, the present invention provides a method of determining chromatin structure in a nucleic acid sample comprising the steps of (i) treating the sample to fragment the nucleic acid therein at multiple HSs; and (ii) analysing fragments formed in step (i) from a plurality of genes. | 08-01-2013 |
20130203605 | MASSIVELY PARALLEL CONTIGUITY MAPPING - Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales. | 08-08-2013 |
20130203606 | Method of Preparing a Nucleic Acid Library - A method of preparing a nucleic acid library in droplets in contact with oil, including: (a) blunt-ending nucleic acid fragments in a droplet in the oil to yield blunt-ended nucleic acid fragments; (b) phosphorylating the blunt-ended nucleic acid fragments in a droplet in the oil to yield phosphorylated nucleic acid fragments; coupling A-tails to the phosphorylated nucleic acid fragments in a droplet in the oil to yield A-tailed nucleic acid fragments; and (d) coupling nucleic acid adapters to the A-tailed nucleic acid fragments in a droplet in the oil to yield the nucleic acid library comprising adapter-ligated nucleic acid fragments. | 08-08-2013 |
20130203607 | METHODS, COMPOSITIONS, SYSTEMS, APPARATUSES AND KITS FOR NUCLEIC ACID AMPLIFICATION - In some embodiments, the present teachings provide methods for paired end sequencing. In some embodiment, a polynucleotide template to be subjected to paired end sequencing comprises at least one cross linking moiety and at least one scissile moiety. In some embodiments, a paired end sequencing reaction comprises (a) a forward sequencing step, (b) a cleavage step, and (c) a reverse sequencing step. In some embodiments, a paired end sequencing reaction comprises (a) a forward sequencing step, (b) a cross-linking step, (c) a cleavage step, and (d) a reverse sequencing step. | 08-08-2013 |
20130203608 | STRUCTURE WITH NANOPORE AND APPARATUS FOR DETERMINING SEQUENCES OF NUCLEIC ACIDS INCLUDING THE SAME - Disclosed are a structure with a nanopore and an apparatus for determining sequences of nucleic acids including the structure, the structure including three or more structures having facing surfaces, a plurality of oligonucleotides attached at one ends thereof to the surfaces, and a pore formed between the structures to which the plurality of oligonucleotides are bound, and allowing a pore of a desired size to be precisely formed by adjusting the length of a plurality of oligonucleotides. | 08-08-2013 |
20130210636 | Method and Kit for Performing Profiling of Endarterectomy Patients - A method of profiling endarterectomy patients for determining one or more post-operative risks includes steps comprising:
| 08-15-2013 |
20130210637 | SOL-GEL CHIP USING POROUS SUBSTRATE FOR ENTRAPPING SMALL MOLECULES AND SCREENING METHOD OF SMALL MOLECULES SPECIFIC MATERIAL USING THEREOF - There is provided a sol-gel chip using a porous substrate for entrapping small molecules and a method for screening a small molecule-specific material using the same, and more particularly, a porous substrate sol-gel chip characterized in that a sol-gel composition for entrapping small molecules is spotted on a surface of the porous substrate, a method for manufacturing the porous substrate sol-gel chip for entrapping small molecules, and a method for screening a material specifically binding to the small molecules using the porous substrate sol-gel chip for entrapping small molecules. | 08-15-2013 |
20130210638 | METHODS FOR SEQUENCING NUCLEIC ACID - The invention generally relates to methods for sequencing a nucleic acid template from both a 5′ and a 3′ end in a single sequencing reaction. In certain embodiments, methods of the invention involve amplifying a nucleic acid template to produce a plurality of amplicons, splitting the amplicons into first and second portions, attaching a first oligonucleotide including a first universal primer site to a 5′ end of the amplicons in the first portion, and attaching a second oligonucleotide including a second universal primer site to a 3′ end of the amplicons in the second portion. The first and second primer sites may be the same or may be different. The method additionally involves pooling the first and second portions, and sequencing the pooled amplicons, thereby sequencing a nucleic acid template from both a 5′ and a 3′ end in a single sequencing reaction. | 08-15-2013 |
20130210639 | MICROFLUIDIC DEVICES - The present invention provides novel microfluidic substrates and methods that are useful for performing biological, chemical and diagnostic assays. The substrates can include a plurality of electrically addressable, channel bearing fluidic modules integrally arranged such that a continuous channel is provided for flow of immiscible fluids. | 08-15-2013 |
20130210640 | ASSAY SYSTEMS FOR GENETIC ANALYSIS - The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual. | 08-15-2013 |
20130210641 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 08-15-2013 |
20130210642 | Hybridization-Mediated Analysis Of Polymorphisms - Described are methods of assay design and assay image correction, useful for multiplexed genetic screening for mutations and polymorphisms, including CF-related mutants and polymorphs, using an array of probe pairs (in one aspect, where one member is complementary to a particular mutant or polymorphic allele and the other member is complementary to a corresponding wild type allele), with probes bound to encoded particles (e.g., beads) wherein the encoding allows identification of the attached probe. The methods relate to avoiding cross-hybridization by selection of probes and amplicons, as well as separation of reactions of certain probes and amplicons where a homology threshold is exceeded. Methods of correcting a fluorescent image using a background map, where the particles also contain an optical encoding system, are also disclosed. | 08-15-2013 |
20130210643 | Method for preparing a counter-tagged population of nucleic acid molecules. - Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications. | 08-15-2013 |
20130210644 | FETAL ANEUPLOIDY DETECTION BY SEQUENCING - The present invention provides apparatus and methods for enriching components or cells from a sample and conducting genetic analysis, such as SNP genotyping to provide diagnostic results for fetal disorders or conditions. | 08-15-2013 |
20130217582 | Library Compositions and Methods for Acyclic Identification of Aptamers - The present invention provides improved aptamer libraries useful for discovery of aptamers that have high binding affinity for a single or a plurality of targets. The libraries contain higher copies of each member candidate such that they are more likely to be available to the application of acyclic identification methods that obviate the most time-consuming and costly step in traditional SELEX method, the multiple cycles of evolutionary selection. | 08-22-2013 |
20130217583 | MICROFLUIDIC DEVICES AND METHODS OF USE IN THE FORMATION AND CONTROL OF NANOREACTORS - The present invention provides novel microfluidic devices and methods that are useful for performing high-throughput screening assays and combinatorial chemistry. Such methods can include labeling a library of compounds by emulsifying aqueous solutions of the compounds and aqueous solutions of unique liquid labels on a microfluidic device, which includes a plurality of electrically addressable, channel bearing fluidic modules integrally arranged on a microfabricated substrate such that a continuous channel is provided for flow of immiscible fluids, whereby each compound is labeled with a unique liquid label, pooling the labeled emulsions, coalescing the labeled emulsions with emulsions containing a specific cell or enzyme, thereby forming a nanoreactor, screening the nanoreactors for a desirable reaction between the contents of the nanoreactor, and decoding the liquid label, thereby identifying a single compound from a library of compounds. | 08-22-2013 |
20130217584 | MICROARRAY-BASED ASSAY INTEGRATED WITH PARTICLES FOR ANALYZING MOLECULAR INTERACTIONS - A microarray-based assay is provided, which is used for analyzing molecular interactions, including polynucleotides, polypeptides, antibodies, small molecule compounds, peptides and carbohydrates. Such method comprises coupling a target molecule to a particle and then binding to a probe molecule on microarray. In particular, multiplexed genetic analysis of nucleic acid fragments can be implemented. Specific genes, single nucleotide polymorphisms or gene mutations, such as deletions, insertions, and indels, can be identified. Coupled with microarray, the particles, themselves or further modified, facilitate the detection of results with non-expensive devices or even naked eyes. This technology enables the detection and interpretation of molecular interactions in an efficient and cost effective way. | 08-22-2013 |
20130217585 | Quantitative Total Definition of Biologically Active Sequence Elements - A method and apparatus include preparing a library of molecules that can be sequenced. The library includes multiple instances of each possible member of a k-mer. The library is sequenced to determine the relative frequency of each member of the k-mer in the library. The library is contacted with a biochemical system. A population of output molecules is sequenced to determine the relative frequency of each member of the k-mer in the population of output molecules. Each output molecule is related to a product of a process of the biochemical system and carries a k-mer related to a corresponding k-mer of a library molecule involved in the process. Effectiveness of each member of the k-mer is determined based on the relative frequency of each member of the k-mer in the population of output molecules and the relative frequency of the corresponding k-mer in the library. | 08-22-2013 |
20130217586 | METHOD OF NUCLEIC ACID AMPLIFICATION - A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc. | 08-22-2013 |
20130217587 | HIGH DENSITY SENSOR ARRAY WITHOUT WELLS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 08-22-2013 |
20130225416 | ELECTRONIC SEQUENCING - A method for sequencing nucleic acid molecules a) amplifies nucleic acid molecules and b) sequences the amplified nucleic acid molecules. Steps (a) and (b) are carried out on an array of field effect transistor (FET) sensor elements, comprising an array of nanowires. Within the array, each FET may include at least one nanowire, or one each FETs can lie between two nanowires, or one nanowire of a nanowire pair is a nanowire FET, with nucleic acids bound to a nanowire surface. A chip includes one or more arrays of field effect transistor sensor elements. A kit for sequencing nucleic acid molecules, may include one or more amplifying reagents or sequencing reagents. | 08-29-2013 |
20130225417 | METHODS AND SYSTEMS FOR UNIVERSAL CARRIER SCREENING - Provided herein are methods, systems, and devices for genetic screening. The genetic screening of two or more individuals can be utilized to predict the phenotype of a child from the group of individuals. Also disclosed is prediction of a phenotype of a child from a subset of biological relatives, such as a potential mother and father, before conception. In many instances, the methods, systems and devices herein are utilized to predict the probability of a child developing a rare genetic disease. | 08-29-2013 |
20130225418 | LABELING AND SAMPLE PREPARATION FOR SEQUENCING - The invention provides methods for sequencing and sample preparation for sequencing and amplification. | 08-29-2013 |
20130225419 | Quantitative Total Definition of Biologically Active Sequence Elements and Positions - A library includes H unique nucleotide sequences involving every position along I continuous positions in a molecule. A method to prepare the library includes obtaining a microarray with a bound probe of up to J nucleotides, J=I+L, for H different probes. The first L nucleotides are reverse complementary to a constant portion in the library at a 5′ end. The remaining nucleotides of different probes are reverse complementary to corresponding different library members. A primer equal to the constant portion in the library is introduced. The primer is extended along the probe as a library strand using DNA polymerase. A first strand of a double stranded linker is ligated with a phosphate group to the library strand. The first strand has a sequence that matches a constant portion in the library at a 3′ end. The library strand is stripped from the probe and from a different second strand of the linker. | 08-29-2013 |
20130225420 | MOLECULAR SUBTYPING OF ORAL SQUAMOUS CELL CARCINOMA TO DISTINGUISH A SUBTYPE THAT IS UNLIKELY TO METASTASIZE - The present invention provides methods of analyzing a sample from a subject having oral epithelial dysplasia or oral SCC or suspected of having oral epithelial dysplasia or oral SCC. | 08-29-2013 |
20130225421 | NUCLEIC ACID AMPLIFICATION - In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components. In some embodiments, methods for nucleic acid amplification comprise a amplifying at least one polynucleotide onto a surface under isothermal amplification conditions, optionally in the presence of a polymer. The polymer can include a sieving agent and/or a diffusion-reducing agent. | 08-29-2013 |
20130225422 | METHODS FOR ALLELE CALLING AND PLOIDY CALLING - Disclosed herein is a system and method for making allele calls, and for determining the ploidy state, in one or a small set of cells, or where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed and the haplotypes are determined using expected similarities between the target genome and the knowledge of the genomes of genetically related individuals. In one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the genetic data from both parents, and possibly one or more sperm and/or sibling embryos. In another embodiment, the chromosome copy number can be determined using the same input data. In another embodiment, these determinations are made for embryo selection during IVF, for non-invasive prenatal diagnosis, or for making phenotypic predictions. | 08-29-2013 |
20130231251 | Methods For Selective Targeting - A selective targeting method is disclosed which comprises contacting a peptide library with an anti-target to allow the peptides to bind; separating non-binding peptides from the anti-target bound peptides, contacting the non-binding anti-target peptides with a target allowing the unbound peptides to bind with the target to form a target-bound peptide complex; separating the target-bound peptide complex from peptides which do not bind to the target, and identifying the target-bound peptides. In one embodiment the target is skin or hair. In another embodiment the anti-target is hair when the target is skin, and the anti-target is skin when the target is hair. | 09-05-2013 |
20130231252 | DETECTING FETAL CHROMOSOMAL ABNORMALITIES USING TANDEM SINGLE NUCLEOTIDE POLYMORPHISMS - The invention provides tandem single nucleotide polymorphisms and methods for their use, for example, in diagnosing Down Syndrome. | 09-05-2013 |
20130231253 | COMPOSITIONS AND METHODS FOR TARGETED NUCLEIC ACID SEQUENCE ENRICHMENT AND HIGH EFFICIENCY LIBRARY REGENERATION - The present invention provides methods, compositions and kits for targeted nucleic acid sequence enrichment in a nucleic acid sample and for high efficiency nucleic acid library generation for next generation sequencing (NGS). Specifically, the methods, compositions and kits provided herein are useful for the production and capture of amplification-ready, target-specific and strand-specific regions of interest from nucleic acid samples containing complex DNA. | 09-05-2013 |
20130231254 | METHOD OF NUCLEIC ACID AMPLIFICATION - A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc. | 09-05-2013 |
20130237427 | Y-SHAPED PROBE AND VARIANT THEREOF, AND DNA MICROARRAY, KIT AND GENETIC ANALYSIS METHOD USING THE SAME - The present disclosure relates to a Y-shaped nucleotide probe having two probe parts in one body, which provides improved sensitivity, specificity and accuracy in genotype and genetic analysis and thus is widely applicable to diagnosis and a variant thereof (d- or b-shaped probe), and a DNA microarray, a kit and a genetic analysis method using the same. The Y-shaped probe comprises a left-side probe part, a left-side stem part, a linker part, a right-side stem part and a right-side probe part. The DNA microarray of the present disclosure can improve accuracy of test by testing the same gene simultaneously or by testing two different target genes at once. Especially, since both the target gene and the control gene can be tested simultaneously from one spot, error can be reduced, quantitative analysis is possible and standardization is easy. The Y-shaped probe of the present disclosure may be widely used for genotyping, analysis of gene expression, analysis of mutation or SNP, diagnosis and prediction of diseases, determination of therapeutic regimen, or the like. | 09-12-2013 |
20130237428 | METHODS FOR HIGH LEVEL MULTIPLEXED POLYMERASE CHAIN REACTIONS AND HOMOGENEOUS MASS EXTENSION REACTIONS - Provided herein are optimized methods for performing multiplexed detection of a plurality of sequence variations. Also provided are methods for performing multiplexed amplification of target nucleic acid. | 09-12-2013 |
20130237429 | DISCOVERY AND UTILIZATION OF SORGHUM GENES (MA5/MA6) - Methods and composition for the production of non-flowering or late flowering | 09-12-2013 |
20130237430 | PROTEIN OR PEPTIDE PRINTING METHOD, PROTEIN ARRAY OR PEPTIDE ARRAY AND FUNCTIONAL PROTEIN OR FUNCTIONAL PEPTIDE IDENTIFICATION METHOD - The present invention relates to a protein or peptide printing method, comprising (a) a step for preparing nucleic acids and a cell-free protein synthesis system in an engraved plate composed of microscopic grooves having a specific opening shape, (b) a step for superimposing a substrate on the engraved plate so as to contact a protein or peptide to be synthesized in the microscopic grooves, and (c) a step for synthesizing the protein or peptide from the nucleic acids using the cell-free protein synthesis system in the microscopic grooves, and immobilizing the protein or peptide on the substrate along the specific opening shapes of the microscopic grooves. | 09-12-2013 |
20130237431 | SIZE-BASED ANALYSIS OF FETAL DNA FRACTION IN MATERNAL PLASMA - A fractional concentration of clinically-relevant DNA in a mixture of DNA from a biological sample is determined based on amounts of DNA fragments at multiple sizes. For example, the fractional concentration of fetal DNA in maternal plasma or tumor DNA in a patient's plasma can be determined. The size of DNA fragments in a sample is shown to be correlated with a proportion of fetal DNA and a proportion of tumor DNA, respectively. Calibration data points (e.g., as a calibration function) indicate a correspondence between values of a size parameter and the fractional concentration of the clinically-relevant DNA. For a given sample, a first value of a size parameter can be determined from the sizes of DNA fragments in a sample. A comparison of the first value to the calibration data points can provide the estimate of the fractional concentration of the clinically-relevant DNA. | 09-12-2013 |
20130237432 | APPLICATION OF A PCR SEQUENCING METHOD, BASED ON DNA BARCODING TECHNIQUE AND DNA INCOMPLETE SHEARING STRATEGY, IN HLA GENOTYPING - The invention provides a PCR sequencing method, wherein the combination of primer indexes, DNA incomplete shearing strategy and the second generation sequencing technique (Paired-End sequencing technique) can make the length of PCR products that can be sequenced by a sequencer longer than the maximum sequencing length of the sequencer whilst making full use of the characteristics of the second generation sequencing technique such as high throughput and low cost, thereby greatly broadening its applicable scope. In addition, the present invention also provides primer indexes for the PCR sequencing method and the use of the method in genotyping, particularly in HLA analysis, and also provides the PCR primers used, particularly the PCR primers for HLA-A, B, HLA-C and HLA-DQB1 gene. | 09-12-2013 |
20130237433 | DETECTION OF NUCLEIC ACIDS AND PROTEINS - The invention generally relates to methods for detecting a target nucleic acid and a target protein in a single assay. | 09-12-2013 |
20130237434 | SEPARATION OF PYROPHOSPHATE RELEASE AND PYROPHOSPHATE DETECTION - The present technology relates to methods and systems for detection of pyrophosphate. As such, disclosed herein are methods and systems that permit improved pyrophosphate detection. Also disclosed herein are methods and systems which utilize improved pyrophosphate detection for nucleotide sequencing. | 09-12-2013 |
20130244882 | MULTIPLEX NUCLEIC ACID REACTIONS - A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array. | 09-19-2013 |
20130244883 | Molecular Display Method - There is provided herein a method for identifying and/or recovering at least one genetically encoded affinity reagent specific for a target molecule by screening using molecular display in conjunction with the sequencing of positive and negative selection pools from the screen. | 09-19-2013 |
20130244884 | Methods for Nucleotide Sequencing and High Fidelity Polynucleotide Synthesis - Methods of obtaining sequence information about target polynucleotide having a predefined sequence are disclosed. The methods include sequencing by ligation and sequencing by polymerase. | 09-19-2013 |
20130244885 | HIGH-THROUGHPUT SEQUENCING METHOD FOR METHYLATED DNA AND USE THEREOF - The present invention provides a high-throughput sequencing method for methylated DNA, and use thereof. Particularly, the present invention provides a high-throughput sequencing method for methylated DNA, which combines methylated DNA immunoprecipitation, removal of repetitive sequences, and bisulfite treatment. The site of sequencing library will be decreased, and the cost will be reduced by using the method disclosed in the present invention. | 09-19-2013 |
20130244886 | COMPOSITIONS AND METHODS FOR SEQUENCING NUCLEIC ACIDS - Disclosed herein are compositions and methods for sequencing nucleic acids. | 09-19-2013 |
20130244887 | RAPID GENOTYPING ANALYSIS AND DEVICES THEREOF - The present invention discloses methods, primer, probes, and kits for genotyping various mutations or disease-causing agent. In one embodiment, the present invention is applied to detecting the presence of multidrug-resistant | 09-19-2013 |
20130244888 | COMPOSITIONS AND METHODS FOR NUCLEOTIDE SEQUENCING - The invention provides nucleoside and nucleotide molecules containing cleavable linkers linking a label such as a dye. The invention also provides nucleosides and nucleotide molecules containing a blocking group, either removable or non-removable. The invention additionally provides methods of using the nucleoside and nucleotide molecules containing a cleavable linker and/or a blocking group. | 09-19-2013 |
20130252821 | METHODS AND COMPOSITIONS FOR THE TREATMENT AND DIAGNOSIS OF DISEASES CHARACTERIZED BY VASCULAR LEAK, HYPOTENSION, OR A PROCOAGULANT STATE - Disclosed herein are methods for treating a vascular leak disorder, hypotension, or a procoagulant state using angiopoietin-2 (Ang-2) antagonist compounds. Also disclosed are methods for treating a vascular leak disorder associated with high dose IL-2 therapy using angiopoietin-2 antagonist compounds. Methods for diagnosing and monitoring vascular leak disorders, hypotension, or a procoagulant state that include the measurement of Ang-2 polypeptide or nucleic acid levels are also disclosed. Methods for inducing a vascular leak using an Ang-2 agonist are also disclosed. | 09-26-2013 |
20130252822 | Methods for Predicting an Antibody Response to Interferon Therapy in Multiple Sclerosis Patients - The present invention relates to a method of diagnosing a predisposition of a multiple sclerosis patient to become less susceptible or resistant to treatment with interferon β, said method comprising determining in a sample obtained from said patient the presence of one or more SNP(s) selected from the group consisting of SNPs defined by the sequences of SEQ ID NOs 12, 17, 2, 3, 5, 7, 8, 1, 4, 6, 9, 10, 11, 13, 14, 15 and 16, wherein the presence of one or more of said SNP(s) in said sample is indicative for said predisposition. | 09-26-2013 |
20130252823 | cDNA SYNTHESIS USING NON-RANDOM PRIMERS - The present invention provides methods for selectively amplifying a target population of nucleic acid molecules in a population of RNA template molecules (e.g., all mRNA molecules expressed in a cell type except for the most highly expressed mRNA species). The invention also provides a method of generating a population of oligonucleotide primers for transcriptome profiling of total RNA from a subject of interest. | 09-26-2013 |
20130252824 | SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA FROM TARGET INDIVIDUALS USING GENETIC DATA FROM GENETICALLY RELATED INDIVIDUALS - A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals. | 09-26-2013 |
20130252825 | Signal Enhancement in Molecular Assays - The present invention relates generally to signal enhancement in single-molecule-assays. In particular, the present invention relates to an array allowing signal enhancement of single molecules. The assay is in particular a Bioassay allowing single molecule analysis of biomolecules. Preferably, the signal enhancement is a fluorescence enhancement based on optical antenna. In another aspect, the present invention relates to a method for measuring irradiation of electromagnetic waves of single compounds. Based on the arrays and methods, it is possible to allow signal enhancement and, consequently, allow single molecule assays with high sensitivity and reproducibility. | 09-26-2013 |
20130252826 | LARGE DELETIONS IN HUMAN PMS2 GENE AND USE THEREOF - Large deletions have been identified in the PMS2 gene in patients. The large deletions predispose the patients to Lynch syndrome associated cancers. Thus, methods for detecting the genetic variants are provided which can be used in detecting a predisposition to cancer. | 09-26-2013 |
20130252827 | DETECTION OF TARGET NUCLEIC ACID SEQUENCES USING DUAL-LABELED IMMOBILIZED PROBES ON SOLID PHASE - The present invention relates to a novel method for detection of target nucleic acid sequences on a solid phase using dual-labeled immobilized probes and its resistance to a 5′ to 3′ exonuclease activity of a DNA polymerase. Because the label is remained on the solid substrate by resistance to nucleases due to labeling of a base component the internal nucleotide, the present invention requires no consideration of a suitability of position of the label for remaining on the solid substrate. The present invention ensures to minimize background signal by positioning labels at a site on probes suitable to maximize quenching efficiency of the dual label system, since it permits to freely determine the position of the internal label on probes. | 09-26-2013 |
20130252828 | CHEMICAL SENSING DEVICE - An apparatus with a transducer having a first output signal and arranged to receive an electrical input. The transducer switches the first output signal between an ON and OFF state. The apparatus has a chemical sensing surface coupled to the transducer arranged to receive a chemical input. A signal generator oscillates one or more of said inputs to vary the switching point of the transducer. The oscillating input may be the chemical input and/or the electrical input. The output signal may be a pulse whose period ON or OFF is determined by the oscillating input modulated by the chemical input. | 09-26-2013 |
20130252829 | Parallel Methods For Insertional Mutagenesis - The present invention provides parallel methods for identifying the locations of insertion elements that are distributed at different sites in the genome among a collection of cells. | 09-26-2013 |
20130252830 | ENHANCED GENE EXPRESSION - The present disclosure is directed to a novel, unexpected approach of expressing exogenous gene(s) at increased levels by predictably, optionally irreversibly, incorporating the gene(s) into a region of increased gene expression (RIDGE) on a chromosome of a host cell. This approach is accomplished by identification of RIDGE(s) and further by integration of integrase-specific sites (e.g., attP or attB) in the presence of or mediated by integrase. The approach renders a high level of gene expression; predictability of the location of the exogenous genes, elimination of genetic instability or unwanted phenotype; and reduction of time and cost in optimizing protein production in host cells, which will be every useful in the production of therapeutic, prophylactic, and diagnostic proteins. | 09-26-2013 |
20130261002 | ASSAYS FOR DETECTING WDR60 MUTATIONS - The present invention relates to compositions and methods for detecting mutations in WD repeat domain 62 (WDR62). | 10-03-2013 |
20130261003 | LIGATION-BASED DETECTION OF GENETIC VARIANTS - The present invention provides assays systems and methods for detection of genetic variants in a sample, including copy number variation and single nucleotide polymorphisms. The invention preferably employs the technique of tandem ligation—e.g., the ligation of two or more fixed sequence oligonucleotides and one or more bridging oligonucleotides complementary to a region between the fixed sequence oligonucleotides—combined with detection of levels of particular genomic regions using array hybridization. | 10-03-2013 |
20130261004 | METHODS FOR NON-INVASIVE PRENATAL PATERNITY TESTING - Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father. | 10-03-2013 |
20130261005 | SYSTEM AND METHODS FOR INDEL IDENTIFICATION USING SHORT READ SEQUENCING - Systems, methods, and analytical approaches for short read sequence assembly and for the detection of insertions and deletions (indels) in a reference genome. A method suitable for software implementation is presented in which indels may be readily identified in a computationally efficient manner. | 10-03-2013 |
20130267423 | PEPTIDE LIBRARIES FOR SCREENING AND OTHER APPLICATIONS - The present invention generally relates to various peptides and particles, for example, for use in screening of particle- or bead-based peptide libraries. In one aspect, the present invention is generally directed to articles including peptides attached to one or more particles, which may have structures such as (particle)-M-Q-Z | 10-10-2013 |
20130267424 | Method of tagging using a split DBR - Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications. | 10-10-2013 |
20130267425 | NONINVASIVE PRENATAL DIAGNOSIS OF FETAL TRISOMY BY ALLELIC RATIO ANALYSIS USING TARGETED MASSIVELY PARALLEL SEQUENCING - Whether a fetus has an aneuploidy associated with a first chromosome is detected using ratios of alleles detected in a maternal sample having a mixture of maternal and fetal DNA. DNA from the sample is enriched for target regions associated with polymorphic loci and then sequenced. Polymorphic loci (e.g., single nucleotide polymorphisms) in the target regions with fetal-specific alleles are identified on a first chromosome and on one or more reference chromosomes. A first ratio of the fetal-specific alleles and shared alleles is determined for the loci on the first chromosome. A second ratio of the fetal-specific alleles and shared alleles is determined for the loci on the reference chromosome(s). A third ratio of the first and second ratio can be compared to a cutoff to determine whether an aneuploidy is present, and whether the aneuploidy is maternally-derived or paternally-derived. | 10-10-2013 |
20130267426 | MICROSATELLITE INSTABILITY MARKERS IN DETECTION OF CANCER - The present application relates to the field of cancer, particularly to mismatch repair (MMR−) deficient tumors. New markers are presented herein that have a high sensitivity to detect whether a tumor is mismatch repair deficient or not. The markers are particularly mutations in microsatellite regions. Accordingly, methods are provided for diagnosing microsatellite instability of a tumor, comprising determining the presence of these markers. Further, kits are provided to detect the presence of these markers (or subsets thereof) in a sample. | 10-10-2013 |
20130267427 | SINGLE CELL ANALYSIS BY POLYMERASE CYCLING ASSEMBLY - The invention provides a method of making measurements on individual cells of a population, particularly cells that have identifying nucleic acid sequences, such as lymphoid cells, in one aspect, the invention provides a method of making multiparameter measurements on individual cells of such a population by carrying out a polymerase cycling assembly (PCA) reaction to link their identifying nucleic acid sequences to other cellular nucleic acids of interest. The fusion products of such PCA reaction are then sequenced and tabulated to generate multiparameter data for cells of the population. | 10-10-2013 |
20130274114 | MULTIPOTENT STEM CELL-BASED CULTURE SYSTEMS AND MODELS - This invention generally relates to multipotent stem cell-based research tools. More particularly, the present invention relates to culture systems and 3-dimensional tissue models that may be used for identifying agents useful for treating diseases and conditions and that are suitable for high throughput screening applications. This present invention is based, in part, on the discovery of a method for propagating multipotent stem cells from human skin fibroblasts and subsequently differentiating those multipotent stem cells into cells of any of the three germ layers. Aspects of the invention include drug discovery tools as a high throughput screen; 3-dimensional tissue engineering model, and drug discovery tools thereof; research tools for identifying genes that are important for acquiring multipotency and for identifying genes that are important for lineage-specific differentiation, and drug discovery tools thereof; diagnostic tools for identifying defective genes; and autologous therapies based on the propagated multipotent stem cells. | 10-17-2013 |
20130274115 | METHOD FOR PAIRWISE SEQUENCING OF TARGET POLYNUCLEOTIDES - The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template. Using the methods of the invention it is possible to obtain two linked or paired reads of sequence information from each double-stranded template on a clustered array, rather than just a single sequencing read from one strand of the template. | 10-17-2013 |
20130274116 | METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING - Disclosed herein are methods for determining the copy number of a chromosome in a fetus in the context of non-invasive prenatal diagnosis. In an embodiment, the measured genetic data from a sample of genetic material that contains both fetal DNA and maternal DNA is analyzed, along with the genetic data from the biological parents of the fetus, and the copy number of the chromosome of interest is determined. In an embodiment, the maternal serum is measured using a single-nucleotide polymorphism (SNP) microarray, along with parental genomic data, and the determination of the chromosome copy number is used to make clinical decisions pertaining to the fetus. | 10-17-2013 |
20130281304 | Comprehensive Methylome Map of Myeloid and Lymphoid Commitment from Hematopoietic Proenitors - Provided herein are differentially methylated regions (DMRs) of multipotent progenitor cells (MPPs) and oligopotent progenitor cells and methods of use thereof. The invention provides methods for detecting and analyzing alterations in the methylation status of DMRs in such progenitor cells as well as methods for differentiating such cells. | 10-24-2013 |
20130281305 | FLOW CELLS FOR HIGH DENSITY ARRAY CHIPS - Biochemical flow cells having sealed inlets and outlets are provided for performing high-volume assays on macromolecules. In one example embodiment, a flow cell with detachable inlet and outlet connectors comprises an inlet manifold, a coverslip, and a substrate disposed below the coverslip to form a reaction chamber, where the substrate is disposed to partially cover the inlet manifold such that a slit is formed along an entire edge of the substrate where fluids can flow from the inlet manifold through the slit, around substantially the entire edge of the substrate, and into the reaction chamber at equalized pressure and without bubbles. In another embodiment, a flow cell comprises an outlet manifold, two or more flow regions each connected to its own loading port via its own flow distribution funnel, each loading port connected to the outlet manifold, and plugs in a wall of the outlet manifold opposite each loading port, such that when a plug is absent from the wall of the outlet manifold, a loading tip may be inserted in its place, passing through the outlet manifold and connecting directly to a loading port. | 10-24-2013 |
20130281306 | SEQUENCING METHODS - The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing. | 10-24-2013 |
20130281307 | NUCLEIC ACID AMPLIFICATION - In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components. In some embodiments, methods for nucleic acid amplification comprise a amplifying at least one polynucleotide onto a surface under isothermal amplification conditions, optionally in the presence of a polymer. The polymer can include a sieving agent and/or a diffusion-reducing agent. | 10-24-2013 |
20130288900 | COMBINATORIAL LIBRARIES OF CONFORMATIONALLY CONSTRAINED POLYPEPTIDE SEQUENCES - The present invention concerns combinatorial libraries of conformationally constrained polypeptide sequences and their uses. In particular, the present invention concerns combinatorial libraries of conformational epitopes and their uses. | 10-31-2013 |
20130288901 | ANALYSIS METHODS - The invention generally relates to methods for analyzing nucleic acids to identify novel mutations associated with diseases. In certain embodiments, methods of the invention involve obtaining nucleic acid from a subject having a disease, identifying at least one mutation in the nucleic acid, and comparing the mutation to a database of mutations known to be associated with the disease, wherein mutations that do not match to the database are identified as novel mutations. | 10-31-2013 |
20130288902 | SYSTEMS AND METHODS FOR PAIRED END SEQUENCING - Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location. | 10-31-2013 |
20130288903 | Methods For The Diagnosis Of Fetal Abnormalities - The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g. fetal cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject, e.g. a fetus by analyzing a cellular sample from the subject. | 10-31-2013 |
20130288904 | PHASE-PROTECTING REAGENT FLOW ORDERINGS FOR USE IN SEQUENCING-BY-SYNTHESIS - A method for nucleic acid sequencing includes: disposing a plurality of template polynucleotide strands, sequencing primers, and polymerases in a plurality of defined spaces of a sensor array; exposing template polynucleotide strands to a series of flows of nucleotide species, the series comprising a sequence of random flows; and obtaining, for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands. | 10-31-2013 |
20130288905 | METHODS FOR DETECTING MODIFICATION RESISTANT NUCLEIC ACIDS - Methods are provided for, inter alia, detecting nucleic acid molecules resistant to degradation, such as a plurality of RNA molecules bound to a ribosome, using various technologies including deep sequencing. | 10-31-2013 |
20130288906 | DIAGNOSIS AND TREATMENT OF ALZHEIMER'S DISEASE - The invention relates to novel variants that associate with Alzheimer's disease AD and their use in kits as a means for diagnosing AD; and also their use in nucleic acid molecules or cells/cell lines for identifying novel therapeutic, label of identification means. | 10-31-2013 |
20130288907 | DNA library, preparation method thereof, and device for detecting SNPs - A DNA library, and a preparing method thereof, a method of determining DNA sequence information, an apparatus and a kit for detecting SNPs, and a method for genotyping may be provided. The method for preparing the DNA library may comprise the steps of: digesting a genomic DNA sample using a restriction endonuclease to obtain a digested product, wherein the restriction endonuclease comprises at least one selected from the group consisting of Mbo II and Tsp 45I; separating the digested product to obtain DNA fragments having a length of 100 bp to 1,000 bp; end-repairing the DNA fragments to obtain an end-repaired DNA fragments; adding a base A to the end of the end-repaired DNA fragments to obtain DNA fragments having a terminal base A; and ligating the DNA fragments having the terminal base A with sequencing adaptors to obtain the DNA library. | 10-31-2013 |
20130288908 | POLYNUCLEOTIDE CONSTRUCT CAPABLE OF DISPLAYING FAB IN A CELL-FREE TRANSLATION SYSTEM, AND METHOD FOR MANUFACTURING AND SCREENING FAB USING SAME - The polynucleotide construct of (1) or (2) below is used to perform ribosome display, CIS display and/or mRNA display in order to screen a Fab against an antigen of interest: (1) a polynucleotide construct which monocistronically comprises a ribosome-binding sequence, Fab first chain-coding sequence, linker peptide-coding sequence, Fab second chain-coding sequence and scaffold-coding sequence in this order, and further comprises at its 3′-end a structure necessary for maintaining a complex with the Fab encoded by itself, and (2) a polynucleotide construct which comprises a Fab first chain-expressing cistron and a Fab second chain-expressing cistron each containing a ribosome-binding sequence, a Fab first chain-coding sequence or Fab second chain-coding sequence, and a scaffold-coding sequence in this order, the first Fab-expressing cistron further comprising at its 3′-end a ribosome stall sequence, said Fab second chain-expressing cistron further comprising at its 3′-end a structure necessary for maintaining a complex with the Fab encoded by itself. | 10-31-2013 |
20130296172 | Methods and Compositions for Analysis of Nucleic Acids - Compositions and methods for analysis of nucleic acids are disclosed. Targets are hybridized to arrays having features that include pairs of co-localized probes within features. The probe pairs may include a first probe type that is oriented so that the 5′ end is free and the 3′ end is attached to the support and a second probe type that is oriented so that the 3′ end is free for extension and the 5′ end is attached to the support. The probes of a feature are complementary to different regions of the same target sequence so they can simultaneously hybridize to a single target with a gap or nick between. The gap may be filled by extension and ligation or ligation. | 11-07-2013 |
20130296173 | PRE-ANCHOR WASH - The present invention is directed to compositions and methods for improving the discordance rate and mapping yield in nucleic acid sequencing reactions. | 11-07-2013 |
20130296174 | Microfluidics System for Sequencing - A microfluidic chip ( | 11-07-2013 |
20130303380 | IDENTIFICATION OF LIGANDS AND THEIR USE - A method to identify a peptide and/or its encoding DNA, wherein the peptide binds to a T-cell receptor and/or an NK-cell receptor and/or an NKT-cell receptor, the method comprising: providing a carrier to which is attached a peptide and its encoding DNA; providing an MHC and/or an MHC-like molecule; and exposing the peptide to a T-cell receptor and/or an NK-cell receptor and/or an NKT-cell receptor in the presence of the MHC or MHC-like molecule. | 11-14-2013 |
20130303381 | ALTERNATIVE NUCLEIC ACID SEQUENCING METHODS - Embodiments are provided that provide for parallel sequencing of nucleic acid segments. In some embodiments, a single sequence is sequenced by at least two different sequencing techniques and the results compared, allowing for deficiencies or strengths of one technique to be complemented by the second technique. | 11-14-2013 |
20130303382 | Integrated Capture And Amplification Of Target Nucleic Acid For Sequencing - The invention provides efficient methods of preparing a target nucleic acid in a form suitable for sequencing. The methods are particularly amenable for preparing high quality nucleic acids for massively parallel sequencing. The methods involve capturing a target nucleic acid from a sample and PCR amplification of the target nucleic acid. The target nucleic acid is captured by binding to a capture probe, which in turn binds to an immobilized probe. The immobilized probe is typically immobilized via a magnetic bead. The captured target nucleic acid is PCR amplified by thermocycling without prior dissociation of the target nucleic acid from the beads. The efficiency of the method lies in part in that both the capture and amplification steps are performed in a single vessel. The amplified nucleic acid can then be sequenced. | 11-14-2013 |
20130303383 | METHODS AND APPARATUS FOR PREDICTING PROTEIN STRUCTURE - The present invention relates to a method for predicting three-dimensional structure of a protein from its sequence. Three-dimensional structure may be determined by: (a) generating a multiple sequence alignment for a candidate protein having a known sequence; (b) identifying a covariance matrix between all pairs of sequence positions in the multiple sequence alignment; (c) inverting the covariance matrix and identifying predicted evolutionary constraints using a statistical model of the candidate protein; and (d) simulating folding of an extended chain structure of the candidate protein using the predicted constraints. | 11-14-2013 |
20130303384 | MODELS FOR ANALYZING DATA FROM SEQUENCING-BY-SYNTHESIS OPERATIONS - A method of modeling a background signal when sequencing a polynucleotide strand using sequencing-by-synthesis includes: flowing a series of nucleotide flows onto a reactor array having multiple reaction confinement regions, one or more copies of the polynucleotide strand being located in a loaded reaction confinement region of the reactor array, the loaded reaction confinement region being located in a vicinity of one or more neighboring reaction confinement regions that may or may not be loaded; receiving output signals from the reactor array; and modeling a background signal for the loaded reaction confinement region using the received output signals and a model adapted to account at least for an exchange of ions between the one or more neighboring reaction confinement regions and a headspace adjacent the loaded reaction confinement region and the one or more neighboring reaction confinement regions. | 11-14-2013 |
20130310260 | METHODS AND COMPOSITIONS FOR ANALYZING NUCLEIC ACID - Technology provided herein relates in part to methods, processes, compositions and apparatuses for analyzing nucleic acid. | 11-21-2013 |
20130310261 | Simplified Method of Determining Predisposition to Scoliosis - The present invention relates to novel genetic markers associated with scoliosis, risk of developing scoliosis and risk of scoliosis curve progression, and simplified methods and materials for determining whether a human subject has scoliosis, is at risk of developing scoliosis or is at risk of scoliosis curve progression. | 11-21-2013 |
20130310262 | NONINVASIVE DETECTION OF ROBERTSONIAN TRANSLOCATIONS - The present invention provides methods for detection of Robertsonian translocations. | 11-21-2013 |
20130310263 | DIAGNOSING CANCER USING GENOMIC SEQUENCING - Methods, systems, and apparatus determine whether a first chromosomal region exhibits a deletion or an amplification associated with cancer in a sample from a subject (e.g., where the sample includes a mixture of cell-free DNA from tumor cells and non-malignant cells. Nucleic acid molecules of the biological sample are sequenced. Respective amounts of a clinically-relevant chromosomal region and of background chromosomal region(s) are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether first chromosomal region exhibits a deletion or an amplification associated with cancer. | 11-21-2013 |
20130310264 | NUCLEIC ACID ANALYSIS BY RANDOM MIXTURES OF NON-OVERLAPPING FRAGMENTS - The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like. | 11-21-2013 |
20130316911 | METHODS AND COMPOSITIONS FOR SCREENING AND TREATING DEVELOPMENTAL DISORDERS - This document provides methods and materials related to genetic variations of developmental disorders. For example, this document provides methods for using such genetic variations to assess susceptibility of developing Autism Spectrum Disorder. | 11-28-2013 |
20130316912 | POLYMERASE ENZYME SUBSTRATES WITH PROTEIN SHIELD - Compositions and methods are provided for nucleotide analogs comprising protein shields for improving enzyme photostability in single molecule real time sequencing. Nucleotide analogs of the invention have a protein shield between the dye moieties and nucleotide moieties of the analog. The protein prevents the direct interaction of the dye moiety with the enzyme carrying out nucleotide synthesis preventing photodamage to the enzyme. The nucleotide analogs of the invention can have multiple dyes and multiple nucleotide moieties. | 11-28-2013 |
20130316913 | Isolation of CpG Islands by Thermal Segregation and Enzymatic Selection-Amplification Method - The present invention concerns isolation, library preparation and selective amplification from a compositionally heterogeneous pool of DNA fragments of a fraction of molecules, such as those originating from promoter CpG islands and characterized by a high GC content. In particular, the process utilizes a heat-induced segregation of DNA molecules into GC-poor, single-stranded molecule fractions and GC-rich, double-stranded molecule fractions, with subsequent enzymatic conversion of the GC-rich, double-stranded DNA molecules into a library, and, optionally, amplification. In specific embodiments, the isolation process is used to generate promoter-enriched genomic and methylome libraries for research and diagnostic applications, for example. | 11-28-2013 |
20130316914 | Methods And Devices For Sequencing Nucleic Acids In Smaller Batches - The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. A plurality of smaller flow cells is employed, each with a relatively small area to be imaged, in order to provide greater flexibility and efficiency. | 11-28-2013 |
20130316915 | METHODS FOR DETERMINING ABSOLUTE GENOME-WIDE COPY NUMBER VARIATIONS OF COMPLEX TUMORS - Methods for interpreting absolute copy number of complex tumors and for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. In certain aspects, genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated. | 11-28-2013 |
20130316916 | CLASSIFICATION OF NUCLEIC ACID TEMPLATES - Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid. | 11-28-2013 |
20130316917 | SELECTIVE ENRICHMENT OF NUCLEIC ACIDS - Methods for the selective enrichment of nucleic acids. | 11-28-2013 |
20130316918 | MODEL-BASED RESIDUAL CORRECTION OF INTENSITIES - A method for improving color calls or base calls utilizes current and prior cycle multi-channel intensity data from a sequencing run to model residual cycle buildup. The model is applied to correct the multi-cycle channel intensity for the current cycle. The corrected multi-cycle channel intensity is used for color calls or base calls for the current cycle. | 11-28-2013 |
20130316919 | BIOMARKERS FOR THE DIAGNOSIS OF MULTIPLE SCLEROSIS - The invention relates to biological markers for use in the diagnosis of multiple sclerosis and the use of said markers for distinguishing between patients with multiple sclerosis and patients with other neurological diseases. The invention further relates to a diagnostic technique for multiple sclerosis using said biological markers. | 11-28-2013 |
20130324416 | Methods and Compositions for Correlating Genetic Markers with Cardiovascular Disease - The present invention provides methods of identifying a subject having an increased or decreased risk of developing cardiovascular disease, comprising: a) correlating the presence of one or more genetic markers in chromosome 3q13.31 with an increased or decreased risk of developing cardiovascular disease; and b) detecting the one or more genetic markers of step (a) in the subject, thereby identifying the subject as having an increased or decreased risk of developing cardiovascular disease. Also provided are methods of identifying subjects with cardiovascular disease as having a good or poor prognosis, as well as methods of identifying effective treatment regimens for cardiovascular disease, based on correlation with genetic markers in chromosome 3q13.31. | 12-05-2013 |
20130324417 | DETERMINING THE CLINICAL SIGNIFICANCE OF VARIANT SEQUENCES - The present invention generally relates to determining the clinical significance of a variant nucleic acid sequence. The invention can involve sequencing a nucleic acid to generate at least one sequence read, identifying a variant sequence within the sequence read, determining the equivalent insertion/deletion region (EIR) of the variant sequence, identifying a functional region including at least a portion of the EIR, and associating the EIR with the identified functional region, thereby to determine the clinical significance of the variant. | 12-05-2013 |
20130324418 | Analysis Of Rare Cell-Enriched Samples - The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g., epithelial cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject by analyzing a cellular sample from the subject. | 12-05-2013 |
20130324419 | METHODS FOR NUCLEIC ACID CAPTURE AND SEQUENCING - Methods of capturing and sequencing target nucleic acid molecules are provided. Methods of determining the methylation status of genomic DNA are also provided. | 12-05-2013 |
20130324420 | NORMALIZING CHROMOSOMES FOR THE DETERMINATION AND VERIFICATION OF COMMON AND RARE CHROMOSOMAL ANEUPLOIDIES - The present invention provides a method capable of detecting single or multiple fetal chromosomal aneuploidies in a maternal sample comprising fetal and maternal nucleic acids, and verifying that the correct determination has been made. The method is applicable to determining copy number variations (CNV) of any sequence of interest in samples comprising mixtures of genomic nucleic acids derived from two different genomes, and which are known or are suspected to differ in the amount of one or more sequence of interest. The method is applicable at least to the practice of noninvasive prenatal diagnostics, and to the diagnosis and monitoring of conditions associated with a difference in sequence representation in healthy versus diseased individuals. | 12-05-2013 |
20130324421 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in the concentration of inorganic pyrophosphate (PPi), hydrogen ions, and nucleotide triphosphates. | 12-05-2013 |
20130331275 | KITS FOR DETECTING RIBONUCLEIC ACID - Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined. | 12-12-2013 |
20130331276 | METHODS OF BEAD MANIPULATION AND FORMING BEAD ARRAYS - According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same. | 12-12-2013 |
20130331277 | PAIRED END RANDOM SEQUENCE BASED GENOTYPING - Method for simultaneous discovery, detection and genotyping of polymorphisms between samples by providing identifier tagged restriction fragments, obtaining sequence information using paired high throughput sequencing technologies, combining the sequence information and identify polymorphisms between the samples. The combination of sequence information from both ends allows for the discovery, detection and genotyping of polymorphisms in highly repetitive genomes. | 12-12-2013 |
20130331278 | COMPLEX SET OF MIRNAS AS NON-INVASIVE BIOMARKERS FOR PROSTATE DISEASES - The present invention relates to non-invasive methods, kits and means for diagnosing and/or prognosing of prostate diseases in a body fluid sample from a subject. Further, the present invention relates to set of polynucleotides or sets of primer pairs for detecting sets of miRNAs for diagnosing and/or prognosing of prostate diseases in a body fluid sample from a subject. In addition, the present invention relates to sets of miRNAs for diagnosing and/or prognosing of prostate diseases in a body fluid sample from a subject. | 12-12-2013 |
20130331279 | RECURRENT SPOP MUTATIONS IN PROSTATE CANCER - The invention relates generally to new prostate cancer markers, and particularly to a class of cancer marked by the presence of missense mutations in SPOP, an E3 ubiquitin ligase component. The invention provides methods and materials for detecting and diagnosing prostate cancer by detecting these mutations and may be useful in predicting disease progression and response to therapy. | 12-12-2013 |
20130338008 | METHOD OF MAKING AN ARRAY OF NUCLEIC ACID COLONIES - A method of making an array of nucleic acid colonies, including the steps of (a) providing a substrate having a patterned surface of features, wherein the features are spatially organized in a repeating pattern on the surface of the substrate; (b) contacting the substrate with a solution of different target nucleic acids to seed no more than a subset of the features that contact the solution; (c) amplifying the nucleic acids on the subset of features; and (d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of nucleic acid colonies. | 12-19-2013 |
20130338009 | HIGH-THROUGHPUT METHODOLOGY FOR IDENTIFYING RNA-PROTEIN INTERACTIONS TRANSCRIPTOME-WIDE - Methods of identifying RNA-protein interaction sites are provided. Systems for identifying RNA-protein interaction sites are provided. Systems for identifying secondary structures are provided. Methods of identifying secondary structures are provided. Methods of identifying RNA-binding proteins are provided. | 12-19-2013 |
20130338010 | FILTER ARCHITECTURE FOR ANALYTICAL DEVICES - An approach to the design of the set of filters which allows for the collection of a larger portion of the optical signal while still distinguishing the presence of the various fluorophores is described. In some embodiments, the filter sets of the invention each block a smaller portion of the spectrum, allowing for a larger portion of the emitted light to be detected. The combined information from the light passing through two or more of the filters is then used to determine the presence of a given fluorophore. The filter sets of the invention can be particularly useful in integrated devices in which the light from a single molecule reaction in a small reaction region is directed to a detector or to a specific portion of a detector. | 12-19-2013 |
20130338011 | METHOD AND SUBSTANCES FOR ISOLATING MIRNAS - A capture probe suitable for use with a method for isolating miRNAs. A method for isolating an miRNA of interest from a sample comprising the miRNA of interest comprising providing the capture probe. A method for identifying an miRNA of interest. | 12-19-2013 |
20130338012 | GENETIC RISK FACTORS OF SICK SINUS SYNDROME - It has been found that certain alleles of the human MYH6 gene are predictive of risk of certain conditions, including Sick Sinus Syndrome, Atrial Fibrillation, Pacemaker implantation and Thoracic aortic aneurysm, in humans. The invention provides diagnostic applications using such alleles, including methods of determining a susceptibility of Sick Sinus Syndrome and related conditions. | 12-19-2013 |
20130345065 | ACTIVE-ELECTRODE INTEGRATED BIOSENSOR ARRAY AND METHODS FOR USE THEREOF - A method and device for performing DNA sequencing and extracting structural information from unknown nucleic acid strands. The device includes a microwell structure, where identical DNA strands are immobilized within the microwell structure on a surface of a micro-bead, an active electrode or a porous polymer. The device further includes a CMOS-integrated semiconductor integrated circuit, where the CMOS-integrated semiconductor integrated circuit includes metal layers on a silicon substrate, where the metal layers form an active electrode biosensor. In addition, a sensing electrode is formed by creating openings in a passivation layer of the CMOS-integrated semiconductor integrated circuit to hold a single bead, on which the DNA strands are immobilized. | 12-26-2013 |
20130345066 | SYSTEMS AND METHODS FOR IDENTIFYING SEQUENCE VARIATION - Systems and method for determining variants can receive mapped reads, align flow space information to a flow space representation of a corresponding portion of the reference. Reads spanning a position with a potential variant can be evaluated in a context specific manner. A list of probable variants can be provided. | 12-26-2013 |
20130345067 | USE OF MICROFLUIDIC SYSTEMS IN THE DETECTION OF TARGET ANALYTES USING MICROSPHERE ARRAYS - The invention relates generally to methods and apparatus for conducting analyses, particularly microfluidic devices for the detection of target analytes. | 12-26-2013 |
20130345068 | Nucleic Acid Analysis by Random Mixtures of Non-Overlapping Fragments - The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like. | 12-26-2013 |
20130345069 | Nucleic Acid Analysis by Random Mixtures of Non-Overlapping Fragments - The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like. | 12-26-2013 |
20130345070 | Nucleic Acid Analysis by Random Mixtures of Non-Overlapping Fragments - The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like. | 12-26-2013 |
20130345071 | Nucleic Acid Analysis by Random Mixtures of Non-Overlapping Fragments - The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like. | 12-26-2013 |
20140005054 | COMPLEX RNA COMPOSITION OF BODILY FLUIDS | 01-02-2014 |
20140005055 | METHODS FOR IMPROVING GENOME ASSEMBLIES | 01-02-2014 |
20140005056 | METHODS AND COMPOSITIONS FOR LONG FRAGMENT READ SEQUENCING | 01-02-2014 |
20140011686 | SELECTION OF SINGLE NUCLEIC ACIDS BASED ON OPTICAL SIGNATURE - The invention provides, inter alia, methods for analyzing populations nucleic acids including nucleic acids from different subjects or different samples such as bacteria in biomes, and for identifying nucleic acids present in such populations. A non-limiting example is an analysis of bacteria in biomes. Another example is an analysis of DNA from different human subjects. | 01-09-2014 |
20140011687 | METHODS FOR THE SURVEY AND GENETIC ANALYSIS OF POPULATIONS - The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine. | 01-09-2014 |
20140018245 | MARKER SEQUENCES FOR MULTIPLE SCLEROSIS AND USE THEREOF - The invention relates to novel marker sequences for multiple sclerosis and to the use thereof in diagnosis as well as to a method for screening potential active ingredients for multiple sclerosis diseases using said marker sequences. The invention further relates to a diagnostic device containing such marker sequences for multiple sclerosis, especially to a protein biochip and the use thereof. | 01-16-2014 |
20140024536 | APPARATUS AND METHODS FOR HIGH-THROUGHPUT SEQUENCING - The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant. | 01-23-2014 |
20140024537 | METHODS AND SYSTEMS FOR DETERMINING HAPLOTYPES AND PHASING OF HAPLOTYPES - The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes. | 01-23-2014 |
20140024538 | MULTIPLEXED SEQUENTIAL LIGATION-BASED DETECTION OF GENETIC VARIANTS - The present invention provides multiplexed sequential ligation-based analysis of genetic variants in a mixed sample, including copy number variations and single nucleotide polymorphisms. The invention employs the techniques of sequential ligation and amplification. | 01-23-2014 |
20140024539 | BIOMARKERS AND METHODS OF USE THEREOF - Methods useful in the prediction and detection of a triple negative cancer subtype using biomarkers are provided herein. | 01-23-2014 |
20140024540 | LIGAND IDENTIFICATION - The present disclosure provides new and improved phage display methodologies. Among other things, the present invention provides methodologies that do not utilize bacterial amplification of phage. Alternatively or additionally, the present invention provides phage display systems that rapidly identify ligands. Alternatively or additionally, the present invention provides phage display methodologies for use in human subjects. Alternatively or additionally, the present invention provides phage display systems that allow detection and/or characterization of low abundance ligands. | 01-23-2014 |
20140031237 | Methods of enriching for and identifying polymorphisms - The invention encompasses methods for enriching for and identifying a polymorphism within a nucleic acid sample either by separating a subset of a nucleic acid sample or by selectively replicating a subset of a nucleic acid sample such that the polymorphism is contained within a nucleic acid population with reduced complexity, and then identifying the polymorphism within the enriched nucleic acid sample. Methods also are disclosed for enriching for and identifying a polymorphism by contacting a nucleic acid sample that includes a subset of nucleic acid molecules having a sequence that binds to a sequence-specific binding activity with a molecule having a sequence-specific binding activity under conditions which permit specific binding, such that the subset of nucleic acid molecules bound to the activity is enriched for nucleic acid molecules having the sequence recognized by the sequence-specific binding activity, and detecting a polymorphism with respect to a reference sequence in the subset of nucleic acid molecules. | 01-30-2014 |
20140031238 | ALTERNATIVE NUCLEOTIDE FLOWS IN SEQUENCING-BY-SYNTHESIS METHODS - A method for sequencing a polynucleotide strand by using sequencing-by-synthesis techniques. To address the problem of incomplete extension (IE) and/or carry forward (CF) errors that can occur in sequencing-by-synthesis reactions, an alternative flow ordering of dNTPs is used. In contrast to conventional flow orderings, the dNTPs are flowed in an ordering that is not a continuous repeat of an ordering of the four different dNTPs. This alternate flow ordering may reduce the loss of phasic synchrony in the population of template polynucleotide strands that result from IE and/or CF errors. | 01-30-2014 |
20140031239 | METHOD OF SEQUENCING - The present invention provides a method of sequencing a single polynucleotide in which the nucleotide base and/or probe which is incorporated during sequencing is labelled with a bead which is detected to identity the base and/or probe which has bound to the single polynucleotide. Particularly, the detection of the bead may be carried out using an apparatus comprising a surface provided with a means for detecting a bead e.g. with one or more light sensitive elements. | 01-30-2014 |
20140031240 | TM-ENHANCED BLOCKING OLIGONUCLEOTIDES AND BAITS FOR IMPROVED TARGET ENRICHMENT AND REDUCED OFF-TARGET SELECTION - The invention is directed to modified oligonucleotide compositions and methods for selectively reducing unwanted nucleic acid contaminants and enriching for desired nucleic acid targets from complex genomic nucleic acid mixtures for sequencing applications. The modified oligonucleotide compositions include one or more modified groups that increase the T | 01-30-2014 |
20140031241 | PAIRED END BEAD AMPLIFICATION AND HIGH THROUGHPUT SEQUENCING - The present invention is related to genomic nucleotide sequencing. In particular, the invention describes a paired end sequencing method that enables the sequencing of unique read pairs by co-localizing both 5′ ends on a single emulsion polymerase chain reaction bead. The method may use a customized forked adaptor primer pair that is compatible with massively parallel sequencing techniques. The compositions and methods disclosed herein contemplate sequencing complex genomes, amplified genomic regions, as well as detecting chromosomal structural rearrangements. | 01-30-2014 |
20140031242 | METHOD FOR DISCOVERING PHARMACOGENOMIC BIOMARKERS - The present invention relates to a method of discovering pharmacogenomic biomarkers that are correlated with varied individual responses (efficacy, adverse effect, and other end points) to therapeutic agents. The present invention provides a mean to utilize archived clinical samples to perform genome-wide association study in order to identify novel pharmacogenomic biomarkers. The newly discovered biomarkers can then be developed into companion diagnostic tests which can help to predict drug responses and apply drugs only to those who will be benefited, or exclude those who might have adverse effects, by the treatment. | 01-30-2014 |
20140038830 | DETECTING AND CLASSIFYING COPY NUMBER VARIATION - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample. | 02-06-2014 |
20140038831 | HIGH THROUGHPUT YEAST TWO-HYBRID SCREENING METHOD AND REAGENT KIT - An approach to collect and interpret results from Y2H screens uses high-throughput next-generation sequencing technologies. In particular, this system is appropriate to generate comprehensive profiles of protein-protein interactions (PPIs), allowing also a side-by-side comparison of specific PPI patterns with that from control samples and allows a direct comparison of PPI patterns displayed by proteins in their wild-type and various mutant conformations. While sample preparation relies to the most part on established transcriptome and RNA sequencing procedures, this invention also encloses a specific DNA preparation step to sequester irrelevant and contaminating sequences from the sample. | 02-06-2014 |
20140045701 | SYTEMS AND METHODS FOR AUTOMATED REUSABLE PARALLEL BIOLOGICAL REACTIONS - A method comprises magnetically holding a bead carrying biological material (e.g., nucleic acid, which may be in the form of DNA fragments or amplified DNA) in a specific location of a substrate, and applying an electric field local to the bead to isolate the biological material or products or byproducts of reactions of the biological material. For example, the bead is isolated from other beads having associated biological material. The electric field in various embodiments concentrates reagents for an amplification or sequencing reaction, and/or concentrates and isolates detectable reaction by-products. For example, by isolating nucleic acids around individual beads, the electric field can allow for clonal amplification, as an alternative to emulsion PCR. In other embodiments, the electric field isolates a nanosensor proximate to the bead, to facilitate detection of at least one of local pH change, local conductivity change, local charge concentration change and local heat. The beads may be trapped in the form of an array of localized magnetic field regions. | 02-13-2014 |
20140045702 | SYSTEMS AND METHODS FOR DISTINGUISHING BETWEEN AUTISM SPECTRUM DISORDERS (ASD) AND NON-ASD DEVELOPMENT DELAY - Methods and systems are presented herein to distinguish children with Autism Spectrum Disorders (ASD) from those with other forms of developmental delay (DD) based on patterns of gene expression levels in blood. | 02-13-2014 |
20140045703 | METHOD OF SEQUENCING - The present invention provides a method of sequencing a polynucleotide using a stepwise ligation and cleavage method in which two or more cleavage enzymes which are specific to two or more test probes are used sequentially to identify which test probe bound and hence the sequence of the target polynucleotide. In a preferred aspect the probes and/or bases used in the reaction are labelled, e.g. with a bead. | 02-13-2014 |
20140045704 | MICROFLUIDIC AND NANOFLUIDIC DEVICES, SYSTEMS, AND APPLICATIONS - The present invention discloses the integration of programmable microfluidic circuits to achieve practical applications to process biochemical and chemical reactions and to integrate these reactions. In some embodiments workflows for biochemical reactions or chemical workflows are combined. Microvalves such as programmable microfluidic circuit with Y valves and flow through valves are disclosed. In some embodiments microvalves of the present invention are used for mixing fluids, which may be part of an integrated process. These processes include mixing samples and moving reactions to an edge or reservoir for modular microfluidics, use of capture regions, and injection into analytical devices on separate devices. In some embodiments star and nested star designs, or bead capture by change of cross sectional area of a channel in a microvalve are used. Movement of samples between temperature zones are further disclosed using fixed temperature and movement of the samples by micropumps. | 02-13-2014 |
20140045705 | Techniques for Determining Haplotype by Population Genotype and Sequence Data - A novel phasing algorithm harnesses sequencing read information from next generation sequencing technologies to guide and improve local haplotype reconstruction from genotypes. Techniques include determining correlated occurrences of single nucleotide polymorphisms (SNPs) in genes of a population of individuals. A plurality of sequences of nucleotide bases in one or more individuals from the populations of individuals is determined based on ultra-high throughput sequencing of a sample from the one or more individuals. Haplotypes included in the population of individuals are determined based on both the correlated occurrences and the plurality of sequences. The inclusion of paired end read data is especially advantageous for the phasing of rare variants, including singletons. | 02-13-2014 |
20140045706 | METHODS AND SYSTEMS FOR HAPLOTYPE DETERMINATION - Embodiments of the present disclosure provide methods and systems for determining the haplotype of a biological sample. Particular embodiments provide methods for long range haplotyping of a genome. | 02-13-2014 |
20140051583 | Noninvasive Diagnosis of Fetal Aneuploidy by Sequencing - Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes. | 02-20-2014 |
20140051584 | Methods and Apparatuses for Estimating Parameters in a Predictive Model for Use in Sequencing-by-Synthesis - A method of estimating a parameter related to sequencing of a sample nucleic acid template includes: receiving signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells; determining sequence information for the sample nucleic acid template using signal data from the first well; and constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells. | 02-20-2014 |
20140051585 | METHODS AND COMPOSITIONS FOR REDUCING GENETIC LIBRARY CONTAMINATION - Embodiments include methods, compositions, and kits for creating genetic libraries useful for massively parallel genetic sequencing. Some embodiments are directed to methods of preventing the contamination of genetic libraries with material generated during the formation of other genetic libraries. In some embodiments, the methods employ adapters comprising universal priming sites. The methods can employ non-ligatable primers to generate non-ligatable amplification products so as to prevent unwanted ligation to adapters. In some embodiments, the non-ligatable primers contain uracil. Genetic material can be treated with uracil N glycosylase to prevent the unwanted ligation of uracil containing amplicons to adapters used for creating a second genetic library. | 02-20-2014 |
20140051586 | HIGH-THROUGHPUT METHODS TO PRODUCE, VALIDATE AND CHARACTERIZE MMABS - Provided herein is a system and method for identifying a biomarker and producing a reagent for detecting the biomarker. The system and method comprises administering to an animal a biological sample and comparing the immune response of the animal to the immune response of another animal. | 02-20-2014 |
20140051587 | CANCER MARKERS - Hence, the invention relates to a method for diagnosis and/or prognosis of cancer, comprising the steps of analyzing in a sample of a subject the DNA methylation status of a genomic region of at least one member of the group of, (i) SFN according to SEQ ID NO. 1, (ii) SLIT2 according to SEQ ID NO. 2, (iii) SERPINB5 according to SEQ ID NO. 3; and (iv) TWIST 1 according to SEQ ID NO 4; wherein, if (i) SFN shows a methylation cut off value of above 80% and/or, (ii) SLIT2 shows a methylation cut-off value of above 45% and/or, (iii) SERPBINB5 shows a methylation cut-off value of above 70%, and/or (iv) TWIST 1 shows a methylation level below 15% the sample is categorized as a sample from a patient with cancer and/of a poor prognosis. | 02-20-2014 |
20140057793 | METHOD OF SIMULTANEOUSLY EVALUATING MULTIPLE GENOMIC SEQUENCES - Methods and systems for simultaneously evaluating genomic sequences across multiple population members, and methods and systems for simultaneously calling normal and cancerous genomic sequences from a mixed sample containing normal and cancerous material are disclosed. This may be achieved by evaluating the probability of one or more hypothesis being correct for a plurality of population members based on genomic sequence information for the population. For related family members, Mendelian inheritance may be integrated into the method. For populations, information from members under evaluation may be used to refine priors to more accurately call population members. Copy number variation and de novo mutations may also be accommodated in the methods. Specific systems for implementing the methods are also disclosed. | 02-27-2014 |
20140057794 | LUNG CANCER SIGNATURE - The present disclosure relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure relates to cancer markers as diagnostic markers and clinical targets for lung cancer. | 02-27-2014 |
20140066316 | DACH1 as a Biomarker for Diabetes - The present invention provides a method for assessing the presence and risk of developing type 2 diabetes or cardiovascular disease in a subject by detecting sequence variation in DACH1 (Dachshund homolog 1) gene. A kit and device useful for such a method are also provided. In addition, the present invention provides a method for treating type 2 diabetes or cardiovascular disease in patients who have been tested and shown to have the pertinent genetic variations. | 03-06-2014 |
20140066317 | SYSTEMS AND METHODS TO DETECT RARE MUTATIONS AND COPY NUMBER VARIATION - The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease. | 03-06-2014 |
20140073511 | System and Method for Operation of Isfet Arrays Using pH Inert Reference Sensors - An embodiment of a method for sequencing a species of nucleic acid template using pH inert reference sensors is described that comprises the steps of: introducing a nucleotide species to an array of wells where a plurality of the wells comprise a species of nucleic acid template and a plurality of the wells comprise a plurality of functional groups with a high pH buffering characteristic, and in at least a first well a polymerase species incorporates the nucleotide species into a plurality of strands complementary to the species of nucleic acid template disposed in the first well and results in a release of a plurality of hydrogen ions; detecting a signal in the first well that is responsive to the hydrogen ions and one or more noise sources; detecting a signal in a second well comprising the functional groups with the high pH buffering characteristic that is responsive to the one or more noise sources; and subtracting the second well signal from the first well signal to generate a corrected signal associated with the detected hydrogen ions. | 03-13-2014 |
20140073512 | Compositions and Methods for Intramolecular Nucleic Acid Rearrangement - Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or MID). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided. | 03-13-2014 |
20140073513 | Self-Assembled Single Molecule Arrays and Uses Thereof - The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences. | 03-13-2014 |
20140073514 | INTEGRATED SEQUENCING APPARATUSES AND METHODS OF USE - Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing. | 03-13-2014 |
20140080715 | NON-INVASIVE DETERMINATION OF METHYLOME OF FETUS OR TUMOR FROM PLASMA - Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer. | 03-20-2014 |
20140080716 | HIGH THROUGHPUT SCREENING OF MUTAGENIZED POPULATIONS - Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation. | 03-20-2014 |
20140080717 | NUCLEIC ACID AMPLIFICATION - In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components. In some embodiments, methods for nucleic acid amplification comprise a amplifying at least one polynucleotide onto a surface under isothermal amplification conditions, optionally in the presence of a polymer. The polymer can include a sieving agent and/or a diffusion-reducing agent. | 03-20-2014 |
20140080718 | Systems and Methods for Identifying Sequence Variation Associated with Genetic Diseases - Systems and method for identifying variants associated with a genetic disease can include obtaining calls for a plurality of individuals for a list of variant positions. The calls can be compared to identify variants that are found in affected individuals and absent in non-affected individuals. Such variants can include loss of heterozygosity, trans-phased compound heterozygotes, increased frequency mitochondrial variants, homozygous recessive variants, de novo variants, sex-linked variants, and combinations thereof. | 03-20-2014 |
20140080719 | METHODS AND APPARATUS FOR DETECTING MOLECULAR INTERACTIONS USING FET ARRAYS - Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. | 03-20-2014 |
20140080720 | FETAL GENOMIC ANALYSIS THAT ACCOUNTS FOR GC BIAS - Systems, methods, and apparatuses for performing a prenatal diagnosis of a sequence imbalance are provided. A shift (e.g. to a smaller size distribution) can signify an imbalance in certain circumstances. For example, a size distribution of fragments of nucleic acids from an at-risk chromosome can be used to determine a fetal chromosomal aneuploidy. A size ranking of different chromosomes can be used to determine changes of a rank of an at-risk chromosome from an expected ranking. Also, a difference between a statistical size value for one chromosome can be compared to a statistical size value of another chromosome to identify a significant shift in size. A genotype and haplotype of the fetus may also be determined using a size distribution to determine whether a sequence imbalance occurs in a maternal sample relative to a genotypes or haplotype of the mother, thereby providing a genotype or haplotype of the fetus. | 03-20-2014 |
20140087954 | QUANTITATIVE NUCLEASE PROTECTION ASSAY (QNPA) AND SEQUENCING (QNPS) IMPROVEMENTS - The present disclosure provides an improvement to quantitative Nuclease Protection Assay (qNPA) and quantitative Nuclease Protection Sequencing (qNPS) methods. The disclosed methods use nuclease protection probes (NPPs) that include 5′-end and/or 3-end flanking sequences, which provide a universal hybridization and/or amplification sequence. The disclosed methods can be used to sequence or detect target nucleic acid molecules, such as those present in fixed or insoluble samples. | 03-27-2014 |
20140094374 | Recombinant Polymerases with Increased Readlength and Stability for Single-Molecule Sequencing - Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing or nucleic acid amplification. Such properties include increased stability, increased readlength, enhanced performance with large nucleotide analogs, and improved detection of modified bases, and can also include resistance to photodamage, enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased accuracy, altered speed, increased cosolvent resistance, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template. | 04-03-2014 |
20140094375 | Recombinant Polymerases for Incorporation of Protein Shield Nucleotide Analogs - Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing or nucleic acid amplification. Such properties include enhanced performance with large nucleotide analogs, increased stability, increased readlength, and improved detection of modified bases, and can also include resistance to photodamage, enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased accuracy, altered speed, increased cosolvent resistance, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template. | 04-03-2014 |
20140100121 | MUTATIONAL ANALYSIS OF PLASMA DNA FOR CANCER DETECTION - A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient. | 04-10-2014 |
20140100122 | METHODS, COMPOSITIONS AND SYSTEMS FOR SAMPLE DEPOSITION - Methods, compositions, systems, apparatus, and kits are provided for depositing samples onto surfaces. The samples can include one or more particles, and the surface can include one or more reaction chambers. In some embodiments, the depositing can include the use of companion particles in combination with sample particles. | 04-10-2014 |
20140106974 | PATHOGEN IDENTIFICATION PROCESS AND TRANSPORT CONTAINER - A process of pathogen identification and a transport container are disclosed. The process includes positioning a porous material containing a sample into an receptacle of a transport container, facilitating transport of the transport container through a mail or parcel service, removing the porous material, the receptacle of the transport container, collecting the sample from the porous material, analyzing the preserved nucleic acid, or a combination thereof. The porous material degrades the sample and preserves nucleic acid. The analyzing identifies a plurality of sequences within the preserved nucleic acid in a parallel manner. | 04-17-2014 |
20140106975 | FETAL ANEUPLOIDY DETECTION BY SEQUENCING - The present invention provides apparatus and methods for enriching components or cells from a sample and conducting genetic analysis, such as SNP genotyping to provide diagnostic results for fetal disorders or conditions. | 04-17-2014 |
20140121116 | System and Methods for Detecting Genetic Variation - The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant. In some aspects, systems and methods of detecting genetic variation are provided. | 05-01-2014 |
20140128268 | Methods of Constructing and Screening Libraries of Peptide Structures - The present invention provides the means for producing libraries of peptide structures for drug screening applications that are capable of folding or assuming their native conformations independently of artificial scaffolds or flanking sequences in the proteins from which they are derived. The libraries can be highly diverse such that they are representative of the repertoire of protein structures existing in nature. The libraries can also be non-redundant or normalized such that the bias towards specific structures existing in source data sets and/or in nature is/are removed. In a particularly preferred embodiment, the present invention provides 30,000 independent fold structures produced by this method. The present invention also provides computer-readable media and systems comprising structural data in relation to the peptide libraries, and methods for displaying and screening the libraries. | 05-08-2014 |
20140128269 | SCAFFOLDED NUCLEIC ACID POLYMER PARTICLES AND METHODS OF MAKING AND USING - The invention provides particle compositions having applications in nucleic acid analysis. Nucleic acid polymer particles of the invention allow polynucleotides to be attached throughout their volumes for higher loading capacities than those achievable solely with surface attachment. In one aspect, nucleic acid polymer particles of the invention comprise polyacrylamide particles with uniform size distributions having low coefficients of variations, which result in reduced particle-to-particle variation in analytical assays. Such particle compositions are used in various amplification reactions to make amplicon libraries from nucleic acid fragment libraries. | 05-08-2014 |
20140128270 | Method of improving microarray performance by strand elimination - The invention is a method of determining nucleotide sequence of a target nucleic acid using microarray analysis. Hybridization signals from probe sets corresponding to the sense and anti-sense strands are compared at each nucleotide position. If there is a substantial difference in performance between the two strands, probe sets from a poorly performing stand are eliminated from the sequence determination calculation for a particular nucleotide. | 05-08-2014 |
20140141979 | METHOD FOR IDENTIFYING ANTIBIOTIC TARGETS - Disclosed is a method for identifying an essential gene which serves as an antibiotic target in a bacterium, the method comprising the steps of:
| 05-22-2014 |
20140141980 | Stratifying and annotating a clinical practice guideline - Personalized medicine involves the use of a patient's molecular markers to guide treatment regimens for the patient. The scientific literature provides multiple examples of correlations between drug treatment efficacy and the presence or absence of molecular markers in a patient sample. Methods are provided herein that permit efficient dissemination of scientific findings regarding treatment efficacy and molecular markers found in patient tumors to health care providers. | 05-22-2014 |
20140141981 | HIGHLY MULTIPLEX PCR METHODS AND COMPOSITIONS - The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons. | 05-22-2014 |
20140148344 | ASSOCIATION MARKERS FOR BETA THALASSEMIA TRAIT - The present invention relates to isolated nucleic acid molecules of SEQ ID NO: 1 to SEQ ID NO: 14 which show a single polymorphic change at position 501, where the wildtype nucleotide is replaced by an indicator nucleotide, respectively. The present invention further relates to the mentioned nucleic acid molecules wherein a panel of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 of the polymorphic, changed sequences comprising the mentioned indicator nucleotides constitutes a marker for beta thalassemia, in particular of beta thalassemia minor. Further envisaged are specific panels comprising SEQ ID NO: 1; or SEQ ID NO 1 and 2; or SEQ ID NO: 1, 2 and 3, or SEQ ID NO: 1, 2, 3 and 4; or SEQ ID NO: 1 to 5; or SEQ ID NO: 1 to 6; or SEQ ID NO: 1 to 7; or SEQ ID NO: 1 to 14; or SEQ ID NO: 8 and 14; or SEQ ID NO: 8 and 9; or SEQ ID NO: 2, 4 and 13. The present invention further relates to a method of detecting or diagnosing beta thalassemia, preferably of beta thalassemia minor, in a subject, comprising the steps of: (a) isolating a nucleic acid from a subject's sample, (b) determining the nucleotide sequence and/or molecular structure present at one or more of the mentioned polymorphic sites, wherein the presence of an indicator nucleotide indicative of the presence of beta thalassemia. Also envisaged are a corresponding composition for detecting or diagnosing beta thalassemia, the use of the mentioned nucleic acid molecules for detecting or diagnosing beta thalassemia or for screening a population for the presence of beta thalassemia, as well as a corresponding kit. The methods, compositions, uses and kits of the invention also relate to the assessment of the risk of developing beta thalassemia in a subject and/or in a subject's progeny. | 05-29-2014 |
20140148345 | NUCLEIC ACID AMPLIFICATION - In some embodiments, the present teachings provide methods for nucleic acid amplification, comprising forming a reaction mixture, and subjecting the reaction mixture to conditions suitable for nucleic acid amplification. In some embodiments, methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components. In some embodiments, methods for nucleic acid amplification comprise a amplifying at least one polynucleotide onto a surface under isothermal amplification conditions, optionally in the presence of a polymer. The polymer can include a sieving agent and/or a diffusion-reducing agent. | 05-29-2014 |
20140148346 | METHODS OF IDENTIFYING AND CLASSIFYING ORGANOHALIDE-RESPIRING BACTERIA - Briefly described, embodiments of the present disclosure relate to methods and systems for identifying and classifying taxa of organohalide-respiring bacteria, including methods and systems for identify and classify two or more taxa of | 05-29-2014 |
20140148347 | High Resolution Analysis of Mammalian Transcriptome Using Gene Pool Specific Primers - The present invention provides methods and systems for analyzing mammalian transcriptomes, particularly, for low abundant transcripts, and with the use of high throughput technologies. Heptamer primers and sequence tags generated by the iterative randomized algorithm, as well as the sequencing-library generation system for amplifying and synthesis-based sequencing low abundant transcripts using the heptamer primers are also provided. The present invention further provides the use of the invention system and method for identifying key embryological lineage specific transcripts that anticipate differentiation of specific cell types. | 05-29-2014 |
20140155271 | METHODS AND COMPOSITIONS FOR DIAGNOSING, PROGNOSING, AND TREATING NEUROLOGICAL CONDITIONS - This document provides methods and materials related to genetic variations of neurological disorders. For example, this document provides methods for using such genetic variations to assess susceptibility of developing Parkinson's disease. | 06-05-2014 |
20140155272 | Use Of Diatomaceous Earth As The Base Substrate For Nucleic Acid Tags - A nucleic acid tag comprising: a nanoparticle nucleotide-support platform attached to a plurality of nucleic acid molecules, each of said nucleic acid molecules comprising identifying information, with a spacer located between the nanoparticle nucleotide-support platform and the identifying information, and where the nanoparticle nucleotide-support platform comprises diatomaceous earth; and an encapsulant surrounding the nanoparticle nucleotide-support platform. | 06-05-2014 |
20140155273 | Method for Detecting the Genus of Bacillus in Samples from Oil Reservoirs - The invention provides a quick method for detecting the genus of | 06-05-2014 |
20140155274 | Single Cell Nucleic Acid Detection and Analysis - Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided. | 06-05-2014 |
20140155275 | SEMI-DIGITAL LIGATION ASSAY - Assays for detecting mutant sequences at particular locations, especially against a background of non-mutant sequences, employ thermocycling ligase reactions. Differentially labeled or sized probes can be used to distinguish wild-type and mutant sequences. Physico-chemical properties of the probes can be critical to successful detection. Mutation detection can be used for diagnosis, monitoring, or prognosticating diseases such as cancers. | 06-05-2014 |
20140155276 | ISOLATION OF POLYMERASE-NUCLEIC ACID COMPLEXES - Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Hook oligonucleotides are used to capture polymerase nucleic acid complexes where the nucleic acids comprise circular nucleic acids having a double stranded central region with hairpin regions on each end. Methods for loading such complexes onto substrates and for single molecule sequencing of such complexes are also provided. | 06-05-2014 |
20140155277 | Adaptive Immunity Profiling and Methods for Generation of Monoclonal Antibodies - Methods are provided for producing monoclonal antibody candidates using adaptive immunity profiling. In some aspects, the method provides for the use of massively parallel signature sequencing. | 06-05-2014 |
20140162885 | Bead Emulsion Nucleic Acid Amplification - Disclosed are methods for nucleic acid amplification wherein nucleic acid templates, beads, and amplification reaction solution are emulsified and the nucleic acid templates are amplified to provide clonal copies of the nucleic acid templates attached to the beads. Also disclosed are kits and apparatuses for performing the methods of the invention. | 06-12-2014 |
20140162886 | METHODS AND MATERIALS FOR ASSESSING ALLELIC IMBALANCE - Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided. | 06-12-2014 |
20140179536 | Genetic Diagnosis of Hepatic Steatosis - Disclosed are methods of identifying a genetic variant in a person determined to have or be predisposed having a fatty liver by determining whether the person has PNPLA3-I148M. Also disclosed are methods of identifying a genetic variant in a person by determining whether the person has PNPLA3-I148M; and prescribing to the person a treatment to reduce liver fat or associated inflammation. | 06-26-2014 |
20140179537 | COMPOSITIONS AND METHODS FOR DIAGNOSING COLON DISORDERS - The present invention relates to methods and compositions for diagnosing, monitoring, prognosticating, analyzing, etc., polymicrobial diseases. The present invention also relates to the microbial community present in the digestive tract and lumen in normal subjects, and subjects with digestive tract diseases, especially diseases of the colon, such as inflammatory bowel disease, including ulcerative colitis, Crohn's syndrome, and pouchitis. The present invention especially relates to compositions and methods for diagnosing and prognosticating the mentioned diseases and conditions, e.g., to determine the presence of the disease in a subject, to determine a therapeutic regimen, to determine a therapeutic regimen, to determine the onset of active disease, to determine the predisposition to the disease, etc. | 06-26-2014 |
20140179538 | MUTATIONS IN PANCREATIC NEOPLASMS - To help reveal the pathogenesis of these lesions, we purified the DNA from Intraductal Papillary Mucinous Neoplasm (IPMN) cyst fluids from 19 patients and searched for mutations in 169 genes commonly altered in human cancers. We identified recurrent mutations at codon 201 of GNAS. We found that GNAS mutations were present in 66% of IPMNs and that either KRAS or GNAS mutations could be identified in 96%. In eight cases, we could investigate invasive adenocarcinomas that developed in association with IPMNs containing GNAS mutations. In seven of these eight cases, the GNAS mutations present in the IPMNs were also found in the invasive lesion. GNAS mutations were not found in other types of cystic neoplasms of the pancreas or in invasive adenocarcinomas not associated with IPMNs. These data suggest that GNAS mutations can inform the diagnosis and management of patients with cystic pancreatic lesions. | 06-26-2014 |
20140187429 | Apparatus and Method for Specific Release of Captured Extension Products - Apparatus and methods for separating different polynucleotide populations in a mixture are provided, wherein different polynucleotides or polynucleotide populations are captured on different solid support. After hybridization, polynucleotides are selectively released from a selected support by altering a physical property of that support. The released polynucleotides can be eluted from a common flow path and isolated. | 07-03-2014 |
20140194295 | Method of Measuring Adaptive Immunity - A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells. | 07-10-2014 |
20140194296 | Multiplex Capture of Nucleic Acids - Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on different subsets of particles or at different selected positions on a spatially addressable solid support. Methods of capturing one or more long nucleic acids and methods of capturing one or more nucleic acid for sequencing are also provided. Compositions, kits, and systems related to the methods are also described. | 07-10-2014 |
20140194297 | Methods and Apparatus for Detecting Molecular Interactions Using FET Arrays - Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. | 07-10-2014 |
20140194298 | Methods and Apparatus for Detecting Molecular Interactions Using FET Arrays - Methods and apparatuses relating to large scale FET arrays for analyte detection and measurement are provided. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. | 07-10-2014 |
20140194299 | COMPOSITIONS, METHODS AND RELATED USES FOR CLEAVING MODIFIED DNA - Compositions, methods and related uses are provided relating to cleaving modified DNA. For example, a set of DNA fragments obtainable by enzymatic cleavage of a large DNA is described where at least 50% are similarly sized and have a centrally positioned modified nucleotide. In addition, an enzyme preparation is provided that includes one or more enzymes that recognize a modified nucleotide in a DNA and cleave the DNA at a site that is at a non-random distance from the modified nucleotide. The one or more enzymes are further characterized by an N-terminal conserved domain with greater than 90% amino acid sequence homology to WXD(X) | 07-10-2014 |
20140194300 | Method and device for genetic map construction, method and device for haplotype analysis - Provided are the method and device for genetic map construction and the method and device for haplotype determination of a single cell. Wherein the method for genetic map construction includes: whole genome sequencing for at least a single cell from a same species, aligning the sequencing data to reference sequences respectively to determine genotypes of SNP sites, determining male parent a/female parent b typing results of SNP genotypes of a single cell based on the genotypes of SNP sites, dividing the chromosome of the species into linkage regions based on the male parent a/female parent b typing results of SNP genotypes, determining the variation ratio of a/b between two linkage regions to obtain recombination rate between every two continuous linkage regions, determining recombination map of a single cell according to the recombination rate, wherein the boundary site of a and b is the recombination site, determining the recombination rate of each recombination rate based on the recombination map to construct a genetic map of the species. | 07-10-2014 |
20140200146 | Methods of Amplifying Whole Genome of a Single Cell - Methods and compositions for amplifying the whole genome of a single cell are provided. | 07-17-2014 |
20140200147 | Methods and Systems for Genetic Analysis - This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions. | 07-17-2014 |
20140206543 | STABLE GENE TARGETS IN BREAST CANCER AND USE THEREOF FOR OPTIMIZING THERAPY - A method for determining genes in breast cancer that are stable in copy number, expression and sequence in tumors from nearly all patients. Certain stable genes are targets of standard chemotherapy. The effectiveness of therapies that act upon these targets depends on maintaining the stability and integrity of these genes in tumors. Mutations in these targets result in poor response to therapies that target these gene products. In the instant invention, ordinarily stable gene targets are characterized as either normal or mutant for the purpose of determining whether to include or exclude particular drugs as potential treatments. | 07-24-2014 |
20140206544 | RNAi-Based Method of Screening and Characterizing Drug Combinations - In one aspect, the invention is directed to a method of characterizing a mechanism of action of a combination of agents. The method comprises contacting a plurality of populations of cells with a combination of agents to be assessed, wherein each population of cells have one gene of interest targeted by a small hairpin RNA (shRNA) and wherein the gene of interest regulates cell death and a plurality of genes that regulate cell death are targeted in the plurality of populations of cells. A responsiveness of each population of cells to the combination of agents is determined, thereby obtaining an shRNA signature of the combination of agents so as to identify one or more genes that mediate a response to the combination of agents, thereby characterizing the mechanism of action of the combination of agents. In another aspect, the invention is directed to a method of determining whether a patient population treated with a first agent would benefit from a treatment using the first agent in combination with one or more additional agents. In yet another aspect, the invention is directed to method of determining whether a formulation of one or more agents maintains a mechanism of action of the one or more agents when unformulated. | 07-24-2014 |
20140206545 | GENE EXPRESSION MARKERS FOR PREDICTION OF PATIENT RESPONSE TO CHEMOTHERAPY - The present invention relates to gene sets useful in assessing prognosis and/or predicting the response of cancer, e.g. colorectal cancer to chemotherapy. In addition, the invention relates to a clinically validated cancer test, e.g. colorectal test, for assessment of prognosis and/or prediction of patient response to chemotherapy, using expression analysis. The present invention accommodates the use of archived paraffin embedded biopsy material for assay of all markers in the relevant gene sets and therefore is compatible with the most widely available type of biopsy material. | 07-24-2014 |
20140206546 | METHODS AND COMPOSITIONS FOR SINGLE CELL EXPRESSION PROFILING - Methods of obtaining a single cell expression profile from a target mammalian cell are provided. Aspects of the methods include contacting a cellular sample which includes the target mammalian cell with a packaged viral barcoded trans-splicing library including a plurality of barcoded trans-splicing constructs under transduction conditions, where a barcoded trans-splicing construct includes a trans-splicing element linked to a barcode element. The methods further include generating expression data from the resultant transduced target mammalian cell to obtain the single cell expression data from the target mammalian cell. Also provided are compositions, e.g., libraries and components thereof, which find use in practicing the methods. | 07-24-2014 |
20140206547 | HAPLOTYING OF HLA LOCI WITH ULTRA-DEEP SHOTGUN SEQUENCING - Methods are provided to determine the entire genomic region of a particular HLA locus including both intron and exons. The resultant consensus sequences provides linkage information between different exons, and produces the unique sequence from each of the two genes from the individual sample being typed. The sequence information in intron regions along with the exon sequences provides an accurate HLA haplotype. | 07-24-2014 |
20140206548 | METHOD OF MEASURING ADAPTIVE IMMUNITY - A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells. | 07-24-2014 |
20140206549 | METHOD OF MEASURING ADAPTIVE IMMUNITY - A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells. | 07-24-2014 |
20140206550 | STEP-WISE NUCLEIC ACID SEQUENCING WITH CATALYTIC AND NON-CATALYTIC METALS - The application relates to methods, and systems for nucleotide sequencing comprising producing polymerase reactions that comprise both catalytic and non-catalytic divalent metal ions. Polymerase/template/primer complexes are immobilized on a substrate. The complexes are exposed to a solution comprising a non-catalytic metal and nucleotides labeled with a detectable label on a portion of the nucleotide that is released upon incorporation. The cognate nucleotide is sequestered in the active site of the polymerase, unable to proceed to incorporation. After observing the sequestered cognate nucleotide, the complex is exposed to a catalytic metal, resulting in the incorporation of the bound cognate nucleotide and consequent release of the label resulting in a single-base extended primer. | 07-24-2014 |
20140206551 | METHOD FOR THE IDENTIFICATION OF THE CLONAL SOURCE OF A RESTRICTION FRAGMENT - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers. | 07-24-2014 |
20140206552 | METHODS FOR PREIMPLANTATION GENETIC DIAGNOSIS BY SEQUENCING - The present disclosure provides methods for determining the ploidy status of an embryo at a chromosome from a sample of DNA from an embryo. The ploidy state is determined by sequencing the DNA from one or more cells biopsied from the embryo, and analyzing the relative amounts of each allele at a plurality of polymorphic loci on the chromosome. In an embodiment, the ploidy state is determined by comparing the observed allele ratios to the expected allele ratios for different ploidy states. In an embodiment, the DNA is selectively amplified at a plurality of polymorphic loci by targeted sequencing. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias. | 07-24-2014 |
20140213461 | EFFICIENT BASE DETERMINATION IN SEQUENCING REACTIONS - The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods. | 07-31-2014 |
20140213462 | STRATEGIES FOR HIGH THROUGHPUT IDENTIFICATION AND DETECTION OF POLYMORPHISMS - The invention relates to a method for the high throughput identification of single nucleotide polymorphisms by performing a complexity reduction on two or more samples to yield two or more libraries, sequencing at least part of the libraries, aligning the identified sequences and determining any putative single nucleotide polymorphisms, confirming any putative single nucleotide polymorphism, generating detection probes for the confirmed single nucleotide polymorphisms, subjection a test sample to the same complexity reduction to provide a test library and screen the test library for the presence or absence of the single nucleotide polymorphisms using the detection probe. | 07-31-2014 |
20140213463 | Method of Measuring Adaptive Immunity - A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells. | 07-31-2014 |
20140213464 | SYSTEM AND APPARATUS FOR SEQUENTIAL PROCESSING OF ANALYTES - An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array. A key feature of the invention is the correlation of the sequence of optical signals generated by each microparticle in the planar array during the analytical process. | 07-31-2014 |
20140221217 | SEQUENCE BASED GENOTYPING BASED ON OLIGONUCLEOTIDE LIGATION ASSAYS - The invention relates to a method for the detection of a target nucleotide sequence in a sample based on an oligonucleotide ligation assay wherein probes are used that contain (a combination of) sequence-based identifiers that can identify the sample and the target sequence (i.e. locus and/or allele combination) wherein after the ligation step, the ligated probes, or after amplification, the amplified ligated probes, are restricted using restriction enzymes to cut of part of the probes and continue with those parts (identifiers and target sequence) that contain the relevant information in the sequencing step. | 08-07-2014 |
20140221218 | METHODS FOR SINGLE-MOLECULE ANALYSIS - Methods for single-molecule preparation and analysis are disclosed herein. The methods can, for example, be used for isolating and analyzing DNA from various biological samples. | 08-07-2014 |
20140221219 | OLIGODENDROGLIOMA DRIVE GENES - Oligodendrogliomas are the second most common malignant brain tumor in adults. These tumors often contain a chromosomal abnormality involving a pericentromeric fusion of chromosomes 1 and 19, resulting in losses of the entire short arm of the former and the long arm of the latter. To identify the molecular genetic basis for this alteration, we performed exomic sequencing of seven anaplastic oligodendrogliomas with chromosome 1p and 19q losses. Among other changes, we found that that CIC (homolog of the | 08-07-2014 |
20140221220 | METHOD OF MEASURING ADAPTIVE IMMUNITY - A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells. | 08-07-2014 |
20140235452 | METHODS AND APPARATUS FOR MEASURING ANALYTES - Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions. | 08-21-2014 |
20140235453 | GLOBAL TRANSCRIPTION MACHINERY ENGINEERING - The invention relates to global transcription machinery engineering to produce altered cells having improved phenotypes. | 08-21-2014 |
20140235454 | MONITORING HEALTH AND DISEASE STATUS USING CLONOTYPE PROFILES - There is a need or improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers. | 08-21-2014 |
20140235455 | USE OF HOXA9 GENE AS A BIOMARKER FOR THE DETECTION OF HEPATOCELLULAR CARCINOMA - A method of detecting hepatocellular carcinoma includes the steps of: detecting a methylation level of a CpG site of HOXA9 gene in a biological sample taken from a suspected subject; and comparing the methylation level to a reference methylation level of a CpG site of HOXA9 gene in another biological sample taken from a normal subject not suffering from hepatocellular carcinoma, wherein when the methylation level is higher than the reference methylation level, the suspected subject is likely to suffer from hepatocellular carcinoma, and wherein each of the biological samples is selected from the group consisting of a blood sample, a serum sample, and a plasma sample. | 08-21-2014 |
20140235456 | Methods and Compositions for Identifying Global Microsatellite Instability and for Characterizing Informative Microsatellite Loci - The disclosure provides methods and systems for assessing microsatellites, for identifying informative microsatellite loci, and for using microsatellite data. Microsatellite information has numerous uses including, for example, to characterize disease risk, to predict responsiveness to therapy, and to non-invasively diagnose subjects. | 08-21-2014 |
20140235457 | SYSTEMS AND METHODS FOR GENETIC AND BIOLOGICAL ANALYSIS - The invention relate to systems and methods for sequencing polynucleotides, as well as detecting reactions and binding events involving other biological molecules. The systems and methods may employ chamber-free devices and nanosensors to detect or characterize such reactions in high-throughput. Because the system in many embodiments is reusable, the system can be subject to more sophisticated and improved engineering, as compared to single use devices. | 08-21-2014 |
20140235458 | METHODS AND TOOLS FOR THE DIAGNOSIS AND PROGNOSIS OF UROGENITAL CANCERS - The present invention provides a microarray useful as a tool in the diagnosis and/or prognosis of certain types of cancers, particularly urogenital cancers. The microarray can include a plurality of genomic regions represented thereon, the genomic regions corresponding to regions wherein alterations, such as copy number aberrations, at such locations correlate to specific, identifiable cancers, particularly prostate, renal, or bladder tumors. The invention further provides methods of diagnosing certain types of cancers, particularly urogenital cancers, more particularly renal cortical cancers. The methods can comprise analyzing genetic material from a human individual to determine the presence or presence of certain aberrations and using a decision tree to classify the subtype of renal cortical neoplasm present in the sample. | 08-21-2014 |
20140235459 | Genotypes, Alleles and Molecular Markers Associated With Asian Soybean Rust, as Well as Methods, Processes and Uses Thereof - The present invention relates to screening methods for rust resistance or tolerance, in particular, Asian soybean rust (ASR— | 08-21-2014 |
20140235460 | QUANTITATIVE NUCLEASE PROTECTION ASSAY (QNPA) AND SEQUENCING (QNPS) IMPROVEMENTS - The present disclosure provides an improvement to quantitative Nuclease Protection Assay (qNPA) and quantitative Nuclease Protection Sequencing (qNPS) methods. The disclosed methods use nuclease protection probes (NPPs) that include 5′-end and/or 3-end flanking sequences, which provide a universal hybridization and/or amplification sequence. The disclosed methods can be used to sequence or detect target nucleic acid molecules, such as those present in fixed or insoluble samples. | 08-21-2014 |
20140235461 | ALGORITHMS FOR SEQUENCE DETERMINATIONS - The invention provides methods of determining a consensus sequence from multiple raw sequencing reads of a nucleic acid target. The nucleic acid target includes an anchor segment of known sequence and an adjacent segment of unknown sequence. The anchor segment provides a means to assess the quality of a raw target sequencing read. Raw target sequencing reads meeting or exceeding a threshold are assigned to an accepted class. The consensus sequence of the adjacent segment can be determined from raw target sequencing reads in the accepted class. Successive polling steps determine successive consensus nucleobases in a nascent sequence of the adjacent segment. Raw target sequencing reads can be removed or reintroduced from the accepted class depending on their correspondence to the most recently determined consensus nucleobase and/or the nascent sequence. | 08-21-2014 |
20140243210 | PURIFICATION OF IMMUNOGLOBULINS USING AFFINITY CHROMATOGRAPHY AND PEPTIDE LIGANDS - An immunoglobulin binding peptide having the general formula, from amino terminus to carboxy terminus, of Z—R | 08-28-2014 |
20140243211 | BLOOD BIOMARKERS FOR SUICIDALITY - Biomarkers and methods for screening expression levels of the biomarkers for predicting and tracking suicidality, as well as for monitoring response to a treatment for suicidal risk and for determining suicidal risk as a side-effect of an antidepressant are disclosed. | 08-28-2014 |
20140243212 | MATERNAL PLASMA TRANSCRIPTOME ANALYSIS BY MASSIVELY PARALLEL RNA SEQUENCING - Methods are provided for diagnosing pregnancy-associated disorders, determining allelic ratios, determining maternal or fetal contributions to circulating transcripts, and/or identifying maternal or fetal markers using a sample from a pregnant female subject. Also provided is use of a gene for diagnosing a pregnancy-associated disorder in a pregnant female subject. | 08-28-2014 |
20140243213 | Analysing Sequencing Bias - The present invention relates to methods for determining the sequence bias of a sequencing technique. Furthermore, the invention relates to methods to reduce or enhance sequence bias during sequencing of nucleic acids via techniques involving adaptor ligations. Specifically the method relates to use of a degenerate RNA sequence to analyse sequence bias when generating small RNA libraries, and to the use of modified adaptors for cloning of small RNAs with degenerate or specific sequences to reduce or enhance sequencing bias, as well as various nucleic acid molecules relating thereto or derived therefrom. | 08-28-2014 |
20140243214 | FET ARRAY SUBSTRATE, ANALYSIS SYSTEM AND METHOD - In an FET configuration having a channel with a small thickness, transistor characteristics vary for different FETs in the same array, and therefore when the same gate voltage is applied, the sensitivities of DNA detection may be insufficient. To this end, the change in the channel current when DNA passes through the nanopore is detected while applying an optimum gate voltage for each nanopore FET to attain a predetermined channel current value to a plurality of nanopore FETs disposed on the same substrate, and four types of bases constituting DNA are distinguished. | 08-28-2014 |
20140243215 | METHOD FOR DIAGNOSING RENAL DISEASES OR PREDISPOSITIONS - The invention provides a method of diagnosing a disease or a predisposition to contract a disease by assaying for mutations of uromodulin (UMOD) within a test subject or patient. The presence of a mutation in the UMOD supports a diagnosis of a disease or a predisposition to contract a disease within the patient. | 08-28-2014 |
20140243216 | METHODS FOR SEPARATING NUCLEIC ACIDS BY SIZE - The present invention pertains to a method for isolating nucleic acids by size from a sample comprising nucleic acids of different sizes using an anion exchange matrix, wherein nucleic acids of a preselected size or a preselected size range are isolated by varying the pH value during elution and/or binding. | 08-28-2014 |
20140249036 | METHOD AND KIT FOR CHARACTERIZING MICROORGANISMS - The present disclosure provides methods of characterizing one or more microorganisms and kits for characterizing at least one microorganism. Exemplary methods include preparing an amplicon library, sequencing a characteristic gene sequence to obtain a gene sequence, and characterizing the one or more microorganisms based on the gene sequence using a computer-based genomic analysis of the gene sequence. Exemplary kits include at least one forward primer including an adapter sequence and a priming sequence, for a target sequence, and at least one reverse primer. | 09-04-2014 |
20140249037 | METHOD AND KIT FOR CHARACTERIZING MICROORGANISMS - The present disclosure provides methods of characterizing one or more microorganisms and kits for characterizing at least one microorganism. Exemplary methods include preparing an amplicon library, sequencing a characteristic gene sequence to obtain a gene sequence, and characterizing the one or more microorganisms based on the gene sequence using a computer-based genomic analysis of the gene sequence. Exemplary kits include at least one forward primer including an adapter sequence and a priming sequence, for a target sequence, and at least one reverse primer. | 09-04-2014 |
20140249038 | Method of detecting a pre-determined event in a nucleic acid sample and system thereof - Disclosed are a method of detecting a pre-determined event in a nucleic acid sample and a system thereof. The method of detecting the pre-determined event in the nucleic acid sample comprises the following steps: constructing a sequencing-library for the nucleic acid sample; sequencing the sequencing-library to obtain a sequencing result consisting of a plurality of sequencing data; determining the sequencing data from a pre-determined region; and determining an occurrence of the pre-determined event in the nucleic acid sample based on a composition of the sequencing data from the pre-determined region. | 09-04-2014 |
20140256558 | Capture Methodologies for Circulating Cell Free DNA - A nucleic acid patch method for amplifying target nucleic acid sequences in circulating free DNA or residual DNA samples where the defining ends of the target nucleic acid sequences are unknown. | 09-11-2014 |
20140256559 | DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING MASSIVELY PARALLEL GENOMIC SEQUENCING - Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. | 09-11-2014 |
20140256560 | DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING MASSIVELY PARALLEL GENOMIC SEQUENCING - Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. | 09-11-2014 |
20140256561 | SURFACE CHEMISTRY AND DEPOSITION TECHNIQUES - Surface chemistries for the visualization of labeled single molecules (analytes) with improved signal-to-noise properties are provided. To be observed, analyte molecules are bound to surface attachment features that are spaced apart on the surface such that when the analytes are labeled adjacent analytes are optically resolvable from each other. One way to express this concept is that binding elements should be spaced apart such that the Guassian point spread functions of adjacent labels do not overlap. Another way of expressing this concept is that the surface binding elements should be spaced apart by a distance equal to at least the diffraction limit for an optical label attached to the bound analytes. | 09-11-2014 |
20140256562 | miRNA-BASED UNIVERSAL SCREENING TEST (UST) - Described are methods for early noninvasive or minimally invasive detection of pathological changes in organ systems/organs/tissues/cells by quantifying organ system-/organ-/tissue-/cells type-enriched miRNA in bodily fluids. | 09-11-2014 |
20140256563 | HIGH THROUGHPUT METHYLATION DETECTION METHOD - Provided is a high throughput methylation detection method, particularly a combined sequence capture and bisulfite sequencing method. The method accurately and effectively analyzes the methylation status of the target area in several samples simultaneously, lowers the difficulty of probe design, enhances operation and application feasibility, and enables high throughput methylation detection of high accuracy on interested target sequences and areas in a complete genome. The method is targeted and conserves energy and time. | 09-11-2014 |
20140256564 | METHODS OF USING HUR-ASSOCIATED BIOMARKERS TO FACILITATE THE DIAGNOSIS OF, MONITORING THE DISEASE STATUS OF, AND THE PROGRESSION OF TREATMENT OF BREAST CANCERS - The present invention relates to methods of identifying gene targets, including methods of using ribonucleoprotein (RNP) immunoprecipitation-microarrays to identify cancer gene targets, such as subsets of RNP-associated mRNAs in breast cancer cell lines. Also presented, are ribonucleotide binding protein-associated biomarkers, panels or sets of ribonucleotide binding protein-associated biomarkers, methods and compositions comprising ribonucleotide-binding protein, associated nucleotides, nucleotide arrays, and kits, plus methods of using HuR-associated biomarkers to facilitate the diagnosis of, monitoring the disease status of, and the progression of treatment of breast cancers to facilitate the diagnosis of and monitoring the disease status or progression of treatment of breast cancers, including drug-resistant breast cancers. | 09-11-2014 |
20140256565 | METHODS FOR HLA TYPING - The present invention relates to methods for reducing the ambiguity in human leukocyte antigen (HLA) allele identification. In particular, the methods comprise using target specific oligonucleotide (TSO) techniques to determine a first set of possible HLA alleles. The methods further comprise using sequence-based typing (SBT) to obtain a second set of possible HLA alleles. The two sets of the possible HLA alleles are then combined to determine at least one common allele identified in the both the TSO and SBT assays, thus reducing the ambiguity associated with current HLA typing procedures. | 09-11-2014 |
20140256566 | SEQUENCE TAGS - The present invention relates to a new class of nucleic acid tagging molecules which are essentially free of homopolymer stretches. Such tagging molecules are helpful for effectively tagging a plurality of individual target molecules and detecting said tags with a high degree of accuracy. | 09-11-2014 |
20140256567 | Method of Measuring Adaptive Immunity - A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells. | 09-11-2014 |
20140256568 | SAMPLE MULTIPLEXING - The invention generally relates to methods for sample multiplexing. In certain embodiments, methods of the invention obtaining a plurality of different reactant molecules, attaching a unique identifier to the reactant molecules, and forming a droplet including the reactant molecules. | 09-11-2014 |
20140256569 | SYSTEM AND METHOD FOR CLEANING NOISY GENETIC DATA FROM TARGET INDIVIDUALS USING GENETIC DATA FROM GENETICALLY RELATED INDIVIDUALS - A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals. | 09-11-2014 |
20140256570 | METHODS FOR ACCURATE SEQUENCE DATA AND MODIFIED BASE POSITION DETERMINATION - Disclosed herein are methods of determining the sequence and/or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample. | 09-11-2014 |
20140274727 | CARIES GENETIC PREDISPOSITION ANALYSIS BY MOLECULAR TESTING - Means and methods of predicting future dental problems are disclosed. Molecular tests use biological matter from a patient to obtain information regarding various genes. The tests and methods generate displays and reports regarding genetic risk pertaining to cavities, tooth decay and other disorders. | 09-18-2014 |
20140274728 | Systems and Methods For Probe Design to Detect the Presence of Simple and Complex Indels - Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions. | 09-18-2014 |
20140274729 | METHODS, COMPOSITIONS AND KITS FOR GENERATION OF STRANDED RNA OR DNA LIBRARIES - The invention provides methods and compositions, including kits, for the construction of directional nucleic acid libraries. The invention further provides methods and compositions for the amplification and sequencing of directional cDNA libraries. | 09-18-2014 |
20140274730 | NUCLEIC ACID SEQUENCING AND ELECTRONIC DETECTION - Embodiments of the present invention provide devices methods for sequencing DNA using arrays of reaction regions containing sensors to monitor changes in solutions or bound molecules contained in the reaction regions. Additional embodiments provide devices and methods for sequencing DNA using arrays of reaction regions that allow for optical monitoring of solutions in the reaction regions. Chemical amplification schemes that allow DNA to be sequenced in which multiple nucleotide addition reactions are performed to detect the incorporation of a base are disclosed. By sequencing DNA using parallel reactions contained in large arrays, DNA can be rapidly sequenced. | 09-18-2014 |
20140274731 | METHODS FOR TARGETED GENOMIC ANALYSIS - The invention provides a method for genetic analysis in individuals that reveals both the genetic sequences and chromosomal copy number of targeted and specific genomic loci in a single assay. The present invention further provide methods for the sensitive and specific detection of target gene sequences and gene expression profiles. | 09-18-2014 |
20140274732 | METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING USING ELECTRONIC SENSING ELEMENTS - The present invention is directed to methods, devices, compositions and systems for obtaining sequence data from nucleic acid templates by utilizing electronic sensing elements. | 09-18-2014 |
20140274733 | Methods and Systems for Local Sequence Alignment - A method for nucleic acid sequencing includes: (a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; (b) exposing the template polynucleotide strands with the sequencing primer and a polymerase operably bound therewith to a series of flows of nucleotide species flowed according to a predetermined ordering; (c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands; and (d) aligning the plurality of sequencing reads using an alignment process comprising a first set of alignment criteria or penalties that are based on biological changes in sequence and a second set of alignment criteria or penalties that are based on a sequencing error mode. | 09-18-2014 |
20140274734 | DNA QUALITY CONTROLS - The present disclosure provides methods, arrays and kits for assessing the quality of genomic DNA samples, especially those obtained from formalin-fixed paraffin-embedded (FFPE) samples. The methods, arrays and kits provided herein use primer pairs specific to regions in the genomes of the organisms from which genomic DNA samples are obtained that have identical or nearly identical copies distributed across multiple chromosomes. | 09-18-2014 |
20140274735 | MULTIPLEX METHYLATION-SPECIFIC AMPLIFICATION SYSTEMS AND METHODS - The present invention relates to systems and methods for performing multiplex amplification reactions. In particular, the present invention relates to multiplex methylation-specific amplification systems and methods. | 09-18-2014 |
20140274736 | MINIMIZING ERRORS USING URACIL-DNA-N-GLYCOSYLASE - Provided herein is technology relating to enzymatic modification of nucleic acids and particularly, but not exclusively, to methods and compositions relating to using uracil-DNA-N-glycosylase for minimizing or eliminating errors in a DNA sequence due to deamination of cytosine residues. | 09-18-2014 |
20140274737 | METHOD FOR ISOLATING NUCLEIC ACID MUTATIONS - The invention includes methods and apparatus for isolating and recovering mutations, especially rare and unknown mutations, without amplifying the sample. In particular, using the disclosed methods, it is possible to separate heteroduplexed nucleic acid strand pair from homoduplexed nucleic acid strand pairs having similar sequences and being at a much higher concentration. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays. | 09-18-2014 |
20140274738 | SEQUENTIAL SEQUENCING - The present invention provides improved methods, compositions and kits for short read next generation sequencing (NGS). The methods, compositions and kits of the present invention enable phasing of two or more nucleic acid sequences in a sample, i.e. determining whether the nucleic acid sequences (typically comprising regions of sequence variation) are located on the same chromosome and/or the same chromosomal fragment. Phasing information is obtained by performing multiple, successive sequencing reactions from the same immobilized nucleic acid template. The methods, compositions and kits provided herein are useful, for example, for haplotyping, SNP phasing, or for determining downstream exons in RNA-seq. | 09-18-2014 |
20140274739 | PORTED PARALLEL PLATE FLOW CHAMBER AND METHODS FOR USE THEREOF - Flow chambers are provided. In some embodiments, the flow chambers include an inner panel having at least one flow channel having an inlet/outlet opening on each end thereof formed therein, wherein the inlet/outlet openings are adapted to releasably receive a septum; one or more ports adapted to releasably receive a plug and for at least liquid communication with the at least one flow channel, and an outer frame that defines an outer portion of the at least one flow channel and that defines a perimeter of the flow chamber. In some embodiments, the flow chamber has overall dimensions of a standard multiwell plate and the at least one flow channel is located in a position that corresponds to a column location of the standard multiwell plate. Also provided are methods for producing the presently disclosed flow chambers and employing the same to assay biological features of cultured cells and/or tissues. | 09-18-2014 |
20140274740 | GENERATING CELL-FREE DNA LIBRARIES DIRECTLY FROM BLOOD - The disclosure provides methods and kits for preparing sequencing library to detect chromosomal abnormality using cell-free DNA (cfDNA) without the need of first isolating the cfDNA from a liquid fraction of a test sample. In some embodiments, the method involves reducing the binding between the cfDNA and nucleosomal proteins without unwinding the cfDNA from the nucleosomal proteins. In some embodiments, the reduction of binding may be achieved by treating with a detergent or heating. In some embodiments, the method further involves freezing and thawing the test sample before reducing the binding between the cfDNA and the nucleosomal proteins. In some embodiments, the test sample is a peripheral blood sample from a pregnant woman including cfDNA of both a mother and a fetus, wherein the methods may be used to detect fetal chromosomal abnormality such as copy number variation. In other embodiments, the test sample is a peripheral blood sample from a patient known or suspected to have cancer, wherein the methods can be used to detect chromosomal abnormalities in the cfDNA of the patient. Kits for detection of copy number variation of the fetus using the disclosed methods are also provided. | 09-18-2014 |
20140274741 | METHODS TO CAPTURE AND SEQUENCE LARGE FRAGMENTS OF DNA AND DIAGNOSTIC METHODS FOR NEUROMUSCULAR DISEASE - The present invention provides methods of sequencing a large fragment of DNA by hybridizing a set of specifically designed probes to the DNA, shearing the DNA, and sequencing the DNA with Next Generation Sequencing. The probes are designed to target genes of interest at intervals to allow the capture of relatively large DNA fragments. The present invention also provides methods of diagnosing a neuromuscular disease (NMD) comprising detecting mutations in one or more of SCML2, CHRND, OFD1, DYNC1H1, COL6A3, EMD, ARHGAP4, FLNA, MID1IP1, MID1, and CFP. | 09-18-2014 |
20140274742 | METHODS TO DETERMINE CARCINOGENESIS, IDENTIFY MARKERS FOR EARLY CANCER DIAGNOSIS AND IDENTIFY TARGETS OF THERAPY - Methods and techniques to identify carcinogenesis pathways and markers for early cancer diagnosis. Cell sampling is performed on a single tumor with multiple samples being taken from the tumor and outward toward the periphery and beyond. Large scale analysis is performed, such as whole genomic sequencing, to identify the differences between the cells of the various samples. The differences are evaluated to determine which differences represent a change along the carcinogenesis pathway. | 09-18-2014 |
20140274743 | NUCLEIC ACID SAMPLE ENRICHMENT FOR SEQUENCING APPLICATIONS - The present invention relates to the field of molecular biology, and more specifically to methods for reducing the complexity of a nucleic acid sample. | 09-18-2014 |
20140274744 | STRATEGIES FOR HIGH THROUGHPUT IDENTIFICATION AND DETECTION OF POLYMORPHISMS - The invention relates to a method for the high throughput identification of single nucleotide polymorphisms by performing a complexity reduction on two or more samples to yield two or more libraries, sequencing at least part of the libraries, aligning the identified sequences and determining any putative single nucleotide polymorphisms, confirming any putative single nucleotide polymorphism, generating detection probes for the confirmed single nucleotide polymorphisms, subjection a test sample to the same complexity reduction to provide a test library and screen the test library for the presence or absence of the single nucleotide polymorphisms using the detection probe. | 09-18-2014 |
20140274745 | METHOD FOR DETECTING MICRO-DELETION AND MICRO-REPETITION OF CHROMOSOME - The present invention relates to the field of genomic mutation detection, and in particular, to the detection of the copy number variation (CNV) in cellular chromosomal DNA fragments. The present invention also relates to the detection of diseases related to the copy number variation in the cellular chromosomal DNA fragments. | 09-18-2014 |
20140287930 | SUB-TOTIPOTENT STEM CELL PRODUCT AND APPARENT HEREDITARY MODIFYING LABEL THEREOF - Provided are a sub-totipotent stem cell product and epigenetic modification label thereof, a method for inducing the generation of the sub-totipotent stem cell product and identification for the epigenetic modification label of the differentiation potential of stem cells. Also provided is a use of histone modification states of sub-totipotent genes and/or differentiation related genes to predict the epigenetic modification label of the differentiation potentials of stem cells. | 09-25-2014 |
20140287931 | METHODS AND COMPOSITIONS FOR PREDICTING RESISTANCE TO ANTICANCER TREATMENT - The instant application provides methods and related compositions pertaining to the identification of resistance to anticancer treatment in. a patient. In a particular embodiment, the invention provides biomarkers for the identification of resistance to anticancer treatment in a breast cancer patient, wherein a reduced expression of a MEDIATOR and/or SWI/SNF complex gene in the breast cancer cells of the patient indicates that the breast cancer cells in the patient may be successfully treated with a PI3K and/or mTOR inhibitor. | 09-25-2014 |
20140287932 | SUPER-ENHANCERS AND METHODS OF USE THEREOF - The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer). | 09-25-2014 |
20140287933 | METHODS FOR MEASURING FEL d 1 CAT ALLERGEN - The present invention relates to a noninvasive method for quantifying Fel d 1 cat allergen expression levels—the major allergen responsible for cat allergies—in individual cats ( | 09-25-2014 |
20140287934 | PROCESSES OF IDENTIFYING AND CHARACTERIZING X-LINKED DISORDERS - The present invention relates to processes for characterizing and screening for the existence or predisposition to X-linked disorders associated with changes in X-chromosome inactivation. The present invention also relates to processes of reducing a disease phenotype associated with an X-linked disorder in a female subject. | 09-25-2014 |
20140287935 | COMPOSITIONS AND METHODS FOR SEQUENCING NUCLEIC ACIDS - Disclosed herein are compositions and methods for sequencing nucleic acids. | 09-25-2014 |
20140296079 | METHODS FOR EARLY DETECTION OF ESOPHAGEAL CANCER - The present invention relates to a method for screening, predicting or prognosing esophageal adenocarcinoma/high grade dysplasia in a subject. | 10-02-2014 |
20140296080 | Methods, Systems, and Computer Readable Media for Evaluating Variant Likelihood - A method for evaluating variant likelihood includes: providing a plurality of template polynucleotide strands, sequencing primers, and polymerase in a plurality of defined spaces disposed on a sensor array; exposing the plurality of template polynucleotide strands, sequencing primers, and polymerase to a series of flows of nucleotide species according to a predetermined order; obtaining measured values corresponding to an ensemble of sequencing reads for at least some of the template polynucleotide strands in at least one of the defined spaces; and evaluating a likelihood that a variant sequence is present given the measured values corresponding to the ensemble of sequencing reads, the evaluating comprising: determining a measurement confidence value for each read in the ensemble of sequencing reads and modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands. | 10-02-2014 |
20140296081 | IDENTIFICATION AND USE OF CIRCULATING TUMOR MARKERS - Methods for creating a library of recurrently mutated genomic regions and for using the library to analyze cancer-specific and patient-specific genetic alterations in a patient are provided. The methods can be used to measure tumor-derived nucleic acids in patient blood and thus to monitor the progression of disease. The methods can also be used for cancer screening. | 10-02-2014 |
20140296082 | DNA Polymerase Variants with Reduced Exonuclease Activity and Uses Thereof - Compositions and methods are described to modify Family B DNA polymerases that contain residual exonuclease activity that interferes with sequencing techniques and with detection of single nucleotide polymorphisms. The compositions are mutant proteins with reduced exonuclease activity compared with presently available “exo | 10-02-2014 |
20140296083 | BIOCHEMICAL ANALYSIS INSTRUMENT - An analysis instrument comprises plural modules connected together over a data network, each module comprising an analysis apparatus operable to perform biochemical analysis of a sample. Each module comprises a control unit that controls the operation of the analysis apparatus. The control units are addressable to select an arbitrary number of modules to operate as a cluster for performing a common biochemical analysis. The control units communicate over the data network, repeatedly during the performance of the common biochemical analysis, to determine the operation of the analysis apparatus of each module required to meet the global performance targets, on the basis of measures of performance derived from the output data produced by the modules. The arrangement of the instrument as modules interacting in this manner provides a scalable analysis instrument. | 10-02-2014 |
20140303000 | COMPOSITIONS AND METHODS FOR DIRECTIONAL NUCLEIC ACID AMPLIFICATION AND SEQUENCING - The invention provides methods and compositions, including kits, for directional nucleic acid amplification and sequencing. The invention further provides methods and compositions for the construction of directional cDNA libraries. | 10-09-2014 |
20140303001 | BLADDER CANCER DETECTION AND MONITORING - Provided are molecular markers for detecting bladder cancer, especially recurrent bladder cancer, and methods of use thereof, including methods of monitoring for the recurrence of bladder cancer. | 10-09-2014 |
20140303002 | Gene Expression Profile Algorithm and Test for Determining Prognosis of Prostate Cancer - The present invention provides algorithm-based molecular assays that involve measurement of expression levels of genes, or their co-expressed genes, from a biological sample obtained from a prostate cancer patient. The genes may be grouped into functional gene subsets for calculating a quantitative score useful to predict a likelihood of a clinical outcome for a prostate cancer patient. | 10-09-2014 |
20140303003 | Fluorescent Dye Compounds, Conjugates and Uses Thereof - The present teachings generally relate to fluorescent dyes, linkable forms of fluorescent dyes, energy transfer dyes, reagents labeled with fluorescent dyes and uses thereof. | 10-09-2014 |
20140303004 | METHOD FOR EXCLUSIVE SELECTION OF CIRCULARIZED DNA FROM MONOMOLECULAR DNA IN CIRCULARIZING DNA MOLECULES - The present invention provides a method for producing a circular DNA molecule having a specific structure that enables to distinguish circular DNA formed from a single DNA molecule (single-molecule circular DNA), from circular DNA formed from multiple DNA molecules (multiple-molecule circular DNA) and also from single-molecule circular DNA derived from the circular DNA formed from multiple DNA molecules. According to the present invention, only single-molecule circular DNA that is not derived from multiple-molecule circular DNA can be selected in the production of circular DNA. | 10-09-2014 |
20140303005 | RARE CELL ANALYSIS AFTER NEGATIVE SELECTION - The invention generally relates to rare cell analysis after negative selection. | 10-09-2014 |
20140303006 | Sequencing System with Memory - The present teachings provide a device including a memory. According to various embodiments, the memory is readable, writable, and rewritable. The present teachings further provide processing stations, e.g., for carrying out electrophoresis, pcr, genetic analysis, sample preparation, and/or sample cleanup, etc., that are capable of reading from and/or writing/rewriting to such memory. | 10-09-2014 |
20140303007 | HIGH THROUGHPUT DETECTION OF MOLECULAR MARKERS BASED ON AFLP AND HIGH THROUGH-PUT SEQUENCING - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker. | 10-09-2014 |
20140303008 | COLORECTAL CANCER ASSOCIATED CIRCULATING NUCLEIC ACID BIOMARKERS - The invention provides methods and reagents for diagnosing colorectal cancer that are based on the detection of biomarkers in the circulating nucleic acids from a patient to be evaluated. In some embodiments, the CNA biomarkers are polynucleotide fragments, e.g., DNA fragments, that are present at an elevated level in blood, e.g., in a serum or plasma sample, of a colorectal cancer patient in comparison to the level in blood, e.g., a serum or plasma sample, obtained from a normal individual who does not have colorectal cancer. | 10-09-2014 |
20140309118 | METHOD OF PREPARING NUCLEIC ACID MOLECULES - Provided is a method of preparing nucleic acid molecules comprising: (a) a step of providing nucleic acid fragments constituting at least a portion of the complete sequence of a target nucleic acid; (b) tagging the nucleic acid fragments with barcode sequences; (c) identifying the sequence of the nucleic acid fragments tagged by the barcode sequences; and (d) recovering desired nucleic acid fragments among the sequence-identified nucleic acid fragments using the barcode sequences. | 10-16-2014 |
20140309119 | Methods and Devices for High Fidelity Polynucleotide Synthesis - Disclosed are methods for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products. | 10-16-2014 |
20140309120 | METHOD AND SUBSTRATE FOR NUCLEIC ACID AMPLIFICATION, AND METHOD AND APPARATUS FOR NUCLEIC ACID ANALYSIS - The present invention relates to a method for nucleic acid amplification, which enables clusters of amplified nucleic acid fragments to be sequenced by a sequencer to be formed at a high density and improves throughput of nucleic acid sequence analysis by amplifying the number of nucleic acids in the cluster to 10,000 molecules or more; and a method for nucleic acid amplification for enhancing read accuracy, which achieves a high cluster density and increases the number of the amplified fragments in the cluster by the steps of previously forming a pattern of primer DNAs on a base material and fixing bulky template DNA molecules synthesized from DNA samples thereon to induce amplification reaction. | 10-16-2014 |
20140315724 | METHODS AND SYSTEMS FOR SEQUENCING LONG NUCLEIC ACIDS - The present invention provides methods and systems for sequencing long nucleic acid fragments. In one aspect of the invention, methods, systems and reagent kits are provided for sequencing nucleic acid target sequences. Some embodiments of the methods, systems and reagent kits are particularly suitable for sequencing a large number of fragments, particularly long fragments. | 10-23-2014 |
20140315725 | SEQUENCE ANALYSIS OF COMPLEX AMPLICONS - The invention is directed to methods of generating sequence profiles of populations of nucleic acids, whose member nucleic acids contain regions of high variability, such as populations of nucleic acids encoding T cell receptors or B cell receptors. In one aspect, the invention provides pluralities of sets of primers for generating nested sets of templates from nucleic acids in such populations, thereby insuring the production of at least one template from which sequence reads are generated, despite such variability, or despite limited lengths or quality of sequence reads. In another aspect, members of such populations are bidirectionally sequenced so that further sequence information is obtained by analyzing overlapping sequence reads in the zones of highest variability. | 10-23-2014 |
20140315726 | METHODS FOR CHARACTERIZING DNA SEQUENCE COMPOSITION IN A GENOME - Methods for the high-throughput analysis of transgenic events are herein disclosed. The methods use libraries of sheared genomic DNA ligated to specialized adapters and pooled for sequence analysis and comparison to known genomic and insert sequence. The method finds use in detecting characterizing insertion site, transgene integrity, and transgene copy number. | 10-23-2014 |
20140315727 | METHOD FOR MULTIPLEXED MOLECULAR DETECTION - Molecular probes to particular targets may be nucleic acids that may generally possess resistance to degradation when bound to a target molecule. For example, the molecular probes may be generally resistant to nuclease degradation when bound to their target molecules, and generally not resistant to nuclease degradation when unbound to their target molecules. This may be utilized, for example, to selectively degrade unbound molecular probes while preserving the bound molecular probes, which may thus serve as an indication of the presence of their target molecules in a sample. | 10-23-2014 |
20140315728 | METHOD FOR HIGH-THROUGHPUT AFLP-BASED POLYMORPHISM DETECTION - The invention relates to a method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of restriction endonuclease digest of DNA, adaptor-ligation, optional pre-amplification, selective amplification, pooling of the amplified products, sequencing the libraries with sufficient redundancy, clustering followed by identification of the genetic markers within the library and/or between libraries and determination of (co-)dominant genotypes of the genetic markers. | 10-23-2014 |
20140315729 | DETECTION OF NUCLEIC ACID REACTIONS ON BEAD ARRAYS - The present invention is directed to methods and compositions for the use of micro sphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays. | 10-23-2014 |
20140323316 | MULTIPLE TAGGING OF INDIVIDUAL LONG DNA FRAGMENTS - This disclosure provides methods and compositions for tagging long fragments of a target nucleic acid for sequencing and analyzing the resulting sequence information in order to reduce errors and perform haplotype phasing, for example. | 10-30-2014 |
20140323317 | MICROFLUIDIC DEVICES AND METHODS OF USE IN THE FORMATION AND CONTROL OF NANOREACTORS - The present invention provides novel microfluidic devices and methods that are useful for performing high-throughput screening assays and combinatorial chemistry. The invention provides for aqueous based emulsions containing uniquely labeled cells, enzymes, nucleic acids, etc., wherein the emulsions further comprise primers, labels, probes, and other reactants. An oil based carrier-fluid envelopes the emulsion library on a microfluidic device, such that a continuous channel provides for flow of the immiscible fluids, to accomplish pooling, coalescing, mixing, sorting, detection, etc., of the emulsion library. | 10-30-2014 |
20140323318 | METHODS OF DETECTING MUTATIONS ASSOCIATED WITH ATAXIA-OCULAR APRAXIA 2 (AOA2) - Methods of identifying polymorphisms associated with ataxia-ocular apraxia 2 (AOA2), are described. The polymorphisms associated with AOA2 include specific mutations in the senataxin (SETX) gene. Also described are methods of diagnosis of AOA2, as well as methods of assessing an individual for carrier status for AOA2. | 10-30-2014 |
20140323319 | SYSTEMS AND METHODS FOR ISOLATING NUCLEIC ACIDS - The present disclosure relates to systems and methods for nucleic acid isolation. In particular, the present disclosure provides systems and methods for isolating nucleic acids from aqueous samples (e.g., blood or urine). | 10-30-2014 |
20140323320 | METHOD OF DETECTING FUSED TRANSCRIPTS AND SYSTEM THEREOF - Provided is a method of detecting method of detecting fusion transcripts in a sample to be analyzed. The method may comprises: subjecting the sample to be analyzed containing a RNA transcriptome to paired-end sequencing, to obtain paired-end RNA-Seq data of the sample to be analyzed; aligning the paired-end RNA-Seq data to a human reference genome sequence, to obtain first paired-end mapped reads, first single-end mapped reads, and first unmapped reads; evaluating an insertsize between two ends of the paired-end mapped reads by means of the first paired-end mapped reads, to obtain a proportion of paired-end mapped reads with overlapped 3′-ends; aligning the first unmapped reads to annotated transcripts, to obtain second single-end mapped reads and second unmapped reads; aligning the second unmapped reads to the annotated transcripts, to filter out unmapped reads caused by indel and obtain third unmapped reads; merging all single-end mapped reads, to obtain a set of single-end mapped reads; obtaining a gene pair linked by a cross-read as a primary set of candidate gene pairs based on the set of single-end mapped reads and combining with a relationship of the mapped paired-end reads; subjecting the primary set of candidate gene pairs to a filtration, to obtain a candidate set of fused gene pairs; bisecting the third unmapped read, to obtain a half-unmapped read; aligning the half-unmapped read to a gene-junction sequence in the candidate set of fused gene pairs, to obtain a potent region of a fused junction site in the gene in which the half-unmap read locates; outputting original reads of mapped half-unmapped reads, to obtain useful unmapped reads; subjecting the candidate set of fused gene pairs to a fusion simulation; aligning the useful unmapped reads to a junction library, to obtain a fused gene supported by the useful unmapped reads; calculating and gathering the fused sequence supported by the useful unmapped reads, to obtain information of the fused gene. And a system for detecting fusion transcripts is also provided. | 10-30-2014 |
20140329690 | PROVIDING NUCLEOTIDE SEQUENCE DATA - A sequencer device generates basic nucleotide sequence data | 11-06-2014 |
20140329691 | Noninvasive Diagnosis of Fetal Aneuploidy by Sequencing - Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes. | 11-06-2014 |
20140329692 | METHOD FOR MEASURING DNA METHYLATION PROFILES - Methods are provided for determining epimutations in a nucleic acid sequence of a cell. | 11-06-2014 |
20140329693 | FORMATION OF LAYERS OF AMPHIPHILIC MOLECULES - To form a layer separating two volumes of aqueous solution, there is used an apparatus comprising elements defining a chamber, the elements including a body of non-conductive material having formed therein at least one recess opening into the chamber, the recess containing an electrode. A pre-treatment coating of a hydrophobic fluid is applied to the body across the recess. Aqueous solution, having amphiphilic molecules added thereto, is flowed across the body to cover the recess so that aqueous solution is introduced into the recess from the chamber and a layer of the amphiphilic molecules forms across the recess separating a volume of aqueous solution introduced into the recess from the remaining volume of aqueous solution. | 11-06-2014 |
20140329694 | INTEGRATED OPTOELECTRONIC READ HEAD AND FLUIDIC CARTRIDGE USEFUL FOR NUCLEIC ACID SEQUENCING - A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir; (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other. | 11-06-2014 |
20140329695 | DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING MASSIVELY PARALLEL GENOMIC SEQUENCING - Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. | 11-06-2014 |
20140329696 | DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING MASSIVELY PARALLEL GENOMIC SEQUENCING - Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. | 11-06-2014 |
20140329697 | CONSTRUCTING METHOD OF HIGH-THROUGHPUT SEQUENCING LIBRARY AND USE THEREOF - The present invention provides a method for constructing a high-throughput sequencing library, which comprises: fragmenting genomic DNA; end-repairing the DNA fragments; adding a base A to the 3′ end of the end-repaired DNA fragments; connecting the DNA fragments having cohesive end A with a methylated adapter; carrying out hybrid capture on the connection products by using specific probes to obtain object fragments; treating the object fragments with bisulfite, to convert non-methylated cytosines to uracils; PCR amplifying the converted object fragments; and separating and purifying the amplification products, wherein the amplification products constitute the high-throughput sequencing library. The present invention also provides a method and an apparatus for identifying methylation information in specified genome regions of a sample. | 11-06-2014 |
20140336055 | GENETIC MARKERS FOR MACULAR DEGENERATION DISORDER TREATMENT - Provided in part herein are genetic variations (e.g., single nucleotide polymorphisms) associated with a vascular endothelial growth factor (VEGF) suppression response to an anti-VEGF agent for treatment of a macular degeneration disorder (e.g., age-related macular degeneration (AMD)). Also provided herein are methods for determining a genotype that includes such genetic variations, methods for predicting a VEGF suppression response for a subject according to a genotype, and methods for selecting a treatment suitable for treating a macular degeneration disorder (e.g., wet AMD) for a subject in need thereof according to a genotype. | 11-13-2014 |
20140336056 | NON-INVASIVE EARLY DETECTION OF SOLID ORGAN TRANSPLANT REJECTION BY QUANTITATIVE ANALYSIS OF MIXTURES BY DEEP SEQUENCING OF HLA GENE AMPLICONS USING NEXT GENERATION SYSTEMS - The invention is a method of detecting or assessing solid organ graft (transplant) rejection by detecting donor-specific HLA alleles in a blood sample of a graft (transplant) recipient. The invention further comprises a method of detecting the presence of maternal cells in a blood sample of an offspring. | 11-13-2014 |
20140336057 | METHOD FOR PAIRWISE SEQUENCING OF TARGET POLYNUCLEOTIDES - The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template. Using the methods of the invention it is possible to obtain two linked or paired reads of sequence information from each double-stranded template on a clustered array, rather than just a single sequencing read from one strand of the template. | 11-13-2014 |
20140336058 | METHOD AND KIT FOR CHARACTERIZING RNA IN A COMPOSITION - The invention relates to a method for determining the sequence and/or quantity of a ribonucleic acid in a composition, comprising the steps of:
| 11-13-2014 |
20140336059 | CLONOTYPES AS BIOMETRIC SPECIMEN TAGS - The invention is directed to methods for biometrically identifying or distinguishing biological specimens, such as patient specimens, as being from the same or different individuals by analysis of specimen clonotypes. The invention provides a direct or backup method for determining or confirming specimen identities. In one aspect, a method of the invention includes generating a first clonotype profile from a first specimen and forming therefrom an identifier set of clonotypes, which serves as a molecular fingerprint of the first specimen. Other specimens are determined to be from the same source individual or from a different source individual by generating clonotype profiles from such specimens and determining the presence or absence in such profiles of clonotypes of the identifier set of the first specimen. | 11-13-2014 |
20140336060 | METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING - The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a sample of DNA from the mother of the fetus and from the fetus, and from genotypic data from the mother and optionally also from the father. The ploidy state is determined by using a joint distribution model to create a set of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias. | 11-13-2014 |
20140342919 | MARKERS RELATED TO AGE-RELATED MACULAR DEGENERATION AND USES THEREFOR - Methods are provided for determining a risk of age-related macular degeneration (AMD), including a risk of a subject developing AMD or a risk of a subject progressing to an advanced form of AMD based on the detection of rare variants in C3, C9, and CFI. | 11-20-2014 |
20140342920 | Biomarkers for Non-Hodkin Lymphomas and Uses Thereof - The disclosure provides a method of identifying a subject as having B-cell non-Hodgkin lymphoma (NHL) such as testing a sample from a subject for a mutation in one or more biomarkers. Also described are methods of classifying or monitoring a subject having, or suspected of having, B-cell non-Hodgkin lymphoma comprising testing the same for a mutation in one or more biomarkers. | 11-20-2014 |
20140342921 | EXPANDED RADIX FOR POLYMERIC TAGS - A method having steps of (a) providing nucleic acids having a tag sequence (N | 11-20-2014 |
20140342922 | NUCLEIC ACID AMPLIFICATION METHOD - A nucleic acid amplification method includes ligating a double-stranded adapter (20) containing adapter DNA strands capable of forming a folded structure to a double-stranded DNA (1, 2) containing a target DNA sequence (1) to prepare a cyclic DNA template composed of double-stranded DNA containing a nick (5). A 3′-end elongation reaction is performed using a strand-displacement DNA polymerase from the nick (5) as an origin, thereby producing a concatemer (29) in which a plurality of the target DNA sequences (1) and the adapter DNA strands capable of forming the folded structure are linked in series as a single-stranded DNA. The concatemer (29) contains a plurality of the target DNA sequences (1) suitable for nucleotide sequence analysis and has a folded shape such that it takes the form of a ball due to its folded structure. | 11-20-2014 |
20140349856 | Neuroendocrine Tumors - The disclosure provides methods for the use of gene expression measurements to classify or identify neuroendocrine cancer in samples obtained from a subject in a clinical setting, such as in cases of formalin fixed, paraffin embedded (FFPE) samples. | 11-27-2014 |
20140349857 | METHOD FOR IN VITRO DIAGNOSIS OR PROGNOSIS OF COLON CANCER - The present invention relates to a method for in vitro diagnosis or prognosis of colon cancer, including a step of detecting at least one expression product of at least one HERV nucleic acid sequence, the use of said isolated nucleic acid sequences as a molecular marker/molecular markers, and a kit including at least one specific binding partner for at least one expression product of the HERV nucleic acid sequences. | 11-27-2014 |
20140349858 | AMPLIFICATION OF A SEQUENCE FROM A RIBONUCLEIC ACID - The present invention relates to methods and compositions for tagging, amplifying, purifying, and or characterizing of ribonucleic acid (RNA) in a sample. In particular, methods are provided for preparing RNA from a sample for subsequent analysis. | 11-27-2014 |
20140349859 | DETECTION OF TARGET NUCLEIC ACIDS USING HYBRIDIZATION - The present invention provides detection systems and methods for detection of loci and genomic regions in a sample, including mixed samples, using hybridization to an array. | 11-27-2014 |
20140357498 | Compositions and Methods for the Detection of DNA Cleavage Complexes - Compositions, methods, and kits for identifying protein-nucleic acid complexes, particularly DNA topoisomerase II-DNA complexes, are disclosed. | 12-04-2014 |
20140357499 | METHODS OF LOW ERROR AMPLICON SEQUENCING (LEA-Seq) AND THE USE THEREOF - This invention is related to nucleic acid sequencing. In particular, the invention relates to manipulative and analytic steps for analyzing and verifying the products of low frequency events. | 12-04-2014 |
20140364320 | Chemical Sensor Array Having Multiple Sensors Per Well - In one embodiment, a device is described. The device includes a material defining a reaction region. The device also includes a plurality of chemically-sensitive field effect transistors have a common floating gate in communication with the reaction region. The device also includes a circuit to obtain respective output signals from the chemically-sensitive field effect transistors indicating an analyte within the reaction region. | 12-11-2014 |
20140364321 | Method for analyzing DNA methylation based on MspJI cleavage - Provided is a method for detecting DNA methylation based on MspJI cleavage and performing bioinformatics analysis of genomic methylation. | 12-11-2014 |
20140364322 | ISOTHERMAL AMPLIFICATION SYSTEMS AND METHODS - The present invention relates to systems and methods for performing isothermal amplification reactions, in particular, denaturation methods for use in isothermal amplification reactions. An exemplary method may comprise: a) contacting a target nucleic acid with an electrode, wherein the electrode surface has a plurality of first and optionally second nucleic acid primers immobilized thereon, and wherein a target nucleic acid hybridizes to at least one of said first and second nucleic acid primers; b) extending at least one of the first and second primers using a DNA polymerase to form extended target nucleic acids; c) applying positive electrical bias to the electrode such that the extended target nucleic acids anneal to one of the first and second primers; d) extending the target nucleic acid with a DNA polymerase to form amplified target nucleic acid; e) reversing the electrical bias such that the amplified target nucleic acid is denatured from the surface. | 12-11-2014 |
20140364323 | MULTI-SAMPLE INDEXING FOR MULTIPLEX GENOTYPING - A method for determining the presence of multiple nucleotide sequences of interest in multiple samples while preserving the identity of each sample, by contacting the samples with a plurality of probe sets. The probes are designed to indicate the presence of the sequences of interest and the identity of the sample containing the sequence of interest in complex mixtures. Applications of the method include genotyping, expression analysis, and identification of individual species in complex samples. Kits of probe sets for use in the methods are also provided. | 12-11-2014 |
20140378315 | ENZYMATIC LIGATION OF NUCLEIC ACIDS - Methods, assays, compositions and kits for the ligation of short polynucleotides are presented herein. The short polynucleotides are optionally no more than 7 nucleotides in length, and can be as short as 3 or 4 nucleotides in length. The ligation is optionally performed by CV ligase. | 12-25-2014 |
20140378316 | METHOD OF PURIFYING RNA BINDING PROTEIN-RNA COMPLEXES - The present invention provides methods for purifying RNA molecules interacting with an RNA binding protein (RBP), and the use of such methods to analyze a gene expression profile of a cell. The invention also provides sequences of RNA molecules that mediate binding to an RBP, proteins encoded by the sequences, a method of identifying the sequences, and the use of the sequences in a screen to identify bioactive molecules. The invention also provides RNA motifs found among the sequences and compounds that bind the RNA motifs. In addition, the invention provides methods of treating diseases associated with a function of an RNA binding protein. | 12-25-2014 |
20140378317 | Amplification and Analysis of Selected Targets on Solid Supports - Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. Targets are circularized by hybridization to probes followed by ligation of the ends of the target to form a closed circle. The targets are then used as template for extension of an array bound probe resulting in extended probes having multiple copies of the target. The extended probes can then be analyzed. The methods may be used for genotyping, sequencing and analysis of copy number. | 12-25-2014 |
20140378318 | CIRCULARIZED TEMPLATES FOR SEQUENCING - The invention provides methods of forming a circular template for sequencing a target nucleic acid. The circular template is generated by amplification of a segment of the target nucleic acid with chimeric primers with complementary 5′ ends. The circular template has a single nick or gap providing a site for initiation of template-directed extension for sequence analysis. Sequencing of a single template generates reads of alternating segments of the same strand of the target nucleic spaced by primer segments. The different reads of the same strand of the target nucleic acid can be compiled to generate a consensus sequence. Because only one strand of the target nucleic acid is sequenced per reaction, the present method avoids errors introduced by unwittingly combining sequences of both strands of a heteroduplex PCR product. Because only one strand of the target nucleic acid is sequenced per reaction, the present method avoids errors introduced by unwittingly combining sequences of both strands of a heteroduplex PCR product. | 12-25-2014 |
20140378319 | Method To Determine Location, Size and In Situ Conditions In Hydrocarbon Reservoir With Ecology, Geochemistry, and Biomarkers - A method of identifying a hydrocarbon system is disclosed A sample from an area of interest is obtained. A first plurality of analyses is used to determine a community structure of an ecology of the sample. A second plurality of analyses is used to determine a community function of the ecology of the sample. The community structure and the community function are used to determine whether the ecology of the sample matches a characteristic ecology of a hydrocarbon system. When the ecology of the sample matches the characteristic ecology, the sample is identified as part of the hydrocarbon system. | 12-25-2014 |
20140378320 | MULTIPLEXED DIGITAL PCR - The invention relates to a method for detecting at least one target molecule and/or product molecule, wherein reaction components are provided in defined regions of a base surface and/or covering device. At least two defined regions with different reaction components are provided, and an amplification reaction is carried out. The invention also relates to a device for carrying out said method. | 12-25-2014 |
20140378321 | Methods and Compositions for Efficient Base Calling in Sequencing Reactions - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence. | 12-25-2014 |
20150011396 | METHODS FOR CREATING DIRECTIONAL BISULFITE-CONVERTED NUCLEIC ACID LIBRARIES FOR NEXT GENERATION SEQUENCING - Provided herein aremethods, compositions and kits for the generation of bisulfite-converted next generation sequencing (NGS) libraries. The methods, compositions and kits provided herein can be useful, for example, for the production of libraries from genomic DNA that allow for determination of the methylation status across the genome, i.e. the methylome. The methods, compositions and kits provided herein can also be utilized to query methylation status at a particular genomic locus or loci. Moreover, the methods provided herein can be employed for high-throughput sequencing of bisulfite-converted DNA while maintaining the directional (strandedness) information of the original nucleic acid sample. | 01-08-2015 |
20150011397 | METHODS FOR QUANTITATIVE DETERMINATION OF MULTIPLE PROTEINS IN COMPLEX MIXTURES - In various embodiments, the present invention relates generally to analysis of complex mixtures and, more specifically, to detection and quantitative determination of multiple proteins, protein modifications, and protein-nucleic acid interactions in those complex mixtures. | 01-08-2015 |
20150011398 | METHODS FOR QUANTITATIVE DETERMINATION OF PROTEIN-NUCLEIC ACID INTERACTIONS IN COMPLEX MIXTURES - In various embodiments, the present invention relates generally to analysis of complex mixtures and, more specifically, to detection and quantitative determination of multiple proteins, protein modifications, and protein-nucleic acid interactions in those complex mixtures. | 01-08-2015 |
20150011399 | DNA Ligation on RNA Template - Disclosed are methods and compositions for detection and amplification of nucleic acids, wherein two DNA strands hybridized to an RNA strand are ligated. In one aspect, the disclosed methods include removal of an energy source, such as ATP, upon charging a ligase to form an enzyme-AMP intermediate, and then adding substrate, which results in one complete round of RNA-templated DNA ligation. In another aspect, the ligation reaction is accomplished by use of a mixture of at least two different ligase enzymes. The disclosed methods and compositions for RNA-templated DNA ligation may be particularly useful for detection of RNA sequence variants, for example RNA splice variants, and for quantitative expression analysis. | 01-08-2015 |
20150011400 | Bacterial Metastructure and Methods of Use - Although metabolic networks have been reconstructed on a genome-scale, the corresponding reconstruction and integration of governing transcriptional regulatory networks has not been fully achieved. Here such an integrated network was constructed for amino acid metabolism in | 01-08-2015 |
20150011401 | Cancer Diagnostics Using Non-Coding Transcripts - Disclosed herein, in certain instances, are methods for the diagnosis, prognosis and determination of cancer progression of a cancer in a subject. Further disclosed herein, in certain instances, are methods for determining the treatment modality of a cancer in a subject. The methods comprise expression-based analysis of non-coding targets and coding targets. Further disclosed herein, in certain instances, are probe sets for use in assessing a cancer status in a subject. | 01-08-2015 |
20150011402 | Nanopore-Based Single DNA Molecule Characterization, Identification and Isolation Using Speed Bumps - The present invention relates to a method of using nanopores to obtain sequence information of sample DNAs in ss test DNAs. The method comprises using speed bumps to stall the ss test DNAs in the nanopores at random positions of the ss test DNAs to obtain sequence information of each and every nucleotides of the sample DNAs, and to construct the whole sequences of the sample DNAs. The present invention also relates to identification and/or isolation of test DNAs having desired sequence(s) using nanopore detectors facilitated by speed bump. | 01-08-2015 |
20150011403 | NON-INVASIVE DETERMINATION OF METHYLOME OF TUMOR FROM PLASMA - Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer. | 01-08-2015 |
20150018222 | METHOD FOR IN VITRO DIAGNOSIS OR PROGNOSIS OF BREAST CANCER - The present invention relates to a method for the in vitro diagnosis or prognosis of breast cancer, which includes a step of detecting at least one expression product of at least one HERV nucleic acid sequence, the use of said nucleic acid sequences, once isolated, as one or more molecular marker(s) and a kit including at least one specific binding partner of at least one of the expression products of the HERV nucleic acid sequences. | 01-15-2015 |
20150024945 | SYSTEMS AND METHODS FOR SEQUENCING IN EMULSION BASED MICROFLUIDICS - Methods, libraries, and kits for nucleotide sequencing are provided. | 01-22-2015 |
20150024946 | METHOD OF DETERMINING HPV INTEGRATION SITE IN GENOME OF HUMAN TISSUE SAMPLE, SYSTEM AND USE THEREOF - Disclosed are a method of determining an HPV integration site in a genome of a human tissue sample and a system thereof. The method comprises: subjecting genome DNA of the human tissue sample to a first sequencing, to obtain a sequencing result; determining DNA fragments containing both HPV sequence and human genome sequence, based on the sequencing result; determining a pair of amplification primers based on the DNA fragments containing both HPV sequence and human genome sequence, subjecting the genome DNA of the human tissue sample to PCR amplification using the pair of amplification primers, to obtain PCR product; and subjecting the PCR product to a second sequencing, to determine the integration site in a genome of the human tissue sample. The method is easy to be operated with low cost, high efficiency and excellent repeatability, which may be used to detect all HPV genotypes one time, and may rapidly and accurately determine detailed sequence information and integration site. | 01-22-2015 |
20150024947 | SYSTEMS AND METHODS FOR DISTINGUISHING BETWEEN AUTISM SPECTRUM DISORDERS (ASD) AND NON-ASD DEVELOPMENTAL DELAY - Methods and systems are presented herein to distinguish children with Autism Spectrum Disorders (ASD) from those with other forms of developmental delay (DD) based on patterns of gene expression levels in blood. | 01-22-2015 |
20150024948 | METHOD FOR DETECTING BALANCED CHROMOSOMAL ABERRATIONS IN A GENOME - The present disclosure provides methods and systems for the capture and enrichment of target nucleic acids and analysis of the enriched target nucleic acids for detecting balanced chromosomal aberrations including translocations and inversions. The present disclosure provides for the enrichment of targeted sequences in a format whereby one fusion partner gene on a capturing platform is represented to allow subsequent sequencing of chimeric nucleic acids (i.e., nucleic acid strands that carry information on different DNA regions of a genome). Such a design enables identification of novel fusion partner genes occurring as a result of a chromosomal translocation or inversion. | 01-22-2015 |
20150024949 | Urine Biomarkers - A method for detecting biomarkers of prostate cancer or other medical condition of the prostate based on the use of microvesicles obtained from urine samples, and the nucleic acids present in the microvesicles. The method disclosed herein are advantageous in that they may be used to support diagnosis, prognosis, monitoring, or therapy selection in lieu of or in conjunction with traditional biopsy-based diagnostics and do not require a digital rectal examination or prostate massage prior to urine sample collection. | 01-22-2015 |
20150031550 | HUMAN ANTIBODIES AND PROTEINS - The present invention provides composite proteins, including antibodies, which show reduced immunogenicity. In particular, composite antibodies for use in humans are provided, in particular antibodies which have been modified to remove one or more T-cell epitopes. Methods for generating such proteins are also provided. | 01-29-2015 |
20150031551 | CONTROL NUCLEIC ACID SEQUENCES FOR USE IN SEQUENCING-BY-SYNTHESIS AND METHODS FOR DESIGNING THE SAME - A method for nucleic acid sequencing includes (a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands comprising a test or control sequence; (b) exposing a plurality of the template polynucleotide strands in the defined spaces to a series of flows of nucleotide species flowed according to a predetermined ordering; and (c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands, wherein the test or control sequence comprises a sequence determined by identifying, using a variant caller, loci with systematic errors present in a plurality of sequencing runs included in a training set of sequencing runs. | 01-29-2015 |
20150031552 | METHOD FOR DETECTING HYDROXYLMETHYLATION MODIFICATION IN NUCLEIC ACID AND USE THEREOF - A method for detecting hydroxymethylation modification in nucleic acid comprises: glycosylating the nucleic acid, digesting with MspI, ligating the digested fragments to a biotin-labeled linker at both ends thereof, digesting with NlaIII; capturing the digested fragments using streptavidin magnetic beads to produce fragments having the biotin-labeled linker at one end and a CATG 4-base sticky end at the other end, wherein these fragments reveal modification information of their adjacent CCGG sites; ligating the CATG sticky end to a linker containing a recognition site of MmeI or Ecop15I, digesting with corresponding restriction endonuclease to produce short sequence fragments that can reveal modification information of their adjacent CCGG sites; and performing a tag number comparison to obtain information about methylation and hydroxymethylation modification relative levels. A use of the method is also provided. | 01-29-2015 |
20150031553 | METHOD OF MEASURING IMMUNE ACTIVATION - The invention is directed to a method of detecting immune activation in an individual by measuring frequencies and sizes of certain groups of related clonotypes, referred to herein as “clans,” in a clonotype profile of the individual. A clan may arise from a single lymphocyte progenitor that gives rise to many related lymphocyte progeny, each possessing and/or expressing a slightly different immunoglobulin receptor due to somatic mutation(s), such as base substitutions, inversions, related rearrangements resulting in common V(D)J gene segment usage, or the like. Immune activation is correlated to frequencies and sizes of clans in a clonotype profile exceeding reference values for those features. | 01-29-2015 |
20150031554 | EXTRACELLULAR TELOMERE ASSAY - Provided herein is a method of detecting a level of cell injury in a subject, the method comprising detecting an amount of extracellular telomeres in a biological sample from the subject. The amount of extracellular telomeres as compared to a control amount indicates the level of cell injury in the subject. Further provided is a kit for detecting a level of apoptosis in a subject, the kit comprises first and second nucleic acid sequences, wherein the first and second nucleic acid sequences hybridize with an extracellular telomere; and a container. The first and second nucleic acid sequences can comprise SEQ ID NO: 1 and SEQ ID NO:2. | 01-29-2015 |
20150031555 | METHOD FOR CORRECTION OF BIAS IN MULTIPLEXED AMPLIFICATION - This invention relates a method to correct for bias inherent to multiplexed sequence amplification. The resulting corrected data is a much more accurate representation of true quantities than unprocessed data. | 01-29-2015 |
20150031556 | SYSTEM AND METHOD OF GENOMIC PROFILING - The present invention relates to a system and method of genomic profiling and is particularly useful in genomic differentiation of heterogeneous and polyclonal neoplastic cell populations, preferably of flow sorted formalin fixed paraffin embedded samples. The present invention includes methods of improving resolution for identifying aberration in variable carcinoma genomes and/or heterogeneous cell populations. The present invention also includes kits configured to improve genomic resolution and the ability to identify genomic aberration in variable and/or heterogeneous cell populations. | 01-29-2015 |
20150031557 | DETECTION OF SHIGA TOXIN GENES IN BACTERIA - The disclosed invention is related to methods, compositions and kits for targeting nucleic acid derived from Shiga toxin-producing bacteria such as | 01-29-2015 |
20150031558 | METHODS, COMPOSITIONS AND SYSTEMS FOR SAMPLE DEPOSITION - Methods, compositions, systems, apparatus, and kits are provided for depositing samples onto surfaces. The samples can include one or more particles, and the surface can include one or more reaction chambers. In some embodiments, the depositing can include the use of companion particles in combination with sample particles. | 01-29-2015 |
20150038335 | CEREBROSPINAL FLUID ASSAY - The present invention is directed to methods of isolating particles, such as nucleic acid-containing particles or microvesicles, from a biological sample and extracting nucleic acids therefrom, wherein the biological sample is cerebrospinal fluid. The present invention further provides methods for aiding diagnosis, prognosis, monitoring and evaluation of a disease or other medical condition in a subject by detecting a biomarker associated with a disease or medical condition thereof. | 02-05-2015 |
20150038336 | METHOD FOR RELATIVE QUANTIFICATION OF NUCLEIC ACID SEQUENCE, EXPRESSION, OR COPY CHANGES, USING COMBINED NUCLEASE, LIGATION, AND POLYMERASE REACTIONS - The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection. | 02-05-2015 |
20150038337 | METHODS OF SELECTING BIOLOGIC-PRODUCING CELL LINES BY NEXT GENERATION SEQUENCING - An optimized multi-step cell line screening method based on next generation sequencing (NGS) and mass spec (MS) is disclosed. The method helps reduce variants in the biologic-producing cell line and improve the efficiency of cell line development process. | 02-05-2015 |
20150038338 | IDENTIFICATION OF OLFACTORY RECEPTORS SENSITIVE TO DIFFERENT ODORANTS - This disclosure provides methods for identification of olfactory sensosry neurons (OSN) that recognize specific odorants. The method comprises introducing into the OSN, a permanent activity marker which exhibits a detectable and permanent change upon activation of the neuron in response to an odorant and exposure to an exteranal stimulus, such as light. The OSN can be isolated and its receptor characterized. | 02-05-2015 |
20150038339 | Methods And Devices For Sequencing Nucleic Acids In Smaller Batches - The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. A plurality of smaller flow cells is employed, each with a relatively small area to be imaged, in order to provide greater flexibility and efficiency. | 02-05-2015 |
20150038340 | METHODS FOR PREDICTING ANTI-CANCER RESPONSE - The present invention is based, in part, on the identification of novel methods for defining predictive biomarkers of response to anti-cancer drugs. | 02-05-2015 |
20150038341 | Digital Amplification - The identification of pre-defined mutations expected to be present in a minor fraction of a cell population is important for a variety of basic research and clinical applications. The exponential, analog nature of the polymerase chain reaction is transformed into a linear, digital signal suitable for this purpose. Single molecules can be isolated by dilution and individually amplified; each product is then separately analyzed for the presence of pre-defined mutations. The process provides a reliable and quantitative measure of the proportion of variant sequences within a DNA sample. | 02-05-2015 |
20150038342 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants. | 02-05-2015 |
20150038343 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants. | 02-05-2015 |
20150038344 | Method of Preparing a Nucleic Acid Library - A method of preparing a nucleic acid library in droplets in contact with oil, including: (a) blunt-ending nucleic acid fragments in a droplet in the oil to yield blunt-ended nucleic acid fragments; (b) phosphorylating the blunt-ended nucleic acid fragments in a droplet in the oil to yield phosphorylated nucleic acid fragments; coupling A-tails to the phosphorylated nucleic acid fragments in a droplet in the oil to yield A-tailed nucleic acid fragments; and (d) coupling nucleic acid adapters to the A-tailed nucleic acid fragments in a droplet in the oil to yield the nucleic acid library comprising adapter-ligated nucleic acid fragments. | 02-05-2015 |
20150045232 | INTEGRATED AND VERSATILE METHODS FOR SYSTEMS DIAGNOSIS OF DISEASES - The disclosure relates to a system diagnosis of a disease or a disease condition whereby a single sample is prepared from a biological specimen which integrates synchronously the methods of protection, isolation and alteration of a biological specimen or a bio-molecule to isolate and study tissues and bio-molecules including DNA, large RNA, small RNA, protein, lipid, carbohydrates, and other metabolite simultaneously or individually resulting in a comprehensive understanding of the cause, prevention, risk, seriousness, confirmation, treatment, triage, and prognosis of a disease or a disease condition. | 02-12-2015 |
20150045233 | MICRO-RNA BIOMARKERS AND METHODS OF USING SAME - A procedure and an apparatus are described for identifying individuals at risk of pulmonary tumour and/or for diagnosing a pulmonary tumour using the study of levels of expression of miRNA in the blood or another biological fluid. Also described are a method and a compound for reducing or eliminating a risk of pulmonary tumour by rebalancing the miRNAs that are underexpressed or overexpressed. | 02-12-2015 |
20150045234 | FLUIDIC SYSTEM FOR REAGENT DELIVERY TO A FLOW CELL - A fluidic system that includes a reagent manifold comprising a plurality of channels configured for fluid communication between a reagent cartridge and an inlet of a flow cell; a plurality of reagent sippers extending downward from ports in the manifold, each of the reagent sippers configured to be placed into a reagent reservoir in a reagent cartridge so that liquid reagent can be drawn from the reagent reservoir into the sipper; at least one valve configured to mediate fluid communication between the reservoirs and the inlet of the flow cell. The reagent manifold can also include cache reservoirs for reagent re-use. | 02-12-2015 |
20150045235 | METHODS FOR SEQUENCING A BIOMOLECULE BY DETECTING RELATIVE POSITIONS OF HYBRIDIZED PROBES - A sequencing method is presented in which a biomolecule is hybridized with a specially chosen pool of different probes of known sequence which can be electrically distinguished. The different probe types are tagged such that they can be distinguished from each other in a Hybridization Assisted Nanopore Sequencing (HANS) detection system, and their relative positions on the biomolecule can be determined as the biomolecule passes through a pore or channel. The methods eliminate, resolve, or greatly reduce ambiguities encountered in previous sequencing methods. | 02-12-2015 |
20150045236 | ACCELERATING THE DEVELOPMENT OF AGRICULTURAL PRODUCTS USING ANCHORED ENRICHMENT - Hybrid enrichment technology as applied to enhancing agricultural production, for example including, but not limited to, crop production, pesticide development, crop trait development, and pest control. The methodology pools samples prior to library production, thus reducing cost and increasing efficiency of sequencing across- and within-species targets. | 02-12-2015 |
20150051081 | METHOD OF SCREENING COMPLEX PROTEIN LIBRARIES TO IDENTIFY ALTERED PROPERTIES - The invention provides methods of making designed and constructed protein (e.g., antibody) libraries and libraries resulting from the same. | 02-19-2015 |
20150051082 | DIAGNOSTIC TEST FOR BACTERIAL PATHOGENS USING INTERNAL CONTROL BACTERIAL STRAIN - The invention relates to a method for detecting the presence or absence of a bacterial pathogen in a biological sample obtained from a human or animal subject, using an internal control. In particular, the invention relates to a method for detecting the presence or absence of | 02-19-2015 |
20150051083 | METHODS AND COMPOSITIONS FOR IDENTIFYING REPEATING SEQUENCES IN NUCLEIC ACIDS - Short Tandem Repeats are currently used by law enforcement and others, for example, for the identification of individuals by DNA matching. A method is described herein that uses WPD to classify and identify repeating sequences in nucleotide sequences from the position and frequency information contained within nucleotide sequences. This decomposition allows for the quick classification of nucleotide sequences (i.e., reads) into two different classes, including, for example, one class that contains sequencer reads that contain a repeat motif with non-repeat sequence on either flank, and another class that contains sequencer reads that do not contain any repeat sequence. | 02-19-2015 |
20150051084 | METHOD FOR DETERMINING PROGNOSIS OF PROSTATE CANCER IN A SUBJECT - A method for determining the prognosis of prostate cancer in a subject is provided which comprises the assessment of the methylation status of the HSPB1 gene in a prostate cancer sample. | 02-19-2015 |
20150051085 | RAPID ANEUPLOIDY DETECTION - Massively parallel sequencing of cell-free, maternal plasma DNA was recently demonstrated to be a safe and effective screening method for fetal chromosomal aneuploidies. Here, we report an improved sequencing method achieving significantly increased throughput and decreased cost by replacing laborious sequencing library preparation steps with PCR employing a single primer pair. Using this approach, samples containing as little as 4% trisomy 21 DNA could be readily distinguished from euploid samples. | 02-19-2015 |
20150051086 | COMPOSITIONS AND METHODS FOR DISCOVERY OF CAUSATIVE MUTATIONS IN GENETIC DISORDERS - The compositions and methods provided herein allow for identification of causative genetic biomarkers for a disease condition or drug response. | 02-19-2015 |
20150051087 | METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING - The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR. | 02-19-2015 |
20150057159 | METHOD TO IDENTIFY ASYMPTOMATIC HIGH-RISK INDIVIDUALS WITH EARLY STAGE LUNG CANCER BY MEANS OF DETECTING miRNAs IN BIOLOGIC FLUIDS - A diagnostic and/or prognostic model of at least 5 serum miRNAs selected among a group of 34 miRNAs that identifies subjects with early stage lung cancer, namely non-small cell lung carcinomas (NSCLCs), in a population of asymptomatic high-risk individuals, with 80% accuracy. The model could also distinguish between benign and malignant lesions and is sensitive enough to capture the disease onset. In addition, the model could also diagnose or confirm a diagnosis of lung cancer in symptomatic patients, and monitor the lung tumor status after treatment with surgery and/or chemotherapy and/or radiotherapy in a subject with such lung cancer. | 02-26-2015 |
20150057160 | PATHOGEN SCREENING - The present invention relates to methods of isolating pathogenic genomes from a clinical sample. | 02-26-2015 |
20150057161 | HIGH-RESOLUTION TRANSCRIPTOME OF HUMAN MACROPHAGES - The invention is based on the finding of specific surface markers for M1-like (classically activated) and M2-like (alternatively activated) macrophages and provides for a method for the identification, characterization and isolation of M1-like and M2-like macrophages based on the abundance of said surface markers and for means for performing such method. | 02-26-2015 |
20150057162 | PEPTIDE ARRAYS - A method is disclosed for identifying a member of a peptide library that interacts with a target molecule in situ, the method including expressing immobilised nucleic acid molecules to produce the peptide library in a way that each member of the peptide library is immobilised on the nucleic acid molecule from which it was expressed; contacting the immobilised peptide library with the target molecule; and detecting an interaction between at least one member of the peptide library and the target molecule. The method further comprises sequencing the plurality of nucleic acid molecules in situ on the solid support, such that the at least one member of the peptide library that interacts with the target molecule can be immediately identified, at least by the sequence of the nucleic acid molecule from which it was expressed, without requiring additional or secondary analysis or characterising procedures in order to identify the useful members of the library. The target molecules may themselves be comprised within a second nucleic acid or peptide library. | 02-26-2015 |
20150057163 | SYSTEMS AND METHODS FOR EPIGENETIC SEQUENCING - The present invention generally relates to microfluidics and/or epigenetic sequencing. In one set of embodiments, cells contained within a plurality of microfluidic droplets are lysed and the DNA (e.g., from nucleosomes) within the droplets are labeled, e.g., with adapters containing an identification sequence. The adapters may also contain other sequences, e.g., restriction sites, primer sites, etc., to assist with later analysis. After labeling with adapters, the DNA from the different cells may be combined and analyzed, e.g., to determine epigenetic information about the cells. For example, the DNA may be separated on the basis of certain modifications (e.g., methylation), and the DNA from the separated nucleosomes may be sequenced using techniques such as chromatin immunoprecipitation (“ChIP”). In some cases, the DNA sequences may also be aligned with genomes, e.g., to determine which portions of the genome were epigenetically modified, e.g., via methylation. | 02-26-2015 |
20150065352 | MONITORING HEALTH AND DISEASE STATUS USING CLONOTYPE PROFILES - There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers. | 03-05-2015 |
20150065353 | REAL-TIME ELECTRONIC SEQUENCING - Real time electronic sequencing methods, devices, and systems are described. Arrays of nanoscale electronic elements comprising capacitive devices with one or two electrodes, or arrays of nanoFET devices are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the nanoscale electronic elements or to the substrate proximate to the nanoscale electronic element. A sequencing reaction mixture comprising nucleotide analogs having impedance labels, capacitive labels, or conductivity labels is introduced to the array of nanoscale electronic elements comprising capacitive devices or nanoFETs under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by identifying the types of labels of the nucleotide analogs that are incorporated into the growing strand using measured impedance, conductivity, or capacitance. | 03-05-2015 |
20150065354 | METHOD FOR CHARACTERISING A POLYNUCELOTIDE BY USING A XPD HELICASE - The invention relates to a new method of characterising a target polynucleotide. The method uses a pore and an XPD helicase. The helicase controls the movement of the target polynucleotide through the pore. | 03-05-2015 |
20150065355 | Epigenetic Signatures as Marker for Cardiomyopathies and Myocardial Insufficiencies - The present invention relates to the use of DNA methylation profiles of patient samples for the diagnosis, prognosis and/or therapy monitoring of a heart disease in a patient, wherein the DNA methylation profile of the patient sample is compared with the DNA methylation profile of a control sample, and wherein a difference in the DNA methylation profile of the patient sample compared to the control sample is indicative of a heart disease or of the risk for developing a heart disease or for a prediction of therapy effects or therapy outcome. The present invention further relates to methods for the diagnosis, prognosis and/or therapy monitoring of a heart disease in a patient, comprising determining the DNA methylation profile in a patient sample comprising genomic DNA from heart cells, heart tissue or peripheral blood; and comparing the DNA methylation profile in the patient sample with the DNA methylation profile from a normal subject not having a heart disease or having a normal heart function. The present invention furthermore relates to kits that are suitable for the methods and uses of the invention. The present invention furthermore relates to the use of ADORA2A, ERBB3, LY75, HOXB13, GF11, CLDN4, FDX1, ID4, NAT1, PPARGC1A, SULF2, TFF1, TKT, AT-P2C, CCDC59, GSTM5m, SLC9A6 and TDG as marker for the diagnosis, prognosis and/or therapy monitoring of a heart disease in a patient. | 03-05-2015 |
20150065356 | METHODS OF BEAD MANIPULATION AND FORMING BEAD ARRAYS - According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same. | 03-05-2015 |
20150065357 | METHODS, SYSTEMS, AND SOFTWARE FOR IDENTIFYING FUNCTIONAL BIO-MOLECULES - The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods. | 03-05-2015 |
20150072865 | Algorithm for Modification of Somatic Cancer Evolution - Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic instability. It has been suggested that the internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex impact on Darwinian species evolution. A similar situation can be expected for somatic cancer evolution as the key mechanisms encountered in species evolution such as duplications, rearrangements or deletions of genes also constitute prevalent mutation mechanisms in cancers with chromosomal instability. The invention is an algorithm which is based on a systems concept describing the putative constraints of the cancer genome architecture on somatic cancer evolution. The algorithm allows the identification of therapeutic target genes in individual cancer patients which do not represent oncogenes or tumor suppressor genes but have become putative therapeutic targets due to constraints of the cancer genome architecture on individual somatic cancer evolution. Target genes or regulatory elements may be identified by their designation as essential genes or regulatory elements in cancer cells of the patient but not in normal tissue cells or they may be identified by their impact on the process of somatic cancer evolution in individual patients based on phylogenetic trees of somatic cancer evolution and on the constructed multilayered cancer genome maps. The algorithm can be used for delivering personalized cancer therapy as well as for the industrial identification of novel anti-cancer drugs. The algorithm is essential for designing software programs which allow the prediction of the natural history of cancer disease in individual patients. | 03-12-2015 |
20150072866 | MARKER PANEL FOR DETECTING CANCER - Provided herein is technology relating to detecting cancer and particularly, but not exclusively, to methods for detecting colorectal cancer by evaluating multiple markers in paired plasma and stool samples. In particular, the technology relates to CRC screening by assaying plasma for methylated Septin 9 and assaying stool DNA for methylated vimentin, NDRG4, BMP3, and/or TFPI2. | 03-12-2015 |
20150072867 | ANALYSIS OF NUCLEIC ACID MOLECULES DISTRIBUTED ON A SURFACE OR WITHIN A LAYER BY SEQUENCING WITH POSITION IDENTIFICATION - The present invention describes a method for identification of areas of a sample from which nucleic acid molecules originate using labeling of said nucleic acid molecules by two-dimensionally distributed oligonucleotide markers. Further analysis of hybrids between the nucleic acid molecules and the oligonucleotide markers allow identification of the original position of the labelled nucleic acid molecules in the sample. | 03-12-2015 |
20150072868 | NANOCAPILLARY DEVICE FOR BIOMOLECULE DETECTION, A FLUIDIC NETWORK STRUCTURE AND A METHOD OF MANUFACTURING THEREOF - A device includes at least one nanoscale capillary and means for applying an electric voltage, said means being adapted to create an electric field at least in said capillary when said electric voltage is applied, so that, when said electric voltage is applied, a charged molecule or particle placed within the created electric field can be electrically controlled. A fluidic network structure includes the at least one nanoscale capillary. A method of using and manufacturing the fluidic network structure is also described. | 03-12-2015 |
20150072869 | METHODS AND COMPOSITIONS FOR NUCLEIC ACID SAMPLE PREPARATION - The present invention provides methods and compositions useful for supplying high throughput nucleic acid sequencing systems with templates. The methods circumvent the need for costly, labor-intensive cloning and cell culture methods and can be scaled to accommodate template production for a variety of sequencing applications, e.g., sequencing individuals' genomes, sequencing subpopulations of transcripts from a gene of interest, and/or gene expression profiling. Particularly preferred embodiments of the methods vastly improve the preparation of cDNA from mRNA samples, e.g., by randomizing errors introduced during the process, thereby allowing these errors to be readily distinguished from true variants present in the mRNA samples. | 03-12-2015 |
20150072870 | Method for Reducing Adapter-Dimer Formation - Methods are provided for ligating a 3′ adapter and a 5′ adapter to a target polynucleotide so as to avoid adapter dimer formation. Embodiments of the methods include adding a blocking oligonucleotide after the first ligation in which a 3′ adapter is ligated to the target polynucleotide so that the blocking oligonucleotide is capable of hybridizing to excess 3′ adapter and the ligated 3′ adapter. Subsequently, a 5′ adapter is ligated to the target polynucleotide thus avoiding adapter dimer formation. | 03-12-2015 |
20150072871 | NUCLEIC ACID SEQUENCING SYSTEM AND METHOD - A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected. | 03-12-2015 |
20150072872 | METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING - The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a sample of DNA from the mother of the fetus and from the fetus, and from genotypic data from the mother and optionally also from the father. The ploidy state is determined by using a joint distribution model to create a set of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias. | 03-12-2015 |
20150080226 | METHODS OF SELECTING BINDING-ELEMENTS AND USES THEREOF - Methods for selecting a binding-element are provided. The method comprised of different steps. A first mixture is formed using at least one target molecule and a plurality of oligomers, followed by incubating the first mixture to form a second mixture comprising at least one target-bound oligomer and at least one target-unbound oligomer. Then a first accelerator is added to cleave the target-unbound oligomer and the target-bound oligomer is separated from the target molecule. This is followed by addition of a second accelerator for ligation, and a third accelerator for amplification followed by sequencing and post sequence analysis to select the binding-element. | 03-19-2015 |
20150080227 | CYCLIC SINGLE MOLECULE SEQUENCING PROCESS - The invention relates to a process for parallel high throughput sequencing of nucleic acid molecules, in particular in the single molecule format. | 03-19-2015 |
20150080228 | Device Preparation Using Condensed Nucleic Acid Particles - A method of sequencing a nucleic acid strand includes receiving particles having nucleic acid strands coupled to a polymer matrix, exposing the particles to a solution including a condensing agent, and applying the particles to a surface, the particles depositing on the surface. | 03-19-2015 |
20150080229 | PLASMA MICRORIBONUCLEIC ACIDS AS BIOMARKERS FOR ENDOMETRIOSIS AND ENDOMETRIOSIS-ASSOCIATED OVARIAN CANCER - The present invention relates to methods and compositions for differentiating between absence of disease, endometriosis, and EAOC or serous ovarian cancer in a subject. It is based, at least in part, on the discovery that certain microRNAs are associated with each of these conditions. | 03-19-2015 |
20150080230 | KINETIC EXCLUSION AMPLIFICATION OF NUCLEIC ACID LIBRARIES - A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated. | 03-19-2015 |
20150087525 | PLASMA MICRORNAS FOR THE DETECTION OF EARLY COLORECTAL CANCER - The present invention relates in general to the field of colorectal cancer detection, and more particularly, to plasma microRNAs for the detection of early colorectal cancer. Specifically, the present invention includes methods, kits and biomarkers for diagnosing or detecting colorectal neoplasia in a human subject comprising the steps of: A method for diagnosing or detecting colorectal neoplasia in a human subject comprising the steps of: obtaining one or more biological samples from the subject suspected of suffering from colorectal neoplasia; measuring an overall expression pattern or level of one or more microRNAs obtained from the one or more biological samples of the subject; and comparing the overall expression pattern of the one or more microRNAs from the biological sample of the subject suspected of suffering from colorectal neoplasia with the overall expression pattern of the one or more microRNAs from a biological sample of a normal subject, wherein the normal subject is a healthy subject not suffering from colorectal neoplasia, wherein overexpression of a combination of miR19a and miR19b, or miR19a and miR19b and miR15b is indicative of colorectal cancer. | 03-26-2015 |
20150087526 | PEPTIDE IDENTIFICATION AND SEQUENCING BY SINGLE-MOLECULE DETECTION OF PEPTIDES UNDERGOING DEGRADATION - The present disclosure provides peptide amino acid sequencing and identification methods and kits for performing such methods. For example, single-molecule detection of fluorophore-labeled peptides is disclosed using multiple rounds of standard Edman degradation or using digestion by chemicals or enzymes. Different fluorophores covalently attached to each of a specific type of amino acid side chain of a peptide provide for the derivation of the peptide's encoded amino acid sequence following image alignments of multiple Edman cycles or following digestion by chemicals or enzymes. The amino acid sequence of a peptide and/or the identity of the peptide can be determined by bioinformatic analysis based on the encoded amino acid sequence. The present disclosure further provides peptide derivatization and immobilization strategies to enable the sequencing and identification of a single peptide or a plurality of peptides. | 03-26-2015 |
20150087527 | METHOD AND KIT FOR THE CLASSIFICATION AND PROGNOSIS OF TISSUE OR ORGAN FIBROSIS IN A REPARATIVE OR REACTIVE PROCESS - The invention relates to methods of diagnosis or prognosis of a tissue or organ fibrosis (e.g., skin fibrosis, hypertrophic scar or a keloid) in a reparative or reactive process comprising the step of determining the levels of expression of genes encoding different molecular markers in a sample of a tissue or organ from a mammalian, wherein different genes markers are studied. | 03-26-2015 |
20150087528 | DNA AMPLIFICATION AND SEQUENCING USING DNA MOLECULES GENERATED BY RANDOM FRAGMENTATION - The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3′ end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention. | 03-26-2015 |
20150087529 | SEQUENCING ANALYSIS OF CIRCULATING DNA TO DETECT AND MONITOR AUTOIMMUNE DISEASES - Systems, methods, and apparatuses are provided for diagnosing auto-immune diseases such as systemic lupus erythematosus (SLE) based on the sizes, methylation levels, and/or genomic characteristics of circulating DNA molecules. Patients provide blood or other tissue samples containing cell-free nucleic molecules for analysis. Massively parallel and/or methylation-aware sequencing can be used to determine the sizes and methylation levels of individual DNA molecules and identify the number of molecules originating from different genomic regions. A level of SLE can be estimated based on: the amount of molecules having sizes below a threshold value; the methylation level(s) of the entire genome or portions of the genome; correlations between the sizes and methylation levels of DNA molecules; and/or comparing the representation of DNA molecules in each of a plurality of genomic regions with a reference value for that region, and determining an amount of genomic regions having increased or decreased measured genomic representation. | 03-26-2015 |
20150087530 | Low-Volume Sequencing System and Method of Use - Various embodiments of a low-volume sequencing system are provided herein. The system can include a low-volume flowcell having at least one reaction chamber of a defined volume (e.g., less than about 100 μl). The system can also include an automated reagent delivery mechanism configured to reversibly couple with the inlet port corresponding to a target reaction chamber thereby placing allowing for reagent to be accurately moved from a storage container to the reaction chamber with minimal reagent waste. The flowcells can include a plurality of reaction chambers (e.g., 6) thereby allowing for parallel analysis of multiple samples. Various methods of analyzing a biomolecule are also provided herein. | 03-26-2015 |
20150087531 | METHOD OF NUCLEIC ACID AMPLIFICATION - A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc. | 03-26-2015 |
20150094209 | AUTONOMOUS REPLICATION SEQUENCES AND EPISOMAL DNA MOLECULES - The present invention provides autonomous replication sequences (ARSs) isolated from | 04-02-2015 |
20150094210 | METHOD, SYSTEM AND COMPUTER READABLE MEDIUM FOR DETERMINING BASE INFORMATION IN PREDETERMINED AREA OF FETUS GENOME - Provided are a method, system and computer readable medium for determining the base information in a predetermined area of a fetus genome, the method comprising following steps: constructing a sequence library for the DNA samples of the fetus genome; sequencing the sequence library to obtain the sequencing result of the fetus, the sequencing result of the fetus comprised of a plurality of sequencing data; and based on the sequencing result of the fetus, determining the base information in the predetermined area according to the hidden Markov model in conjunction with the genetic information of an individual related hereditarily to the fetus. | 04-02-2015 |
20150094211 | POLYMERASE COMPOSITIONS, METHODS OF MAKING AND USING SAME - The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having lower systematic error as compared to a reference polymerase. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered properties. | 04-02-2015 |
20150094212 | Systems and Methods for Detecting Structural Variants - Systems and method for identifying long deletions can obtain sequencing information for a plurality of amplicons in and around a potential region from a nucleic acid sample. The sequencing information can include a plurality of reads that can be mapped to a reference sequence. Using information, such as where reads map to a reference sequence and relative abundance of reads for the amplicons, structural variants can be identified and a determination can be made if the nucleic acid sample is homozygous or heterozygous for the structural variant. | 04-02-2015 |
20150099642 | METHODS AND DEVICES FOR DNA SEQUENCING AND MOLECULAR DIAGNOSTICS - The present invention is directed to methods for capturing, amplifying and identifying one or more of a plurality of target nucleotide sequences in a sample. The present invention is further directed to a device comprising a solid support having a plurality of wells or pillars and a plurality of oligonucleotides attached to the wells or pillars. Other aspects of the invention are directed to methods of making such devices. | 04-09-2015 |
20150099643 | BLOOD-BASED GENE EXPRESSION SIGNATURES IN LUNG CANCER - The invention pertains to a method for diagnosing or detecting lung cancer in human subjects based on ribonucleic acid (RNA) expression, in particular based on RNA from blood. The invention discloses 361 genes which are differentially expressed in blood from lung cancer patients and discloses that at least 4 of the mRNAs must be determined in order to have an AUC of at least 0.8. | 04-09-2015 |
20150099644 | Method of Performing Digital PCR - A method of detection of a target nucleic acid is provided. The method includes fractionating a sample into a plurality of sample volumes wherein more than 50% of the fractions contain no more than 1 target nucleic acid molecule per sample volumes, and subjecting the plurality of sample volumes to conditions for amplification. The method further includes detecting a change in ion concentration in a sample volume wherein a target nucleic acid is present, counting the number of fractions with an amplified target nucleic acid, and determining the quantity of target nucleic acid in the sample. | 04-09-2015 |
20150105263 | BIOLOGICAL SAMPLE ANALYSIS SYSTEM AND METHOD - Disclosed are a biological sample analysis system and method for determining whether or not each of a plurality of biological samples has a test-target property using the plurality of biological samples and a plurality of pools generated by pooling samples. The system includes a determiner configured to determine whether or not there is a possibility of a determination of a false positive according to test values for the test-target property of the plurality of pools, an additional sample selector configured to select a minimum number of additional test-target samples on which an individual test of whether or not a sample has the test-target property will be carried out from among the plurality of samples when it is determined that there is the possibility of a determination of a false positive, and a test result determiner configured to determine whether or not each of the plurality of samples has the test-target property according to test results of the additional test-target samples. | 04-16-2015 |
20150105264 | METHOD AND SYSTEM FOR IDENTIFYING TYPES OF TWINS - Provided are a method and a system for identifying whether the twins are dizygotic twins, the method comprising: typing at least one polymorphic loci of the twins fetuses to obtain the fetal polymorphism types, comparing the fetal polymorphism types with the corresponding polymorphism types of their parents, determining whether the twins are dizygotic twins on the basis of the comparison result. | 04-16-2015 |
20150105265 | METHODS TO ASSESS THE LIKELIHOOD OF DYSPLASIA OR ESOPHAGEAL ADENOCARCINOMA - In some embodiments, a method for aiding assessment of the likelihood of dysplasia or esophageal adenocarcinoma being present in a subject can include (a) providing an esophagal sample from said subject (b) determining the methylation status of (i) SLC22A18, (ii) PIGR, (iii) GJA12 and (iv) RIN2 in said sample wherein if 2 or more of said genes are methylated then an increased likelihood of presence of dysplasia or esophageal is determined. The invention also relates to apparatus for same. | 04-16-2015 |
20150105266 | METHODS FOR SELECTING BINDERS BY PHAGE DISPLAY AND MASKED SELECTION - The present invention relates to methods for selecting binders by phage display and masked selection. More particularly, the present invention relates to a method for selecting a plurality of binders specific for at least one relevant target comprising screening a phage binder library of binders against the relevant target in presence of a plurality of binders obtained from a library of binders directed against at least one irrelevant target and positively selecting the binders that are specific for the at least one relevant target. | 04-16-2015 |
20150105267 | WHOLE GENOME SEQUENCING OF A HUMAN FETUS - Methods of genome sequencing of a fetus are provided herein. In some embodiments, such methods include steps of predicting inheritance or transmission of an allele from one or more maternal-only heterozygous sites from a maternal genomic sequence to a fetal genome sequence; and predicting inheritance or transmission of an allele from one or more paternal-only heterozygous sites from a paternal genomic sequence to a fetal genome sequence. In some embodiments, the methods may also include predicting transmission of one or more genomic variants at one or more heterozygous sites that are present on both a maternal genomic sequence and a paternal genomic sequence. According to these embodiments, the paternal genomic sequence and the maternal genomic sequence are derived from a biological sample containing DNA. According to other embodiments, the sequencing methods may include a step of predicting de novo mutations in a fetal genomic sequence. | 04-16-2015 |
20150105268 | RARE BIOMARKERS FOR INCREASED RISK OF DRUG-INDUCED ELONGATED QT INTERVAL AND TORSADES DE POINTES FROM EXOME SEQUENCING STUDIES - The present disclosure provides a method for predicting the risk of a patient for developing adverse drug reactions, particularly drug-induced prolonged QT interval or TdP. The disclosure also provides a method of identifying a subject afflicted with, or at risk of, developing TdP. In some aspects, the methods comprise analyzing at least one genetic marker, wherein the presence of the at least one genetic marker indicates that the subject is afflicted with, or at risk of, developing TdP. | 04-16-2015 |
20150105269 | BIOMARKERS FOR INCREASED RISK OF DRUG-INDUCED OSTEONECROSIS OF THE JAW - The present disclosure provides a method for predicting the risk of a patient for developing adverse drug reactions, particularly drug-induced osteonecrosis of the jaw (ONJ). The disclosure also provides a method of identifying a subject afflicted with, or at risk of, developing ONJ. In some aspects, the methods comprise analyzing at least one genetic marker, wherein the presence of the at least one genetic marker indicates that the subject is afflicted with, or at risk of, developing ONJ. | 04-16-2015 |
20150105270 | BIOMARKERS FOR INCREASED RISK OF DRUG-INDUCED LIVER INJURY FROM EXOME SEQUENCING STUDIES - The present invention provides a method for predicting the risk of a patient for developing adverse drug reactions, particularly Drug-Induced Liver Injury (DILI) or hepatotoxicity. The invention also provides a method of identifying a subject afflicted with, or at risk of, developing DILI. In some aspects, the methods comprise analyzing at least one genetic marker, wherein the presence of the at least one genetic marker indicates that the subject is afflicted with, or at risk of, developing DILI. | 04-16-2015 |
20150105271 | BIOMARKERS FOR INCREASED RISK OF DRUG-INDUCED ACUTE HYPERSENSITIVITY SYNDROME - The present disclosure provides a method for predicting the risk of a patient for developing adverse drug reactions, particularly drug-induced acute hypersensitivity syndrome (AHSS). The disclosure also provides a method of identifying a subject afflicted with, or at risk of, developing AHSS. In some aspects, the methods comprise analyzing at least one genetic marker, wherein the presence of the at least one genetic marker indicates that the subject is afflicted with, or at risk of, developing AHSS. | 04-16-2015 |
20150105272 | BIOMOLECULAR EVENTS IN CANCER REVEALED BY ATTRACTOR METAGENES - The present invention is directed to compositions and methods for the independent and unconstrained identification of attractor metagenes as surrogates of pure biomolecular events as well as the use of such attractor metagenes in performing medical diagnosis, prognosis, and developing appropriate therapeutic regimes. | 04-16-2015 |
20150105273 | REAL-TIME SEQUENCING METHODS AND SYSTEMS - The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions. | 04-16-2015 |
20150111757 | METHODS FOR DETERMINING CARRIER STATUS - The invention generally relates to methods for determining carrier status with respect to a condition or disease. In certain embodiments, the method involves exposing a sample to a plurality of molecular inversion probes capable of capturing DNA from at least one genomic region suspected of having an altered copy number and at least one internal control DNA known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the molecular inversion probes, and determining a copy number state of the at least one genomic region based on the sequence results. | 04-23-2015 |
20150111758 | GENE SIGNATURES ASSOCIATED WITH EFFICACY OF POSTMASTECTOMY RADIOTHERAPY IN BREAST CANCER - The present invention relates to compositions, kits, and methods for providing a prognosis and/or determining a treatment course of action in a subject diagnosed with breast cancer. In particular, the present invention relates to gene expression signatures useful in the prognosis, diagnosis, and treatment of breast cancer. | 04-23-2015 |
20150111759 | METHOD OF PREPARATION OF NANOPORE AND USES THEREOF - This disclosure provides systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore. In aspects, this disclosure is related to composition, method, and system for sequencing a nucleic acid using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule. | 04-23-2015 |
20150111760 | HIGHLY CONSERVED GENES AND THEIR USE TO GENERATE PROBES AND PRIMERS FOR DETECTION OF MICROORGANISMS - Provided herein are compositions and methods for the detection of | 04-23-2015 |
20150111761 | SUPER-ENHANCERS AND METHODS OF USE THEREOF - The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer). | 04-23-2015 |
20150119255 | Digital Counting of Individual Molecules by Stochastic Attachment of Diverse Labels - Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample. | 04-30-2015 |
20150119256 | Digital Counting of Individual Molecules by Stochastic Attachment of Diverse Labels - Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample. | 04-30-2015 |
20150119257 | Digital Counting of Individual Molecules by Stochastic Attachment of Diverse Labels - Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample. | 04-30-2015 |
20150119258 | Digital Counting of Individual Molecules by Stochastic Attachment of Diverse Labels - Compositions, methods and kits are disclosed for high-sensitivity single molecule digital counting by the stochastic labeling of a collection of identical molecules by attachment of a diverse set of labels. Each copy of a molecule randomly chooses from a non-depleting reservoir of diverse labels. Detection may be by a variety of methods including hybridization based or sequencing. Molecules that would otherwise be identical in information content can be labeled to create a separately detectable product that is unique or approximately unique in a collection. This stochastic transformation relaxes the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed labels are present. The methods may be used, for example, to estimate the number of separate molecules of a given type or types within a sample. | 04-30-2015 |
20150119259 | NUCLEIC ACID SEQUENCING BY NANOPORE DETECTION OF TAG MOLECULES - This disclosure provides systems and methods for sequencing nucleic acids using nucleotide analogues and translocation of tags from incorporated nucleotide analogues through a nanopore. In aspects, this disclosure is related to composition, method, and system for sequencing a nucleic acid using tag molecules and detection of translocation through a nanopore of tags released from incorporation of the molecule. | 04-30-2015 |
20150119260 | CIRCULATING CANCER BIOMARKER AND ITS USE - The present invention provides a chimera nucleic acid obtained from circulatory system for monitoring tumor status. The nucleic acid comprises partial sequence derived from host genome and partial sequence derived from non-host genome. The partial sequence derived from host genome and the partial sequence derived from non-host genome form a chimera junction. The chimera junction is obtained from cell-free nucleic acids and is indicative of disease status. | 04-30-2015 |
20150119261 | Enrichment of Target Sequences - Methods and compositions are provided for enriching for target sequences from a population of nucleic acids, that includes: combining in solution, a population of nucleic acids and a target isolation probe wherein the target isolation probe comprises an affinity binding domain; permitting a single stranded region of the target isolation probe to hybridize to all or a portion of a target sequence in the population of nucleic acids; selectively immobilizing the hybridized nucleic acids from the population containing the target sequences by associating the target isolation probe with a capture domain and removing unbound material; removing non-target sequences from the 3′ end of the target sequence by means of one or more 3′ exonucleases thereby generating a blunt ended duplex or a staggered end at the 3′ end of the target sequence; optionally ligating a 3′ duplex adaptor or a duplex end of a hairpin adaptor to the 3′ end of the target sequence and the 5′ end of the target isolation probe; extending the 3′ end of the target isolation probe to form a blunt end or a staggered end at the 5′ end of the target sequence suitable for ligating and ligating an adapter to the 5′ end of the target sequence and the 3′ extended end of the target isolation probe. | 04-30-2015 |
20150126373 | ULTRA-HIGH SENSITIVE MONITORING OF EARLY TRANSPLANTATION FAILURE - The present invention provides a method for detecting transplantation failure of a transplanted organ or cells which comprises detecting a donor-positive but recipient-negative DNA marker in the recipient's plasma using pyrophosphorolysis activated polymerization. Because of the high sensitivity, specificity and selectivity of pyrophosphorolysis activated polymerization, transplantation failure can be detected at early stages and treatment can be initiate earlier. | 05-07-2015 |
20150126374 | HYPERMETHYLATED GENE MARKERS FOR HEAD AND NECK CANCER - Methods and kits for diagnosing or predicting head and neck squamous cell carcinoma (HNSCC) and for predicting responsivity to therapeutic regimens for treating HNSCC are disclosed. | 05-07-2015 |
20150126375 | ASSEMBLY AND METHOD FOR ANALYZING NUCLEIC ACID SEQUENCES - An assembly and a method are disclosed for analyzing nucleic acid sequences by way of so-called sequencing-by-synthesis. According to an embodiment of the invention, a chemical substance group that is released when a nucleotide bonds to a nucleic acid sequence to be sequenced is detected. The reagents are applied by way of a spraying device to a sensor that detects the released substance group. This has the advantage that no lateral flow occurs. The rate of false-negative and false-positive results is significantly reduced. Furthermore, a small amount of the reagent is sufficient to completely wet the sensor. Filling of the supply and discharge lines as for a flow cell is not necessary. | 05-07-2015 |
20150126376 | COMPOSITIONS AND METHODS FOR SENSITIVE MUTATION DETECTION IN NUCLEIC ACID MOLECULES - The present disclosure provides methods for detecting mutations in a target nucleic acid molecule by rolling circle amplification of a library of double-stranded circular bar-coded template molecules. Also provided herein are methods for enriching a target nucleic acid molecule. | 05-07-2015 |
20150126377 | SELECTION OF NUCLEIC ACIDS BY SOLUTION HYBRIDIZATION TO OLIGONUCLEOTIDE BAITS - Methods of selection of nucleic acids using solution hybridization, methods of sequencing nucleic acids including such selection methods, and products for use in the methods are disclosed. | 05-07-2015 |
20150126378 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in the concentration of inorganic pyrophosphate (PPi), hydrogen ions, and nucleotide triphosphates. | 05-07-2015 |
20150133309 | Compositions and Methods for Diagnosing and Treating Neoplasia - The present invention relates to mutations associated with neoplasia, such as meningioma. Thus, the invention relates to compositions and methods useful for the assessment, characterization, classification and treatment of neoplasia, including meningioma, based upon the presence or absence of mutations that are associated with neoplasia, including meningioma. | 05-14-2015 |
20150133310 | NUCLEIC ACID SEQUENCING SYSTEMS AND METHODS - The present invention relates to systems and methods for performing isothermal amplification reactions. In particular, the present invention relates to denaturation methods for use in isothermal amplification reactions. | 05-14-2015 |
20150133311 | METHOD FOR ASSESSING ENDOMETRIOSIS - The present invention provides a diagnostic agent for endometriosis for measuring the concentration of at least one miRNA selected from the group consisting of hsa-miR-708, hsa-miR-127-3p and hsa-miR-518d-3p in a sample derived from the blood of a subject, the agent containing an amplification primer for the miRNA as a main component. The present invention also provides a method of detecting endometriosis, including a step of measuring the concentration of at least one miRNA selected, from the group consisting of hsa-miR-708, hsa-miR-127-3p and hsa-miR-518d-3p in a sample derived from the blood of the subject. The diagnostic agent for endometriosis of the present invention and the diagnostic method using the agent are simple and low invasive and have high sensitivity and specificity. | 05-14-2015 |
20150133312 | COMPOSITIONS AND METHODS FOR DETECTING RARE NUCLEIC ACID MOLECULE MUTATIONS - The present disclosure relates to compositions and methods for detecting rare nucleic acid molecule mutations in a plurality of nucleic acid molecules. Also disclosed are methods for determining the size of a nucleic acid molecule using droplet digital PCR. | 05-14-2015 |
20150133313 | METHOD FOR IDENTIFYING VARIETY OF HOP - The present invention relates to a method for identifying the variety of a hop by using an identification marker comprising at least one single nucleotide polymorphism that differs among varieties, and a method for preparing said identification marker. The present invention also provides a primer or a probe to be used in the method for identifying the variety of a hop, and a nucleic acid of a region including said identification marker. The present invention further provides a method for detecting the intrusion of different varieties in a hop sample. | 05-14-2015 |
20150133314 | REAGENTS AND METHODS FOR SEQUENCING - The disclosure provides a plurality of nucleic acid sequences comprising multiple variants of a reference sequence. The disclosure further provides plasmids, cells, methods and kits comprising the same. | 05-14-2015 |
20150133315 | CELL-BASED GENOMIC RECORDED ACCUMULATIVE MEMORY - The present invention relates to a cell based genomic Recorded Accumulative Memory (geRAM) system (also referred to herein as Genomically Encoded Memory (GEM)) for recoding data (i.e., changes in nucleic acid sequences in cellular DNA in response to physical and/or chemical signal(s)) from the cellular environment. | 05-14-2015 |
20150133316 | METHOD FOR GENOME COMPLEXITY REDUCTION AND POLYMORPHISM DETECTION - The present invention provides methods to produce a reduced representation of a genome for sequencing and DNA polymorphism detection. In particular, the invention provides PCR-based methods, with normalization of the amplified products using a duplex-specific nuclease, in order to reduce over-representation of PCR products. Oligonucleotides for use in the disclosed method are also provided. | 05-14-2015 |
20150141256 | COMPOSITIONS AND METHODS FOR BISULFITE CONVERTED SEQUENCE CAPTURE - This invention relates generally to composition and methods for characterizing a methylome which comprises all or substantially all methylation states of a genome. In particular, a plurality of oligonucleotides, each representing nearly every possible methylation state of the cytosine position of each CG dinucleotide pair within a target nucleic acid of interest, and methods of using the plurality are provided herein. | 05-21-2015 |
20150141257 | SEQUENCE CAPTURE METHOD USING SPECIALIZED CAPTURE PROBES (HEATSEQ) - The present invention is a novel protocol for the massively parallel production of improved MIPs. The molecular improvements to the MIP cover the manufacturing of the probes, the workflow, the addition of unique sequence elements which connote sample specificity, and a sequence tag which uniquely identifies a specific molecule present in the initial sample population. Lastly, this invention also is combined with an empirical optimization strategy that overcomes issues of both locus representation and allelic bias. This improved technique is scalable and can be utilized to amplify targets comprised of a single locus' amplicon up to targeting more than 1 million loci. | 05-21-2015 |
20150141258 | TARGETED DNA ENRICHMENT AND SEQUENCING - The invention relates to a method for enriching one or more target sequences of a deoxyribonucleic acid (DNA) in a composition, comprising the steps of providing a composition comprising one or more deoxyribonucleic acid (DNA) molecules, hybridizing to said one or more DNA molecules, one or more target specific ribonucleic acid (RNA) hybridization probes, thereby forming one or more RNA/DNA hybrids, capturing the RNA/DNA hybrids with one or more antibodies being specific for such RNA/DNA hybrids, thereby forming one or more RNA/DNA/antibody hybrids, isolating the one or more RNA/DNA/antibody hybrids, amplifying the one or more DNA molecules of the one or more RNA/DNA/antibody hybrids if necessary, and, optionally, sequencing the one or more DNA molecules of the one or more RNA/DNA/antibody hybrids or the amplification product, wherein the sequencing is preferably done by means of next generation sequencing. The invention also relates to a kit comprising a first an antibody which is specific for a DNA/RNA hybrid molecule, wherein optionally the antibody is bound to a magnetic particle, and additionally comprising one or more target specific RNA hybridization probes. | 05-21-2015 |
20150141259 | Aptamer-Based Multiplexed Assays - The present disclosure describes methods, devices, reagents, and kits for the detection of one or more target molecules that may be present in a test sample. The described methods, devices, kits, and reagents facilitate the detection and quantification of a non-nucleic acid target (e.g., a protein target) in a test sample by detecting and quantifying a nucleic acid (i.e., an aptamer) where the aptamer-aptamer interactions are significantly reduced or eliminated while maintaining the aptamer-target interaction. | 05-21-2015 |
20150141260 | METHODS OF DETECTING DISEASES OR CONDITIONS USING CIRCULATING DISEASED CELLS - This invention provides methods of using circulating diseased cells in the diagnosis, prognosis, or monitoring of diseases or conditions. The invention also provides methods of using circulating diseased cells to identify markers of diseases or conditions. This invention also provides methods for assessing the risk of developing a disease or condition, prognosing said disease, monitoring said disease progression or regression, assessing the efficacy of a treatment, or identifying a compound capable of ameliorating or treating said disease or condition. | 05-21-2015 |
20150141261 | HIGH THROUGHPUT SEQUENCING OF MULTIPLE TRANSCRIPTS OF A SINGLE CELL - The present disclosure generally relates to sequencing two or more genes expressed in a single cell in a high-throughput manner. More particularly, the present disclosure relates to a method for high-throughput sequencing of pairs of transcripts co expressed in single cells (e.g., antibody VH and VL coding sequence) to determine pairs of polypeptide chains that comprise immune receptors. | 05-21-2015 |
20150141262 | METHYLATION BIOMARKERS FOR BREAST CANCER - Different combinations of methylation status based biomarkers can be used to test for breast cancer with high sensitivity and high specificity. | 05-21-2015 |
20150141263 | MASSIVELY PARALLEL COMBINATORIAL GENETICS - The invention relates to methods and compositions that enable the rapid generation of high-order combinations of genetic elements, and that provide a barcoded basis for rapid characterization of the specific combination of genetic elements encoded within a single cell or in a pooled population. | 05-21-2015 |
20150141264 | IN-FIELD DNA EXTRACTION, DETECTION AND AUTHENTICATION METHODS AND SYSTEMS THEREFOR - The invention provides a method for in-field detection of a distinctive marker. The method includes providing a sample from an article of interest and analyzing the sample to detect the presence of the distinctive marker. The analysis is performed using an in-field detection instrument. The in-field detection instrument includes a microsystem configured to perform sample in-answer out analysis and detect the presence of the distinctive marker in the sample. | 05-21-2015 |
20150141265 | METHODS FOR ANALYZING LARIAT RNA - The present invention relates to compositions and methods useful for analyzing lariat RNA, which plays a role in the regulation of gene expression. A sample of RNA is specifically treated to remove linear mRNA and enrich for lariat RNA. The enriched lariat RNA sample may be analyzed further to identify introns, branch point sequences, alternative splicing patters, and gene transcription levels. The enriched lariat RNA sample may also be exploited as a detection or compound screening tool, as well as other uses. | 05-21-2015 |
20150141266 | SINGLE MOLECULE LOADING METHODS AND COMPOSITIONS - Methods, compositions and arrays for non-random loading of single analyte molecules into array structures are provided. For example, methods are presented for providing a surface comprising the plurality of array regions by exposing the surface to a solution comprising polymerase enzymes where each polymerase enzyme is bound to a binding structure having several functional moieties. The functional moieties of the binding structure react with the binding elements on the array regions such that the functional moieties on the binding structure react with other available binding sites in an array region, preventing other polymerase-binding structures from loading, and resulting in a single polymerase molecule bound to each of these regions. | 05-21-2015 |
20150141267 | INTEGRATED DEVICE WITH EXTERNAL LIGHT SOURCE FOR PROBING DETECTING AND ANALYZING MOLECULES - Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits radiation; at least one element for directing the emission radiation in a particular direction; and a light path along which the emission radiation travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the integrated device. Each sensor may detect emission radiation from a sample in a respective sample well. The instrument includes an excitation light source for exciting the sample in each sample well. | 05-21-2015 |
20150141268 | ACTIVE-SOURCE-PIXEL, INTEGRATED DEVICE FOR RAPID ANALYSIS OF BIOLOGICAL AND CHEMICAL SPECIMENS - An active-source-pixel, integrated device capable of performing biomolecule detection and/or analysis, such as single-molecule nucleic acid sequencing, is described. An active pixel of the integrated device includes a sample well into which a sample to be analyzed may diffuse, an excitation source for providing excitation energy to the sample well, and a sensor configured to detect emission from the sample. The sensor may comprise two or more segments that produce a set of signals that are analyzed to differentiate between and identify tags that are attached to, or associated with, the sample. Tag differentiation may be spectral and/or temporal based. Identification of the tags may be used to detect, analyze, and/or sequence the biomolecule. | 05-21-2015 |
20150148238 | DROPLET-BASED SURFACE MODIFICATION AND WASHING - The present invention relates to droplet-based surface modification and washing. According to one embodiment, a method of splitting a droplet is provided, the method including providing a droplet microactuator including a droplet including one or more beads and immobilizing at least one of the one or more beads. The method further includes conducting one or more droplet operations to divide the droplet to yield a set of droplets including a droplet including the one or more immobilized beads and a droplet substantially lacking the one or more immobilized beads. | 05-28-2015 |
20150291942 | MODIFIED TRANSPOSASES FOR IMPROVED INSERTION SEQUENCE BIAS AND INCREASED DNA INPUT TOLERANCE - Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same. | 10-15-2015 |
20150292001 | Methods for Standardized Sequencing of Nucleic Acids and Uses Thereof - Methods for standardized sequencing of nucleic acids and uses thereof are described. The identification of genetic information is becoming a key piece of information for the diagnosis and treatment of many diseases. In order to make such diagnostic tool readily available, it is desired that this identification be as efficient and as inexpensive as possible. | 10-15-2015 |
20150292002 | Multiplex Amplification of Polynucleotides - The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis. | 10-15-2015 |
20150292009 | Measurement and Comparison of Immune Diversity by High-Throughput Sequencing - A precise measurement of the immunological receptor diversity present in a sample is obtained by sequence analysis. Samples of interest are generally complex, comprising more than 10 | 10-15-2015 |
20150292011 | Biomarkers for Diabetes and Usages Thereof - Biomarkers for diabetes and usages thereof are provided. And the biomarkers are nucleotides having polynucleotide sequences defined in SEQ ID NOs: 1-50. | 10-15-2015 |
20150292013 | NOVEL MIRNAS AS DIAGNOSTIC MARKERS - The invention relates to novel miRNA markers useful for diagnosis or therapy of disease, in particular for neuronal disorders such as Alzheimer's Disease (AD). | 10-15-2015 |
20150292014 | METHOD AND SYSTEM TO PREDICT RESPONSE TO TREATMENTS FOR MENTAL DISORDERS - The present inventions relates to methods and assays to predict the response of an individual to psychiatric treatment and to a method to improve medical treatment of a disorder, which responsive to treatment with a psychiatric treatment. | 10-15-2015 |
20150292027 | PAPANICOLAOU TEST FOR OVARIAN AND ENDOMETRIAL CANCERS - The recently developed liquid-based Papanicolaou (Pap) smear allows not only cytologic evaluation but also collection of DNA for detection of HPV, the causative agent of cervical cancer. We tested these samples to detect somatic mutations present in rare tumor cells that might accumulate in the cervix once shed from endometrial and ovarian cancers. A panel of commonly mutated genes in endometrial and ovarian cancers was assembled and used to identify mutations in all 46 endometrial or cervical cancer tissue samples. We were able also able to identify the same mutations in the DNA from liquid Pap smears in 100% of endometrial cancers (24 of 24) and in 41% of ovarian cancers (9 of 22). We developed a sequence-based method to query mutations in 12 genes in a single liquid Pap smear without prior knowledge of the tumor's genotype. | 10-15-2015 |
20150292041 | METHODS AND COMPOSITIONS FOR IDENTIFYING ENTEROVIRUS - Certain embodiments of the invention include, but are not limited to PCR primer pairs, sequencing primers, and/or associated thermocycling protocols targeting a region identified by the inventors within the 5′ untranslated region of enteroviruses for the purpose of identifying, subtyping, and/or classifying of virus in samples using nucleic acid sequencing. The sequencing procedures can use nucleic acid templates, such as cDNA or PCR amplicons, as a template for sequencing in medium to high throughput format that is cost effective and easily deployed to other clinical microbiology laboratories. | 10-15-2015 |
20150292042 | FLAVIVIRUS ASSOCIATED WITH THEILER'S DISEASE - This disclosure relates to Theiler's disease-associated virus (“TDAV”), reagents relating thereto, and methods for detecting, using, and/or treating diseases associated with TDAV. | 10-15-2015 |
20150299753 | WHOLE GENOME AMPLIFICATION METHOD AND APPLICATION THEREOF - Provided are a whole genome sample amplification method, a whole genome sequencing method, and a method for determining whether an abnormal state occurs in a whole genome, a whole genome sample amplification apparatus, a whole genome sequencing device, and a system for determining whether an abnormal state occurs in a whole genome. The whole genome sample amplification method comprises: subjecting a whole genome sample to a first amplification reaction, so as to obtain a first amplification product; and subjecting the first amplification product to a second amplification reaction, so as to obtain a second amplification product. The first amplification reaction is one of the PCR-based amplification reaction and the isothermal amplification reaction, and the second amplification reaction is the other of the PCR-based amplification reaction and the isothermal amplification reaction. | 10-22-2015 |
20150299781 | OXIDIZING AGENT FOR MODIFIED NUCLEOTIDES - This invention relates to the use of metal (VI) oxo complexes to catalyse the selective oxidation of 5hmC residues in polynucleotides to 5fC residues. This may be useful in the identification of modified cytosine residues in a population of polynucleotides comprising a sample nucleotide sequence. A first portion of the population is oxidised with a metal (VI) oxo complex and then the first portion and a second portion of said population are both treated with bisulfite. The residues in the first and second portions that correspond to a cytosine residue in the sample nucleotide sequence are identified following treatment and the identities of these residues are used to determine the modification of the cytosine residue in the sample nucleotide sequence. Methods, reagents and kits are provided. | 10-22-2015 |
20150299786 | UNIQUELY TAGGED REARRANGED ADAPTIVE IMMUNE RECEPTOR GENES IN A COMPLEX GENE SET - Compositions and methods are disclosed for uniquely tagging each rearranged gene segment that encodes a T cell receptor (TCR) and/or an immunoglobulin (Ig), in a DNA (or mRNA or cDNA reverse transcribed therefrom) sample from lymphoid cells. These and related embodiments permit accurate, high throughput quantification of distinct TCR and/or Ig encoding sequences. Also provided are compositions and methods for quantitatively sequencing the genes that encode both chains of a TCR or Ig heterodimer in a single cell, for example, to characterize the degree of T or B cell clonality in a sample. | 10-22-2015 |
20150299787 | IMMOBILIZED BUFFER PARTICLES AND USES THEREOF - The disclosure relates to novel particle compositions and methods of making said compositions having applications in nucleic acid analysis, as well as apparatuses and systems for the same. | 10-22-2015 |
20150299791 | DNA METHYLATION BIOMARKERS OF POST-PARTUM DEPRESSION RISK - The present invention relates to the field of post-partum depression. More specifically, the present invention relates to the use of biomarkers to diagnose post-partum depression or predict a risk thereof. In a specific embodiment, a method for identifying a likelihood of PPD in a patient comprises the steps of (a) providing a sample from the patient; (b) measuring white blood cell type counts and DNA methylation levels of a panel of biomarkers in the sample collected from the patient, wherein the panel of biomarkers comprises HP1BP3 and TTC9B and the white blood cell type counts comprise monocytes and non-monocytes; and (c) identifying the patient as likely to develop PPD based on the relative DNA methylation levels at the biomarker loci relative to the ratio of monocytes:non-monocytes. | 10-22-2015 |
20150299795 | CANCER-ASSOCIATED GERM-LINE AND SOMATIC MARKERS AND USES THEREOF - The invention provides methods and compositions for identifying subjects, including canine subjects, having an elevated risk of developing cancer or having an undiagnosed cancer. These subjects are identified based on the presence of germ-line allele(s) and markers and various somatic mutations. | 10-22-2015 |
20150299800 | MONITORING MANTLE CELL LYMPHOMA CLONOTYPES IN PERIPHERAL BLOOD AFTER IMMUNOTRANSPLANT - The invention is directed to a method of monitoring a mantle cell lymphoma residual disease in an immunotransplant patient by post-treatment analysis of clonotype profiles from patient blood samples. In some embodiments, methods of the invention comprising steps of (a) treating a patient by immunotransplanting the patient with vaccine-primed autologous T cells; (b) obtaining a peripheral blood sample from the patient comprising B-cells and/or cell-free nucleic acids; (c) amplifying molecules of nucleic acid from the B-cells of the sample and/or cell-free nucleic acids in the sample, the molecules of nucleic acid comprising recombined DNA sequences from immunoglobulin genes; (d) sequencing the amplified molecules of nucleic acid to form a clonotype profile; and (e) determining from the clonotype profile a presence, absence and/or level of the one or more patient-specific clonotypes correlated with the mantle cell lymphoma, including phylogenic clonotypes thereof. | 10-22-2015 |
20150299814 | Reagents and methods for HIV coreceptor tropism genotyping - The present disclosure relates to oligonucleotide sequences for amplification primers and their use in performing nucleic acid amplifications of HIV, in particular regions that encode the V3 region of the env glycoprotein. In some embodiments the primers are used in nested PCR methods for the detection or sequencing of the V3 region of the env glycoprotein. The oligonucleotide sequences are also provided assembled as kits that can be used to detect or sequence the V3 region of the env glycoprotein. Control nucleic acids for use in methods and kits of the present disclosure are also provided. | 10-22-2015 |
20150301053 | SURROGATE FUNCTIONAL DIAGNOSTICS TEST FOR CANCER - The present invention relates to diagnostic methods that are relevant to various cancers and which comprise improvements on a BH3 profiling diagnostic method. | 10-22-2015 |
20150302143 | GENE FUSIONS AND ALTERNATIVELY SPLICED JUNCTIONS ASSOCIATED WITH BREAST CANCER - The present invention relates to gene fusions and alternative spliced junctions associated with breast cancer. The present invention also relates to novel methods of identifying gene fusions and alternative spliced junctions in RNA sequencing data. The present invention further relates to predicting prognosis of a breast cancer patient based on the number of gene fusion events. | 10-22-2015 |
20150307833 | IDENTIFICATION OF THERMOTOLERANCE GENES IN YEAST - The disclosure relates to a method for identifying genes that are important determinators of thermotolerance in yeast. The disclosure relates further to genes, identified with the method, especially specific alleles of PRP42 and the use of such alleles to increase thermotolerance. It relates further to recombinant strains transformed with such alleles. | 10-29-2015 |
20150307868 | YEAST STRAIN IMPROVEMENT METHOD - The present invention relates to a method for improving an industrial yeast strain of industrial interest, particularly a sterile hybrid strain, without resorting to recombinant DNA techniques | 10-29-2015 |
20150307920 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants. | 10-29-2015 |
20150307922 | METHOD FOR THE DIAGNOSIS OF ROSACEA - A method of characterizing specific microbiota associated with | 10-29-2015 |
20150307935 | NON-MASS DETERMINED BASE COMPOSITIONS FOR NUCLEIC ACID DETECTION - The present invention provides systems, methods, and compositions for nucleic acid detection based on non-mass determined base compositions. For example, in certain embodiments, base count data for a template nucleic acid is generated using an approach that does not measure molecular mass of the template nucleic acid (e.g., by sequencing the template nucleic acid) and a database comprising base count entries is queried to identify the target nucleic acid. In particular embodiments, sequencing is employed which is conducted in substantially real-time. | 10-29-2015 |
20150307936 | SYSTEM AND METHOD FOR DNA SEQUENCING AND BLOOD CHEMISTRY ANALYSIS - A DNA sequencing and blood chemistry analysis device is provided including one or more sensor chips and one or more sample wells, wherein each sample well is configured to form a seal with one of the sensors. The one or more sensor chips may comprise Graphene transistors, and each transistor having an associated sequencing probe. The sensor chips interact with a biological sample introduced into the sample well, wherein changes in the current, transconductance, and resistance of the Graphene transistors are indicative of a DNA binding process. Based on the associated sequencing probes, the DNA sequence present in a biological sample can be identified. | 10-29-2015 |
20150307947 | MOLECULAR PROFILING FOR CANCER - Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments that have likely benefit for a cancer, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease. The molecular profiling can be used to identify likely have lack of benefit for treating the cancer. | 10-29-2015 |
20150310165 | EFFICIENT COMPARISON OF POLYNUCLEOTIDE SEQUENCES - The disclosure relates to rapid detection of oligonucleotide sequence in a nucleic acid sequence database through the configuration of the database into rapidly searchable index classes built around perfect Hamming code oligonucleotides. | 10-29-2015 |
20150315571 | Method of Nucleic Acid Fragmentation - A method of preparing an at least partially randomly sheared library of nucleic acids is provided. The method includes the steps of providing a source of nucleic acids, randomly incorporating modified bases into the nucleic acids, and digesting the modified nucleic acids with one or more modification-dependent restriction endonucleases to produce the nucleic acid library. The practice of the method can be facilitated using a kit for performing the method. The method can be used to form nucleic acid libraries and as part of a method of next generation sequencing. | 11-05-2015 |
20150315640 | IDENTIFICATION OF THE DCPS GENE ON 11Q24.2, WHICH ENCODES THE HUMAN DECAPPING ENZYME SCAVENGER, IN NON-SYNDROMIC AUTOSOMAL RECESSIVE MENTAL RETARDATION, DIAGNOSTIC PROBES THEREOF AND METHODS OF IDENTIFYING SUBJECTS WITH SAME - Provided herein is a DCPS nucleotide sequence on 11q24.2, which encodes the human decapping enzyme scavenger, associated with non-syndromic autosomal recessive mental retardation, diagnostic probes thereof, mutant proteins encoded thereby and methods of identifying subjects with same. | 11-05-2015 |
20150315641 | NEW DIAGNOSTIC MIRNA MARKERS FOR PARKINSON DISEASE - The invention relates to methods for diagnosing Parkinson's Disease PAD) with miRNA markers. Towards the identification of biomarkers for diagnosis of PD, a comprehensive analysis of miRNA expression patterns was obtained. Significantly deregulated miRNAs were identified. | 11-05-2015 |
20150315643 | BLOOD TRANSCRIPTIONAL SIGNATURES OF ACTIVE PULMONARY TUBERCULOSIS AND SARCOIDOSIS - The present invention includes a method of determining a lung disease from a patient suspected of sarcoidosis, tuberculosis, lung cancer or pneumonia comprising: obtaining a sample from whole blood of the patient suspected of sarcoidosis, tuberculosis, lung cancer or pneumonia; detecting expression of (although not exclusive) six or more disease genes, markers, or probes selected from SEQ ID NOS.: 1 to 1446, wherein increased expression of mRNA of upregulated sarcoidosis, tuberculosis, lung cancer and pneumonia markers of SEQ ID NOS.: 1 to 1446 and/or decreased expression of mRNA of downregulated sarcoidosis, tuberculosis, lung cancer or pneumonia markers of SEQ ID NOS.: 1 to 1446 relative to the expression of the mRNAs from a normal sample; and determining the lung disease based on the expression level of the six or more disease markers of SEQ ID NOS.: 1 to 1446 based on a comparison of the expression level of sarcoidosis, tuberculosis, lung cancer, and pneumonia. | 11-05-2015 |
20150315645 | METHODS OF IDENTIFYING BIOMARKERS ASSOCIATED WITH OR CAUSATIVE OF THE PROGRESSION OF DISEASE - Provided are methods of identifying biomarkers that cause or promote progression of disease. The successful application of the methods is demonstrated by the identification of biomarkers associated with and/or causative of the onset and/or progression and/or severity and/or recurrence of glaucoma and POAG. Many of these biomarkers were not previously associated with glaucoma or POAG. Predictive methods are also described, as well as applications in prognosis, diagnosis, and therapy. Testing for onset, progression, severity, and/or recurrence can be carried out. A key advantage in at least some embodiments is that a patient can receive earlier treatment for the disease such as POAG by use of the methods, screenings, and predictions described herein. Another key advantage in at least some embodiments is that a patient can receive more personalized or particular treatment for the disease such as POAG by use of the methods, screenings, and predictions described herein. | 11-05-2015 |
20150316523 | SYSTEMS AND METHODS FOR IDENTIFYING EXPLOSIVES - A method and a system for identifying an explosive in a sample are disclosed. The method comprises receiving an explosive fingerprint defined by a set of kinetic parameters, describing a plurality of interactions between the explosive and each of a respective plurality of functional moieties. The method further comprises using a data processor for accessing a database of explosive fingerprints, and searching the database for a database fingerprint matching the received fingerprint. The system comprises a plurality of sensing devices, each comprising semiconductor nanostructures (e.g. Si nanowires) having attached thereto a functional moiety selected to interact with a nitro-containing and/or peroxide-containing explosive sample. | 11-05-2015 |
20150316555 | DEVICES AND METHODS FOR ENRICHMENT AND ALTERATION OF CIRCULATING TUMOR CELLS AND OTHER PARTICLES - The invention features devices and methods for detecting, enriching, and analyzing circulating tumor cells and other particles. The invention further features methods of diagnosing a condition, e.g., cancer, in a subject by analyzing a cellular sample from the subject. | 11-05-2015 |
20150322474 | IN VITRO PRODUCTION OF CYCLIC PEPTIDES - This invention relates to the in vitro production of cyclic peptides using cyanobacterial enzymes, such as patellamide biosynthesis enzymes. Linear peptide substrates are cyclized using an isolated cyanbacterial macrocyclase, such as PatG from | 11-12-2015 |
20150322490 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants. | 11-12-2015 |
20150322495 | COMPOSITIONS AND METHODS FOR DETECTING GASTROINTESTINAL PATHOGEN NUCLEIC ACID - Disclosed are nucleic acid oligomers, including amplification oligomers, detection probes, and combinations thereof, for detection of one or more gastrointestinal pathogens selected from | 11-12-2015 |
20150322507 | METHODS FOR SIMULTANEOUS AMPLIFICATION OF TARGET LOCI - The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons. | 11-12-2015 |
20150322508 | METHOD FOR COMPLETE TRACKING OF A SET OF BIOLOGICAL SAMPLES CONTAINING DNA OR RNA THROUGH MOLECULAR BARCODE IDENTIFICATION DURING LABORATORIAL WORKFLOW AND KIT FOR COLLECTING BIOLOGICAL SAMPLES CONTAINING DNA OR RNA - The present invention discloses a method for complete tracking of a set of biological samples containing DNA or RNA through the use of molecular barcode identification during the course of laboratorial workflow, wherein the sample is contacted with primers comprising a molecular barcode and a universal primer sequence immediately after its collection and the amplification of the target regions occurs concomitantly to the barcode insertion, in one or both ends of said target region, in the same annealing temperature through a one step PCR. Finally, the invention also discloses kits for collecting biological samples containing DNA or RNA. | 11-12-2015 |
20150322509 | GENOTYPING METHOD - The present invention relates to a genotyping method, and more particularly to an ID sequence, which is assigned to each genotype, and a multiplex genotyping method which uses the ID sequence. When pyrosequencing is performed using the ID sequence, a unique and simple pyrogram can be obtained for each genotype. Thus, the use of the ID sequence makes it possible to genotype viral genes, disease genes, bacterial genes and identification genes in a simple and efficient manner. In addition, a genotyping primer of the invention can be used in various genotyping methods which are performed using dispensation orders and sequencing methods. | 11-12-2015 |
20150322518 | BIOMARKERS FOR AUTISM SPECTRUM DISORDERS - Methods of determining the risk of ASD in an individual are provided which comprise identifying the presence of one or more genomic mutations in one or more of the genes, PTCHD1, SHANK3, NFIA, DPP6, DPP10, DYPD, GPR98, PQBP1, ZNF41 and FTSJ1. | 11-12-2015 |
20150322524 | METHODS FOR DETECTING ANEUPLOIDY - The invention generally relates to methods for determining aneuploidy of cells with respect to a control sample. In certain embodiments, the method involves exposing a sample to a plurality of probes capable of capturing DNA from at least one chromosome suspected of having an altered copy number, and at least one control DNA sample known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the probes, calculating a chromosomal read fraction; determining a sample specific scaling factor; scaling the chromosomal read fractions, normalizing the scaled read fractions, and determining a copy number state of at least one chromosome. | 11-12-2015 |
20150322526 | COMPOSITION, KIT, AND METHOD FOR DIAGNOSING ADHD RISK - Provided is a method for predicting the risk of attention deficit hyperactivity disorder (ADHD). The method comprises: 1) isolating a nucleic acid species from a biological species derived from a subject; 2) identifying the nucleotide of rs550818 single nucleotide polymorphism (SNP) in the GIT1 gene, which is the 24926101st nucleotide residue on human chromosome 17, from the nucleic acid isolated from stage 1); and 3) determining the risk of ADHD to be high when the genotype of rs550818 SNP that is identified in stage 2) carries T nucleotide; wherein the composition comprising a primer pair for amplifying a rs550818 single nucleotide polymorphism (SNP), wherein the primer pair comprises a primer having a sequence of SEQ ID NO:18 and a primer having a sequence of SEQ ID NO: 45. | 11-12-2015 |
20150322528 | BIOMARKERS ASSOCIATED WITH CDK INHIBITORS - The invention provides methods of monitoring differential gene expression of biomarkers to determine patient sensitivity to Cyclin Dependent kinase inhibitors (CDKi), methods of determining the sensitivity of a cell to a CDKi, methods of treating a patient with a CDKi and methods of screening for candidate CDKi. | 11-12-2015 |
20150324518 | Genetic Affinity of Microorganisms and Viruses - Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism. | 11-12-2015 |
20150329855 | AMPLIFICATION PRIMERS AND METHODS - The present invention provides methods, compositions, and kits for performing amplification (e.g., whole genome amplification) employing primers that have a 5′ restriction site, a 3′ random sequence (e.g., a random hexamer), and an identifiable barcode sequence. In certain embodiments, the amplification generates individual amplified sequenced that are ligated together to form concatamers containing at least two amplified sequences (e.g., not contiguous on the original target sequence) that are separated by the barcode sequences. In particular embodiments, a plurality of the concatamers are sequenced and aligned with an alignment algorithm that uses the barcode sequences to identify artificial junctions between amplified sequences. | 11-19-2015 |
20150329903 | PREDICTING RESISTANCE TO DISEASE - The Invention relates to a method of predicting resistance to infectious pancreatic necrosis in salmon, the method comprising determining the alleles present at a DNA polymorphism in the salmon and predicting whether or not the salmon is resistant to infectious pancreatic necrosis based on the determination of the alleles. The invention also relates to a method of selecting a salmon for use as broodstock, wherein the salmon is selected based on the prediction by the first method that the salmon will have resistance to infectious pancreatic necrosis. | 11-19-2015 |
20150329904 | METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis. | 11-19-2015 |
20150329911 | NUCLEIC ACID BIOMARKERS FOR PROSTATE CANCER - This invention relates to microRNA biomarkers useful in the diagnosis and prognosis of prostate cancer. The biomarkers are also useful for the monitoring and/or treatment of prostate cancer. | 11-19-2015 |
20150336068 | CREATION OF LIBRARIES OF DROPLETS AND RELATED SPECIES - The present invention is generally related to systems and methods for producing a plurality of droplets. The droplets may contain varying species, e.g., for use as a library. In some cases, the fluidic droplets may be rigidified to form rigidified droplets (e.g., gel droplets). In certain embodiments, the droplets may undergo a phase change (e.g., from rigidified droplets to fluidized droplets), as discussed more herein. In some cases, a species may be added internally to a droplet by exposing the droplet to a fluid comprising a plurality of species. | 11-26-2015 |
20150336070 | CREATION OF LIBRARIES OF DROPLETS AND RELATED SPECIES - The present invention is generally related to systems and methods for producing a plurality of droplets. The droplets may contain varying species, e.g., for use as a library. In some cases, the fluidic droplets may be rigidified to form rigidified droplets (e.g., gel droplets). In certain embodiments, the droplets may undergo a phase change (e.g., from rigidified droplets to fluidized droplets), as discussed more herein. In some cases, a species may be added internally to a droplet by exposing the droplet to a fluid comprising a plurality of species. | 11-26-2015 |
20150336071 | CREATION OF LIBRARIES OF DROPLETS AND RELATED SPECIES - The present invention is generally related to systems and methods for producing a plurality of droplets. The droplets may contain varying species, e.g., for use as a library. In some cases, the fluidic droplets may be rigidified to form rigidified droplets (e.g., gel droplets). In certain embodiments, the droplets may undergo a phase change (e.g., from rigidified droplets to fluidized droplets), as discussed more herein. In some cases, a species may be added internally to a droplet by exposing the droplet to a fluid comprising a plurality of species. | 11-26-2015 |
20150337295 | INTEGRATED SINGLE CELL SEQUENCING - This disclosure provides a method of forming tagged nucleic acid sequences. A target polynucleotide is immobilized on a solid support; a recognition-oligonucleotide is hybridized thereto; the recognition-oligonucleotide-target polynucleotide hybrid is cleaved; and an adapter nucleic acid is ligated to the cleaved target polynucleotide, thereby forming a tagged nucleic acid sequence. Also provided is a method of forming a tagged single stranded cDNA; a method of forming a plurality of tagged heterogeneous nucleic acid sequences; a library of recognition-oligonucleotides; and methods for amplifying a cDNA sequence immobilized on a solid support. These methods and products can be used alone or in combination for integrated single cell sequencing, and can be adapted for use in a microfluidic apparatus or device. | 11-26-2015 |
20150337296 | Arrays and Methods of Use - Methods are provided for producing a molecular array comprising a plurality of molecules immoblised to a solid substrate at a density which allows individual immobilised molecules to be individually resolved, wherein each individual molecule in the array is spatially addressable and the identity of each molecule is known or determined prior to immobilization. The use of spatially addressable low density molecular arrays in single molecule detection and analysis techniques is also provided. Novel assays and methods are also provided. | 11-26-2015 |
20150337299 | Methods and Apparatuses for Nucleic Acid Shearing by Sonication - Methods and kits for preparing nucleic acid fragments from a sample of purified nucleic acid are provided. Alternatively, chromatin or other long polymers can be sheared with similar methods and kits. | 11-26-2015 |
20150337368 | METHODS AND PRIMER SETS FOR HIGH THROUGHPUT PCR SEQUENCING - The invention relates to a method for amplifying a target nucleic acid sequence t | 11-26-2015 |
20150337369 | SINGLE CELL ANALYSIS OF T CELLS USING HIGH-THROUGHPUT MULTIPLEX AMPLIFICATION AND DEEP SEQUENCING - Methods and oligonucleotide reagents for analyzing individual T cells are disclosed. In particular, the present disclosure provides methods for analyzing individual T cells using high-throughput multiplex amplification and deep sequencing of nucleic acids encoding T cell receptors (TCRs) and various other T cell phenotypic markers. The present disclosure further provides methods of reconstituting TCRs from individual T cells for functional studies, ligand discovery, or screening therapeutics. | 11-26-2015 |
20150337376 | Core Transcriptional Circuitry in Human Cells and Methods of Use Thereof - Disclosed herein are methods for identifying the core regulatory circuitry or cell identity program of a cell or tissue, and related methods of diagnoses, screening, and treatment involving the core regulatory circuitry and/or cell identity programs identified using the methods. | 11-26-2015 |
20150337383 | METHOD OF USING FOXO3A POLYMORPHISMS AND HAPLOTYPES TO PREDICT AND PROMOTE HEALTHY AGING AND LONGEVITY - The invention provides methods and compositions relating to identification and use of genetic information from the FOXO3A gene that can be used for determining and increasing an individual's likelihood of longevity and of retaining physical and cognitive function during aging, and for determining and decreasing an individual's likelihood of developing a cardiovascular-, metabolic- or age-related disease, including coronary artery (heart) disease, stroke, cancer, chronic pulmonary disease, diabetes, Parkinson's disease and dementia. | 11-26-2015 |
20150338428 | SYSTEMS AND METHODS FOR MULTI-ANALYSIS - Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample. | 11-26-2015 |
20150344516 | LABELLED NUCLEOTIDES - The invention provides a nucleotide or nucleoside having a base attached to a detectable label via a cleavable linker, characterised in that the cleavable linker contains a moiety selected from the group comprising: Formula (I) (wherein X is selected from the group comprising O, S, NH and NQ wherein Q is a C | 12-03-2015 |
20150344873 | Whole Genome Mapping by DNA Sequencing With Linked-Paired-End Library - The present invention relates to innovative means of generating sequence-linked DNA fragments and subsequent uses of such linked DNA fragments for de novo haplotype-resolved whole genome mapping and massively parallel sequencing. In various embodiments described herein, the methods of the invention relate to methods of generating paired-end nucleic acid fragment sharing common linker nucleic acid sequences using a nicking endonuclease, a T7 endonuclease, a restriction enzyme, or a transposase, methods of analyzing the nucleotides sequences from the linked-paired-end sequenced fragments, and methods of de novo whole genome mapping. Thus, the methods of this invention allow establishing sequence contiguity across the whole genome, and achieving high-quality, low-cost de novo assembly of complex genomes. | 12-03-2015 |
20150344938 | MULTIPLEX TRANSCRIPTOME ANALYSIS - In some embodiments, the disclosure relates generally to methods, compositions, systems, apparatuses and kits comprising a multiplex nucleic acid amplification reaction that employs a plurality (e.g., hundreds, thousands, tens-of-thousands or hundreds-of-thousands) of different target-specific primer pairs that enable substantially simultaneous amplification of a plurality of different target sequences-of-interest in a single reaction mixture. In some embodiments, the multiplex nucleic acid amplification reaction generates a plurality of amplicons having sequences derived from a sample containing RNA or DNA, including whole transcriptome or genomic samples. In some embodiments, the sequences and abundances of at least some of the plurality of amplicons are characterized, optionally simultaneously or through a single assay, by suitable detection methods, including sequencing or other procedures known in the art. | 12-03-2015 |
20150344942 | METHODS AND PRODUCT FOR OPTIMISING LOCALISED OR SPATIAL DETECTION OF GENE EXPRESSION IN A TISSUE SAMPLE - The present invention relates to methods and products for localized or spatial detection and/or analysis of RNA in a tissue sample or a portion thereof, comprising: (a) providing an object substrate on which at least one species of capture probe, comprising a capture domain, is directly or indirectly immobilized such that the probes are oriented to have a free 3′ end to enable said probe to function as a reverse transcriptase (RT) primer; (b) contacting said substrate with a tissue sample and allowing RNA of the tissue sample to hybridise to the capture probes; (c) generating cDNA molecules from the captured RNA molecules using said capture probes as RT primers; (d) labelling the cDNA molecules generated in step (c), wherein said labelling step may be contemporaneous with, or subsequent to, said generating step; (e) detecting a signal from the labelled cDNA molecules; and optionally (f) imaging the tissue sample, wherein the tissue sample is imaged before or after step (c). | 12-03-2015 |
20150344947 | GENOTYPING BY NEXT-GENERATION SEQUENCING - Provided herein is technology relating to genotyping and particularly, but not exclusively, to methods for genotyping one or more organisms by genome sequencing. | 12-03-2015 |
20150344956 | Methods For The Diagnosis Of Fetal Abnormalities - The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g. fetal cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject, e.g. a fetus by analyzing a cellular sample from the subject. | 12-03-2015 |
20150346149 | BIOCHEMICAL ANALYSIS INSTRUMENT - An analysis instrument comprises plural modules connected together over a data network, each module comprising an analysis apparatus operable to perform biochemical analysis of a sample. Each module comprises a control unit that controls the operation of the analysis apparatus. The control units are addressable to select an arbitrary number of modules to operate as a cluster for performing a common biochemical analysis. The control units communicate over the data network, repeatedly during the performance of the common biochemical analysis, to determine the operation of the analysis apparatus of each module required to meet the global performance targets, on the basis of measures of performance derived from the output data produced by the modules. The arrangement of the instrument as modules interacting in this manner provides a scalable analysis instrument. | 12-03-2015 |
20150346228 | GENETIC TESTING DEVICE, GENETIC TESTING METHOD AND PROGRAM - In the past, genetic testing systems for exclusive use were needed due to the difference in type or property of specimens. Therefore, a genetic testing system includes: an extraction unit; an assay preparation unit; a reading unit; a first conveying mechanism for conveying a sample among the extraction unit, the assay preparation unit, and the reading unit; multiple sample loading units which are provided corresponding to at least two units of the extraction unit, the assay preparation unit, and the reading unit; and multiple second conveying mechanisms which are provided corresponding to the multiple sample loading units and convey test samples to the inside of the system from the sample loading units. | 12-03-2015 |
20150353926 | POLYNUCLEOTIDE MODIFICATION ON SOLID SUPPORT - The present disclosure relates to the field of molecular biology and more specifically to methods for capturing and amplifying target polynucleotides on a solid surface. | 12-10-2015 |
20150353991 | MIRNA TARGETS - The present invention provides systems and methods for identifying, isolating, and/or characterizing microRNAs, their targets, and microRNA response elements, and for predicting their biological function. | 12-10-2015 |
20150353994 | BI-DIRECTIONAL SEQUENCING COMPOSITIONS AND METHODS - In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template, In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis. | 12-10-2015 |
20150354000 | METHOD OF ANALYSIS OF COMPOSITION OF NUCLEIC ACID MIXTURES - When sequencing is used for the analysis of composition of nucleic acid mixtures with a large dynamic range of concentrations of individual components, the reliability of results significantly differs for abundant and rare components. The present invention relates to methods for analysis of concentrations of components of nucleic acid mixtures by sequencing, wherein relative abundances of at least two components for which concentrations should be measured is changed before sequencing in a reproducible way using locus-specific oligonucleotides. | 12-10-2015 |
20150354002 | Identification of Traits Associated with DNA Samples Using Epigenetic-Based Patterns Detected Via Massively Parallel Sequencing - Illustrative embodiments of systems and methods for the identification of traits associated with DNA samples using epigenetic-based patterns detected via massively parallel sequencing (MPS) are disclosed. Illustrative embodiments may involve digesting a DNA sample with a methylation-dependent endonuclease, amplifying loci of the digested DNA sample (including a positive control locus that does not contain a restriction site for the methylation-dependent endonuclease) using a multiplex PCR to produce amplicons, sequencing the amplicons using an MPS instrument to generate sequence reads, determining a sequence count for each of the loci by comparing each of the sequence reads to reference sequences, normalizing the sequence count for each of the loci to the sequence count of the positive control locus, and identifying a trait associated with the DNA sample by applying a classification algorithm to the normalized sequence counts. | 12-10-2015 |
20150354003 | METHODS FOR ANALYZING NUCLEIC ACIDS - The invention generally relates to methods for analyzing nucleic acids. In certain aspects, methods of the invention involve obtaining a sample including a nucleic acid template. A plurality of molecular inversion probes are tiled across a portion of the template. The probes are designed such that immediately adjacent probes hybridize to opposite strands of the nucleic acid template and probes on the same strand hybridize to the template in an overlapping manner. A region between targeting arms of a plurality of the molecular inversion probes is filled-in with nucleotides, and the filled-in region of a plurality of the probes is analyzed to obtain sequence information about the nucleic acid template. | 12-10-2015 |
20150354006 | MARKERS FOR ACUTE LYMPHOBLASTIC LEUKEMIA - The invention provides methods of detecting a NSD2 mutation in a cancer cell, methods cancer diagnosis and methods of screening for NSD2 inhibitors. | 12-10-2015 |
20150354009 | COLORECTAL CANCER CLASSIFICATION WITH DIFFERENTIAL PROGNOSIS AND PERSONALIZED THERAPEUTIC RESPONSES - The present invention relates to gene sets, the expression levels of which are useful for classifying colorectal tumors and predicting disease-free prognosis and response of patients to specific therapies that are either novel or currently available in the clinics for colorectal cancer patients. | 12-10-2015 |
20150354010 | MARKERS FOR BREAST CANCER - Correlations between polymorphisms and breast cancer are provided. Methods of diagnosing, prognosing, and treating breast cancer are provided. Systems and kits for diagnosis, prognosis and treatment of breast cancer are provided. Methods of identifying breast cancer modulators are also described. | 12-10-2015 |
20150354013 | DETECTING NEOPLASM - This document relates to methods and materials for detecting premalignant and malignant neoplasms. For example, methods and materials for determining whether or not a stool sample from a mammal contains nucleic acid markers or polypeptide markers of a neoplasm are provided. | 12-10-2015 |
20150355189 | QUANTITATIVE ANALYSIS OF TRANSGENIC PROTEIN 5-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE - The invention relates to methods for quantitative multiplex analysis of complex protein samples from plants using mass spectroscopy. In some embodiments, the disclosure concerns methods for maintaining a transgenic plant variety, for example by analyzing generations of a transgenic plant variety for selective and sensitive quantitation of multiplexed transgenic proteins. | 12-10-2015 |
20150360194 | Enrichment of DNA Sequencing Libraries from Samples Containing Small Amounts of Target DNA - Provided herein is a method for capturing DNA molecules in solution. The method may comprise: extracting DNA from a sample that comprises endogenous DNA and environmental DNA to produce extracted DNA; ligating universal adaptors to the extracted DNA; hybridizing the extracted DNA, in solution, with affinity-tagged RNA probes generated by: in vitro transcribing a library of fragmented reference genomic DNA that has been ligated to an RNA promoter adaptor, in the presence of an affinity-tagged ribonucleotide; binding the product with a capture agent that is tethered to a substrate in the presence of RNA oligonucleotides that are complementary to the adaptors, thereby capturing the hybridized DNA molecules on the substrate; washing the substrate to remove any unbound DNA molecules; and releasing the captured DNA molecules. A kit for performing the method is also provided. | 12-17-2015 |
20150361502 | METHOD FOR SCREENING CANCER - Disclosed in the present invention is a method for screening cancer, comprising the following steps: (1) providing a specimen to be detected; (2) detecting the methylation status of CpG sequence of at least one target gene which is at least one of ADRA1D, AJAP1, HS3ST2, MAGI2, POU4F2, POU4F3, PTGDR, SOX17 and SYT9 in genomic DNA of the specimen; (3) determining whether cancer or precancerous lesions are present in the specimen according to the methylation status of at least one target gene. | 12-17-2015 |
20150361507 | TERT PROMOTER MUTATIONS IN GLIOMAS AND A SUBSET OF TUMORS - We surveyed 1,230 tumors of 60 different types and found that tumors could be divided into types with low (<15%) and high (≧15%) frequencies of TERT promoter mutations. The nine TERT-high tumor types almost always originated in tissues with relatively low rates of self renewal, including melanomas, liposarcomas, hepatocellular carcinomas, urothelial carcinomas, squamous cell carcinomas of the tongue, medulloblastomas, and subtypes of gliomas (including 83% of primary glioblastoma, the most common brain tumor type). TERT and ATRX mutations were mutually exclusive, suggesting that these two genetic mechanisms confer equivalent selective growth advantages. In addition to their implications for understanding the relationship between telomeres and tumorigenesis, TERT mutations provide a biomarker for the early detection of urinary tract and liver tumors and aid in the classification and prognostication of brain tumors. | 12-17-2015 |
20150361509 | DIAGNOSIS OF MELANOMA AND SOLAR LENTIGO BY NUCLEIC ACID ANALYSIS - The present invention provides methods for diagnosing melanoma and/or solar lentigo in a subject by analyzing nucleic acid molecules obtained from the subject. The present invention also provides methods for distinguishing melanoma from solar lentigo and/or dysplastic nevi and/or normal pigmented skin. The methods include analyzing expression or mutations in epidermal samples, of one or more skin markers. The methods can include the use of a microarray to analyze gene or protein profiles from a sample | 12-17-2015 |
20150361510 | GENES/GENETIC ELEMENTS ASSOCIATED WITH MATING IMPAIRMENT IN TRICHODERMA REESEI QM6A AND ITS DERIVATIVES AND PROCESS FOR THEIR IDENTIFICATION - The invention relates to a process for identifying gene(s)/genetic element(s) associated with mating impairment in strains of | 12-17-2015 |
20150368694 | METHODS FOR CLOSED CHROMATIN MAPPING AND DNA METHYLATION ANALYSIS FOR SINGLE CELLS - Methods of identifying DNase I Hyper-Resistant Sites (DHRS), or in board sense, highly compact chromatin and characterizing the DNA methylation status of DMRs such as CpG islands and CpG island shores are provided. The methods are particularly useful for analysis of genomic DNA from low quantities of cells, for example, less than 1,000 cells, less than 100 cells, less than 10 cells, or even one cell, and can be used to generate chromatin and methylation profiles. The downstream analyses include in parallel massive sequencing, microarray, PCR and Sanger sequencing, hybridization and other platforms. These methods can be used to generate chromatin and DNA methylation profiles in drug development, diagnostics, and therapeutic applications are also provided. | 12-24-2015 |
20150368708 | SYSTEMS AND METHODS TO DETECT RARE MUTATIONS AND COPY NUMBER VARIATION - The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease. | 12-24-2015 |
20150368709 | Method and Kit for Detecting a Wild-Type and/or a Mutated Target DNA Sequence - The present invention relates to a method for detecting a first and/or a second target DNA sequence from a DNA library, differing in that a mutation generates/eliminates a restriction site for a restriction endonuclease, comprising the steps of: (a) providing the DNA library, in which each of the DNA sequences comprises a first sequence segment, a second sequence segment of genomic DNA as cleaved by the restriction endonuclease, and a third sequence segment reverse complementary to the union of said first sequence segment and | 12-24-2015 |
20150368719 | DENDRITIC CELL RESPONSE GENE EXPRESSION, COMPOSITIONS OF MATTERS AND METHODS OF USE THEREOF - This invention relates generally to compositions and methods for identifying the regulatory network that modulates, controls or otherwise influences dendritic cell (DC) response(s), for example, dendritic cell maturation, dendritic cell antiviral response(s) and/or dendritic cell inflammatory response(s), as well compositions and methods for exploiting the regulatory network that modulates, controls or otherwise influences dendritic cell response(s) in a variety of therapeutic and/or diagnostic indications. | 12-24-2015 |
20150368720 | METHODS AND COMPOSITIONS OF PREDICTING ACTIVITY OF RETINOID X RECEPTOR MODULATOR - The present invention describes genomic biomarkers that have been discovered to correlate with varied individual responses (efficacy, adverse effect, and other end points) to therapeutic retinoid X receptor modulator, such as bexarotene, in treating diseases such as, non small cell lung cancer. The newly discovered biomarkers and others in linkage disequilibrium with them can be used in companion diagnostic tests which can help to predict drug responses and apply drugs only to those who will be benefited, or exclude those who might have adverse effects, by the treatment. | 12-24-2015 |
20150376691 | RAPID ANEUPLOIDY DETECTION - Massively parallel sequencing of cell-free, maternal plasma DNA was recently demonstrated to be a safe and effective screening method for fetal chromosomal aneuploidies. Here, we report an improved sequencing method achieving significantly increased throughput and decreased cost by replacing laborious sequencing library preparation steps with PCR employing a single primer pair. Using this approach, samples containing as little as 4% trisomy 21 DNA could be readily distinguished from euploid samples. | 12-31-2015 |
20150376692 | SYSTEMS AND METHODS FOR BIOLOGICAL ANALYSIS - Provided herein are devices and methods suitable for sequencing, amplifying, analyzing, and performing sample preparation procedures for nucleic acids and other biomolecules. | 12-31-2015 |
20150376694 | Integrated Analytical System and Method - An analytical assembly within a unified device structure for integration into an analytical system. The analytical assembly is scalable and includes a plurality of analytical devices, each of which includes a reaction cell, an optical sensor, and at least one optical element positioned in optical communication with both the reaction cell and the sensor and which delivers optical signals from the cell to the sensor. Additional elements are optionally integrated into the analytical assembly. Methods for forming and operating the analytical system are also disclosed. | 12-31-2015 |
20150376704 | BIOMARKER ASSAY FOR DIAGNOSIS AND CLASSIFICATION OF CARDIOVASCULAR DISEASE - The disclosed methods, assays and kits identify biomarkers, particularly miRNA and/or protein biomarkers, for assessing the cardiovascular health of a human. In certain embodiments, methods, assays and kits, circulating miRNA and/or protein biomarkers are identified for assessing the cardiovascular health of a human. | 12-31-2015 |
20150376705 | METHOD TO PREDICT THE PATTERN OF LOCOMOTION IN HORSES - The present invention provides methods for predicting the pattern of locomotion in a horse including the ability of a horse to use different gaits and the ability to trot at a fast speed. The methods comprise determining in a sample of DNA obtained from a horse the presence or absence of at least one genetic marker, wherein said at least one genetic marker is located on horse chromosome 23, said marker being associated with the ability to use different gaits. The invention further provides primers that amplify markers being associated with the ability to use different gaits and hybridization probes to detect markers being associated with the ability to use different gaits and the ability to trot at a fast speed. | 12-31-2015 |
20150376717 | METHODS AND KITS FOR DETECTING MELANOMA - This invention is directed to a method for detecting melanoma in a tissue sample by measuring a level of methylation of one or more regulatory elements differentially methylated in melanoma and benign nevi. The invention provides methods for detecting melanoma, related kits, and methods of screening for compounds to prevent or treat melanoma. | 12-31-2015 |
20160002719 | LABELLED NUCLEOTIDES - Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group. | 01-07-2016 |
20160002720 | Enrichment of Target Sequences - Methods and compositions are provided for enriching for target sequences from a population of nucleic acids, that includes combining in solution, a population of nucleic acids and a target isolation probe wherein the target isolation probe includes an affinity binding domain; permitting a single stranded region of the target isolation probe to hybridize to all or a portion of a target sequence in the population of nucleic acids; selectively immobilizing the hybridized nucleic acids from the population containing the target sequences by associating the target isolation probe with a capture domain and removing unbound material; and removing from the 3′ end of the target sequence, a non-target sequence by means of one or more 3′ single strand specific exonucleases. Target enrichment may be used to detect variations in nucleotide sequence for detecting phenotypic changes related to health or disease. | 01-07-2016 |
20160002729 | RISK CALCULATION FOR EVALUATION OF FETAL ANEUPLOIDY - The present invention provides processes for determining accurate risk probabilities for fetal aneuploidies. Specifically, the invention provides non-invasive evaluation of genomic variations through chromosome-selective sequencing and non-host fraction data analysis of maternal samples. | 01-07-2016 |
20160002731 | IMMUNOCOMPETENCE ASSESSMENT BY ADAPTIVE IMMUNE RECEPTOR DIVERSITY AND CLONALITY CHARACTERIZATION - Disclosed are methods for determining the immunological status of the adaptive immune system of a subject by identifying and quantifying rearranged DNA (and/or subsequently transcribed RNA) sequences encoding T cell receptor (TCR) and/or immunoglobulin (IG) polypeptides, in a lymphoid DNA-containing sample from the subject. TCR and/or IG sequence diversity and sequence distribution permit immunocompetence and immune repertoire assessment and reflect the degree of T cell or B cell clonality and clonal expansion in the sample. Methods for stratifying patient populations on the basis of immunocompetence including likelihood of responding to immunotherapy are also described. | 01-07-2016 |
20160002737 | Analysis of Rare Cell-Enriched Samples - The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g., epithelial cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject by analyzing a cellular sample from the subject. | 01-07-2016 |
20160002739 | PROSTATE CANCER ASSOCIATED CIRCULATING NUCLEIC ACID BIOMARKERS - The invention provides methods and reagents for diagnosing prostate cancer that are based on the detection of biomarkers in the circulating nucleic acids from a patient to be evaluated. | 01-07-2016 |
20160003844 | SCREENING AND ENGINEERING METHOD OF SUPER-STABLE IMMUNOGLOBULIN VARIABLE DOMAINS AND THEIR USES - There are provided a method named Tat-associated protein engineering (TAPE), of screening a target protein having higher solubility and excellent thermostability, in particular, an immunoglobulin variable domain (VH or VL) derived from human germ cells, by preparing a gene construct where the target protein and an antibiotic-resistant protein are linked to a Tat signal sequence, and then expressing this within | 01-07-2016 |
20160003849 | Diagnostic Method for Diagnosing Depression and Monitoring Therapy Effectiveness - The present invention relates to new biomarkers and new sets of biomarkers for diagnosing a mood disorder, preferably depression or monitoring the effectiveness of therapy for said mood disorder. | 01-07-2016 |
20160010150 | SINGLE MOLECULE SEQUENCING WITH TWO DISTINCT CHEMISTRY STEPS | 01-14-2016 |
20160010163 | DUAL SEQUENCE-CAPTURE METHOD FOR QUANTIFYING TRANS RENAL HPV DNA IN URINE | 01-14-2016 |
20160011215 | SYSTEMS AND METHODS FOR MULTI-ANALYSIS | 01-14-2016 |
20160011225 | SYSTEMS AND METHODS FOR MULTI-ANALYSIS | 01-14-2016 |
20160012180 | GENETIC ADDICTION RISK ANALYSIS FOR RDS SEVERITY INDEX | 01-14-2016 |
20160016140 | Integrated Analysis System - The invention provides systems, devices, methods, and kits for performing an integrated analysis. The integrated analysis can include sample processing, library construction, amplification, and sequencing. The integrated analysis can be performed within one or more modules that are fluidically connected to each other. The one or more modules can be controlled and/or automated by a computer. The integrated analysis can be performed on a tissue sample, a clinical sample, or an environmental sample. The integrated analysis system can have a compact format and return results within a designated period of time. | 01-21-2016 |
20160017396 | POLYNUCLEOTIDE ENRICHMENT USING CRISPR-CAS SYSTEMS - A method for enriching a target nucleic acid comprising providing an endonuclease system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid; contacting the target nucleic acid with the endonuclease system to form a complex; and separating the complex and thereby enriching for the target nucleic acid. | 01-21-2016 |
20160017412 | NON-INVASIVE PRENATAL DIAGNOSIS OF FETAL GENETIC CONDITION USING CELLULAR DNA AND CELL FREE DNA - Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother. In various embodiments, the method can determine one or more sequences of interest in a test sample that comprises a mixture of maternal cellular DNA and mother-and-fetus cfDNA. In some embodiments, methods are provided for determining whether the fetus has a genetic disease. In some embodiments, methods are provided for determining whether the fetus is homozygous in a disease causing allele when the mother is heterozygous of the same allele. In some embodiments, methods are provided for determining whether the fetus has a copy number variation (CNV) or a non-CNV genetic sequence anomaly. | 01-21-2016 |
20160017415 | METHODS AND KITS FOR IDENTIFYING AND ADJUSTING FOR BIAS IN SEQUENCING OF POLYNUCLEOTIDE SAMPLES - Disclosed are methods for determining one or more nucleotides at one or more nucleotide positions of a polynucleotide sample, the polynucleotide sample comprising heterogeneous polynucleotides having different nucleotides at the nucleotide positions. The disclosed, methods may be utilized to control for sequencing bias during sequencing of the polynucleotide sample. Suitable samples may include patient samples for use in diagnosing, prognosing, and treating the patient. | 01-21-2016 |
20160017417 | METHODS AND SYSTEMS FOR GENETIC ANALYSIS - This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions. | 01-21-2016 |
20160017419 | METHYLATION PATTERN ANALYSIS OF TISSUES IN A DNA MIXTURE - The contributions of different tissues to a DNA mixture are determined using methylation levels at particular genomic sites. Tissue-specific methylation levels of M tissue types can be used to deconvolve mixture methylation levels measured in the DNA mixture, to determine fraction contributions of each of the M tissue types. Various types of genomic sites can be chosen to have particular properties across tissue types and across individuals, so as to provide increased accuracy in determining contributions of the various tissue types. The fractional contributions can be used to detect abnormal contributions of a particular tissue, indicating a disease state for the tissue. A differential in fractional contributions for different sizes of DNA fragments can also be used to identify a diseased state of a particular tissue. A sequence imbalance for a particular chromosomal region can be detected in a particular tissue, e.g., identifying a location of a tumor. | 01-21-2016 |
20160017420 | METHODS FOR PROFILING AND QUANTITATING CELL-FREE RNA - The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected. | 01-21-2016 |
20160017421 | NON-INVASIVE EARLY DETECTION OF SOLID ORGAN TRANSPLANT REJECTION BY QUANTITATIVE ANALYSIS OF HLA GENE AMPLICONS - The invention is a method of detecting or assessing solid organ graft (transplant) rejection and acute dysfunction—no rejection condition by detecting donor-specific HLA alleles in a blood sample of a graft (transplant) recipient. | 01-21-2016 |
20160017425 | Detection of Genomic Rearrangements by Sequence Capture - Provided herein is a method of sample analysis. In some embodiments, the method comprises hybridizing fragmented genomic DNA from a test genome with a population of first oligonucleotides of the formula V | 01-21-2016 |
20160017426 | METHODS AND SYSTEMS FOR ASSESSING INFERTILITY AND RELATED PATHOLOGIES - Methods for assessing infertility and related pathologies and informing treatment type and timing thereof are provided. According to certain embodiments, methods of the invention include determining levels of one or more transcripts present in a sample obtained from a subject suspected of having endometriosis, identifying transcript levels that correspond to a regulation pattern specific to a time-point in a uterine cycle, and characterizing endometriosis of the subject based upon the identified transcript levels. The invention includes methods for assessing age-associated increase in aneuploidy rates based on FSH levels and IVF success rates based on obesity in PCOS patients. | 01-21-2016 |
20160017427 | TREATING FEMALE PELVIC ORGAN PROLAPSE - Provided are methods for diagnosing an increased risk of failure in a female pelvic organ prolapse surgery. Also provided are devices and kits for detection of a SNP associated with increased risk of failure in a female pelvic organ prolapse surgery. | 01-21-2016 |
20160017436 | ARTIFICIAL SYNTHETIC CDNA AND METHOD FOR DETECTING SECONDARY GLIOBLASTOMA - The present invention provides an artificial synthetic cDNA (complementary deoxyribonucleic acid). The said artificial synthetic cDNA encodes a fused protein which is specifically presented in secondary glioblastoma, and the said artificial synthetic cDNA can be used as a biomarker for detecting the secondary glioblastoma. The present invention further provides a method for detecting secondary glioblastoma. According to the above technical solutions, the accuracy in distinguishing the secondary glioblastoma from primary glioblastoma is effectively improved in the present invention. | 01-21-2016 |
20160018400 | DIAGNOSTIC AND PROGNOSTIC BIOMARKERS FOR PROSTATE CANCER AND OTHER DISORDERS - The present invention relates to the use of VPS28 and/or VPS13A as biomarkers for diagnosing prostate cancer, prostate intraepithelial neoplasia (PIN) or atypical small acinar proliferation (ASAP) and to the use of VPS13A, VPS28 and/or NAALADL2 as biomarkers for predicting the prognosis of prostate cancer. The invention also relates to the use of VPS13A, VPS28 and/or NAALADL2 as biomarkers for determining the grade or pathological stage of prostate cancer and monitoring progression of prostate cancer. In addition, the invention relates to the use of NAALADL2 as a biomarker for diagnosing colon, pancreatic or breast cancer. Assays, systems and storage media based on the use of these biomarkers are also provided. | 01-21-2016 |
20160024493 | UNIQUELY TAGGED REARRANGED ADAPTIVE IMMUNE RECEPTOR GENES IN A COMPLEX GENE SET - Compositions and methods are disclosed for uniquely tagging each rearranged gene segment that encodes a T cell receptor (TCR) and/or an immunoglobulin (Ig), in a DNA (or mRNA or cDNA reverse transcribed therefrom) sample from lymphoid cells. These and related embodiments permit accurate, high throughput quantification of distinct TCR and/or Ig encoding sequences. Also provided are compositions and methods for quantitatively sequencing the genes that encode both chains of a TCR or Ig heterodimer in a single cell, for example, to characterize the degree of T or B cell clonality in a sample. | 01-28-2016 |
20160024556 | ENRICHMENT AND NEXT GENERATION SEQUENCING OF TOTAL NUCLEIC ACID COMPRISING BOTH GENOMIC DNA AND cDNA - The present invention relates to methods of enriching and sequencing a mixture of nucleic acids comprising genomic DNA sequences and cDNA sequences obtained from the test sample. | 01-28-2016 |
20160024564 | METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING - Disclosed herein are methods for determining the copy number of a chromosome in a fetus in the context of non-invasive prenatal diagnosis. In an embodiment, the measured genetic data from a sample of genetic material that contains both fetal DNA and maternal DNA is analyzed, along with the genetic data from the biological parents of the fetus, and the copy number of the chromosome of interest is determined. In an embodiment, the maternal serum is measured using a single-nucleotide polymorphism (SNP) microarray, along with parental genomic data, and the determination of the chromosome copy number is used to make clinical decisions pertaining to the fetus. | 01-28-2016 |
20160024572 | Massively Multiplexed RNA Sequencing - A method for parallel sequencing target RNA from samples from multiple sources while maintaining source identification is provided. The method includes providing samples of RNA comprising target RNA from two or more sources; labeling, at the 3′ end, the RNA from the two or more sources with a first nucleic acid adaptor that comprises a nucleic acid sequence that differentiates between the RNA from the two or more sources; reverse transcribing the two or more sources to create a single stranded DNA comprising the nucleic acid sequence that differentiates between the RNA from the two or more sources; amplifying the single stranded DNA to create DNA amplification products that comprise the nucleic acid sequence that differentiates between the RNA from the two or more sources; sequencing the DNA amplification products thereby parallel sequencing target RNA from samples from multiple sources while maintaining source identification. | 01-28-2016 |
20160024573 | PHOTOCLEAVABLE DEOXYNUCLEOTIDES WITH HIGH-RESOLUTION CONTROL OF DEPROTECTION KINETICS - Provided herein are new classes of photocleavable deoxynucleotides that allow for more precise control over deprotection kinetics compared to previously described compounds. The compounds further feature more favorable solubility properties. The nucleotides find use in methods such as next-generation sequencing. A series of molecules are provided with defined organic substituents that allow fine tuning of the deprotection kinetics when irradiated with an appropriate light source. | 01-28-2016 |
20160024574 | DNA SEQUENCING WITH NON-FLUORESCENT NUCLEOTIDE REVERSIBLE TERMINATORS AND CLEAVABLE LABEL MODIFIED NUCLEOTIDE TERMINATORS - This invention provides a process for sequencing nucleic acids using 3′ modified deoxynucleotide analogues or 3′ modified deoxyinosine triphosphate analogues, and 3′ modified dideoxynucleotide analogues having a detectable marker attached to a base thereof. | 01-28-2016 |
20160024575 | CIRCULATING SMALL NONCODING RNA MARKERS - This application describes small noncoding RNA markers that can be found in a biological sample taken from an individual. The level of such markers are useful for determining the individual's health status, especially in comparison with others. Methods and kits for the use of these markers are provided as well. | 01-28-2016 |
20160024578 | METHOD FOR IDENTIFYING THE QUANTITATIVE CELLULAR COMPOSITION IN A BIOLOGICAL SAMPLE - The present invention provides an epigenetic haemogram, also referred to as an epigenetic blood cell count that identifies the quantitative, comprehensive picture of cellular composition in a biological sample, wherein advantageously a normalization standard is used. The normalization standard is a nucleic acid molecule comprising at least one marker-region being specific for each of the blood cells to be detected, and at least one control-region being cell-unspecific, wherein said regions are present in the same number of copies on said molecule and/or a natural blood cell sample of known composition. Furthermore, the present invention relates to a kit and the use of a kit for performing the epigenetic assessment of comprehensive, quantitative cellular composition of a biological sample. The biological sample is derived from e.g. a mammalian body fluid, including peripheral, capillary or venous blood samples or subfractions thereof, such as peripheral blood mononuclear cells or peripheral blood monocytes, or a tissue sample, organ sample, or from frozen, dried, embedded, stored or fresh body fluids or tissue samples. | 01-28-2016 |
20160024579 | NON-INVASIVE DETERMINATION OF FETAL INHERITANCE OF PARENTAL HAPLOTYPES AT THE GENOME-WIDE SCALE - The present invention provides a method, device and a computer program for haplotyping single cells, such that a sample taken from a pregnant female, without directly sampling the fetus, provides the ability to non-invasively determine the fetal genome. The method can be performed by determining the parental and inherited haplotypes, or can be performed merely on the basis of the mother's genetic information, obtained preferably in a blood or serum sample. The novel device allows for sequence analysis of single chromosomes from a single cell, preferably by partitioning single chromosomes from a metaphase cell into long, thin channels where a sequence analysis can be performed. | 01-28-2016 |
20160024584 | METHODS AND SYSTEMS FOR INFERRING BOVINE TRAITS - Methods, compositions, and systems are provided for managing bovine subjects in order to maximize their individual potential performance and edible meat value, and to maximize profits obtained in marketing the bovine subjects. The methods and systems draw an inference of a trait of a bovine subject by determining the nucleotide occurrence of at least one bovine SNP that is identified herein as being associated with the trait. The inference is used in methods of the present invention to establish the economic value of a bovine subject, to improve profits related to selling beef from a bovine subject; to manage bovine subjects, to sort bovine subjects; to improve the genetics of a bovine population by selecting and breeding of bovine subjects, to clone a bovine subject with a specific trait, to track meat or another commercial product of a bovine subject; and to diagnose a health condition of a bovine subject. Methods are also disclosed for identifying additional SNPs associated with a trait, by using the associated SNPs identified herein. | 01-28-2016 |
20160024587 | MARKERS ASSOCIATED WITH WNT INHIBITORS - The invention provides methods of monitoring differential gene expression of biomarkers to determine patient sensitivity to Wnt inhibitor, methods of determining the sensitivity of a cell to an Wnt inhibitor by measuring biomarkers, methods of screening for candidate Wnt inhibitor, Wnt inhibitor for use in head and neck squamous cell carcinoma. | 01-28-2016 |
20160024588 | OSTEOSARCOMA-ASSOCIATED RISK MARKERS AND USES THEREOF - Provided herein are methods and compositions for identifying subjects, including canine subjects, as having an elevated risk of developing cancer or having an undiagnosed osteosarcoma. These subjects are identified based on the presence of germ-line risk markers. | 01-28-2016 |
20160025726 | METHODS FOR DETECTING PEPTIDE/MHC/TCR BINDING - Provided herein are compositions and methods for detecting the binding of a peptide to an MHC molecule, and the binding of a peptide: MHC complex to a TCR. In preferred embodiments, the compositions and methods are in a highly-multiplexed way. The compositions and methods disclosed herein can be used to provide direct information on which peptides are bound to an MHC molecule. Also provided is a method for simultaneously detecting a large number of peptides for binding to an MHC molecule and/or a T cell. A method for detecting competitive binding of a large number of peptides to an MHC molecule and/or a T cell is also disclosed. Also provided herein is a method for simultaneously detecting a large number of specific TCRs. The compositions and methods of the present invention are useful for vaccine design, research and monitoring of autoimmune and infectious disease, immunogenicity testing of therapeutics, and tissue typing. | 01-28-2016 |
20160026759 | Detecting Chromosomal Aneuploidy - A method for detecting a chromosomal aneuploidy relating to a target nucleic acid region includes the following steps. A reference database is obtained. At least one normalizing factor is determined based on the reference database. A cutoff value is determined based on the reference database. A biological sample under test is sequenced by the sequencing platform to obtain a number of target reads of the biological sample under test. The target reads of the biological sample under test originate from the target nucleic acid region. The number of the target reads of the biological sample under test is normalized by the normalizing factor and then is compared with the cutoff value. Whether the chromosomal aneuploidy relating to the target nucleic acid region is present in the fetus is determined based on the comparison | 01-28-2016 |
20160032273 | CHARACTERIZATION OF MRNA MOLECULES - The present invention describes methods for the characterization of mRNA molecules during mRNA production. Characterizing mRNA includes processes such as oligonucleotide mapping, reverse transcriptase sequencing, charge distribution analysis, and detection of RNA impurities. Oligonucleotide mapping includes using an RNase to digest antisense duplexes from an RNA transcript, and then subjecting the digested RNA to reverse phase HPLC, anion exchange HPLC, and/or mass spectrometry analysis. Reverse transcriptase sequencing involves reverse transcription of an RNA transcript followed by DNA sequencing. Charge distribution analysis can comprise procedures such as anion exchange HPLC, or capillary electrophoresis. Detection of impurities includes detecting short mRNA transcripts, RNA-RNA hybrids, and RNA-DNA hybrids. | 02-04-2016 |
20160032275 | NANOPIPETTE DEVICE AND METHOD FOR SUBCELLULAR ANALYSIS - Described herein are devices and methods for extracting cellular material from living cells and then depositing them into to a receptacle in a nanoliter scale. Using a nanopipette integrated into a scanning ion conductance microscope (SICM), extraction of mitochondrial DNA from human BJ fibroblasts and Green Fluorescent Protein (GFP) transcripts from HeLa/GFP cells was achieved with minimal disruption to the cellular milieu and without chemical treatment prior to obtaining the isolated sample. Success of the extraction was confirmed by fluorescence microscopy and PCR analysis of the extracted material. The method and apparatus may be applied to many different cell types and intracellular targets, allowing not only single cell analysis, but single subcellular compartment analysis of materials extracted in their native state. | 02-04-2016 |
20160032371 | MATRIX ARRAYS AND METHODS FOR MAKING SAME - A method of forming a polymer matrix array includes applying an aqueous solution into wells of a well array. The aqueous solution includes polymer precursors. The method further includes applying an immiscible fluid over the well array to isolate the aqueous solution within the wells of the well array and polymerizing the polymer precursors isolated in the wells of the well array to form the polymer matrix array. An apparatus includes a sensor array, a well array corresponding to the sensor array, and an array of polymer matrices disposed in the well array. | 02-04-2016 |
20160032376 | NUCLEOTIDE ANALOGS FOR SEQUENCING - Provided herein is technology relating to sequencing nucleic acids, but not exclusively, to compositions, methods, systems, and kits related to nucleotides comprising an electrochemically detectable moiety and one or more photolabile synthesis-inhibiting moieties. | 02-04-2016 |
20160032386 | GENETIC MARKERS FOR OSTEOARTHRITIS - A method for predicting the severity or progression of OA in a human subject, comprising: determining the identity of at least one allele at each of at least 4 positions of single nucleotide polymorphism (SNPs) selected from the group consisting of: rs2206593, rs10465850, rs780094, rs1374281, rs1143634, rs2073508, rs2243250, rs4720262, rs917760, rs7838918, rs12009, rs730720, rs874692, rs893953, rs1799750, rs10845493, rs11054704, rs7986347, rs1802536, rs10519263, rs7342880, rs16947882 and rs10413815, and one or more SNPs in linkage disequilibrium at a level of at least R | 02-04-2016 |
20160032396 | Identification and Use of Circulating Nucleic Acid Tumor Markers - Methods for creating a selector of mutated genomic regions and for using the selector set to analyze genetic alterations in a cell-free nucleic acid sample are provided. The methods can be used to measure tumor-derived nucleic acids in a blood sample from a subject and thus to monitor the progression of disease in the subject. The methods can also be used for cancer screening, cancer diagnosis, cancer prognosis, and cancer therapy designation. | 02-04-2016 |
20160032397 | MAST CELL CANCER-ASSOCIATED GERM-LINE RISK MARKERS AND USES THEREOF - Provided herein are methods and compositions for identifying subjects, including canine subjects, as having an elevated risk of developing cancer or having an undiagnosed cancer. These subjects are identified based on the presence of germ-line risk markers. | 02-04-2016 |
20160034640 | METHODS AND PROCESSES FOR NON-INVASIVE ASSESSMENT OF GENETIC VARIATIONS - Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of nucleic acid fragment length information. | 02-04-2016 |
20160040143 | METHODS FOR AMPLIFICATION AND SEQUENCING USING THERMOSTABLE TTHPRIMPOL - The present invention is directed to methods for replicating, amplifying, and sequencing of nucleic acids using the thermostable, bifunctional replicase “TthPrimPol” from | 02-11-2016 |
20160040212 | Methods for the Detection of DNA-RNA Proximity in Vivo - Disclosed is a method for detecting spatial proximity relationships between RNA and DNA molecules in a cell. The method includes: providing a sample of RNA and DNA wherein the RNA and fDNA have ends capable of joining to other DNA and RNA, respectively; joining at least one end of the fragmented RNA to the end of at least one fragmented DNA, to create at least one joined RNA-DNA hybrid molecule, wherein the join encodes the information about the proximity of the RNA and DNA in the cell; reverse transcribing the at least one joined rRNA-DNA hybrid molecule to create least one target join DNA molecule that retains the information of the join, and determining the sequence of the target join thereby detecting spatial proximity relationships between RNA and DNA molecules in a cell. | 02-11-2016 |
20160040215 | Methods for Pathogen Detection and Enrichment from Materials and Compositions - Provided are methods and compositions for characterization of bacterial compositions for the maintenance or restoration of a healthy microbiota in the gastrointestinal tract of a mammalian subject, and the resulting characterized compositions. Provided are methods of characterizing bacterial compositions including subjecting the compositions to various detecting processes. | 02-11-2016 |
20160040218 | Selective Purification of RNA and RNA-Bound Molecular Complexes - Disclosed are methods for isolating a target nucleic molecule of interest from a sample. The methods include contacting a sample comprising a target nucleic molecule of interest with at least one single stranded nucleic acid targeting probe comprising a nucleic acid sequence between about 30 nucleotide and the length of the target nucleic acid length that hybridizes to the target nucleic molecule of interest under highly stringent hybridization conditions. The probe comprises a capture moiety covalently linked to one or more nucleotide bases in the probe. The targeting probes can be captured with a specific binding agent that specifically binds the capture moiety, thereby isolating the target nucleic molecule of interest. In some embodiments, the sample is further contacted with a crosslinking agent before contacting the sample with a targeting probe. Thus, complexes formed with the target nucleic acid can also be isolated. | 02-11-2016 |
20160040220 | METHODS FOR THE DETECTION OF BREAKPOINTS IN REARRANGED GENOMIC SEQUENCES - Methods for detecting the amplifications of sequences in the BRCA1 locus, which sequences have ends consisting of or are framed with sequence stretches present at least twice in the BRCA1 locus, and which amplification results in at least two or at least three, especially three, tandem copies of the amplified sequence; methods for determining a predisposition to diseases or disorders associated with these amplifications, including predisposition to ovarian cancer or breast cancer and methods for detecting amplifications with similar features in other loci and/or for predicting breakpoints of such amplifications. | 02-11-2016 |
20160040226 | MANIPULATION OF MICROPARTICLES IN MICROFLUIDIC SYSTEMS - An array of transportable particle sets is used in a microfluidic device for performing chemical reactions in the microfluidic device. The microfluidic device comprises a main channel and intersecting side channels, the main channel and side channels forming a plurality of intersections. The array of particle sets is disposed in the main channel, and the side channels are coupled to reagents. As the particle sets are transported through the intersections of the main channel and the side channels, reagents are flowed through the side channels into contact with each array member (or selected array members), thereby providing a plurality of chemical reactions in the microfluidic system. | 02-11-2016 |
20160040228 | SEQUENCING STRATEGIES FOR GENOMIC REGIONS OF INTEREST - The disclosure relates to methods for determining the sequence of a genomic region of interest comprising a target nucleotide sequence comprising: providing a DNA comprising a genomic region of interest, fragmenting the DNA, separating the DNA fragments, fragmenting and ligating the DNA fragments to provide for ligated fragments of the DNA fragments (or ligated DNA subfragments), and determining at least part of the sequences of at least part of the ligated DNA subfragments that comprise the target nucleotide sequence. | 02-11-2016 |
20160040229 | SYSTEMS AND METHODS TO DETECT RARE MUTATIONS AND COPY NUMBER VARIATION - The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease. | 02-11-2016 |
20160040230 | Compositions, Devices, Systems, and Methods for Using a Nanopore - Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof. | 02-11-2016 |
20160040234 | METHODS OF SEQUENCING THE IMMUNE REPERTOIRE - The invention provides a non-invasive technique for the detection and quantification of the immune repertoire, in a biological sample containing a plurality of distinct cell populations. Methods are conducted using sequencing technology to detect and enumerate immune repertoire within a heterogeneous biological sample. | 02-11-2016 |
20160040239 | METHODS FOR PREDICTING CARDIOVASCULAR RISKS AND RESPONSIVENESS TO STATIN THERAPY USING SNPS - Methods and compositions for the effect of Cholesteryl ester transfer protein (CETP) polymorphisms on mRNA splicing, statin treatment outcome, response to CETP inhibitor drugs, and myocardial infarction risk are described. | 02-11-2016 |
20160040244 | METHOD FOR DETECTING GASTRIC POLYP AND GASTRIC CANCER MARKER GENE OF GASTRIC POLYP AND GASTRIC CANCER-SPECIFIC METHYLATION - The present invention relates to the novel use of syndecan-2 (SDC2; NM_002998) gene as a gastric polyp- and gastric cancer-specific methylation biomarker, and more particularly, to the use of the syndecan-2 gene as a biomarker that enables gastric polyp and gastric cancer to be diagnosed in an early stage by measuring the methylation level thereof. The present invention has an effect in that the methylation of the CpG island of the gastric polyp- and gastric cancer-specific marker gene can be detected to thereby provide information for diagnosing gastric cancer. The use of the methylation detection method according to the present invention or the diagnostic composition, kit or nucleic acid chip according to the present invention makes it possible to diagnose gastric cancer at an early transformation stage, thus enabling the early diagnosis of gastric cancer. In addition, the method of the present invention enables gastric cancer to be effectively diagnosed in an accurate and rapid manner compared to conventional methods. | 02-11-2016 |
20160040246 | DETECTING NEOPLASM - Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as pancreatic and colorectal cancer. Accordingly, provided herein is technology for pancreatic cancer screening markers and other gastrointestinal cancer screening markers that provide a high signalto-noise ratio and a low background level when detected from samples taken from a subject (e.g., stool sample). As described herein, the technology provides a number of methylated DNA markers and subsets thereof (e.g., sets of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more markers) with high discrimination for G1 neoplasms overall and/or at individual tumor sites. | 02-11-2016 |
20160046926 | NUCLEIC ACID SAMPLE PREPARATION - The present invention includes methods, devices and systems for isolating a nucleic acid from a fluid comprising cells. In various aspects, the methods, devices and systems may allow for a rapid procedure that requires a minimal amount of material and/or results in high purity nucleic acid isolated from complex fluids such as blood or environmental samples. | 02-18-2016 |
20160046978 | COMPOSITIONS AND METHODS OF NUCLEIC ACID-TARGETING NUCLEIC ACIDS - This disclosure provides for compositions and methods for the use of nucleic acid-targeting nucleic acids and complexes thereof. | 02-18-2016 |
20160046979 | METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for determining copy number variation of one or more nucleic acids present in a sample. In some aspects, the method includes various target-specific primers that allow for the selective amplification of one or more target nucleic acids in the sample. In yet another aspect, the invention relates to determining copy number variation with respect to gene or chromosome representation of a nucleic acid in the sample. In some aspects, the method for determining copy number variation of different target nucleic acids in a sample using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including diagnosis, predictive therapeutic regimes or other therapeutic purposes. | 02-18-2016 |
20160046980 | TRANSPOSON NUCLEIC ACIDS COMPRISING A CALIBRATION SEQUENCE FOR DNA SEQUENCING - Transposon nucleic acids comprising a transposon end sequence and a calibration sequence for DNA sequencing in the transposon end sequence. In one embodiment, the transposon end sequence is a Mu transposon end. A method for the generation of DNA fragmentation library based on a transposition reaction in the presence of a transposon end with the calibration sequence providing facilitated downstream handling of the produced DNA fragments, e.g., in the generation of sequencing templates. | 02-18-2016 |
20160046989 | IN VITRO METHOD FOR PREDICTIVE ASSESSMENT OF THE PROSPECTS OF SUCCESS OF AN IMPLANT AND/OR TRANSPLANT - An in vitro method of prognostically assessing tissue regeneration capacity and/or cellular potency and/or the prospects of success of an implantation and/or transplantation, wherein the transcriptome and/or the gene expression of cells, said gene expression originating from the transcriptome, are analyzed. | 02-18-2016 |
20160046994 | NOVEL CD177 HAPLOTYPES, THEIR ROLE IN HNA-2 DEFICIENCY, AND METHODS OF USING - This disclosure describes a novel CD177 haplotype and its involvement in HNA-2 deficiency. Methods of determining the CD177 haplotype of an individual are provided. | 02-18-2016 |
20160046996 | Common and Rare Genetic Variations Associated with Common Variable Immunodeficiency (CVID) and Methods of Use Thereof for the Treatment and Diagnosis of the Same - Compositions and methods useful for the diagnosis and treatment of common variable immunodeficiency are disclosed. | 02-18-2016 |
20160047002 | METHOD OF ESTIMATING THE AMOUNT OF A METHYLATED LOCUS IN A SAMPLE - A method of estimating the amount of a methylated locus is provided. In certain embodiments the method comprises: digesting a nucleic acid sample that contains both unmethylated and methylated copies of a genomic locus with an MspJI family member to produce a population of fragments that are in the range of 20-40 nucleotides in length, ligating adaptor sequence A and adaptor sequence B to the respective ends of a target fragment of sequence X, and quantifying the amount of ligation products of formula A-X-B. A kit for performing the method is also provided. | 02-18-2016 |
20160047003 | HIGH THROUGHPUT METHOD OF SCREENING A POPULATION FOR MEMBERS COMPRISING MUTATION(S) IN A TARGET SEQUENCE - The present invention provides high-throughput methods of screening for members of a population comprising mutation(s) in one or more target sequence(s). The methods may comprise the steps of: pooling genomic DNA isolated from each member of said population; amplifying the one or more target sequence(s) in the pooled genomic DNA; pooling the amplification products of step (b) to create a library of amplification products; sequencing the amplified products by pair-end sequencing to produce paired-end reads for each sequencing reaction or obtaining paired-end sequence reads for the amplified products; merging the paired-end reads into composite read(s); mapping the composite read(s) to reference sequence(s) to identify mutation(s) in the one or more target sequence(s); and identifying member(s) of the population comprising one or more of the identified mutations in the target sequence(s). The invention further provides kits for use with the methods. | 02-18-2016 |
20160053305 | RNA AMPLIFICATION METHODS - Methods of detecting and amplifying short RNAs are provided. | 02-25-2016 |
20160053307 | LIGASE-ASSISTED NUCLEIC ACID CIRCULARIZATION AND AMPLIFICATION - Provided herein are methods for generation and amplification of a single-stranded DNA circle in a single reaction vessel from a linear DNA without any intervening purification steps. The single-stranded DNA circle is generated via a template-independent single-stranded DNA ligation. Whole-genome amplification of linear chromosomal DNA in a single tube using ligation-assisted DNA amplification is also provided. | 02-25-2016 |
20160053310 | KINETIC EXCLUSION AMPLIFICATION OF NUCLEIC ACID LIBRARIES - A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated. | 02-25-2016 |
20160053311 | MULTIPLEX Y-STR ANALYSIS - Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci. | 02-25-2016 |
20160053325 | miRNA FINGERPRINT IN THE DIAGNOSIS OF MULTIPLE SCLEROSIS - The present invention provides novel methods for diagnosing diseases based on the determination of specific miRNAs that have altered expression levels in disease states compared to healthy controls. | 02-25-2016 |
20160053328 | PERSONALIZED BIOMARKERS FOR CANCER - The invention provides methods and reagents for identifying personalized tumor biomarkers for a patient that has a solid tumor and methods of using such biomarkers to monitor patient responses to therapeutic treatments. | 02-25-2016 |
20160054343 | SYSTEMS AND METHODS FOR MULTI-ANALYSIS - Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample. | 02-25-2016 |
20160055296 | Method And System For Assessing A Health Condition - The present invention relates to a method of assessing whether a subject mammal has a target condition, comprising a step of formulating a function of abundances of a first group of biomarkers and abundances of a second group of biomarkers that is useful for assessing whether the subject mammal has the target condition. The present invention also relates to a computer-aided system for assessing whether a subject mammal has a target condition. The present invention further relates to a computer-readable medium for assessing whether a subject mammal has a target condition | 02-25-2016 |
20160060686 | STRATEGIES FOR HIGH THROUGHPUT IDENTIFICATION AND DETECTION OF POLYMORPHISMS - The invention relates to a method for the high throughput identification of single nucleotide polymorphisms by performing a complexity reduction on two or more samples to yield two or more libraries, sequencing at least part of the libraries, aligning the identified sequences and determining any putative single nucleotide polymorphisms, confirming any putative single nucleotide polymorphism, generating detection probes for the confirmed single nucleotide polymorphisms, subjection a test sample to the same complexity reduction to provide a test library and screen the test library for the presence or absence of the single nucleotide polymorphisms using the detection probe. | 03-03-2016 |
20160060687 | METHODS AND COMPOSITIONS TO IDENTIFY, QUANTIFY, AND CHARACTERIZE TARGET ANALYTES AND BINDING MOIETIES - Proximity coupling and sequencing methods to screen identify, validate and/or characterize interactions between analytes and binding moieties are disclosed. Also disclosed herein are proximity coupling methods and sequencing methods to determine or quantify levels of target analytes. The disclosed methods can be multiplexed in two dimensions, and can be used to determine the affinity and specificity of each of a plurality of binding moieties for each of a plurality of target analytes. Also disclosed herein are substrates, arrays, and reagents for use in the methods, and methods of their preparation. | 03-03-2016 |
20160060691 | Transposition of Native Chromatin for Personal Epigenomics - Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided. | 03-03-2016 |
20160060692 | LABELLED NUCLEOTIDES - Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group. | 03-03-2016 |
20160060693 | Compositions and Methods for Intramolecular Nucleic Acid Rearrangement - Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or MID). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided. | 03-03-2016 |
20160060695 | METHOD AND KIT FOR MULTIPLEX DNA TYPING OF HLA GENE - The purpose of the present invention is to provide a method and kit for highly precise DNA typing, in which a high throughput sequencer is used and ambiguity derived from phase ambiguity is eliminated. The present invention provides a method for the DNA typing of HLA, which is characterized by comprising: (1) a step of preparing sets of primers which respectively hybridize specifically to an upstream region and a downstream region of at least 2 genes selected from genes belonging to HLA class I and HLA class II in a human genome sequence, and are capable of amplifying under the same PCR conditions; (2) a step of simultaneously amplifying said at least 2 genes in a test sample (DNA) using the sets of primers in a single container under the same PCR conditions; (3) a step of determining the nucleotide sequences of PCR amplified products; and (4) a step of optionally carrying out a homology search within a database. | 03-03-2016 |
20160060699 | SLE AND SLE-RELATED DISEASE-ASSOCIATED RISK MARKERS AND USES THEREOF - Provided herein are methods and compositions for identifying subjects, including canine subjects, as having an elevated risk of developing systemic lupus erythematosus (SLE) or an SLE-related immune-mediated rheumatic disorder or having undiagnosed SLE or an SLE-related immune-mediated rheumatic disorder. These subjects are identified based on the presence of gem-line risk markers. | 03-03-2016 |
20160060714 | SYSTEMS AND METHODS FOR GENOTYPING SEED COMPONENTS - The invention provides methods for obtaining genetic material from plant embryos while preserving their viability as well as methods for performing a molecular analysis of plant embryos, particularly with small quantities of genetic material. The methods may include the steps of collecting shed cellular material from one or more plant embryos; obtaining DNA from the shed cellular material; performing a molecular analysis of the DNA; and germinating at least one of said one or more plant embryos. A further extension of this method includes determining whether to germinate and grow the embryo or to discard the embryo based on its genotype as part of a breeding process. Also provided are methods of genotyping embryos using embryo shed cellular material contained in or on agar and methods of analyzing plant embryonic tissue derived from microspores. | 03-03-2016 |
20160060715 | SYSTEMS AND METHODS FOR GENOTYPING SEED COMPONENTS - The invention provides methods for obtaining genetic material from plant embryos while preserving their viability as well as methods for performing a molecular analysis of plant embryos, particularly with small quantities of genetic material. The methods may include the steps of collecting shed cellular material from one or more plant embryos; obtaining DNA from the shed cellular material; performing a molecular analysis of the DNA; and germinating at least one of said one or more plant embryos. A further extension of this method includes determining whether to germinate and grow the embryo or to discard the embryo based on its genotype as part of a breeding process. Also provided are methods of genotyping embryos using embryo shed cellular material contained in or on agar and methods of analyzing plant embryonic tissue derived from microspores. | 03-03-2016 |
20160067711 | SYSTEMS AND METHODS FOR SINGLE CELL ISOLATION AND ANALYSIS - The present disclosure relates to devices, systems, and methods for single cell isolation and analysis. In particular, the present disclosure relates to systems and methods for isolating single cells present at low numbers. | 03-10-2016 |
20160068798 | SYSTEMS AND METHODS FOR SINGLE CELL ISOLATION AND ANALYSIS - The present disclosure relates to devices, systems, and methods for single cell isolation and analysis. In particular, the present disclosure relates to laser detachment systems and methods for isolating single cells suitable for culture and molecular analysis. | 03-10-2016 |
20160068885 | AGENTS PROVIDING CONTROLS AND STANDARDS FOR IMMUNOPRECIPITATION ASSAYS - Control agents for immunoprecipitation assays, methods of using the control agents and kits comprising the control agents are provided. | 03-10-2016 |
20160068889 | METHODS FOR SELECTIVELY SUPPRESSING NON-TARGET SEQUENCES - The invention generally relates to negative selection of nucleic acids. The invention provides methods and systems that remove unwanted segments of nucleic acid in a sample so that a target gene or region of interest may be analyzed without interference from the unwanted segments. A sample is obtained that includes single-stranded nucleic acid with one or more unwanted segments. Complementary nucleic acid is added to the single-stranded nucleic acid to create a double-stranded region that includes the unwanted segment. The double-stranded region is then digested, leaving single-stranded nucleic acid that includes the target gene or region of interest. This allows paralogs, pseudogenes, repetitive elements, and other segments of the genome that may be similar to the target gene or region of interest to be removed from the sample. | 03-10-2016 |
20160068890 | GENE SIGNATURES OF INFLAMMATORY DISORDERS THAT RELATE TO THE LIVER - This invention is related to the area of characterization of inflammation in relation with the gut microbiota, in metabolic and autoimmune disorders. In particular, it relates to the identification of gene signatures which can be used as a marker predictive of inflammation associated diseases, such as liver-related metabolic disorders, in particular to the evolution of benign steatosis towards its most severe forms (steatohepatitis and cirrhosis) or autoimmune disorders, in particular inflammatory bowel diseases (Crohn's and Ulcerative Colitis). These gene signatures can therefore be used as a means of diagnosis, prognosis, stratification for drug studies, for monitoring patient and for assigning an appropriate treatment. | 03-10-2016 |
20160068901 | Analysis of DNA - The invention provides pyrosequencing-based methods of analyzing and synthesizing DNA, including methods of DNA error correction, determining DNA size distribution, screening for nucleotide repeat disorders such as fragile X syndrome, determining size distribution and bias in a DNA library, and determining pyrosequencing read length. The methods include on-bench protocols as well as droplet-based protocols that may be conducted on a droplet actuator. | 03-10-2016 |
20160068906 | METHOD OF SCREENING NEWBORNS FOR GENE VARIANTS - Disclosed are methods, systems, and kits for screening a newborn infant for one or more gene variants comprising, obtaining a genomic DNA containing sample from the newborn infant; sequencing at least one target region of each of two or more genes selected from the group consisting of PCCA, PCCB, MUT, MMAA, MMAB, MMADHC, MCEE, IVD, ACAT1, ACADM, ACADVL, HADHA, ASL, BCKDHA, BCKDHB, DBT, DLD, CYP21A2, GALT, and ACAD8 in the genomic DNA; and screening for a gene variant from the sequenced target regions of each gene to identify gene variants present in the genomic DNA, wherein the sequencing does not include whole genome sequencing or whole exome sequencing. | 03-10-2016 |
20160068915 | METHODS AND COMPOSITIONS FOR CLASSIFICATION OF SAMPLES - Disclosed herein are kits, compositions, and methods relating to the classification of samples. Methods disclosed herein can also be used to diagnose conditions or to support treatment-related decisions. | 03-10-2016 |
20160069806 | Illumination of Integrated Analytical Systems - An analytical device including an optically opaque cladding, a sequencing layer including a substrate disposed below the cladding, and a waveguide assembly for receiving optical illumination and introducing illumination into the device. The illumination may be received from a top, a side edge, and a bottom of the device. The waveguide assembly may include a nanoscale aperture disposed in the substrate and extending through the cladding. The aperture defines a reaction cell for receiving a set of reactants. In various aspects, the device includes a sensor element and the illumination pathway is through the sensor element. Waveguides and illumination devices, such as plasmonic illumination devices, are also disclosed. Methods for forming and operating the devices are also disclosed. | 03-10-2016 |
20160069863 | DEVICES AND METHODS FOR SINGLE CELL ANALYSIS - The present disclosure provides systems, methods, and devices for the simultaneous determination of a single cell's response to a stimuli and characterization of its cell response. The present disclosure further provides methods for detection of disease state, clinical management of a subject suffering from a disease, drug screening, prediction of drug response, and stands to help direct drug and diagnostic development for the treatment of disease. | 03-10-2016 |
20160069898 | Methods for Determining Responsiveness to an Anti-CD47 Agent - Methods and kits are provided for determining whether an individual is responsive to an anti-CD47 agent and for determining whether an individual is maintaining responsiveness to an anti-CD47 agent by assaying biological samples for the level of at least one biomarker in a biological sample. | 03-10-2016 |
20160069919 | SYSTEMS AND METHODS FOR MULTI-ANALYSIS - Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample. | 03-10-2016 |
20160070853 | DETECTING AND CLASSIFYING COPY NUMBER VARIATION - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample. | 03-10-2016 |
20160070857 | METHOD FOR EXTRACTING BIOMARKER FOR DIAGNOSING BILIARY TRACT CANCER, COMPUTING APPARATUS THEREFOR, BIOMARKER FOR DIAGNOSING BILIARY TRACT CANCER AND APPARATUS FOR DIAGNOSING BILIARY TRACT CANCER COMPRISING SAME - Disclosed are a method for extracting a biomarker for diagnosing biliary tract cancer and a computing apparatus therefor, and the biomarker for diagnosing biliary tract cancer and an apparatus for diagnosing biliary tract cancer comprising same. More particularly, disclosed are a method for extracting a biomarker for diagnosing biliary tract cancer using a gene specifically expressed in a biliary tract cancer patient, or a microRNA obtained from blood or a tissue, capable of forming a pair with the gene and a computing apparatus therefor, and the biomarker for diagnosing biliary tract cancer and an apparatus for diagnosing biliary tract cancer comprising same. | 03-10-2016 |
20160076089 | A METHOD FOR DNA AMPLIFICATION WITH A BLOCKING OLIGONUCLEOTIDE - The invention relates to an in vitro method for selectively amplifying a target DNA sequence from a nucleic acid sample, which method comprises running a PCR amplification of a nucleic acid sample suspected of comprising at least one target DNA sequence that differs from a reference DNA sequence at at least one predetermined target mutation site; wherein said method employs a blocking oligonucleotide complementary to a portion of the reference DNA sequence comprising the target mutation site, with the exception of a least one mismatch outside the target mutation site. | 03-17-2016 |
20160076093 | MULTIPLEX HOMOLOGY-DIRECTED REPAIR - Disclosed is a method for introducing a plurality of programmed nucleotide modifications into a single locus of a desired genomic DNA sequence in a single experiment. The method entails synthesizing a homology-directed repair (HDR) library comprising a plurality of oligonucleotides, wherein each oligonucleotide comprises a programmed nucleotide modification in the locus of the desired genome, and co-transfecting a population of cells with (i) an expression system capable of expressing Cas9 and a single guide RNA (sgRNA) and (ii) introducing a plurality of programmed nucleotide modifications to the locus of the desired genomic DNA sequence in one or more cells of the population. Also disclosed are methods for analyzing the functional consequence of a genomic mutation and for genomic screening. | 03-17-2016 |
20160076094 | Efficient Deep Sequencing and Rapid Genomic Speciation of RNA Viruses (vRNAseq) - A method for limited input whole genome sequencing of RNA viruses includes isolating a viral RNA sample, converting the viral RNA sample to a double-stranded viral cDNA sample, constructing a double-stranded viral cDNA amplicon library from the double-stranded viral cDNA sample, and sequencing the double-stranded viral cDNA amplicon library to obtain a double-stranded viral cDNA sample sequencing read. | 03-17-2016 |
20160076103 | miRNA FINGERPRINT IN THE DIAGNOSIS OF DISEASES - The present invention provides novel methods for diagnosing a state of health based on the determination of specific miRNAs that have altered expression levels in different conditions, e.g. disease states compared to healthy controls. | 03-17-2016 |
20160076980 | Method of Partial Lysis and Assay - The present disclosure describes a method of treating a sample comprising cells with a process of partial lysing. Cells are exposed to a process such as bead beating that lyses some cells in the mixture. The process generates a resultant sample mixture that is suitable for both cell morphology screening and genetic screening. A first portion of the partially lysed sample can be mounted on a slide and observed for atypical cells and cytologic abnormalities. A second portion of the partially lysed sample can be screened for genetic markers known to correlate with a risk of cervical cancer. Surprisingly the presence of beads in the mixture from the partial lysing process does not interfere with slide processing or cellular analysis. The method is particularly useful for cervical screening, where a combination of cytology and genetic screening present a more complete picture of cervical health. The disclosed method streamlines the diagnostic process for protocols that require both types of assays, without compromising screening accuracy. | 03-17-2016 |
20160080384 | METHOD AND APPARATUS FOR DNA-BASED AUTHENTICATION SYSTEM - Techniques for biochemcally-enabled security/authentication mechanisms are described herein. In an example embodiment, a security system receives a biological sample from a key. The biological sample includes a set of deoxyribonucleic acid (DNA) oligos that represent a code assigned to the key. The set of DNA oligos is sequenced to obtain a set of read sequences. The set of read sequences is then filtered to identify a set of filtered sequences. The set of filtered sequences is matched to sets of expected sequences, where the sets of expected sequences are assigned to respective keys issued for the security system. Access to a resource is then granted or denied based on whether the set of filtered sequences matches with any set from the sets of expected sequences. | 03-17-2016 |
20160083721 | MULTIPLEXED SEQUENTIAL LIGATION-BASED DETECTION OF GENETIC VARIANTS - The present invention provides multiplexed sequential ligation-based analysis of genetic variants in a mixed sample, including copy number variations and single nucleotide polymorphisms. The invention employs the techniques of sequential ligation and amplification. | 03-24-2016 |
20160083788 | METHOD FOR TARGETED SEQUENCING - The method of the present invention now provides a technique for generating sequence information from nucleic acid samples based on knowledge from part(s) of the nucleotide sequence. The knowledge of the partial sequence may include knowledge about the presence of restriction sites. The knowledge of the partial sequence can be used to generate adaptor-ligated or nucleotide-elongated fragments. From the combination of information on the ligated adaptor and the Known Nucleotide Sequence Section, probes can be designed. The probes can be used in the provision of circularized fragments that can be sequenced. Combining the known and determined sequences adds sequence information to the already existing sequence information and complements the available genomic sequence information. | 03-24-2016 |
20160083789 | NUCLEIC ACID SEQUENCING WITH NANOSCALE ELECTRODE PAIRS - Sequencing methods, devices, and systems are described. Arrays of nanoscale electronic elements comprising two electrodes separated by an insulating layer are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the insulating region. A sequencing reaction mixture comprising nucleotide analogs having impedance labels is introduced to the array of nanoscale electronic elements under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by identifying the types of labels of the nucleotide analogs that are incorporated into the growing strand using measured impedance. | 03-24-2016 |
20160083790 | REGULATOR TARGETTING FATTY ACID SYNTHASE AND METHOD OF USING THE SAME FOR IMPROVING MEAT QUALITY - A miRNA miR-4749-5 represented by the sequence of SEQ ID NO: 1 is disclosed. | 03-24-2016 |
20160083791 | SYSTEM AND METHOD FOR DETECTING ABNORMALITIES IN CERVICAL CELLS - The present disclosure is directed to a method for identifying an abnormal sample of cells by (a) hybridizing a set of chromosomal probes to the sample, wherein the set comprises probes to 3q, 5p, CEP7, and 20; (b) evaluating cells of the sample to detect and quantify the presence of each probe in the set; (c) categorizing the evaluated cells of the sample as normal or abnormal, wherein the normal cells contain exactly two copies of each probe in the set and the abnormal cells do not contain exactly two copies of each probe in the set; (d) calculating the percentage of the abnormal cells in the evaluated cells of the sample; and (e) identifying the sample of cells as abnormal if the percentage of abnormal cells in the evaluated cells is greater than or equal to a predetermined cut-off threshold value. | 03-24-2016 |
20160083797 | BIOMARKER FOR BLADDER CANCER - The present invention relates to new methods for diagnosing or identifying bladder cancer in a subject for predicting the clinical outcome or determining the treatment course in a subject afflicted with bladder cancer as well as for the stratification of the therapeutic regimen of a subject with bladder cancer and for monitoring the progress of bladder cancer in a subject. The methods are based on the determination of the level or amount of methylation of the promoter of the ECRG4- and/or the promoter of the ITIH5-gene in a sample of said subject. In addition, the present invention relates to the use of a kit in a method according to the present invention. Finally, the present invention relates to new biomarkers, namely, the promoter of the ECRG4-gene or the promoter of the ITIH5-gene; in particular, the level or amount of methylation of said promoters as biomarkers for bladder cancer. | 03-24-2016 |
20160083802 | METHODS FOR DETERMINING RESPONSE TO A HYPOMETHYLATING AGENT - Disclosed are methods for predicting a response of a subject with myelodysplastic syndrome to treatment with a hypomethylating agent, for example using a sample obtained from the subject. The methods can be used to select a subject for treatment with a hypomethylating agent, and/or measure a subject's response to therapy and/or disease progression/regression. The methods include detecting, in a nucleic acid sample obtained from a subject, one or more mutations of any one or more genes selected from Table 3a. | 03-24-2016 |
20160084863 | SYSTEMS AND METHODS FOR MULTI-ANALYSIS - Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample. | 03-24-2016 |
20160090590 | HIGH THROUGHPUT SEQUENCING OF END REGIONS OF LONG LINEAR DNAs - This invention relates to linking, amplifying and sequencing of two ends of long linear DNAs. In particular, this invention provides methods for pairing and sequencing VH and VL genes that encode two parts of one immunoglobulin. The method of the present invention can be applied to rapid antibody discovery and engineering. | 03-31-2016 |
20160090631 | METHOD FOR DETECTION OF FETAL ABNORMALITIES - Disclosed are methods for non-invasive fetal genetic analysis involving enrichment of trophoblast cells in a maternal cervical sample, followed by isolation and genetic analysis of the isolated trophoblasts. | 03-31-2016 |
20160090633 | USE OF FGFR MUTANT GENE PANELS IN IDENTIFYING CANCER PATIENTS THAT WILL BE RESPONSIVE TO TREATMENT WITH AN FGFR INHIBITOR - Disclosed herein are methods of identifying a cancer patient that will be responsive to treatment with a fibroblast growth factor receptor (FGFR) inhibitor and methods of treating cancer patients. The methods involve evaluating a biological sample from the patient for the presence of one or more FGFR mutants from a FGFR mutant gene panel. Kits and primers for identifying the presence of one or more FGFR mutant genes in a biological sample are also disclosed herein. | 03-31-2016 |
20160090634 | DETECTING CHOLANGIOCARCINOMA - Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting neoplasms such as cholangiocarinoma. | 03-31-2016 |
20160097088 | Methods of Genome Sequencing and Epigenetic Analysis - Novel methods of ChIP-seq are disclosed herein. These methods of ChIP-seq employ carrier DNA to prevent loss of DNA samples. The greater DNA yields achieved by this invention permit ChIP-seq of a small number of cells, permitting epigenetic analysis of primary cells of limited quantity. | 04-07-2016 |
20160097091 | SEQUENCING METHODS, COMPOSITIONS AND SYSTEMS - In some embodiments, the disclosure relates generally to methods, as well as compositions, systems, kits and apparatuses, for performing nucleotide incorporation, comprising: (a) providing a surface including one or more reaction sites containing a polymerase and a nucleic acid template that has, or is hybridized to, an extendible end; (b) performing a first nucleotide flow by contacting one or more of the reaction sites with a first solution including one or more types of terminator nucleotide; (c) incorporating at least one type of terminator nucleotide at the extendible end of the nucleic acid template contained within at least one of the reaction sites using the polymerase; and (d) detecting a non-optical signal indicating the nucleotide incorporation using a sensor that is attached or operatively linked to the at least one reaction site. | 04-07-2016 |
20160097094 | Hydrophilic Polymeric Particles and Methods for Making and Using Same - A method of forming a particle includes, in a disperse phase within an aqueous suspension, polymerizing a plurality of mer units of a hydrophilic monomer having a hydrophobic protection group, thereby forming a polymeric particle including a plurality of the hydrophobic protection groups. The method further includes converting the polymeric particle to a hydrophilic particle. | 04-07-2016 |
20160098518 | HLA TYPING USING SELECTIVE AMPLIFICATION AND SEQUENCING - Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads. | 04-07-2016 |
20160102347 | METHODS FOR HIGH LEVEL MULTIPLEXED POLYMERASE CHAIN REACTIONS AND HOMOGENEOUS MASS EXTENSION REACTIONS - Provided herein are optimized methods for performing multiplexed detection of a plurality of sequence variations. Also provided are methods for performing multiplexed amplification of target nucleic acid. | 04-14-2016 |
20160102349 | METHODS FOR SEQUENCING POLYNUCLEOTIDES - The invention relates to methods and systems for sequencing and constructing a high resolution physical map of a polynucleotide. In accordance with the invention, nucleotide sequences are determined at the ends of restriction fragments produced by a plurality of digestions with a plurality of combinations of restriction endonucleases so that a pair of nucleotide sequences is obtained for each restriction fragment. A physical map of the polynucleotide is constructed by ordering the pairs of sequences by matching the identical sequences among the pairs. | 04-14-2016 |
20160102358 | METHODS AND COMPOSITIONS FOR CORRELATING GENETIC MARKERS WITH CANCER RISK - The present invention provides methods of assessing an individual subject's risk of developing different types of cancer, comprising calculating a genetic risk score (GRS) for the subject. | 04-14-2016 |
20160103093 | APPARATUSES, METHODS, SYSTEMS, AND COMPUTER-READABLE MEDIA FOR FLUID POTENTIAL ARTIFACT CORRECTION IN REAGENT DELIVERY SYSTEMS - A method for correcting nucleotide incorporation signals for fluid potential effects or disturbances arising in nucleic acid sequencing-by-synthesis includes: disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, the template polynucleotide strands having a sequencing primer and a polymerase bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed through a fluid manifold, the fluid manifold comprising passages for flowing nucleotide species and a branch passage for flowing a solution, the branch passage comprising a reference electrode and a sensing electrode; obtaining a plurality of nucleotide incorporation signals corresponding to the plurality of defined spaces, the nucleotide incorporation signals having a signal intensity related to a number of nucleotide incorporations; and correcting at least some of the plurality of nucleotide incorporation signals for fluid potential effects or disturbances. | 04-14-2016 |
20160103959 | Methods and Systems for Universal Carrier Screening - Provided herein are methods, systems, and devices for genetic screening. The genetic screening of two or more individuals can be utilized to predict the phenotype of a child from the group of individuals. Also disclosed is prediction of a phenotype of a child from a subset of biological relatives, such as a potential mother and father, before conception. In many instances, the methods, systems and devices herein are utilized to predict the probability of a child developing a rare genetic disease. | 04-14-2016 |
20160108462 | METHOD FOR GENETIC DETECTION USING INTERSPERSED GENETIC ELEMENTS: A MULTIPLEXED DNA ANALYSIS SYSTEM - By utilizing a Mini-Primer strategy targeting the target site duplication (TSD) sequence of retrotransposons, insertion and null allele (INNUL) markers, which include short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), and composite SVA retrotransposons (SINE/VNTR/Alu, where VNTR represents “variable number of tandem repeats” and Alu represents a type of primate specific SINE that has reached a copy number in excess of one million in the human genome), can be effectively used as markers for human identification and bio-ancestry studies regardless of the size of the inserted element. The size of the amplicons for INNULs and the difference between allelic states can be reduced substantially such that these markers have utility for analyzing high and low quality human DNA samples. Multiplexes including either 15 or 20 retrotransposable element (RE) markers plus Amelogenin for single tube amplification of DNA in four color detection were successfully designed. The multiplexes provided power of discrimination suitable for forensic and paternity analyses. | 04-21-2016 |
20160108470 | Compositions And Methods Of Nucleic Acid-Targeting Nucleic Acids - This disclosure provides for compositions and methods for the use of nucleic acid-targeting nucleic acids and complexes thereof. Genome engineering can refer to altering the genome by deleting, inserting, mutating, or substituting specific nucleic acid sequences. The altering can be gene or location specific. Genome engineering can use nucleases to cut a nucleic acid thereby generating a site for the alteration. Engineering of non-genomic nucleic acid is also contemplated. | 04-21-2016 |
20160108472 | System and Method for Authentication and Tamper Detection Using Nucleic Acid Taggants - A method for authenticating an item of interest. A nucleic acid tag comprised of a nucleotide-support platform attached to a first nucleic acid molecule is added to the item of interest, where information about the item of interest is contained within the first nucleic acid molecule. A portion of an item is sampled for the presence of the nucleic acid tag, where the item is potentially the item of interest. The presence of the nucleic acid tag is detected in the sample, where the presence of the first nucleic acid tag authenticates the item as the item of interest. | 04-21-2016 |
20160108475 | PRE-IMPLANTATION GENETIC SCREENING AND ANEUPLOIDY DETECTION - Provided herein are methods for determining ploidy of an embryo. The methods can include the steps of amplifying, using a primer pair that amplifies a plurality of human genomic loci, nucleic acid from a preimplantation embryo to generate a plurality of amplicons, sequencing the amplicons to generate a plurality of sequence reads, matching the sequence reads to the genomic loci and counting a number of matches, and determining chromosome count based on the number of matches. Also provided herein are systems for determining chromosome count comprising a processor coupled to a tangible memory subsystem storing instructions. When executed by the processor, the instructions cause the system to implement the methods provided. | 04-21-2016 |
20160108476 | COLORECTAL CANCER MARKERS - The invention relates to the identification and selection of novel genomic regions (biomarker) and the identification and selection of novel genomic region combinations which are hypermethylated in subjects with colorectal cancer compared to subjects without colorectal cancer. Nucleic acids which selectively hybridize to the genomic regions and products thereof are also encompassed within the scope of the invention as are compositions and kits containing said nucleic acids and nucleic acids for use in diagnosing prostate cancer. Further encompassed by the invention is the use of nucleic acids which selectively hybridize to one of the genomic regions or products thereof to monitor disease progression or regression in a patient and the efficacy of therapeutic regimens. | 04-21-2016 |
20160110499 | METHODS, SYSTEMS, AND COMPUTER-READABLE MEDIA FOR BLIND DECONVOLUTION DEPHASING OF NUCLEIC ACID SEQUENCING DATA - Embodiments disclose methods, systems, and computer-readable media for base-calling of sequencing data in the presence of systematic or phasic synchrony errors. These techniques may be adapted to rapidly and accurately resolve signal data arising from a variety of different nucleic acid sequencing platforms. In various embodiments, techniques for blind deconvolution dephasing of nucleic acid sequencing data may be adapted to perform raw signal processing, basecalling, and/or sequence determination. | 04-21-2016 |
20160115444 | AGE-MODIFIED CELLS AND METHODS FOR MAKING AGE-MODIFIED CELLS - Provided are age-modified cells and method for making age modified cells using progerin or a progerin-like protein. The aging and/or maturation process can be accelerated and controlled for young and/or immature cells, such as a somatic cell, a stem cell, a stem cell-derived somatic cell, including an induced pluripotent stem cell-derived cell, by contacting with progerin or a progerin-like protein. Methods described by the present disclosure can produce age-appropriate cells from a somatic cell or a stem cell, such as an old cell and/or a mature cell. Such age-modified cells constitute model systems for the study of late-onset diseases and/or disorders. | 04-28-2016 |
20160115521 | BACILLUS THURINGIENSIS TOXIN RESISTANCE ASSAY - A method for monitoring resistance to a | 04-28-2016 |
20160115523 | METHODS AND COMPOSITIONS FOR DETECTION OF SMALL RNAS - Currently, the circularization of small RNAs is broadly regarded as an obstacle in ligation-related assays and explicitly avoided while short lengths of linear RNA targets is broadly recognized as a factor limiting use of conventional primers in PCR-related assays. In contrast, the disclosed invention capitalizes on circularization of small RNA targets or their conjugates with oligonucleotide adapters. The circular RNA templates provide amplification of the target sequences via synthesis of multimer nucleic acids that can be either labeled for direct detection or subjected to PCR amplification and detection. Structure of small circular RNAs and corresponding multimeric nucleic acids provide certain advantages over current methods including flexibility in design of conventional RT and PCR primers as well as use of 5′-overlapping dimer-primers for efficient and sequence-specific amplification of short target sequences. Our invention also reduces number of steps and reagents while increasing sensitivity and accuracy of detection of small RNAs with both 2′OH and 2′-OMe at their 3′ ends. Our invention increase sensitivity and specificity of detection of microRNAs and other small RNAs with both 2′OH and 2′-OMe at their 3′ ends while allowing us to distinguish these two forms from each other. | 04-28-2016 |
20160115533 | SEQUENCING BY ORTHOGONAL SYNTHESIS - A method for sequencing includes steps of (a) providing first and second nucleic acid templates, wherein the two templates have different sequences; (b) extending a first primer bound to the first template using a first polymerase species and a first set of nucleotide analogs; (c) extending a second primer bound to the second template using a second polymerase species and a second set of nucleotide analogs, wherein the first polymerase species is different from the second polymerase species and wherein the first set of nucleotide analog is different from the second set of nucleotide analog, (d) detecting the first and second primer extension products; and (e) repeating steps (b) through (d), thereby determining the different sequences of the first and second templates. | 04-28-2016 |
20160115553 | METHODS FOR PERSONALIZING CANCER TREATMENT - Personalized medicine involves the use of a patient's molecular markers to guide treatment regimens for the patient. The scientific literature provides multiple examples of correlations between drug treatment efficacy and the presence or absence of molecular markers in a patient sample. Methods are provided herein that permit efficient dissemination of scientific findings regarding treatment efficacy and molecular markers found in patient tumors to health care providers. | 04-28-2016 |
20160121325 | INSTRUMENT SYSTEMS FOR INTEGRATED SAMPLE PROCESSING - An integrated system for processing and preparing samples for analysis may include a microfluidic device including a plurality of parallel channel networks for partitioning the samples including various fluids, and connected to a plurality of inlet and outlet reservoirs, at least a portion of the fluids comprising reagents, a holder including a closeable lid hingedly coupled thereto, in which in a closed configuration, the lid secures the microfluidic device in the holder, and in an open configuration, the lid is a stand orienting the microfluidic device at a desired angle to facilitate recovery of partitions or droplets from the partitioned samples generated within the microfluidic device, and an instrument configured to receive the holder and apply a pressure differential between the plurality of inlet and outlet reservoirs to drive fluid movement within the channel networks. | 05-05-2016 |
20160122717 | DIFFERENTIATION OF PLURIPOTENT STEM CELLS AND CARDIAC PROGENITOR CELLS INTO STRIATED CARDIOMYOCYTE FIBERS USING LAMININS LN-511, LN-521 AND LN-221 - The present disclosure describes methods of differentiating cardiomyocyte progenitor cells and mature cardiomyocyte cells from pluripotent stem cells. The methods may include differentiating pluripotent stems cells on a substrate including (i) laminin-511 or 521 and (ii) laminin 221. The mature cardiomyocyte cells produced by the method may form a human heart muscle cell line for use in regenerative cardiology. | 05-05-2016 |
20160122747 | TARGET ANTIGEN DISCOVERY, PHENOTYPIC SCREENS AND USE THEREOF FOR IDENTIFICATION OF TARGET CELL SPECIFIC TARGET EPITOPES - The invention provides methods and compositions for identifying binding polypeptides (e.g., antibodies or antigen binding fragments thereof) that specifically binds to a cell-surface antigen. The methods of the invention generally comprise contacting a variegated nucleic acid-display library of binding polypeptides with a cell-surface antigen displayed on the exterior surface of a cell; and isolating from the library at least one library member that specifically binds to the cell-surface antigen on the exterior surface of the cell. | 05-05-2016 |
20160122752 | Methods for Obtaining Information from Single Cells Within Populations Using DNA Origami Nanostructures Without the Need for Single Cell Sorting - Methods for construction of DNA origami nanostructures, as well as for binding, isolation, linking, and deep sequencing information, such as both of TCR alpha and beta CDR3 mRNA, from individual cells within a mixed population of cells without the need for single cell sorting. | 05-05-2016 |
20160122755 | Compositions, Methods and Apparatus for Oligonucleotides Synthesis - Aspects of the invention relate to methods, compositions for synthesizing oligonucleotides having a predefined sequence. | 05-05-2016 |
20160122814 | METHODS OF SEQUENCING WITH LINKED FRAGMENTS - The invention generally relates to sequencing library preparation methods. In certain embodiments, two template nucleic acids are joined together by a linking molecule, such as a PEG derivative. The linked template nucleic acids is amplified, creating linked amplicons. | 05-05-2016 |
20160122819 | METHOD FOR QUANTIFYING THE LEVEL OF MINIMAL RESIDUAL DISEASE IN A SUBJECT - The present invention belongs to the field of diagnosis of disease. Thus the present invention is focused on a method and kit for quantifying the level of minimal residual disease (MRD) in a subject who has been treated for said disease, which comprises: | 05-05-2016 |
20160122830 | METHODS FOR PERSONALIZING CANCER TREATMENT - Personalized medicine involves the use of a patient's molecular markers to guide treatment regimens for the patient. The scientific literature provides multiple examples of correlations between drug treatment efficacy and the presence or absence of molecular markers in a patient sample. Methods are provided herein that permit efficient dissemination of scientific findings regarding treatment efficacy and molecular markers found in patient tumors to health care providers. | 05-05-2016 |
20160122833 | Quasispecies analysis of JC virus DNA present in urine of healthy subjects - JC virus (JCV) is a human polyomavirus that infects the majority of people without apparent symptoms in healthy subjects. A neuropathogenic JCV variant is the causative agent of progressive multifocal leucoencephalopathy (PML), a disorder following lytic infection of oligodendrocytes that mainly manifests itself under immunosuppressive conditions. A hallmark for JCV isolated from PML-brain is the presence of rearrangements in the non-coding control region (NCCR) interspersed between the early and late genes on the viral genome. Such rearrangements are believed to originate from the archetype JC virus variant which is shed in urine by healthy subjects and PML patients. Next generation sequencing (pyro-sequencing) has been performed to explore the NCCR variability in urine of healthy subjects in search for JCV quasispecies and rearrangements reminiscent of PML. | 05-05-2016 |
20160123852 | PARTICLE RELEASE AND COLLECTION - Particles are released from a particle-containing area of a first surface of a porous matrix. The particle-containing area is contacted with a liquid medium and sonic energy is applied to an opposing area on a second surface of the porous matrix, wherein the opposing area is opposite to the particle-containing area. The particles may be biological particles or non-biological particles. | 05-05-2016 |
20160124009 | SYSTEMS AND METHODS FOR FLUID AND COMPONENT HANDLING - Systems and methods are provided for sample processing. A device may be provided, capable of receiving the sample, and performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing multiple assays. The device may comprise one or more modules that may be capable of performing one or more of a sample preparation, sample assay, and detection step. The device may be capable of performing the steps using a small volume of sample. | 05-05-2016 |
20160130643 | ACCURATE IN VITRO COPYING OF DNA METHYLATION - A method of copying a methylated nucleic acid molecule is provided. The method includes copying a nucleic acid molecule into a plurality of nucleic acid molecules; and contacting the plurality of nucleic acid molecules with a DNA methyltransferase enzyme and an E3 ubiquitin ligase. The method results in the copying of the methylated nucleic acid molecule. | 05-12-2016 |
20160130646 | METHODS AND COMPOSITIONS FOR SEQUENCING MODIFIED NUCLEIC ACIDS - Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid. | 05-12-2016 |
20160130647 | SIGNAL CONFINEMENT SEQUENCING (SCS) AND NUCLEOTIDE ANALOGUES FOR SIGNAL CONFINEMENT SEQUENCING - Novel fluorescent nucleotide analogues are provided herein. Also provided herein are methods of using the nucleotide analogues in sequencing-by-synthesis and signal confinement methods. | 05-12-2016 |
20160130651 | Biological Analysis Systems, Devices, And Methods - A device for performing biological sample reactions may include a plurality of flow cells configured to be mounted to a common microscope translation stage, wherein each flow cell is configured to receive at least one sample holder containing biological sample. Each flow cell also may be configured to be selectively placed in an open position for positioning the at least one sample holder into the flow cell and a closed position for reacting biological sample contained in the at least one sample holder. The plurality of flow cells may be configured to be selectively placed in the open position and the closed position independently of each other. | 05-12-2016 |
20160132632 | System, Method and Software for Improved Drug Efficacy and Safety in a Patient - The present invention provides systems, methods and software predicting drug efficacy for treating a disorder in a patient, the method including providing a drug score database (DSD) based on pathway manifestation strengths (PMSs) for a plurality of biological pathways associated with the drug in the treatment of the disorder and comparing the pathway manifestation strengths of the plurality of biological pathways of the patient with the drug score database to provide a predictive indication if the patient is a responder or non-responder to the drug to determine whether the drug should be used in treating the patient. | 05-12-2016 |
20160132635 | DIRECTED STRATEGIES FOR IMPROVING PHENOTYPIC TRAITS - The present invention provides a method for improving at least one phenotypic trait of interest in subsequent generation(s) of a population of individuals, preferably crop plants or cattle. Particularly, the method identifies the combination of at least three individuals that gives, upon subsequent intercrossing, the highest estimated probability of improving the at least one phenotypic trait of interest in the subsequent generation(s). Also provided is a computer-readable medium comprising instructions for performing the method. | 05-12-2016 |
20160136643 | MICROFLUIDIC METHODS FOR MANIPULATING DNA - Techniques are provided for generating, manipulating, and measuring fluidic droplets in mixed phase systems based on establishing transient continuities between otherwise spatially separated phases. In certain methods of the invention, electrodes in contact with the continuous phases allow electrical monitoring of continuity or proximity of separated phases as a means to characterize droplets. In other methods of the invention, fluidic continuity provides a means for generating droplets, injecting or extracting the contents of droplets, and sorting droplets. Chemical techniques are also provided that use these droplet-based methods, or others, to quantify and identify nucleic acids through incorporation into hydrogel particles. The nucleic acids are entrapped either actively by chemical incorporation during gel polymerization or passively by chain entanglement. After incorporation into the hydrogel particles, the nucleic acids are solvent accessible either at the particle periphery or within internal pores for further biochemical manipulations and characterization. In one important aspect, the invention combines the high specificity, high sensitivity, and unbiased performance of clonal DNA amplification in free solution with the simplicity of permanently co-localizing the separate reaction products onto rigid substrates for myriad biochemical applications. | 05-19-2016 |
20160138091 | METHODS AND SYSTEMS FOR DETERMINING SPATIAL PATTERNS OF BIOLOGICAL TARGETS IN A SAMPLE - The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature. | 05-19-2016 |
20160138094 | Direct, Programmable Detection of Epigenetic DNA Cytosine Modifications using TAL Effectors - The present invention relates to methods for the differentiation of a 5-hydroxymethyl modification of a cytosine residue of interest in a nucleic acid molecule from (i) a 5-methyl modification of said cytosine residue of interest o,r (ii) said unmodified cytosine residue of interest, said methods making use of the capability of transcription-activator-like effector (TALE) proteins to preferentially bind with strong affinity to nucleic acid sequences containing non-modified cytosine residues or 5-methyl modified cytosine residues, and to bind, if at all, with only strongly reduced affinity to nucleic acid sequences containing 5-hydroxymethyl modified cytosine residues. The present invention further relates to respective uses of TALE proteins for the differentiation of a 5-hydroxymethyl modification of a cytosine residue of interest in a nucleic acid molecule from (i) a 5-methyl modification of said cytosine residue of interest or (ii) said unmodified cytosine residue of interest. | 05-19-2016 |
20160138101 | METHOD AND DEVICE FOR IDENTIFYING NUCLEOTIDE, AND METHOD AND DEVICE FOR DETERMINING NUCLEOTIDE SEQUENCE OF POLYNUCLEOTIDE - The present invention provides technology that uses current measurements to identify nucleotides and determine a nucleotide sequence in polynucleotides. The present invention calculates a modal value of a tunnel current that arises when a nucleotide or polynucleotide for analysis passes through between electrodes, and then employs the calculated modal value. The present invention accordingly enables direct rapid implementation to identify nucleotides and to determine a nucleotide sequence in a polynucleotide without marking. | 05-19-2016 |
20160138104 | METHODS FOR DETERMINING THE QUALITY OF AN EMBRYO - The present invention relates generally to the fields of reproductive medicine. More specifically, the present invention relates to in vitro non invasive methods and kits for determining the quality of an embryo by determining the level of the cell free nucleic acids and/or determining the presence and/or expression level of at least one specific nucleic acid sequence in the nude is acid extraction. | 05-19-2016 |
20160138107 | Mutations Associated With Cystic Fibrosis - The present invention provides novel mutations identified in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that can be used for a more accurate diagnosis of cystic fibrosis (CF) and CF related disorders. Methods for testing a sample obtained from a subject to determine the presence of one or more mutations in the CFTR gene are provided wherein the presence of one or more mutations indicates that the subject has CF or a CF related disorder, or is a carrier of a CFTR mutation. | 05-19-2016 |
20160138115 | METHODS AND CHARACTERISTICS FOR THE DIAGNOSIS OF ACUTE LYMPHOBLASTIC LEUKEMIA - Methods for identification of leukemia or a genetic predisposition to leukemia are provided that are particularly applicable to acute lymphoblastic leukemia (ALL). A novel heterozygous germline variant, c.547G>A (p.Gly183Ser) in the octapeptide domain of PAX5, is used to identify those individuals with an enhanced risk or predisposition to ALL. | 05-19-2016 |
20160138116 | METHODS FOR MONITORING TREATMENT RESPONSE AND RELAPSE IN BREAST CANCER - The present invention provides a method for monitoring the response to treatment in a patient undergoing breast cancer therapy, comprising detecting the presence of a loss-of-function-related genetic alteration in the PAPPA gene or its regulatory or promoter sequences in a sample obtained from the patient wherein if the genetic alteration is present but its quantitative level decreases during treatment, this is indicative of response to therapy, whereas, if there is no change or upward change in its quantitative level during therapy, this is indicative of non-response to therapy. The invention also relates to the use of specific biological markers for monitoring for relapse, and aiding the screening, primary diagnosis and staging of breast cancer. | 05-19-2016 |
20160145666 | Poly(UG) Polymerase, Constructs, and Methods of Making and Using the Same - Methods, kits, and compositions of matter relating to poly(UG) polymerases are disclosed. In one embodiment, a method includes: contacting an RNA substrate with a poly(UG) polymerase; and allowing the poly(UG) polymerase to add a poly(UG) sequence to the end of the RNA substrate by retaining contact between the RNA substrate and the poly(UG) polymerase for a period of time from about 1 second to about 28 days. The poly(UG) polymerase can be | 05-26-2016 |
20160145677 | SPATIALLY ENCODED BIOLOGICAL ASSAYS USING A MICROFLUIDIC DEVICE - The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents, in particular, microfluidic device based instrumentation; and a decoding scheme providing a readout that is digital in nature. | 05-26-2016 |
20160145681 | METHODS AND MATERIALS FOR ASSESSING ALLELIC IMBALANCE - Methods and systems for detecting allelic imbalance using nucleic acid sequencing are provided. | 05-26-2016 |
20160145684 | METHODS OF DETECTING SYNTHETIC URINE AND MATCHING A URINE SAMPLE TO A SUBJECT - Provided herein are methods for determining if a urine sample comprises synthetic urine, methods for matching a urine sample to a subject, and methods for amplifying DNA. Also provided are kits that include a set of at least 3 pairs of a pre-amplification forward and reverse primer, where each pair of pre-amplification forward and reverse primers is designed to amplify 250 to 300 nucleotides of genomic DNA that contains one of at least 3 SNPs, where the pre-amplification forward and reverse primers in each of the three or more pairs of pre-amplification primers contains (i) a sequence of about 17 to about 25 contiguous nucleotides that is complementary to a sequence in the genomic DNA and (i) a tag sequence of about 17 to about 25 contiguous nucleotides that is not complementary to a sequence in the genomic DNA. | 05-26-2016 |
20160145687 | Method of Predicting Risk for Type 1 Diabetes - The present invention relates to methods, transcriptome profiles and kits useful for determining, before seroconversion, the risk that an individual will develop Type 1 diabetes (T1D). | 05-26-2016 |
20160145689 | STRATEGIES FOR HIGH THROUGHPUT IDENTIFICATION AND DETECTION OF POLYMORPHISMS - The invention relates to a method for the high throughput identification of single nucleotide polymorphisms by performing a complexity reduction on two or more samples to yield two or more libraries, sequencing at least part of the libraries, aligning the identified sequences and determining any putative single nucleotide polymorphisms, confirming any putative single nucleotide polymorphism, generating detection probes for the confirmed single nucleotide polymorphisms, subjection a test sample to the same complexity reduction to provide a test library and screen the test library for the presence or absence of the single nucleotide polymorphisms using the detection probe. | 05-26-2016 |
20160145693 | METHODS FOR THE DIAGNOSIS OF ONCOLOGICAL DISORDERS USING EPIMETABOLIC SHIFTERS, MULTIDIMENSIONAL INTRACELLULAR MOLECULES, OR ENVIRONMENTAL INFLUENCERS - Methods and formulations for diagnosing onocological disorders in humans using epimetabolic shifters, multidimensional intracellular molecules or environmental influencers are described. | 05-26-2016 |
20160145694 | METHOD FOR DETECTING METHYLATION OF COLORECTAL CANCER SPECIFIC METHYLATION MARKER GENE FOR COLORECTAL CANCER DIAGNOSIS - The present invention relates to a method for detecting methylation of the bowel-cancer-specific methylation marker GPM6A (NM_201591, glycoprotein M6A) gene in order to diagnose bowel cancer, and more specifically relates to a method for providing information for diagnosing bowel cancer by detecting the methylation of a bowel-cancer-specific marker gene that is specifically methylated in bowel cancer cells. The method for detecting methylation and a diagnostic composition, kit and nucleic-acid chip according to the present invention can be used to advantage in diagnosing bowel cancer more accurately and quickly than by normal methods as they permit bowel cancer to be diagnosed at the initial genetic transformation step and so allow early diagnosis. | 05-26-2016 |
20160145697 | A Method for Determining the Vase Life or Storage History of One or More Cut Flowers, Wherein the Method Comprises Assaying Xylose Concentration or Beta-Xylosidase Expression/Activity - A method for determining the vase life or storage history of one or more cut flowers, wherein the method comprises assaying a test sample obtained from the one or more cut flowers for one or more of: (a) an indicator representative of xylose concentration; (b) an indicator representative of β-xylosidase expression; and (c) an indicator representative of β-xylosidase activity; to determine a value for (each of) the one or more indicators in the test sample. | 05-26-2016 |
20160146786 | Method of monitoring cellular trafficking of peptides - This disclosure provides a method of isolating peptides having cell-penetrating function, wherein the peptides are detected as biotinylated molecules only following their translocation through the cell membrane. The disclosure also provides methods for validating the cell-penetrating function of the peptides, or that may be employed in their own right to isolate such peptides, wherein the peptides are detectable by virtue of their ability to transport a detectable cargo into the cytoplasm, such as a cargo toxin or a fragment of a green fluorescent protein (GFP) that is required for complementation of a functional GFP. The disclosure also provides non-canonical peptides having cell-penetrating function that differ structurally from known CPPs such as TAT, VP22, transportan and penetratin, and that are capable of translocating cell membranes and escaping the endosome. The disclosed peptides have utility in transporting cargo therapeutics and diagnostics into cells. | 05-26-2016 |
20160146830 | PROTEOMIC IDENTIFICATION OF ANTIBODIES - Methods and compositions for identification of candidate antigen-specific variable regions as well as generation of antibodies or antigen-binding fragments that could have desired antigen specificity are provided. For example, in certain aspects, methods for determining amino acid sequences of serum antibody CDR3 and abundancy levels are described. In some aspects, methods for determining nucleic acid sequences of antibody variable region sequences and the frequency thereof in biological samples are provided. Furthermore, the invention provides methods for identification and generation of antibodies or antigen-binding fragments that comprise highly-represented CDR domains. | 05-26-2016 |
20160152977 | ANALYZING METHOD FOR MICRO RNA ID AND BIOMARKERS RELATED TO COLON CANCER THROUGH THIS METHOD | 06-02-2016 |
20160153029 | DNA SEQUENCES TO ASSESS CONTAMINATION IN DNA SEQUENCING | 06-02-2016 |
20160153039 | COMPOSITIONS AND METHODS FOR TARGETED NUCLEIC ACID SEQUENCE ENRICHMENT AND HIGH EFFICIENCY LIBRARY GENERATION | 06-02-2016 |
20160153042 | MARKERS TO PREDICT MACROCYCLIC LACTONE DRUG RESISTANCE IN DIROFILARIA IMMITIS, THE CAUSATIVE AGENT OF HEARTWORM DISEASE | 06-02-2016 |
20160153045 | Biomarkers for Increased Risk of Drug-Induced 5-Aminosalicylate Nephrotoxicity | 06-02-2016 |
20160153046 | Biomarkers for Increased Risk of Drug-Induced Thiopurine-Induced Pancreatitis | 06-02-2016 |
20160153054 | BIOMARKERS FOR COLORECTAL CANCER | 06-02-2016 |
20160153056 | RICE WHOLE GENOME BREEDING CHIP AND APPLICATION THEREOF | 06-02-2016 |
20160160275 | WHOLE-GENOME AND TARGETED HAPLOTYPE RECONSTRUCTION - The present invention relates to methods for haplotype determination and, m particular, haplotype determination at the whole genome level as well as targeted haplotype determination. | 06-09-2016 |
20160160277 | METHOD FOR SEQUENCING A POLYNUCLEOTIDE TEMPLATE - The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which permit the sequential determination of nucleotide sequences in two distinct and separate regions on complementary strands of the double-stranded polynucleotide template. The two regions for sequence determination may or may not be complementary to each other. | 06-09-2016 |
20160160281 | CYSTIC FIBROSIS GENE MUTATIONS - The present invention provides novel mutations of the CFTR gene related to cystic fibrosis or to conditions associated with cystic fibrosis. Also provided are probes for detecting the mutant sequences. Methods of identifying if an individual has a genotype containing one or more mutations in the CFTR gene are further provided. | 06-09-2016 |
20160160287 | METHOD FOR DETERMINING THE RISK OF DEVELOPING RADIATION-INDUCED TOXICITY AFTER EXPOSURE TO RADIATION - The invention is in the art of medical treatments, in particular the treatment of tumors with ionizing radiation. It provides means and methods for predicting whether a subject is likely to develop radiation damage upon radiotherapy. The invention provides tools that allow individualized and optimized radiation treatment of a subject in need of a radiation treatment. The invention also provides methods of determining the risk of developing severe dyspnea after radiation treatment. More in particular, the invention relates to an in vitro method for predicting the risk of developing radiation induced toxicity comprising the steps of obtaining mitochondrial DNA from a sample of a subject, determining the number of non-synonymous variations present in at least one gene encoding a mitochondrial protein, attributing a value to the number of non-synonymous variations, wherein a higher value corresponds to a higher risk of developing radiation induced lung toxicity. | 06-09-2016 |
20160160295 | NON-CODING RNAS AND USES THEREOF - Provided herein are compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, provided herein are non-coding RNAs as diagnostic markers and clinical targets for cancer. | 06-09-2016 |
20160162636 | SYSTEM AND METHOD FOR INTER-SPECIES DNA MIXTURE INTERPRETATION - Methods and systems for characterizing two or more nucleic acids in a sample. The method can include the steps of providing a hybrid machine learning approach that enables rapid and automated deconvolution of DNA mixtures of multiple contributors. The input is analyzed by an expert system which is implemented in the form of a rule set. The rule set establishes requirements based on expectations on the biology and methods used. The methods and systems also include a machine learning algorithm that is either incorporated into the expert system, or utilizes the output of the expert system for analysis. The machine learning algorithm can be any of a variety of different algorithms or combinations of algorithms used to perform classification in a complex data environment. | 06-09-2016 |
20160168611 | METHODS AND APPARATUS FOR SYNTHESIZING NUCLEIC ACIDS | 06-16-2016 |
20160168632 | DNA SEQUENCING AND EPIGENOME ANALYSIS | 06-16-2016 |
20160168634 | Windowed Sequencing | 06-16-2016 |
20160168635 | INTEGRATED SENSOR ARRAYS FOR BIOLOGICAL AND CHEMICAL ANALYSIS | 06-16-2016 |
20160168639 | GENETIC POLYMORPHISMS ASSOCIATED WITH STROKE, METHODS OF DETECTION AND USES THEREOF | 06-16-2016 |
20160168644 | Method for the quantitative analysis of nucleic acid fragmentation and amplificability | 06-16-2016 |
20160169865 | High-Speed Molecular Diagnostics | 06-16-2016 |
20160169898 | METHODS FOR PREDICTING AND IMPROVING THE SURVIVAL OF COLORECTAL CANCER PATIENTS | 06-16-2016 |
20160171152 | METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING | 06-16-2016 |
20160177359 | METHOD FOR CONTROLLED DNA FRAGMENTATION | 06-23-2016 |
20160177373 | POLYMERASE COMPOSITIONS AND METHODS OF MAKING AND USING SAME | 06-23-2016 |
20160177380 | COMPOSITIONS FOR RNA-CHROMATIN INTERACTION ANALYSIS AND USES THEREOF | 06-23-2016 |
20160177385 | HIGH DATA RATE INTEGRATED CIRCUIT WITH POWER MANAGEMENT | 06-23-2016 |
20160177392 | METHODS FOR MEASURING VIRULENCE IN SOYBEAN CYST NEMATODE | 06-23-2016 |
20160177393 | LAFORA'S DISEASE GENE | 06-23-2016 |
20160177398 | DNA Methylation Biomarkers for Bladder Cancer | 06-23-2016 |
20160177399 | A KIT FOR THE PROGNOSIS OF COLORECTAL CANCER | 06-23-2016 |
20160178615 | RGD-BINDING COMPOUNDS AND METHODS OF USE | 06-23-2016 |
20160180018 | MOLECULAR AND BIOINFORMATICS METHODS FOR DIRECT SEQUENCING | 06-23-2016 |
20160184829 | NUCLEIC ACID AMPLIFICATION APPARATUS AND SYSTEM - This present disclosure relates to devices, systems, and methods for performing biological assays. In particular, the present disclosure provides microfluidic devices, systems, and methods for performing fast amplification reactions. | 06-30-2016 |
20160186146 | HUMAN PLURIPOTENT STEM CELL-BASED MODELS FOR PREDICTIVE DEVELOPMENTAL NEURAL TOXICITY - The present invention relates to three-dimensional (3D) tissue constructs and methods of using such 3D tissue constructs to screen for neurotoxic agents. In particular, provided herein are methods of producing and using complex, highly uniform human tissue models comprising physiologically relevant human cells, where the tissue models have the degree of sample uniformity and reproducibility required for use in quantitative high-throughput screening applications. | 06-30-2016 |
20160186252 | PH MEASUREMENT FOR SEQUENCING OF DNA - The present method involves sequencing by synthesis in which a template strand having an attached primer is immobilized in a small volume reaction mixture. In one embodiment, the reaction mixture is in contact with a sensitive heat sensor, which detects the heat of reaction from incorporation of a complementary base (dNTP) in the presence of appropriate reagents (DNA polymerase, and polymerase reaction buffer). Alternatively, or in addition, a change in pH resulting from the incorporation of nucleotides in the DNA polymerase reaction is measured. A device is provided having delivery channels for appropriate reagents, including dNTPs, which may be delivered sequentially or in a mixture. Preferably, the dNTPs are added in a predetermined sequence, and the dNTP is incorporated or not depending on the template sequence. | 06-30-2016 |
20160186253 | NON-INVASIVE PRENATAL DIAGNOSIS OF FETAL GENETIC CONDITION USING CELLULAR DNA AND CELL FREE DNA - Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother. In various embodiments, the method can determine one or more sequences of interest in a test sample that comprises a mixture of fetal cellular DNA and mother-and-fetus cfDNA. In some embodiments, methods are provided for determining whether the fetus has a genetic disease. In some embodiments, methods are provided for determining whether the fetus is homozygous in a disease causing allele when the mother is heterozygous of the same allele. In some embodiments, methods are provided for determining whether the fetus has a copy number variation (CNV) or a non-CNV genetic sequence anomaly. | 06-30-2016 |
20160186254 | Sequencing Biopolymers - The invention relates to a method and a corresponding arrangement for sequencing at least two biopolymers ( | 06-30-2016 |
20160186256 | IN VITRO EVOLUTION IN MICROFLUIDIC SYSTEMS - The invention describes a method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising the steps of: (a) compartmentalising genetic elements into microcapsules; and (b) sorting the genetic elements which express the gene product having the desired activity; wherein at least one step is under microfluidic control. The invention enables the in vitro evolution of nucleic acids and proteins by repeated mutagenesis and iterative applications of the method of the invention. | 06-30-2016 |
20160186261 | PREVOTELLA COPRI AND ENHANCED SUSCEPTIBILITY TO ARTHRITIS - Methods, reagents and compositions thereof for predicting risk for NORA onset in susceptible individuals, diagnosing NORA onset, and/or evaluating efficacy of a therapeutic regimen for treating RA are described herein. Determining the amount of at least one of SEQ ID NOs: 1-19 and/or at least one of a KO presented in either of Tables S4 or S5 serves as a biomarker for the above indications. | 06-30-2016 |
20160186262 | COMPOSITIONS AND METHODS FOR GENETIC ANALYSIS OF EMBRYOS - This disclosure provides compositions and methods for determining a presence or absence of a genomic copy number alteration (CNA) in an embryo, wherein the method comprises analysis of RNA from an embryo or cDNA derived from this RNA. Generally, the compositions and methods provide for the acquisition of a sample containing RNA produced by an embryo, application of one or more of at least 3 different methods for detecting CNAs. One method can identify CNAs based on the identification of alterations in expression of loci or alleles affected by the CNA. Another can identify CNAs based on the identification of associated breakpoint. A third can identify CNAs based on expression profiles that are associated with CNAs. A variety of other genetic and biologic analyses can be performed on the RNA in combination with the copy number analyses. Analysis of copy number in embryos can provide information that can provide important clinical information pertaining to the health and developmental potential of an embryo that can impact the plans of the parents and clinical staff for the embryo. | 06-30-2016 |
20160186266 | MOLECULAR PROFILING FOR PERSONALIZED MEDICINE - Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease. | 06-30-2016 |
20160186267 | METHODS, COMPOSITIONS, AND KITS FOR NUCLEIC ACID ANALYSIS - Aspects of the invention relate to methods and kits for assessing cancer. Some aspects of the invention relate to methods and kits for preparing a sample library for sequencing. Some aspects of the invention relate to methods and kits for allele detection. Some aspects of the invention relate to high efficiency ligation methods and kits. Some aspects of the invention relate to sensitive detection of amplicons. | 06-30-2016 |
20160187347 | BIOMARKER TEST FOR PREDICTION OR EARLY DETECTION OF PREECLAMPSIA AND/OR HELLP SYNDROME - Disclosed are specific biomarkers that allow for early testing of preeclampsia/HELLP syndrome. Thus, a method is provided predicting preeclampsia in a pregnant woman. Also disclosed is a kit comprising means for assaying a sample from a pregnant woman for the concentrations of the specific biomarkers. | 06-30-2016 |
20160187352 | METHODS AND KITS FOR PREDICTING THE RISK OF HAVING A CARDIOVASCULAR DISEASE OR EVENT - The present invention relates to a method for diagnosing a cardiovascular event or disease in a subject by measuring sTREM-1 level in a sample. | 06-30-2016 |
20160188792 | Methods and Compositions for the Detection, Classification, and Diagnosis of Schizophrenia - Disclosed are compositions and methods for the diagnosis and classification of schizophrenia. | 06-30-2016 |
20160188793 | Method For Determining Genotypes in Regions of High Homology - Described herein are methods directed to determining the carrier status or genotype of a subject. Described herein is a method that combines experimental and computational approaches to resolve the structure of genomic loci (i.e., the genotype) whose sequences are highly homologous to other sequences in the genome. In particular, the determination of carrier status and/or copy number of a gene in a subject, wherein the gene has a corresponding highly homologous homolog, e.g., gene or pseudogene, utilizes Next Generation Sequencing. Also described herein is a computer-assisted method for such determinations. | 06-30-2016 |
20160194629 | SCAFFOLDED NUCLEIC ACID POLYMER PARTICLES AND METHODS OF MAKING AND USING | 07-07-2016 |
20160194686 | Efficient Arrays of Amplified Polynucleotides | 07-07-2016 |
20160194691 | DNA MUTATION DETECTION EMPLOYING ENRICHMENT OF MUTANT POLYNUCLEOTIDE SEQUENCES AND MINIMALLY INVASIVE SAMPLING | 07-07-2016 |
20160194692 | SCREENING FOR STRUCTURAL VARIANTS | 07-07-2016 |
20160194696 | Detecting, Sequencing and/or Mapping 5-Hydroxymethylcytosine and 5-Formylcytosine at Single-Base Resolution | 07-07-2016 |
20160194703 | DETECTING AND CLASSIFYING COPY NUMBER VARIATION | 07-07-2016 |
20160194716 | MIRNA in Gulf War Illness | 07-07-2016 |
20160195514 | Methods for Genetically Diversified Stimulus-Response Based Gene Association Studies | 07-07-2016 |
20160196382 | VARIETY IDENTIFICATION-ENCODING SYSTEM AND ENCODING METHOD USING THE SAME | 07-07-2016 |
20160200772 | BINDING POLYPEPTIDES HAVING A MUTATED SCAFFOLD | 07-14-2016 |
20160201026 | MICROBIAL CONSORTIA FOR PROGRAMMABLE OUTPUT VIA PHOTOAUTOTROPH-HETEROTROPH INTERACTIONS | 07-14-2016 |
20160201052 | METHODS FOR RETRIEVING SEQUENCE-VERIFIED NUCLEIC ACID FRAGMENTS AND APPARATUSES FOR AMPLIFYING SEQUENCE VERIFIED NUCLEIC ACID FRAGMENTS | 07-14-2016 |
20160201126 | EFFICIENT BIOMOLECULE RECYCLING METHOD AND SYSTEM | 07-14-2016 |
20160201128 | METHODS FOR SELECTING COMPETENT OOCYTES AND COMPETENT EMBRYOS WITH HIGH POTENTIAL FOR PREGNANCY OUTCOME | 07-14-2016 |
20160201129 | DETERMINATION OF IMMUNE CELLS AND OTHER CELLS | 07-14-2016 |
20160201131 | Method for Identifying Drug Resistance Related Mutations | 07-14-2016 |
20160201134 | NONINVASIVE PRENATAL DIAGNOSIS OF FETAL TRISOMY BY ALLELIC RATIO ANALYSIS USING TARGETED MASSIVELY PARALLEL SEQUENCING | 07-14-2016 |
20160201143 | LKB1 Levels and Brain Metastasis from Non-Small-Cell Lung Cancer (NSCLC) | 07-14-2016 |
20160203259 | DIGITAL MEASUREMENTS FROM TARGETED SEQUENCING | 07-14-2016 |
20160203260 | APPLICATIONS OF PLASMA MITOCHONDRIAL DNA ANALYSIS | 07-14-2016 |
20160251697 | METHODS OF IDENTIFYING MULTIPLE EPITOPES IN CELLS | 09-01-2016 |
20160251704 | SYSTEMS AND METHODS TO DETECT RARE MUTATIONS AND COPY NUMBER VARIATION | 09-01-2016 |
20160251710 | METHOD OF CHARACTERIZING A TARGET RIBONUCLEIC ACID (RNA) COMPRISING FORMING A COMPLEMENTARY POLYNUCLEOTIDE WHICH MOVES THROUGH A TRANSMEMBRANE PORE | 09-01-2016 |
20160251711 | SEQUENTIAL SEQUENCING | 09-01-2016 |
20160251712 | Sequential Sequencing | 09-01-2016 |
20160251718 | Endometriosis Classifier | 09-01-2016 |
20160251719 | METHODS FOR COPY NUMBER DETERMINATION | 09-01-2016 |
20160251721 | METHOD OF MEASURING ADAPTIVE IMMUNITY | 09-01-2016 |
20160251725 | METHOD FOR PREDICTING CLINICAL TOXICITY AND OUTCOME | 09-01-2016 |
20160251727 | DETECTING GASTROINTESTINAL NEOPLASMS | 09-01-2016 |
20160251728 | MONITORING HEALTH AND DISEASE STATUS USING CLONOTYPE PROFILES | 09-01-2016 |
20160376644 | TARGETED SEQUENCING TECHNIQUE FOR WHOLE GENOME DNA METHYLATION - This invention is directed to a guide positioning sequencing technology of whole-genome DNA methylation. The invention provides a new detection method of nucleic acid methylation. In particular, a concept of “positioning” in the detection of nucleic acid methylation is provided. Specifically, a portion of a sequence is used for genome wide positioning and the other portion of the sequence is used for methylation detection in sequencing, thereby solving/defeating previously existing challenges in methylation detection and bioinformatics analysis of a genome. | 12-29-2016 |
20160376647 | SEQUENCING USING CONCATEMERS OF COPIES OF SENSE AND ANTISENSE STRANDS - Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions. | 12-29-2016 |
20160376649 | COMPOSITIONS AND METHODS FOR SEQUENCING NUCLEIC ACIDS - Disclosed herein are compositions and methods for sequencing nucleic acids. | 12-29-2016 |
20180023125 | SYSTEMS AND METHODS TO DETECT RARE MUTATIONS AND COPY NUMBER VARIATION | 01-25-2018 |
20180023133 | SYSTEMS AND METHODS FOR EPIGENETIC SEQUENCING | 01-25-2018 |
20180023135 | SEQUENCE BASED GENOTYPING BASED ON OLIGONUCLEOTIDE LIGATION ASSAYS | 01-25-2018 |
20180023143 | MONITORING HEALTH AND DISEASE STATUS USING CLONOTYPE PROFILES | 01-25-2018 |
20190144928 | MOLECULAR TAG ATTACHMENT AND TRANSFER | 05-16-2019 |
20190147978 | METHODS FOR GENOME ASSEMBLY AND HAPLOTYPE PHASING | 05-16-2019 |