Entries |
Document | Title | Date |
20080200340 | Bead Bound Combinatorial Oligonucleoside Phosphorothioate And Phosphorodithioate Aptamer Libraries - The present invention includes composition and methods for making and using a combinatorial library having two or more beads, wherein attached to each bead is a unique nucleic acid aptamer that have disposed thereon a unique sequence. The library aptamers may be attached covalently to the one or more beads, which may be polystyrene beads. The aptamers may include phosphorothioate, phosphorodithioate and/or methylphosphonate linkages and may be single or double stranded DNA, RNA or even PNAs. | 08-21-2008 |
20080248958 | System for pulling out regulatory elements in vitro - Disclosed are methods for identifying molecular interactions between proteins and DNA sequences in vitro. All of the methods of the invention employ known or suspected DNA-binding proteins and genomic DNA from a stable library. Interacting molecules direct the expression of a reporter gene, the expression of which is then assayed. Also disclosed are genetic constructs useful in practicing the methods of the invention. | 10-09-2008 |
20080254994 | Classification and diagnosis of the molecular basis of cholestasis - The methods and compositions of the invention find use in the clinical diagnosis of cholestasis related syndromes, particularly PFIC types 1, 2, and 3; BRIC types 1 and 2; Alagille syndrome, and alpha 1-antitrypsin deficiency. The compositions of the invention include isolated nucleic acid molecules and oligonucleotide pairs suitable for use in amplifying regions of cholestasis related genes. Compositions of the invention include a cholestasis related gene resequencing microarray suitable for determining the nucleotide sequence of a region of a cholestasis related gene. Knowledge of the nucleotide sequence of one or more regions of a patient's cholestasis related gene allows diagnosis of the patient's syndrome. | 10-16-2008 |
20080254995 | NANOPORE ARRAYS AND SEQUENCING DEVICES AND METHODS THEREOF - Provided are devices comprising one or more nanoscale pores for use in, inter alia, analyzing various biological molecules. Also provided are methods for the fabrication of nanoscale pores in solid-state substrates, methods for functionalizing nanopores in solid-state substrates, and methods for sequencing polymers using devices containing nanoscale pores. | 10-16-2008 |
20080274905 | MICROFLUIDIC CELLS WITH PARALLEL ARRAYS OF INDIVIDUAL DNA MOLECULES - Nucleic acid arrays and methods of using nucleic acid arrays are disclosed. | 11-06-2008 |
20080287305 | Method for Nucleic Acid Analysis - This invention provides methods for nucleic acid analysis. A closed complex of nucleic acid template, nucleotide and polymerase can be formed during polymerase reaction, absent divalent metal ion. This is used to trap the labeled nucleotide complementary to the next template nucleotide in the closed complex. Detection of the label allows determination of the identity of this next correct nucleotide. Identification can be either in place, as part of the complex, or as the dye is eluted from the complex when the reaction cycle is completed by the addition of divalent metal ion. In this way, sequential nucleotides of a DNA can be identified, effectively determining the DNA sequence. This method can be applied to nucleic acid single molecules or to collections of identical or nearly identical sequence such as PCR products or clones. Multiple templates can be sequenced in parallel, particularly if they are immobilized on a solid support. | 11-20-2008 |
20080287306 | Methods and devices for sequencing nucleic acids - The invention provides methods and devices for high throughput single molecule sequencing of a plurality of target nucleic acids using a universal primer. Devices of the invention comprise a plurality of oligonucleotides, each having the same sequence, bound to a solid support, and ligated to a plurality of target nucleic acids. | 11-20-2008 |
20080300140 | Methods for Antibody Library Screening - The present invention provides a method of screening a library of molecules to identify and/or select one or more members thereof which are candidate binding partners for one or more ligands comprising: a) contacting an expression library in solution with one or more ligands; b) capturing ligands which have become bound to one or more members of the expression library onto a solid phase; and c) detecting the presence of a ligand, thereby detecting the presence of one or more members of the expression library which are candidate binding partners for the ligand. | 12-04-2008 |
20080305957 | Method for Obtaining Structural Information Concerning an Encoded Molecule and Method for Selecting Compounds - In one aspect, the present invention relates to a method for obtaining structural information about an encoded molecule. The encoded molecule may be produced by a reaction of a plurality of chemical entities and may be capable of being connected to an identifier oligonucleotide containing codons informative of the identity of the chemical entities which have participated in the formation of the encoded molecule. In a certain embodiment, primers are designed complementary to the codons appearing on the identifier oligonucleotide, and the presence, absence or relative abundance of a codon is evaluated by mixing a primer with the identifier oligonucleotide in the presence of a polymerase and substrate (deoxy)ribonucleotide triphosphates and measuring the extension reaction. In another aspect, the invention provides a method for selecting compounds which binds to a target. More specifically, the invention relates to a method in which a target associated with an oligonucleotide initially is mixed with a library of complexes, each complex comprising a display molecule and an oligonucleotide identifying said display molecule. Next, due an increased proximity, the target oligonucleotide is coupled to the identifier oligonucleotide of complexes having a display molecule with affinity towards the target. In a final stage the coupled nucleotides are analysed to deduce at least the identity of the display molecule. | 12-11-2008 |
20080305958 | Process for Liquid or gas Chromatography/Mass Spectrometry Based Biomolecular Screening for Drug Discovery - Methods of achieving realistic hit rates and reducing or eliminating false positive rates in medicinal compound high throughput screening are provided. The methods of the invention include chromatographic resolution, for example by liquid or gas chromatography of biological substrates and/or substrate products, followed by sensitive with mass spectrometry to measure biological activity screening to generate meaningful drug leads. The methods of the invention save significant method development and thus are directly applicable to the high throughput screening time scale while providing high accuracy and sensitivity. | 12-11-2008 |
20080312091 | INVERTEBRATE ACETYLCHOLINESTERASE INHIBITORS - Methods for determining invertebrate- and insect-specific, such as mosquito-specific, residues of acetylcholinesterases are provided herein. The methods can be used to design pesticides and insecticides that are specific for the invertebrate or insect (e.g., mosquito) enzymes, resulting in reduced toxicity concerns for mammals. Compositions for inhibiting invertebrate and insect (e.g., mosquito) acetylcholinesterases and methods for preparing the same are also provided. | 12-18-2008 |
20090011943 | High throughput genome sequencing on DNA arrays - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished. | 01-08-2009 |
20090011944 | METHOD AND TEST KIT FOR DETECTING NUCLEOTIDE VARIATIONS - The present invention is related to a method for a simultaneous determination of the relative amounts of more than one target polynucleotide sequence and nucleotide variations in said targets. The method is carried out by separating and recording single-stranded probes, which have hybridized to the targets and which are determined and distinguished by their defined properties including size and optional detectable label. The probes are complementary to a region in the target that has a sequence being contiguous to the nucleotide variations to be determined. After being hybridized with affinity-tagged targets, the probes are attached to a solid support and purified. The target probe hybrids are elongated using enzyme-assisted elongations. The elongated probes are recorded after release from the solid supports and the amount of each of the targets and their nucleotide variations and the ratio of modified and modified target polynucleotide sequences are calculated from the recorded results. Also disclosed is a test kit, which kit comprises in a packaged form devices equipments and reagents as well as instructions for carrying out the method. The method is useful for several diagnostic purposes. | 01-08-2009 |
20090023589 | METHODS FOR IDENTIFYING CONDITIONS AFFECTING A CELL STATE - The present invention is directed to methods for identifying agents which affect cell state. The instant invention provides rapid and efficient methods for identifying agents which affect cell state. Methods are directed toward the screening of complex combinations of agents for their ability to affect cell state. In one embodiment, cells are incubated under suitable conditions and subjected to different agents. After an appropriate amount of time, the cells are assayed to determine what, if any, characteristics they possess. Cell characteristics can be organized in a manner such that different and novel cell states can be identified. | 01-22-2009 |
20090036316 | Random array DNA analysis by hybridization - The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization. | 02-05-2009 |
20090082212 | SYSTEM AND METHODS FOR NUCLEIC ACID SEQUENCING OF SINGLE MOLECULES BY POLYMERASE SYNTHESIS - This invention relates to improved methods for sequencing and genotyping nucleic acid in a single molecule configuration. The method involves single molecule detection of fluorescent labeled PPi moieties released from NTPs as a polymerase extension product is created. | 03-26-2009 |
20090088327 | Method for sequencing a polynucleotide template - 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. | 04-02-2009 |
20090099027 | Methods of Modifying Support Surfaces for the Immobilization of Particles and the Use of the Immobilized Particles for Analyzing Nucleic Acids - Methods of modifying a nucleophilic surface of a support are described. The methods involve reacting a multifunctional electrophilic reagent with nucleophilic groups on the surface of the support. The resulting electrophilic surface can be used for the covalent attachment of particles (e.g. beads) having nucleophilic functional groups. For example, nucleic acid templates with nucleophilic (e.g., amine) groups can be attached to a surface of the particles. The nucleophilic groups on the nucleic acid templates can then be used to attach the particles to the modified surface of the support. The resulting support-bound particles can be used to analyze (e.g., sequence) the nucleic acid templates on the particles. | 04-16-2009 |
20090131263 | Normalization methods for G-protein coupled receptor membrane array - Reference membrane components are either pre-labeled or labeled during assays for purposes of normalizing signals associated with binding or functional assays employing G-protein coupled receptor microarrays. A reference component may be included in a membrane in which the target GPCR is embedded or may be present in another membrane printed in conjunction with the target membrane on a microspot. Or, a GPCR microarray may be pre-labeled by incorporating a label on an exposed substrate in a defect in the printed microspot. | 05-21-2009 |
20090143233 | DEVICE AND METHOD FOR DIGITAL MULTIPLEX PCR ASSAYS - A method and device for digital multiplex PCR assays employ a microfluidic chip for performing real-time, continuous flow PCR within microchannels of the chip. A stream of sample material is introduced into each microchannel and alternating boluses of assay-specific reagents and buffer are introduced into the stream to form sequentially configured test boluses. A PCR procedure is performed on the test boluses followed by a thermal melt procedure. During the thermal melt procedure, fluorescent output is detected and fluorescence vs temperature data is collected and compared to expected normal correlations. The results, positive or negative, are converted to digital format, with positive results designated as “1” and negative results designated as “0”, or vice versa. | 06-04-2009 |
20090143234 | QUALITY CONTROL METHODS FOR ARRAYED OLIGONUCLEOTIDES - We disclose quality controls methods that allow quick and accurate verification of a test oligonucleotide deposited on a solid support. It is especially useful for the verification of oligonucleotides representing alleles of a multi-allelic locus. It employs single base extension, with labeled dideoxynucleotides, to locate and verify the identity of test oligonucleotides. This approach involves synthesizing a complement probe oligonucleotide for each oligonucleotide being tested. Probe oligonucleotides are optionally grouped. They are then hybridized to test oligonucleotides, and the hybridized pair is subject to single base extension and detection. It requires the presence of one unique base, either in the last two bases at the free hanging end of the test oligonucleotide—as opposed to the end anchored to the solid support surface, or in the last two bases at one end of the probe oligonucleotide. | 06-04-2009 |
20090163366 | TWO-PRIMER SEQUENCING FOR HIGH-THROUGHPUT EXPRESSION ANALYSIS - The disclosure provides a method of sequencing a nucleic acid molecule that contains two or more target regions to be sequenced (such as, for example, barcodes). The invention is advantageous for sequencing by synthesis two or more target regions whose combined lengths plus the length of any intermediate sequence exceeds the available read length on a given sequencing platform. The methods of the invention utilize nucleic acid constructs containing at least the following elements: a complement of a first universal primer, a first target sequence, an optional polynucleotide spacer, a complement of a second universal primer, and a second target sequence. A first round of sequencing by synthesis is performed to sequence the first target sequence by elongating the first universal primer. Once the sequence of the first target region is obtained, and before the complement of the second primer is reached, the first round of sequencing is terminated. Thereafter, a second round of sequencing by synthesis is initiated—this time, by elongating the second universal primer, thereby sequencing the second target region. | 06-25-2009 |
20090209430 | TEMPLATE DIRECTED SPLIT AND MIX SYSTHESIS OF SMALL MOLECULE LIBRARIES - The present invention provides a method for combining the advantages of encoded molecule fragments made by split and mix synthesis with the advantages of template directed synthesis of molecules. The method provided in the invention comprises the steps of: Adding a linker molecule L to one or more reaction wells; Adding a molecule fragment to each of said reaction wells; Adding an oligonucleotide identifier to each of said reaction wells; Subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; Combining the contents of said one or more reaction wells; Optionally, distributing the combined product to one or more new reaction wells; Optionally, repeating steps b) to e) one or more times; Contacting the resulting bifunctional molecule(s) of step e) or g) with one or more Contacting the resulting bifunctional molecule(s) of step e) or g) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added in step c). | 08-20-2009 |
20090215633 | HIGH THROUGHPUT SEQUENCE-BASED DETECTION OF SNPS USING LIGATION ASSAYS - Method for the detection the presence or absence of one or more target sequences in one or more samples based on oligonucleotide ligation assays with a variety of ligatable probes containing identifiers and the subsequent identification of the identifiers in the amplicons or ligated probes using high throughput sequencing technologies. | 08-27-2009 |
20090221428 | Methods of Genome-Wide Location Analysis in Stem Cells - The invention relates to improved methods of identifying the genomic regions to which a protein of interest binds, and in particular, to methods that apply to stem cells such as but not limited to; embryonic stem cells and adult stem cells. The invention also provides methods of identifying agents which modulate differentiation of stem cells. The invention also provides methods of defining the differentiation potential of a cell and of designing array oligonucleotides. | 09-03-2009 |
20090221429 | Method for Detecting Target Nucleic Acid with Specific Base Sequence and Set of Nucleic Acids for Detection - It is intended to provide a method for detecting a target nucleic acid with a specific base sequence existing in a sample mixture with high specificity and sensitivity by utilizing the formation of a hybrid with a complementary strand as a detection principle, and a nucleic acid for the detection. The invention relates to a set of nucleic acids for detecting a target nucleic acid with a specific base sequence comprising a photoligating nucleic acid composed of a nucleic acid (with the proviso that in the nucleic acid, a nucleic acid and a peptide nucleic acid are included) having a group represented by the formula I, II, III, IV or V described in claims at the 5′ end or 3′ end as a base moiety, and a photoligated nucleic acid having a base with a carbon-carbon double bond at the 3′ end or 5′ end as a base moiety capable of photoligating to the photoligating nucleic acid, wherein either of the photoligating nucleic acid and the photoligated nucleic acid has a labeling moiety and the other remaining nucleic acid is immobilized on a substrate, and the method for detecting a target nucleic acid with a specific base sequence by using the set of nucleic acids. | 09-03-2009 |
20090264300 | ENZYMATIC ENCODING METHODS FOR EFFICIENT SYNTHESIS OF LARGE LIBRARIES - Disclosed is a method for obtaining a bifunctional complex comprising a molecule linked to a single stranded identifier oligonucleotide, wherein a nascent bifunctional complex comprising a chemical reaction site and a priming site for enzymatic addition of a tag is a) reacted at the chemical reaction site with one or more reactants, and b) reacted enzymatically at the priming site with one or more tag(s) identifying the reactant(s). | 10-22-2009 |
20090280993 | Method of Analyzing the Accuracy of a Sequence of Probe Nucleic Acid Immobilized on a Microarray Substrate - A method of analyzing an accuracy of a sequence of a probe nucleic acid immobilized in a microarray includes providing a microarray in which regions where a probe nucleic acid is immobilized on a substrate are arrayed, hybridizing the probe nucleic acid with a target nucleic acid that is complementary to the probe nucleic acid to form a hybridization product, wherein the target nucleic acid is labeled with a detectable signal material on at least one end, reacting the hybridization product with an enzyme to remove the detectable signal material from the target nucleic acid, wherein the at least one end of the target nucleic acid remains unpaired with the probe nucleic acid, measuring a residual signal generated from the resultant enzyme reaction product, comparing the measured signal value with a signal value generated from a control group experiment; and analyzing an accuracy of the probe nucleic acid sequence. | 11-12-2009 |
20090286688 | COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS - Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence. | 11-19-2009 |
20090318299 | DEVELOPMENT AND USE OF FLUORESCENT PROBES OF UNBOUND ANALYTES - A method for high throughput screening of probes is described. These probes are useful for characterization and measurement of unbound metabolites in a fluid sample, particularly characterization and measurement of levels of unbound free fatty acids. By practice of the disclosed invention, a profile of unbound metabolites can be determined for an individual which can be used to determine the individual's relative risk for disease such as stroke, cardiac disease and cancer. | 12-24-2009 |
20100016170 | HIGH THROUGHPUT METHOD FOR DISCOVERY OF GENE CLUSTERS - A method for identifying gene cluster is disclosed. The method may be used for identifying gene clusters involved in the biosynthesis of natural products. A small insert library of DNA fragments of genomic DNA and a large insert library of DNA fragments of genomic DNA are prepared. Fragments in the small insert library are sequenced and compared by homology comparison under computer control to a database containing genes, gene fragments or proteins known to be involved in the biosynthesis of microbial natural products. Fragments having similar structure to genes, gene fragments or proteins known to be involved in the biosynthesis of naturally occurring metabolites are used as probes to screen the large insert library of genomic DNA to detect gene clusters involved in the biosynthesis of microbial natural products. | 01-21-2010 |
20100069250 | Digital PCR Calibration for High Throughput Sequencing - Disclosed is a method for accurately determining the number of template molecules in a library of nucleic acids (e.g., DNA) to be sequenced. The method does not require large amounts of the DNA sample, nor does it require the preparation of a standard curve. The method is especially applicable to methodologies for “sequencing by synthesis,” where quantitation of the starting library is important. The method uses quantitative real time PCR, especially digital PCR, which measures the number of individual molecules in a sample. The present method particularly may use a microfluidic device for running large numbers of PCR reactions. Each PCR reaction is monitored in real time by a primer/probe combination. The forward primer is adapted to contain a sequence not on the adapter but which corresponds to a probe sequence. A short probe which generates fluorescence during the PCR process is used. | 03-18-2010 |
20100075858 | BIOLOGICAL BAR CODE - The invention provides coding compositions comprising mixtures of coding oligonucleotides and methods of using such compositions to code samples. The compositions and methods are useful for identifying, verifying, or authenticating any type of sample, whether the sample is biological or non-biological. | 03-25-2010 |
20100081576 | METHOD FOR GENOME ANALYSIS - A method of sample analysis is provided. In certain embodiments, the method may comprise: a) contacting under primer extension conditions a genomic sample comprising a test genome with a set of at least ten sequence-specific primers that are complementary to sites in only one strand of a reference chromosomal region, to produce primer extension products, and b) analyzing the primer extension products to identify a chromosomal rearrangement in the test genome. | 04-01-2010 |
20100113283 | MASSIVELY MULTIPLEXED SEQUENCING - The present invention provides multiplexed methods for analyzing polynucleotides associated with sample tags. The multiplexed information is deconvoluted by single-molecule and more generally single-particle detection methods. In particular, a method for determining nucleic acid sequence information is provided. | 05-06-2010 |
20100152050 | Detection Device And Methods Of Use - An imaging system for exciting and measuring fluorescence on or in samples comprising fluorescent materials (e.g. fluorescent labels, dyes or pigments). In one embodiment, a device is used to detect fluorescent labels on nucleic acid. In a preferred embodiment, the device is configured such that fluorescent labels in a plurality of different DNA templates are simultaneously detected. | 06-17-2010 |
20100173786 | Method for Absolute Quantification of Polypeptides - The present invention relates to a method for absolute quantification of polypeptides. | 07-08-2010 |
20100173787 | DETECTION OF NUCLEIC ACID SEQUENCE DIFFERENCES USING THE LIGASE DETECTION REACTION WITH ADDRESSABLE ARRAYS - The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support. | 07-08-2010 |
20100298152 | USE OF APTAMERS IN PROTEOMICS - The present invention is a method for measuring the amount of at least one molecule in a biological sample, the method comprising a) combining the sample, or a derivative thereof, with one or more aptamers and allowing one or more molecules in the sample to bind to the aptamer(s); b) separating bound from unbound molecules; and c) quantifying the molecule(s) bound to the or each aptamer, wherein quantification of the bound molecule(s) is carried out by sequencing at least part of the or each aptamer. Uses of and products derived from the method are also contemplated. | 11-25-2010 |
20100317531 | Labelled nucleotides - Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group. | 12-16-2010 |
20110034340 | Systems and Methods for Immunosorbent Assays for Single and Multiple Analytes - The present invention discloses systems and methods for minimizing or eliminating steps in immunosorbent assays for single and multiple analytes by eliminating both the need to attach target molecules to the test well and the need to remove unbound antibodies through rinsing. The immunosorbent assay (ISA) is utilized for a single analyte or target and includes the step of mixing the immunologic molecules with the sample and detection. The present invention further discloses an immunosorbent assay for multiple analytes (ISAMA) for testing a plurality of analytes or targets in a single well using a modified ISA test wherein different tags are attached to different antibody pairs. Alternate embodiments use multiple types of scavenger antigens with corresponding elimination of the need for scavenger antibodies. The present invention discloses various types of test wells for the rapid and simultaneous testing of fluids for a plurality of components and a methodology for a continuous immunosorbent assay. Also disclosed is a method for immunosorbent assay of micro-organisms to determine serotype. | 02-10-2011 |
20110082046 | METHOD AND DEVICE FOR THE MANIPULATION OF MICROCARRIERS FOR AN IDENTIFICATION PURPOSE - The present invention relates to a method for the manipulation for an identification purpose of a microcarrier comprising the steps of: (a) an identification purpose step of the microcarrier; and (b) a positioning and orientation step prior to or during the identification purpose step, wherein the identification purpose step is a detection step for the detection of an encoded microcarrier having an anisotropy in its shape. The invention further relates to an apparatus for the manipulation for identification purposes of a microcarrier comprising means for identification purposes such as a microscoper and means for the positioning and orientation of the microcarriers. | 04-07-2011 |
20110118125 | NEONATAL SALIVARY GENOMICS - The present invention provides systems for assessing neonatal development and/or conditions by analyzing neonatal saliva RNA. Methods of identifying genes involved in neonatal development and/or conditions affecting neonates, are provided. Methods of determining a diagnosis of a neonate comprising detection of one or more differentially expressed genes are also provided. | 05-19-2011 |
20110136676 | GEOMETRIC PATTERNS AND LIPID BILAYERS FOR DNA MOLECULE ORGANIZATION AND USES THEREOF - The invention is related to nucleic acid arrays and methods of using nucleic acid arrays. | 06-09-2011 |
20110166027 | INTERACTION SCREENING METHODS, SYSTEMS AND DEVICES - An interaction screening method for identifying binding moieties encapsulates candidate binding moieties in droplets with a first known moiety and a second known moiety. The candidate binding moieties are different in the different droplets. The method further comprises determining for one or more of the droplets whether the candidate binding moiety is bound to the first known moiety and/or the second known moiety. Optionally, the method further comprises segregating at least one droplet in which the candidate binding moiety is bound to the first known moiety or to the first and second known moiety. | 07-07-2011 |
20110301042 | METHODS OF SAMPLE ENCODING FOR MULTIPLEX ANALYSIS OF SAMPLES BY SINGLE MOLECULE SEQUENCING - The invention generally relates to methods for sequencing a plurality of nucleic acids from different samples. In certain embodiments, methods of the invention provide contacting a nucleic acid duplex including a primer nucleic acid hybridized to a template nucleic acid with a polymerase enzyme in the presence of a first detectably labeled nucleotide under conditions that permit the polymerase to add nucleotides to the primer in a template-dependent manner, in which a unique oligonucleotide sequence is attached to the template nucleic acid so that the template nucleic acid may be differentiated from other template nucleic acid molecules, detecting a signal from the incorporated labeled nucleotide, and sequentially repeating the contacting and detecting steps at least once, wherein sequential detection of incorporated labeled nucleotide determines the sequence of the nucleic acid. | 12-08-2011 |
20110301043 | RISK ASSESSMENT FOR CUTANEOUS ADVERSE DRUG REACTIONS FROM ANTIRETROVIRAL AGENT - The present invention provides a method of predicting the risk of a patient for developing cutaneous adverse drug reaction to non-nucleoside reverse transcriptase inhibitors such as nevirapine by using HLA-B*3505 allele and/or polymorphisms in the CCHCR1 gene. | 12-08-2011 |
20110301044 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention. | 12-08-2011 |
20120046178 | PRODUCTS AND PROCESSES FOR MULTIPLEX NUCLEIC ACID IDENTIFICATION - Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the oligonucleotides include distinguishable labels and a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing and detecting the distinguishable label, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the distinguishable label. | 02-23-2012 |
20120071329 | METHODS FOR IDENTIFYING COMPOUNDS OF INTEREST USING ENCODED LIBRARIES - The present invention provides a method for identifying a compound of interest by screening libraries of molecules which include an encoding oligonucleotide tag. | 03-22-2012 |
20120071330 | MULTIPLEXED IDENTIFICATION OF NUCLEIC ACID SEQUENCES - A method for the rapid identification of a target nucleic acid sequence is provided, as well as corresponding devices, products and kits. Such methods are useful for the rapid detection, identification and/or quantification of target nucleic acid sequences associated with, for example, a pathogen. | 03-22-2012 |
20120071331 | INCREASING CONFIDENCE OF ALLELE CALLS WITH MOLECULAR COUNTING - 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. | 03-22-2012 |
20120142540 | Methods For Sequencing Nucleic Acid Molecules - Methods and compositions for determining the nucleic acid sequence of polynucleotides that are at least 1500 nucleotides in length are provided. | 06-07-2012 |
20120178635 | COMPOSITIONS AND METHODS FOR IDENTIFYING AND DETECTING SITES OF TRANSLOCATION AND DNA FUSION JUNCTIONS - The present invention provides a powerful technique based on ultra high-throughput sequencing that finds structural aberrations of chromosomes and defines breakpoints. It is disclosed herein that, Anchored ChromPET, a technique to capture and interrogate targeted sequences in the genome, is a cost-effective means to identify chromosomal aberrations and define breakpoints. Using this method, we defined the BCR-ABL1 translocation DNA breakpoint to a base-pair resolution in Philadelphia chromosome positive cell lines and patient cells. This DNA-based method is highly sensitive and can detect signal using samples from which it is hard to obtain RNA or cells where the RNA expression has been silenced. These data demonstrate that ChromPET is a cost-effective and powerful technology that can identify and follow the appearance of chromosomal aberrations in various organisms, including, but not limited to, humans. | 07-12-2012 |
20120196758 | METHOD FOR NUCLEOTIDE DETECTION - A method of inhibiting light-induced degradation of nucleic acids includes irradiating a portion of the nucleic acids in the presence of a detection solution comprising a polyphenolic compound. A method of detecting a nucleic acid having a fluorescent tag includes irradiating at least a portion of the nucleic acid with light of a suitable wavelength to induce a fluorescence emission and detecting the fluorescence emission. Optionally, the polyphenolic compound is gallic acid, a lower alkyl ester thereof, or mixtures thereof. A kit includes one or more nucleotides, an enzyme capable of catalyzing incorporation of the nucleotides into a nucleic acid strand and a polyphenolic compound suitable for preparing a detection solution. | 08-02-2012 |
20120220468 | TD PROBE AND ITS USES - The present invention relates to a target discriminative probe (TD probe) and its uses or applications. The TD probe is hybridized with a target nucleic acid sequence through both of the 5′-second hybridization portion and the 3′-first hybridization portion. When the TD probe is hybridized with a non-target nucleic acid sequence, both the 5′-second hybridization portion and the separation portion are not hybridized with the non-target nucleic acid sequence such that both portions form a single strand due to its low Tm value. As such, the TD probe exhibits distinctly different hybridization patterns for each of the target and the non-target nucleic acid sequence, discriminating the target nucleic acid sequence from the non-target nucleic acid sequence with much higher specificity. | 08-30-2012 |
20120238456 | RATIONAL LIBRARY - The invention relates to a method to generate rational libraries comprising genetic elements which are involved in transcriptional and/or translational regulation of a gene and devised to increase the production yield of the encoded protein as well as to the rational library and to the application of said rational library. | 09-20-2012 |
20120238457 | RNA ANALYTICS METHOD - The present invention relates to a method of ordering nucleic acid molecule fragment sequences derived from a pool of potentially diverse RNA molecules comprising
| 09-20-2012 |
20120245040 | METHODS FOR SYNTHESIS OF ENCODED LIBRARIES - The present invention provides a method of synthesizing libraries of molecules which include an encoding oligonucleotide tag. | 09-27-2012 |
20120245041 | BASE-BY-BASE MUTATION SCREENING - Aspects of the present invention are drawn to screening assays for isolating polynucleotides having a sequence variation or mutation. Embodiments of the screening assays include generating a population of polynucleotide duplexes having 5′ overhang regions on one strand of the duplex (the “template” or “bottom strand”) followed by isolating polynucleotide duplexes from the mixture that have one or more mismatched base at the 3′ end of the other strand of the duplex (the “test” or “top” strand). | 09-27-2012 |
20120258870 | Methods, Systems, and/or Use of Oligonucleotide Conjugates to Develop Panels for Use in Assays and Detections - The present disclosure is directed to methods systems, and/or uses of oligonucleotide conjugates to develop panels for use in assays and detections and related systems and/or kits. Certain methods are directed to a method for detecting one or more biological targets of a sample in a detection assay, comprising: providing a molecular probe, comprising a binding moiety and an oligonucleotide sequence, to a sample comprising one or more biological targets; binding the one or more biological targets with the binding moiety; providing a detectable component to the sample, wherein the detectable component comprises a signal generating moiety conjugated to an oligonucleotide sequence complementary to the oligonucleotide sequence of the molecular probe; hydridizing the oligonucleotide sequence of the target-bound molecular probe to the detectable component; and detecting a signal generated from the hydridized detectable component. Various other embodiments, applications etc. are disclosed herein. | 10-11-2012 |
20120258871 | PEPTIDE CONSTRUCTS AND ASSAY SYSTEMS - The present invention provides methods for constructing peptide construct sets and methods of use of these peptide construct sets in assay systems for peptide analysis, and in particular for use in high throughput peptide analysis. The methods allow for analysis of large sets of peptide constructs in a cost-effective manner, employing molecular biological techniques that are both robust and easily parallelized. Thus, the methods allow for the construction of peptide construct sets encompassing, e.g., the human proteome. | 10-11-2012 |
20120264620 | METHODS FOR DIAGNOSIS AND TREATMENT OF ENDOMETRIAL CANCER - The present invention discloses methods of using endothelial membrane protein 2 (EMP2) as a biomarker for stratification of endometrial premalignancy, diagnosing, staging and imaging of endometrial neoplasia. Further, methods for identifying pharmaceutical/therapeutic modalities are described, including compositions which modulate glycolipid-enriched lipid raft microdomains (GEMs). | 10-18-2012 |
20120264621 | PHASE-PROTECTING REAGENT FLOW ORDERINGS FOR USE IN SEQUENCING-BY-SYNTHESIS - A method for nucleic acid sequencing includes disposing template polynucleotide strands in defined spaces on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed according to a predetermined ordering; and determining, for each of the series of flows of nucleotide species, how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands, wherein the predetermined ordering (a) is not a series of consecutive repetitions of a 4-flow permutation of four different nucleotide species, (b) is not specifically tailored to a particular combination of a particular template polynucleotide strand to be sequenced and a particular sequencing primer to be used, and (c) comprises a phase-protecting flow ordering. | 10-18-2012 |
20120264622 | COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS - Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence. | 10-18-2012 |
20120277107 | Methods and Compositions for Tagging and Identifying Polynucleotides - The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g. by hybridization of the oligonucleotide tag to its tag complement on an addressable array; or such analysis can be carried out serially by successive hybridizations of labeled word complements. | 11-01-2012 |
20120283109 | METHOD OF ANALYZING TARGET NUCLEIC ACID OF BIOLOGICAL SAMPLES - This invention provides a method of analyzing target nucleic acids of biological samples for multiplex nucleic acid analysis of disease associated genetic changes of biological samples in biomedical research and clinical diagnostics. | 11-08-2012 |
20120283110 | METHODS FOR RETRIEVAL OF SEQUENCE-VERIFIED DNA CONSTRUCTS - In some embodiments, methods of recovering a sequence-verified target nucleic acid are provided. In some embodiments, such methods may include tagging each member of a nucleic acid library with a set of adaptor sequences; sequencing the tagged members of the nucleic acid library; and recovering the sequence-verified target nucleic acid from the tagged and sequenced members of the nucleic acid library using a dial-out selection method. In certain embodiments, the members of the nucleic acid library may be tagged with a second set of adaptor sequences. | 11-08-2012 |
20120289413 | METHODS FOR OPERATING AN ARRAY OF CHEMICALLY-SENSITIVE SENSORS - 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. | 11-15-2012 |
20120289414 | METHOD FOR MULTIPLEXED NUCLEIC ACID PATCH POLYMERASE CHAIN REACTION - The invention encompasses a method for amplifying at least two different nucleic acid sequences. In particular, the method encompasses a multiplexed nucleic acid patch polymerase chain reaction. | 11-15-2012 |
20120295795 | METHODS FOR OPERATING CHEMICALLY-SENSITIVE SAMPLE AND HOLD SENSORS - 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. | 11-22-2012 |
20120322669 | METHODS OF MARKING MATERIALS - Methods for marking a material and subsequently detecting that it has been marked, comprising adding or applying a marker comprising a nucleic acid tag to the material, sampling a portion of the material, and detecting the presence of the tag. The quantity of the tag present in the sample provides an indication of the quantity of marker present in the material. The tag may comprise one or more identifying sequences, and the tag is amplified by means of a nucleic acid amplification reaction. | 12-20-2012 |
20130012400 | METHOD AND DEVICE FOR SEPARATING MOLECULAR TARGETS IN A COMPLEX MIXTURE - The invention relates to a method of analysing molecular targets contained in a complex mixture, comprising the following steps consisting in: a) bringing the mixture of molecular targets to be analysed into contact with an array of different types of primary probes, whereby each type of primary probe forming the array can bind specifically to a type of target selected from among the molecular targets, under conditions that enable specific binding between the molecular targets and the primary probes; b) optionally eliminating the primary probes that are not bound specifically to a molecular target; c) separating the molecular targets and the primary probes which are bound specifically in a probe/target complex, such as to recover the array of primary probes representing a fingerprint of the molecular targets to be analysed; and d) quantitatively analysing the primary probes eluted in step c. | 01-10-2013 |
20130017960 | PRODUCTS AND PROCESSES FOR MULTIPLEX NUCLEIC ACID IDENTIFICATION - Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the extended oligonucleotides include a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing the extended oligonucleotide by competition with a competitor; detecting the extended oligonucleotide, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the extended oligonucleotide. | 01-17-2013 |
20130023422 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention. | 01-24-2013 |
20130029854 | Method for Determining an Attribute Profile of Biological Samples - A method of identifying attributes in a plurality of biological samples including the steps of determining a source tag sharing number “d” for each of the attributes; providing a plurality of pools for the source tag sharing number “d” wherein each pool comprising a pooled subset of biological samples; for each pool of the plurality of pools, producing at least one pooled pool comprising attribute-specific reaction products comprising a marker tag that uniquely identifies an attribute and a source tag identifying said pool; and identifying said attribute-specific reaction products to identify the attributes. If “d” is equal to or larger than a maximum pool size, the reaction products may not comprise a source tag identifying each pool. Attributes may be binned together. | 01-31-2013 |
20130029855 | Sieving of Nucleic Acid Samples - A method of selecting nucleic acid samples from a plurality of nucleic acid samples based on desired alleles including the steps of performing a first reaction in a plurality of pools of the alleles to be identified to produce reaction products including a source tag identifying said each pool; pooling the pools to provide pooled pools; for each of the desired alleles to be identified, performing a second reaction using said reaction products to produce allele-specific second reaction products comprising a marker tag and a derived source tag; identifying said allele-specific second reaction products to select nucleic acid sample. In some embodiments, the first reaction may not be performed. A source tag sharing number “d” may be determined for each of the alleles. Alleles may be binned together. | 01-31-2013 |
20130059740 | Sequencing Small Amounts of Complex Nucleic Acids - The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example. | 03-07-2013 |
20130059741 | BINDING ASSAYS FOR MARKERS - This invention provides compositions and methods for assaying the presence of a target analyte in a sample using a solid support. Embodiments of the present invention provide a solid support having a binding protein, such as an antibody, antibody fragment or protein receptor, immobilized to the solid support and at least two separate nucleic acid primers immobilized near the binding protein. This invention also provides a method for tethering two or more polypeptide subunits to generate a multifunctional fusion protein, which can have a primary function, e.g., binding a target analyte, such as a target protein, or an enzymatic activity, and one or more of the subunits of the fusion protein carries out a secondary function, e.g., capture on a solid matrix or quantitation. | 03-07-2013 |
20130065770 | Methods and Compositions for Tagging and Identifying Polynucleotides - The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g. by specific hybridization of the oligonucleotide tag to its tag complement on an addressable array; or such analysis can be carried out serially by successive specific hybridizations of labeled word complements, or the like. | 03-14-2013 |
20130096015 | Massive Parallel Method For Decoding DNA And RNA - This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3′-position of the deoxyribose. | 04-18-2013 |
20130109577 | REAL-TIME REDOX SEQUENCING | 05-02-2013 |
20130116130 | Digital Counting of Individual Molecules by Stochastic Attachment of Diverse Label-Tags - Compositions, methods and kits are disclosed for high-sensitivity counting of individual molecules by stochastic labeling of a identical molecules in mixtures of molecules by attachment of a unique label-tags from a diverse pool of label tags to confer uniqueness to otherwise identical or indistinguishable events. Individual occurrences of target molecules randomly choose from a non-depleting reservoir of diverse label-tags. Labeled molecules may be detected by hybridization or sequencing based methods. Molecules that would otherwise be identical in information content are labeled to create a separately detectable product that can be distinctly detected. The disclosed stochastic transformation methods reduce the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed label-tags are present. The methods may be used, for example, to count a given species of molecule within a sample. | 05-09-2013 |
20130123118 | Metal Nanoparticle Structures For Enhancing Fluorescence-Based Arrays - Provided, among other things, is a multiplex assay comprising: conducting a fluorescence-developing assay on microtabs having at least one surface that shows plasmonic enhancement, wherein a plurality of the microtabs have unique probes affixed to their plasmonically enhanced surfaces; and measuring the fluorescence associated with the substrates and identifying the correlated probe by for the microtab. The microtabs can be, for example, MTPs that send a unique identifier, and the correlated probe can be identified by querying the MTPs for their identifier. | 05-16-2013 |
20130130922 | ANALYSIS OF METHYLATION SITES - A method for labeling unmethylated CpG dinucleotides within a DNA fragment, and use of the method in profiling of genomic DNA methylation. The present invention further provides modified DNA methyltransferase enzymes and compounds which are capable of being used by the enzymes as cofactors for use in the labeling method. | 05-23-2013 |
20130172199 | SPATIAL POSITIONING OF SPECTRALLY LABELED BEADS - Devices, systems, kits, and methods for detecting and/or identifying a plurality of spectrally labeled bodies well-suited for performing multiplexed assays. By spectrally labeling the beads with materials which generate identifiable spectra, a plurality of beads may be identified within the fluid. Reading of the beads is facilitated by restraining the beads in arrays, and/or using a focused laser. | 07-04-2013 |
20130190192 | Methods And Systems For Long Distance Tagging, Tracking, And Locating Using Wavelength Upconversion - Methods and systems for plasmonically enhanced bionanoantennas for tagging, tracking, and locating targets of interest at long distances in both day and nighttime conditions. The nanoantennas are used to tag a target of interest and emit a wavelength to impart a unique biometric signature. The nanoantennas are detectable by selectively harvesting and plasmonically enhancing incident light in the visible region, then upconverting that energy through an activated phosphor. | 07-25-2013 |
20130210645 | PERSONALIZED TUMOR BIOMARKERS - Clinical management of human cancer is dependent on the accurate monitoring of residual and recurrent tumors. We have developed a method, called personalized analysis of rearranged ends (PARE), which can identify translocations in solid tumors. Analysis of four colorectal and two breast cancers revealed an average of nine rearranged sequences (range 4 to 15) per tumor. Polymerase chain reaction with primers spanning the breakpoints were able to detect mutant DNA molecules present at levels lower than 0.001% and readily identified mutated circulating DNA in patient plasma samples. This approach provides an exquisitely sensitive and broadly applicable approach for the development of personalized biomarkers to enhance the clinical management of cancer patients. | 08-15-2013 |
20130267428 | High throughput digital karyotyping for biome characterization - The invention herein describes a method for identifying a DNA sequence, and oligonucleotide adaptors used in the identification of a DNA sequence. | 10-10-2013 |
20130274117 | High-Throughput Single Cell Barcoding - Methods and compositions for high-throughput, single cell analyses are provided. The methods and compositions can be used for analysis of genomes and transcriptomes, as well as antibody discovery, HLA typing, haplotyping and drug discovery. | 10-17-2013 |
20130281308 | Methods for sorting nucleic acids and preparative in vitro cloning - Methods and compositions relate to the sorting and cloning of high fidelity nucleic acids using high throughput sequencing. Specifically, nucleic acid molecules having the desired predetermined sequence can be sorted from a pool comprising a plurality of nucleic acids having correct and incorrect sequences. | 10-24-2013 |
20130303385 | 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. | 11-14-2013 |
20130316920 | 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. | 11-28-2013 |
20130324422 | DETECTING DISEASE-CORRELATED CLONOTYPES FROM FIXED SAMPLES - The invention is directed to a method for determining immunophenotypes of tissue-infiltrating lymphocytes in a solid tissue of a patient by (a) generating clonotype profiles from a sample of nucleic acid extracted from a fixed tissue sample from a solid tissue of the patient, where such tissue contains tissue-infiltrating lymphocytes; and (b) determining immunophenotypes of the tissue-infiltrating lymphocytes by (i) obtaining a sample of lymphocytes from peripheral blood of the patient; (ii) sorting the lymphocytes from peripheral blood into at least one subset based on different immunophenotypes of the lymphocytes; (iii) generating a clonotype profile for each of the at least one subset of lymphocytes; and (iv) determining immunophenotypes of lymphocytes in the fixed tissue sample by a correspondence between clonotypes of the fixed tissue sample and clonotypes of the at least one subset. | 12-05-2013 |
20130331280 | COMPOSITIONS AND METHODS FOR FUNCTIONAL GYLCOMICS - The disclosure relates to labeling glycans and glycosphingolipids from undefined mixtures with chemical moieties that emit light when exposed to electromagnetic radiation and uses of these labeled glycans and glycosphingolipids in microarrays for research and diagnostic purposes. In certain embodiments, the disclosure relates to derivatizing glycosphingolipids with a marker. | 12-12-2013 |
20130338014 | Calibration Standards For Digital Histocytometry - An analytical reference for digital histochemistry is constituted of an on-slide standard used to calibrate biomarker expression in biopsy material and tissue sections. The standard consists of one or more calibration standards, which are derived from cell lines that express biomarkers, and are arranged into a calibration array. Expression of the desired biomarkers is validated by Western blotting, flow cytometry, or other methods. The calibration array is applied to a microscopy slide in such a manner that test samples from biopsies or tissue sections, or other cellular material, can also be mounted on the same slide, adjacent to the calibration array. Data obtained from the calibration array can be used to quantify expression of biomarkers in the biopsy material, tissue sections, tissue microarrays, and cellular material, via digital histochemistry. | 12-19-2013 |
20140011688 | 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. | 01-09-2014 |
20140018246 | 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. | 01-16-2014 |
20140038832 | COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS - Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence. | 02-06-2014 |
20140045707 | CENTROID MARKERS FOR IMAGE ANALYSIS OF HIGH DENSITY CLUSTERS IN COMPLEX POLYNUCLEOTIDE SEQUENCING - Improved compositions, methods, apparatus, and kits for high-throughput nucleic acid amplification, detection and sequencing are disclosed. A nucleic acid cluster having an identifiable center is produced by generating on a solid support an immobilized nucleic acid complement from a template, one of which comprises a detectable label; and amplifying the complement and the template to obtain a nucleic acid cluster on the support, the cluster having a substantially central location marked by the detectable label and a surrounding region comprising immobilized copies. Also disclosed are nucleotide sequence determination in nucleic acid clusters so produced, center position annotation in the clusters, assignment of sequence information to overlapping clusters, and related compositions and methods. | 02-13-2014 |
20140045708 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention. | 02-13-2014 |
20140051588 | Sequencing Small Amounts of Complex Nucleic Acids - The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example. | 02-20-2014 |
20140051589 | PEPTIDE CONSTRUCTS AND ASSAY SYSTEMS - The present invention provides methods for constructing peptide construct sets and methods of use of these peptide construct sets in assay systems for peptide analysis, and in particular for use in high throughput peptide analysis. The methods allow for analysis of large sets of peptide constructs in a cost-effective manner, employing molecular biological techniques that are both robust and easily parallelized. Thus, the methods allow for the construction of peptide construct sets encompassing, e.g., the human proteome. | 02-20-2014 |
20140080721 | METHODS FOR REDUCING NUCLEIC ACID DAMAGE - Provided herein is a method of inhibiting degradation of nucleic acids during a nucleic acid processing step selected from fragmentation and detection comprising contacting the nucleic acids with a solution comprising gallic acid, analogues, derivatives thereof or mixtures thereof, during the processing step, wherein the contacting inhibits degradation of the nucleic acids. Also provided herein is a method of inhibiting light-induced degradation of nucleic acids. Additionally, provided herein is a method of reducing or inhibiting nucleic acid damage during preparation of a nucleic acid sample comprising fragmenting the nucleic acid sequences in the sample in a solution comprising one of more compounds, the compounds inhibiting degradation of the nucleic acid sequences in the sample. | 03-20-2014 |
20140087955 | DEVICES AND METHODS FOR EFFICIENT CAPTURE OF NUCLEIC ACIDS - The present invention relates a device for the efficient binding of nucleic acids on a microarray, comprising a reaction zone comprising a microarray, and a capture zone comprising a porous membrane substrate, wherein the capture zone is capable of specifically capturing sense strands of target molecules, whereas complementary antisense strands are captured in the reaction zone, or vice versa. The invention further envisages temperature regulating units in the device allowing to bring or keep the capture at a temperature not allowing hybridizing or binding of nucleic acid(s) to the capture molecules or to a temperature suitable for nucleic acid hybridization. The invention also relates to a method of efficiently binding nucleic acids on a microarray, comprising introducing a medium containing one or more target molecules in denatured form into a capture zone of a device of the present invention, performing an interaction reaction between the target molecules and immobilized capture molecules in said capture zone, and transporting not bound target molecule strands to a reaction zone comprising a microarray, thereby allowing an interaction between the target molecule strands and immobilized capture molecules on the microarray. In a further aspect the invention relates to the use of such a device for enriching target molecules, specifically selecting a target molecules, expression analysis, comparative genomic hybridization, the detection of SNPs, or for microarray-based genomic selection-based sequencing. | 03-27-2014 |
20140094376 | MULTIPLEX PYROSEQUENCING USING NON-INTERFERING NOISE CANCELLING POLYNUCLEOTIDE IDENTIFICATION TAGS - The present disclosure generally pertains to a multiplex method for analyzing samples comprising using polynucleotide amplification to produce amplified products wherein one or more target sequences are tagged with a non-interfering, non-canceling target-specific polynucleotide identification tag, pyrosequencing the amplified products through the non-canceling target-specific polynucleotide identification tag sequence to detect the presence of one or more specific polynucleotide identification tags. The presence of a specific polynucleotide identification tag being correlated with the presence of a specific target sequence. | 04-03-2014 |
20140121117 | SAMPLE ANALYSIS BY MASS CYTOMETRY - In a mass cytometer system, a tissue sample labeled with multiple metal tags is supported on an encoded substrate for distribution profile mapping by laser ablation. Groups of elemental ions from each plume generated by each laser pulse are detected by the mass cytometer and the data is mapped according to the encoded substrate. This configuration allows for the production of a 3-dimentional distribution profile of the multiple metal tags in the tissue sample. | 05-01-2014 |
20140121118 | METHODS, SYSTEMS AND COMPOSITIONS REGARDING MULTIPLEX CONSTRUCTION PROTEIN AMINO-ACID SUBSTITUTIONS AND IDENTIFICATION OF SEQUENCE-ACTIVITY RELATIONSHIPS, TO PROVIDE GENE REPLACEMENT SUCH AS WITH TAGGED MUTANT GENES, SUCH AS VIA EFFICIENT HOMOLOGOUS RECOMBINATION - A method is provided to construct libraries of nucleic acids that comprise a plurality of mutations, each of which may be identified with particularity, such as following a selection or screening. | 05-01-2014 |
20140128271 | ASSAY METHOD USING ENCODED PARTICLE-BASED PLATFORM - Provided is an assay method using an encoded particle-based platform. In the assay method, first, a plurality of encoded particles having codes distinguishable from one another according to kinds of included target materials are prepared. The plurality of encoded particles are provided onto a plate including a plurality of wells by pipetting, and disposed in the plurality of wells by a self-assembly method. An analyte is provided into the plurality of wells. The codes of the plurality of encoded particles disposed in the plurality of wells are decoded. The target materials of the plurality of encoded particles are released to cause a reaction between the target materials and the analyte. | 05-08-2014 |
20140141982 | Methods for sorting nucleic acids and multiplexed preparative in vitro cloning - Methods and compositions relate to the sorting and cloning of high fidelity nucleic acids using high throughput sequencing. Specifically, nucleic acid molecules having the desired predetermined sequence can be sorted from a pool comprising a plurality of nucleic acids having correct and incorrect sequences. | 05-22-2014 |
20140155278 | SYSTEM AND METHOD FOR DETECTING BIOLOGICAL MATERIALS - A method of identifying a target biological material by using captures and probes. Each capture is specific for a kind of target. Each probe is designed to distinguish the type of the target. The captures and probes are each labeled with one or more detectable labels. | 06-05-2014 |
20140206553 | MASSIVE PARALLEL METHOD FOR DECODING DNA AND RNA - This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3′-position of the deoxyribose. | 07-24-2014 |
20140206554 | Methods and Systems for Processing Polynucleotides - The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. | 07-24-2014 |
20140249039 | METHODS OF MACROMOLECULAR ANALYSIS USING NANOCHANNEL ARRAYS - Methods of analyzing features such as the physical size of macromolecules or biomarkers along large genomic DNA molecules were disclosed as wen as the devices for carrying out such high throughput analysis in a massively parallel fashion. Methods of fabricating such devices are also disclosed. | 09-04-2014 |
20140303009 | Compositions, Methods, and Kits for Identifying Candidate Molecules from Encoded Chemical Libraries - The subject matter relates to relates to a one-bead-one-sequence composition, a library of tagged chemicals comprising a plurality of one-bead-one-sequence compositions, a method for identifying a candidate molecule from a library of tagged chemicals, and a composition produced by a process, all as described herein. | 10-09-2014 |
20140315730 | SCALABLE CHARACTERIZATION OF NUCLEIC ACIDS BY PARALLEL SEQUENCING - A method for detecting the presence or absence of a target polynucleotide in a sample is described. | 10-23-2014 |
20140323321 | DETECTION OF HEAD AND NECK CANCER USING HYPERMETHYLATED GENE DETECTION - Methods and kits for detection of a cell proliferative disorder, such as head and neck cancer are provided utilizing analysis of the methylation state of targeted genes or regulatory regions of genes in a saliva or serum sample are described. The presence of hypermethylation of the genes or their regulatory regions is indicative of the presence, or a stronger possibility of recurrence and or a poorer prognosis in subjects with cancer. | 10-30-2014 |
20140329698 | 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. | 11-06-2014 |
20140336061 | METHODS FOR OPTICALLY ENCODING AN OBJECT WITH UPCONVERTING MATERIALS AND COMPOSITIONS USED THEREIN - The present invention relates generally to encoding samples. More specifically, it relates to barcodes and compositions involving upconverters and methods including them. In a composition aspect of the invention, a composition comprising two or more lanthanide materials is provided. Each lanthanide material comprises a host, an absorber, and an emitter, and the materials emit detectable electromagnetic radiation upon excitation with absorbable electromagnetic energy. One or more relative ratios of emission intensities uniquely identify the composition. | 11-13-2014 |
20140349860 | IDENTIFYING PEPTIDES AT THE SINGLE MOLECULE LEVEL - The present invention relates to methods for identifying amino acids in peptides. In one embodiment, the present invention contemplates labeling the N-terminal amino acid with a first label and labeling an internal amino acid with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level. | 11-27-2014 |
20140357500 | SINGLE CELL BAR-CODING FOR ANTIBODY DISCOVERY - Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding for heavy and IgL pairing if antibodies. | 12-04-2014 |
20140378322 | COMPOSITIONS AND METHODS FOR SAMPLE PROCESSING - This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device. | 12-25-2014 |
20150024950 | COMPOSITIONS AND METHODS FOR ACCURATELY IDENTIFYING MUTATIONS - The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods. | 01-22-2015 |
20150031559 | Increased Confidence of Allele Calls with Molecular Counting - 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. | 01-29-2015 |
20150031560 | 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. | 01-29-2015 |
20150038346 | MONITORING IMMUNE RESPONSIVENESS TO CANCER VACCINATION - The invention is direct to a method for determining a cancer patient's immune responsiveness to anti-cancer vaccination. In one aspect, for each of a plurality of vaccinations, pairs of clonotype profiles are obtained, one immediately prior to vaccination and one during the period of peak immune response, usually within two to twenty days after the vaccination. Responsiveness is correlated to successive increases in identical clonotypes within each pair of clonotype profiles in at least two successive vaccinations. | 02-05-2015 |
20150045237 | METHOD FOR IDENTIFICATION OF THE SEQUENCE OF POLY(A)+RNA THAT PHYSICALLY INTERACTS WITH PROTEIN - The invention relates to an in vitro method for identifying the sequence of one or more poly(A)+RNA molecules that physically interacts with protein. The present invention provides a method to define the protein-bound transcriptome under any given cellular condition, such as a disease condition or after treatment with any given substance, drug, or other cellular perturbation. The invention also relates to a method for identification of a drug target and a method for the identification of one or more biomarkers, preferably for identification of a panel of biomarkers, for any given medical condition, comprising the method of the invention. | 02-12-2015 |
20150051088 | NEXT-GENERATION SEQUENCING LIBRARIES - Provided herein is technology relating to next-generation sequencing and particularly, but not exclusively, to methods and compositions for preparing a next-generation sequencing library comprising short overlapping DNA fragments and using the library to sequence one or more target nucleic acids. | 02-19-2015 |
20150051089 | Quantification of Adaptive Immune Cell Genomes in a Complex Mixture of Cells - Compositions and methods are described for highly sensitive quantification of the relative representation of DNA from adaptive immune cells (e.g., T and/or B lymphocytes) in DNA extracted from complex mixtures of cells that include cells which are not adaptive immune cells. Included are methods for determining the relative presence in a tumor of tumor infiltrating lymphocytes (TIL), the relative presence of lymphocytes infiltrating a somatic tissue that is the target of an autoimmune disease, and the relative presence of lymphocytes infiltrating a transplanted organ. | 02-19-2015 |
20150057164 | HIGH THROUGHPUT METHODS FOR FUNCTIONALLY DETERMINING RNA INTERFERENCE EFFICIENCY - Provided is a single construct combining a sequence encoding an RNAi molecule, a sequence encoding a reporter, and a target sequence specific for the RNAi molecule. The construct can be used to determine the potency of the encoded RNAi molecule in a direct and unbiased way. These results can be used to inform the design of potent RNAi molecules of various types and can be extended to several other applications, including: (1) generation of tiled libraries comprising every possible RNAi molecule-encoding sequence for a given gene target; (2) large-scale parallel validation of RNAi molecules targeting many genes to generate validated RNAi molecule-encoding libraries; (3) experimental comparison of design algorithms and strategies; and (4) investigation of RNAi biology in target site mutagenesis assays by screening pools containing single nucleotide changes in target sites and/or in the RNAi molecule to identify the most relevant sequence characteristics of potent RNAi-target site predictions. | 02-26-2015 |
20150065358 | METHOD FOR VERIFYING BIOASSAY SAMPLES - The present invention relates to a method for verifying the integrity of biological source samples subjected to multistep bioassays that comprise massively parallel sequencing of the sample genomic nucleic acids. The integrity of the biological source samples is verified using unique marker nucleic acids that are combined with the biological source sample, and are sequenced concomitantly with the genomic nucleic acids of the biological source sample. The method provides verification of individual samples in single- and multiplex massively parallel sequencing assays. | 03-05-2015 |
20150065359 | Culture Based Screening Assay and Methods of Use Thereof to Identify Agents Which Modulate Tumor Development, Invasion and Differentiation - A 3D organotypic culture which phenocopies aggressive, invasive cancer and methods of use thereof are provided. | 03-05-2015 |
20150072873 | METHOD AND APPARATUS FOR PRODUCING SEQUENCE VERIFIED DNA - A method of retrieving a subset of polynucleotide molecules from a mixture of polynucleotide molecules includes receiving a mixture of nucleotide sequences comprising one or more polynucleotide molecules, synthesizing one or more identifier (ID) regions onto the one or more polynucleotide molecules, and sequencing members of the population of polynucleotide molecules to associate the sequence of one or more of the molecules (the “Polynucleotide Sequence”) with the sequence of the attached ID region (the “ID Sequence”). The method also includes generating a bead-bound library of one or more beads comprising subsets of identical polynucleotide molecules. Each bead is identified by the ID Sequence of the associated Polynucleotide Sequence. The method further includes sequencing the one or more ID regions of each bead to generate ID Sequence information for each bead, combining the Polynucleotide Sequence information, the one or more ID Sequences, and coordinates of each bead to identify the Polynucleotide Sequence on the bead, and retrieving the bead with its associated Polynucleotide Sequence from the flow cell based on the absolute coordinate position of the bead. | 03-12-2015 |
20150072874 | METHOD FOR DETECTING HLA-A*31:01 ALLELE - Provided is a method for detection of HLA-A*31:01 allele. One or more single nucleotide polymorphisms which characterize HLA-A*31:01 are analyzed and the presence or absence of HLA-A*31:01 is determined based on the result of the analysis. | 03-12-2015 |
20150072875 | IDENTIFICATION OF NUCLEIC ACIDS - This disclosure relates to methods for identifying target nucleic acids in a sample by detecting an amplified sequence corresponding to the target using a detectable probe and by monitoring its melting temperature (T | 03-12-2015 |
20150080232 | DNA SEQUENCING BY SYNTHESIS USING RAMAN AND INFRARED SPECTROSCOPY DETECTION - This invention provides nucleoside triphosphate analogues having the structure: | 03-19-2015 |
20150080233 | MULTIPLEXED IMAGING OF TISSUES USING MASS TAGS AND SECONDARY ION MASS SPECTROMETRY - A method of generating a high resolution two-dimensional image of a sample comprising cells and extracellular structures is provided. In certain embodiments, the method comprises: labeling a sample with at least one mass tag, thereby producing a labeled sample; scanning the sample with a secondary ion mass spectrometer (SIMS) ion beam to generate a data set that comprises spatially-addressable measurements of the abundance of the mass tag across an area of the sample; and outputting the data set. In many embodiments, the data set contains the identity and abundance of the mass tag. A system for performing the method is also provided. | 03-19-2015 |
20150080234 | Cell Patterning - The present disclosure provides technologies for achieving cell patterning, as well as patterned cell arrays achieved with such technologies. Provided apparatus and methods are useful in a variety of contexts and provide particular advantages with respect to assessing living cell arrays and/or their responsiveness to stimuli, including identifying and/or characterizing complex cellular responses. | 03-19-2015 |
20150080235 | ASSAYS AND REAGENTS FOR DIAGNOSING TYPE 1 DIABETES - Described herein are compositions and methods for diagnosing or monitoring type 1 diabetes. | 03-19-2015 |
20150087534 | METHODS OF NUCLEIC ACID SEQUENCING - Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand. | 03-26-2015 |
20150087535 | MEASUREMENT OF NUCLEIC ACID VARIANTS USING HIGHLY-MULTIPLEXED ERROR-SUPPRESSED DEEP SEQUENCING - Methods and compositions are disclosed for measuring low-abundance DNA variants from a complex mixture of DNA molecules. Embodiments of the methods allow for extremely sensitive detection and can distinguish true variants from sequencer misreads and PCR misincorporations. | 03-26-2015 |
20150087536 | USE OF APTAMERS IN PROTEOMICS - The present invention is a method for measuring the amount of at least one molecule in a biological sample, the method comprising a) combining the sample, or a derivative thereof, with one or more aptamers and allowing one or more molecules in the sample to bind to the aptamer(s); b) separating bound from unbound molecules; and c) quantifying the molecule(s) bound to the or each aptamer, wherein quantification of the bound molecule(s) is carried out by sequencing at least part of the or each aptamer. Uses of and products derived from the method are also contemplated. | 03-26-2015 |
20150087537 | Methods, Systems, Computer Readable Media, and Kits for Sample Identification - A method for sequencing a polynucleotide sample having a barcode sequence includes: introducing a series of nucleotides to the polynucleotide sample according to a predetermined order of nucleotide flows; obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-correcting code that is (i) designed based on and adapted for use with the predetermined order of nucleotide flows, and (ii) capable of distinguishing any codeword in the error-correcting code from the other codewords in the error-correcting code in the presence of zero, one, and two errors. | 03-26-2015 |
20150094213 | Comparative Ligand Mapping from MHC Positive Cells - A method of comparative ligand mapping to identify peptide ligands presented by MHC positive cells that distinguish an infected/transfected cell from an uninfected/non-transfected cell is disclosed. | 04-02-2015 |
20150099646 | NUCLEIC ACID AMPLIFICATION PRIMERS FOR PCR-BASED CLONALITY STUDIES - The invention relates to PCR-based clonality studies for among others early diagnosis of lymphoproliferative disorders. Provided is a set of nucleic acid amplification primers comprising a forward primer, or a variant thereof, and a reverse primer, or a variant thereof, capable of amplifying a rearrangement selected from the group consisting of a VH-JH IGH rearrangement, a DH-JH IGH rearrangement, a VK-JK IGK rearrangement, a VK/intron-Kde IGK rearrangement, a Vλ-Jλ IGL rearrangement, a Vβ-Jβ TCRB rearrangement, a Dβ-Jβ TCRB rearrangement, a Vγ-Jγ TCRG rearrangement, a Vδ-Jδ TCRD rearrangement, a Dδ-Dδ TCRD rearrangement, a Dδ-Jδ TCRD rearrangement, a Vδ-Dδ TCRD rearrangement, or a translocation selected from t(11;14) (BCL1-IGH) and t(14;18) (BCL2-IGH). The primers can be used in PCR-based clonality studies for early diagnosis of lymphoproliferative disorders and detection of minimal residual disease (MRD). Also provided is a kit comprising at least one set of primers of the invention. | 04-09-2015 |
20150099647 | Methods And Solutions For Inhibiting Undesired Cleaving Of Labels - 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. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses. | 04-09-2015 |
20150099648 | SOYBEAN TRANSFORMATION METHOD - The present disclosure relates in part to a method for identifying a soybean germline transformant from a population of soybean transformants by incorporating a selection agent within rooting medium used in tissue culture during the soybean transformation process. The soybean germline transformants are selected from a population of soybean transformants which are comprised of a combination of non-germline and germline soybean transformants. The soybean non-germline transformants are identified and eliminated early in the transformation process. The soybean germline transformants are identified and selected for culturing into mature soybean plants. The method is readily applicable for screening and obtaining a soybean germline transformant at an early stage in the soybean transformation process. | 04-09-2015 |
20150111762 | DNA SEQUENCING - Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using one or more labels and signal amplitude to distinguish bases. | 04-23-2015 |
20150111763 | DNA SEQUENCING - Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, and systems for sequencing a nucleic acid using two or more labels and signal ratios to distinguish bases. | 04-23-2015 |
20150126379 | LONG INSERT-BASED WHOLE GENOME SEQUENCING - The present invention is directed to a method of detecting a genomic rearrangement in a nucleic acid sample with Long Insert Whole Genome Sequencing (LI-WGS). The method may include obtaining a nucleic acid sample and then fragmenting the nucleic acid sample (e.g., via sonication). In particular, the fragmenting may result in the production of a plurality of inserts. Thereafter, the method comprises purifying the plurality of inserts using magnetic beads and then amplifying the purified plurality of inserts. In addition, the method further comprises sequencing the purified and amplified plurality of inserts. In some aspects, the plurality of inserts have a length of between about 800 and about 1,100 base pairs. | 05-07-2015 |
20150126380 | METHOD FOR ANALYZING MATERNAL DNA IN LARGE PLANT POPULATIONS - The present invention relates to a non-destructive method for analyzing maternal DNA of a seed. In this method the DNA may be dislodged from the seed coat surface and may be used to collect information on the genome of the maternal parent of the seed. Also, the present invention provides a high throughput DNA analysis system for large plant populations. | 05-07-2015 |
20150126381 | TEMPLATE DIRECTED SPLIT AND MIX SYNTHESIS OF SMALL MOLECULE LIBRARIES - The invention combines the advantages of split and mix synthesis with the advantages of template directed synthesis. The method comprises the steps of: a) adding a linker molecule L to one or more reaction wells; b) adding a molecule fragment to each of said reaction wells; c) adding an oligonucleotide identifier to each of said reaction wells; d) subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; e) combining the contents of said one or more reaction wells; and f) contacting the resulting bifunctional molecule(s) of step e) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added in step c). | 05-07-2015 |
20150133317 | IDENTIFICATION OF POLYNUCLEOTIDES ASSOCIATED WITH A SAMPLE - Disclosed herein are compositions and methods for sequencing, analyzing, and utilizing samples such as single samples. Also disclosed herein are compositions and methods for matching together two or more sequences from a sample. Also disclosed herein are compositions and methods for expressing and screening molecules of interest. | 05-14-2015 |
20150133318 | ENZYMATIC METHOD TO ENRICH FOR CAPPED RNA, KITS FOR PERFORMING SAME, AND COMPOSITIONS DERIVED THEREFROM - The instant invention is based, at least in part, on the identification of novel methods for the enzymatic enrichment of capped RNAs. The invention provides, e.g., methods for enrichment of capped RNAs, kits for making such capped RNAs, and compositions of enriched RNAs or cDNA libraries derived therefrom. | 05-14-2015 |
20150133319 | COMPOSITIONS AND KITS FOR MOLECULAR COUNTING - Methods, kits and systems are disclosed for analyzing one or more molecules in a sample. Analyzing the one or more molecules may comprise quantitation of the one or more molecules. Individual molecules may quantitated by PCR, arrays, beads, emulsions, droplets, or sequencing. Quantitation of individual molecules may further comprise stochastic labeling of the one or more molecules with a plurality of oligonucleotide tags to produce one or more stochastically labeled molecules. The methods may further comprise amplifying, sequencing, detecting, and/or quantifying the stochastically labeled molecules. The molecules may be DNA, RNA and/or proteins. | 05-14-2015 |
20150133320 | 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. | 05-14-2015 |
20150141270 | SINGLE-STRANDED NUCLEIC ACID APTAMERS SPECIFICALLY BINDING TO KLEBSIELLA PNEUMONIAE AND METHOD FOR DETECTING K. PNEUMONIA USING THE SAME - Provided is a single-stranded nucleic acid aptamer specifically binding to | 05-21-2015 |
20150148240 | UNIVERSAL METHYLATION PROFILING METHODS - This invention provides methods of derivatizing a double-stranded DNA comprising contacting double-stranded DNA with a CpG methyltransferase and an s-adenosylmethionine analog. This invention also provides methods of sequencing DNA to determine methylation patterns. | 05-28-2015 |
20150148241 | METHOD FOR GENOME 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. | 05-28-2015 |
20150292007 | Spatial Sequencing of Nucleic Acids Using DNA Origami Probes - A method of sequencing nucleic acids by probe hybridization and/or ligation is provided using DNA origami as a barcode for a nucleic acid probe. | 10-15-2015 |
20150292008 | SHORT CYCLE METHODS FOR SEQUENCING POLYNUCLEOTIDES - The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or full completion. | 10-15-2015 |
20150292019 | Array-based Translocation and Rearrangement Assays - Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array. | 10-15-2015 |
20150299694 | METHODS OF MARKING MATERIALS - A method of marking a material and subsequently detecting that it has been marked is disclosed, comprising adding or applying a marker comprising a nucleic acid tag to the material, sampling a portion of the material containing such marker, and detecting the presence of nucleic acid tag in the sample. The method is characterized in that the quantity of the nucleic acid tag present in the sample is determined to provide an indication of the quantity of marker present in the material. The nucleic acid tag may comprise one or more identifying sequences, and the tag is amplified by means of a nucleic acid amplification reaction. Also disclosed are a method of marking a material with a nucleic acid tag, a method of detecting whether a material has been marked by a marker comprising a nucleic acid tag, a method of detecting the quantity of a marker comprising a nucleic acid tag in a material that has previously been marked, a method of marking a material and subsequently determining the quantity of marker in the material, and a method of and a kit for determining which particular nucleic acid tag from a known pool of nucleic acid tags has been used to mark a material. | 10-22-2015 |
20150299783 | Methods and Compositions for Incorporating Nucleotides - 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. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses. | 10-22-2015 |
20150299784 | MASSIVELY PARALLEL SINGLE CELL ANALYSIS - The disclosure provides for methods, compositions, and kits for multiplex nucleic acid analysis of single cells. The methods, compositions and systems may be used for massively parallel single cell sequencing. The methods, compositions and systems may be used to analyze thousands of cells concurrently. The thousands of cells may comprise a mixed population of cells (e.g., cells of different types or subtypes, different sizes). | 10-22-2015 |
20150299812 | 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. | 10-22-2015 |
20150307875 | Restriction Enzyme-Free Target Enrichment - Provided herein are various methods for enriching a target fragment that is present in randomly sheared genomic DNA. In some embodiments, the method may involve hybridizing randomly sheared genomic DNA to a halo probe to produce a first circular complex, and then enzymatically digesting the overhanging ends of the genomic fragment. Other embodiments may include hybridizing randomly sheared genomic DNA to an RNA oligonucleotide that comprises a region that hybridizes to a fragment of the randomly sheared genomic DNA to produce an RNA/DNA duplex. The overhanging ends of the genomic fragment in the RNA/DNA duplex can then be enzymatically digested. | 10-29-2015 |
20150307942 | METHOD AND A KIT FOR NON-INVASIVELY DETECTING FETAL DEAFNESS PATHOGENIC GENE MUTATIONS - The present invention is directed to a method, kit and primers for detecting fetal deafness pathogenic gene mutations. The method of the invention comprises: (a) designing primers according to the pre-determined mutation loci of deafness pathogenic genes; (b) extracting plasma DNAs in a pregnant woman; (c) connecting the extracted plasma DNAs with pre-amplification linkers to obtain connected products; (d) PCR pre-amplifying the connected product to obtain pre-amplified products; (e) cyclizing the pre-amplified products to obtain cyclised DNAs; (f) PCR amplifying the cyclised DNAs using the designed primers to obtain amplified products; and (g) high throughput sequencing the amplified products and analyzing the mutations of the fetal deafness pathogenic genes. The invention can effectively determine whether the pre-determined loci on deafness pathogenic genes have been mutated as well as the mutation type. | 10-29-2015 |
20150315568 | Sieving Nucleic Acid Samples - A method of selecting nucleic acid samples including particular desired alleles from a plurality of nucleic acid samples including the steps of performing a first reaction in a plurality of pools containing the samples to produce reaction products including a source tag identifying said each pool; pooling the pools to provide pooled pools; for each of the desired alleles to be identified, performing a second reaction using said reaction products to produce allele-specific second reaction products comprising a marker tag and a derived source tag; identifying said allele-specific second reaction products, and further identifying nucleic acid samples with the desired alleles. A source tag sharing number “d” may be determined for each of the alleles. Alleles may also be binned together. | 11-05-2015 |
20150321164 | METHOD FOR SYNTHESIZING AND SCREENING LEAD COMPOUND AND REAGENT TESTING KIT - A method for synthesizing and screening a lead compound, comprising the following steps: (1) retrieving raw materials: retrieving an i-number of synthetic blocks and an (i+2)-number of single-stranded DNA fragments; (2) synthesizing a compound by using a combinatorial chemistry method, acquiring a library of a single-stranded DNA-marked compound; (3) screening: screening the library of the DNA-marked compound; and, (4) sequencing: retrieving the DNA-marked compound screened in step (3), and sequencing the DNA on the DNA-marked compound, where the synthesis blocks and reaction mechanism of the compound can be determined on the basis of the DNA sequencing. Also disclosed are a synthesis and screening reagent testing kit for the lead compound and a combinatorial chemistry library. | 11-12-2015 |
20150322492 | METHODS AND KITS FOR IDENTIFYING MICROORGANISMS IN A SAMPLE - Disclosed herein are compositions with uniquely designed oligonucleotide primers for identifying a plurality of microorganisms in a sample, and improved methods for detection of microbial populations from diverse biological and environmental samples. | 11-12-2015 |
20150329852 | INCREASING DYNAMIC RANGE FOR IDENTIFYING MULTIPLE EPITOPES IN CELLS - The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection. | 11-19-2015 |
20150329899 | SYSTEMS AND METHODS FOR VALIDATION OF SEQUENCING RESULTS - Systems and method for validation of sequencing results can amplify a target region of a nucleic acid sample in the presence of a primer pool including target specific and variant specific primers. The variant specific primers can include variant specific barcodes and variant specific sequences. An amplicon can be sequenced to determine the sequence of the variant specific barcode. The variant can be identified based on the sequence of the variant specific barcode, and the location of the variant can be determined by mapping the amplicon to a reference sequence. | 11-19-2015 |
20150329906 | 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. | 11-19-2015 |
20150329909 | AUTISM-ASSOCIATED BIOMARKERS AND USES THEREOF - The invention discloses biomarkers for human autism. The invention provides methods for treating, preventing, and diagnosing human autism and autism-related disorders. | 11-19-2015 |
20150330978 | TARGETED MORPHOLINO LIGANDS AND USES THEREOF - Morpholino ligands that have high specificity for targets, such as proteins, and that bind their targets through non Watson-Crick base pairing, are described. The use of such morpholino ligands for targeted delivery of loads, such as drugs or labels, are disclosed. | 11-19-2015 |
20150337364 | Isothermal Methods and Related Compositions for Preparing Nucleic Acids - According to some aspects of the invention preparative methods and related compositions are provided for nucleic acid sequencing. | 11-26-2015 |
20150344872 | METHODS OF SYNTHESIS OF OLIGONUCLEOTIDE TAGGED COMBINATORIAL LIBRARIES AND USES THEREOF - Provided herein are methods of synthesis of a compound which includes a functional moiety operatively linked to a tagging oligonucleotide, libraries thereof and methods of using the compound and libraries thereof to identify compounds which bind to a target. | 12-03-2015 |
20150344946 | 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. | 12-03-2015 |
20150344970 | Personalized Tumor Biomarkers - Clinical management of human cancer is dependent on the accurate monitoring of residual and recurrent tumors. We have developed a method, called personalized analysis of rearranged ends (PARE), which can identify translocations in solid tumors. Analysis of four colorectal and two breast cancers revealed an average of nine rearranged sequences (range 4 to 15) per tumor. Polymerase chain reaction with primers spanning the breakpoints were able to detect mutant DNA molecules present at levels lower than 0.001% and readily identified mutated circulating DNA in patient plasma samples. This approach provides an exquisitely sensitive and broadly applicable approach for the development of personalized biomarkers to enhance the clinical management of cancer patients. | 12-03-2015 |
20150353925 | TRANSPOSON END COMPOSITIONS AND METHODS FOR MODIFYING NUCLEIC ACIDS - The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5′-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5′- and 3′-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5′-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3′-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5′- and 3′-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing.) | 12-10-2015 |
20150361489 | BIOMOLECULAR PROCESSING PLATFORM AND USES THEREOF - The present invention relates to a device comprising a biomolecular processor. Each biomolecular processor has one or more bioreactor chambers defined by a solid substrate; a support structure within each bioreactor; a cleaving enzyme immobilized to the support structure and operatively positioned within the bioreactor chamber to cleave monomer or multimer units of a biopolymer molecule operatively engaged by the cleaving enzyme; and one or more time-of-flight channels formed in the solid substrate and fluidically coupled to said one or more bioreactor chambers. Each of the time-of-flight channels have two or more sensors including at least (i) a first sensor contacting the time-of-flight channel proximate to the input end of the channel and (ii) a second sensor contacting the time-of-flight channel proximate to the output end of channel. The present invention further relates to methods of sequencing and identifying biopolymer molecules using the device. | 12-17-2015 |
20150361492 | SAFE SEQUENCING SYSTEM - The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ≧95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells. | 12-17-2015 |
20150363551 | PROCESS FOR IDENTIFYING RARE EVENTS - A method for identifying a subpopulation of specific cells among a large population of cells, includes:
| 12-17-2015 |
20150368638 | METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING - Embodiments of the present invention relate to sequencing nucleic acids. In particular, embodiments of the methods and compositions provided herein relate to preparing nucleic acid templates and obtaining sequence data therefrom. | 12-24-2015 |
20150368704 | METHODS AND COMPOSITIONS FOR SINGLE CELL GENOMICS - Presented are methods and compositions for obtaining sequence information from one or more individual cells. The methods are useful for obtaining sequence information for a single nucleotide sequence, and for multiplex generation of sequence information from one or more individual cells. | 12-24-2015 |
20150368706 | 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. | 12-24-2015 |
20150368710 | CHEMICAL METHODS FOR PRODUCING TAGGED NUCLEOTIDES - This disclosure provides systems and methods for attaching nanopore-detectable tags to nucleotides. The disclosure also provides methods for sequencing nucleic acids using the disclosed tagged nucleotides. | 12-24-2015 |
20150368711 | METHOD FOR HIGH THROUGHPUT SCREENING OF NUCLEIC ACIDS - A scalable reaction and detection system for automated high throughput sequencing of nucleic acids involving a combination of chemical processes and observation processes independent of the chemistry processes. Discrete functional units may be configured in a manner that allows the system to interchangeably utilize different sequencing reaction components in conjunction with discrete apparatus components for optical image collection and/or analysis. | 12-24-2015 |
20150376609 | Methods of Analyzing Nucleic Acids from Individual Cells or Cell Populations - Methods, compositions and systems for analyzing individual cells or cell populations through the partitioned analysis of contents of individual cells or cell populations. Individual cells or cell populations are co-partitioned with processing reagents for accessing cellular contents, and for uniquely identifying the contents of a given cell or cell population, and subsequently analyzing the cell's contents and characterizing it as having derived from an individual cell or cell population, including analysis and characterization of the cell's nucleic acids through sequencing. | 12-31-2015 |
20150376690 | MOLECULAR REDUNDANT SEQUENCING - Methods, systems and compositions where a target nucleic acid includes a registration sequence disposed therein for identification of the number or relative position of determined sequence from the template sequence. Particularly preferred aspects include a registration sequence in a circular template nucleic acid sequence which is, in turn, used in sequence by incorporation processes that rely upon template dependent, polymerase mediated primer extension in the identification of the sequence of the template. | 12-31-2015 |
20150376700 | ANALYSIS OF NUCLEIC ACID SEQUENCES - The present disclosure relates to methods, compositions and systems for haplotype phasing and copy number variation assays. Included within this disclosure are methods and systems for combining the barcode comprising beads with samples in multiple separate partitions, as well as methods of processing, sequencing and analyzing barcoded samples. | 12-31-2015 |
20150379195 | SOFTWARE HAPLOTYING OF HLA LOCI - Methods are provided to determine the genomic sequence of the alleles at the HLA gene. The resultant sequences provide linkage information between different exons, and produces the unique sequence at each gene from the two alleles of the individual sample being typed. The sequence information provides an accurate HLA haplotype. Methods to decrease allele dropout during long range PCR reactions are also disclosed. | 12-31-2015 |
20160001248 | METHODS AND COMPOSITIONS FOR TAGGING AND ANALYZING SAMPLES - The invention relates to methods of tagging analytes in a sample. | 01-07-2016 |
20160003812 | METHODS FOR MAINTAINING THE INTEGRITY AND IDENTIFICATION OF A NUCLEIC ACID TEMPLATE IN A MULTIPLEX SEQUENCING REACTION - The invention generally relates to methods for maintaining the integrity and identification of a nucleic acid template in a multiplex sequencing reaction. In certain embodiments, methods of the invention involve obtaining a template nucleic acid, incorporating a pair of sequence identifiers into the template, and sequencing the template. | 01-07-2016 |
20160010085 | HETEROLOGOUS DNA BARCODING METHOD | 01-14-2016 |
20160017416 | BIOCHEMICALLY ACTIVATED ELECTRONIC DEVICE - A method of nucleic acid sequencing. The method can include the steps of (a) providing a polymerase tethered to a solid support charge sensor; (b) providing one or more nucleotides, whereby the presence of the nucleotide can be detected by the charge sensor; and (c) detecting incorporation of the nucleotide into a nascent strand complementary to a template nucleic acid. | 01-21-2016 |
20160024571 | Scalable Characterization of Nucleic Acids by Parallel Sequencing - A method for detecting the presence or absence of a target polynucleotide in a sample is described. | 01-28-2016 |
20160026758 | METHODS AND USES FOR MOLECULAR TAGS - Methods and uses for molecular tags are disclosed. Molecular tags may be attached to nucleic acid molecules. The attachment of the nucleic acid molecules prior to PCR amplification and sequencing improves the accuracy of genetic analysis and detection of genetic variations and diversity. Molecular tags may also be used for detection of drug-resistant variants. Methods for using molecular tags for determining and correcting PCR errors and/or sequencing error are also disclosed. | 01-28-2016 |
20160032375 | 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. | 02-04-2016 |
20160032379 | ENZYME-LINKED NUCLEOTIDES - Presented herein are polymerase-linked nucleotides for improved distinguishing nucleotide sequences for different nucleic acid molecules. Also presented are methods and systems using the polymerase-linked nucleotides for improved distinguishing nucleotide sequences for different nucleic acid molecules. | 02-04-2016 |
20160040227 | PARALLEL POLYMER SEQUENCING METHODS - The present invention relates to a method of sequencing a target polynucleotide by enzymatic and/or chemical means. The sequencing method includes a method for characterizing multiple alleles in a sample, a method of calculating confidence levels in ascertained sequences, a method for comparing polynucleotide sequences and a method of resolving ambiguities in a polynucleotide sequence. It also provides methods for appropriately preparing samples, for immobilising template molecules, for organising the template molecules and to conduct the sequencing of many molecules in parallel. The method involves analysing molecules as members of an array. Many target polynucleotides or many segments of a single target polynucleotide can be sequenced simultaneously. In a preferred embodiment the method involves analysing individual molecules within an array and base calls are based on the signals from two or more molecules. A method to prevent non-specific signal in sequencing is also provided. The invention is readily automated, both for small-scale and large-scale operation and relevant algorithms and the composition of kits and systems are provided. | 02-11-2016 |
20160041095 | OPTICAL SYSTEM AND ASSAY CHIP FOR PROBING, DETECTING AND ANALYZING MOLECULE - Apparatus and methods for analyzing single molecule and performing nucleic acid sequencing. An apparatus can include an assay chip that includes multiple pixels with sample wells configured to receive a sample, which, when excited, emits emission energy; at least one element for directing the emission energy in a particular direction; and a light path along which the emission energy travels from the sample well toward a sensor. The apparatus also includes an instrument that interfaces with the assay chip. The instrument includes an excitation light source for exciting the sample in each sample well; a plurality of sensors corresponding the sample wells. Each sensor may detect emission energy from a sample in a respective sample well. The instrument includes at least one optical element that directs the emission energy from each sample well towards a respective sensor of the plurality of sensors. | 02-11-2016 |
20160041179 | METHOD FOR DETECTING MULTIPLE PREDETERMINED COMPOUNDS IN A SAMPLE - This invention provides methods for detecting the presence of a plurality of predetermined compounds in a sample using a plurality of tag moieties and at least one nanopore. This invention also provides methods for determining the quantity of each of a plurality of predetermined compounds in a sample using a plurality of tag moieties and at least one nanopore. This invention further provides methods for detecting interaction of at least two predetermined compounds using at least one tag moiety and at least one nanopore. | 02-11-2016 |
20160046930 | METHODS OF SEQUENCING NUCLEIC ACIDS IN MIXTURES AND COMPOSITIONS RELATED THERETO - This disclosure relates to analyzing the end-to-end sequence and the relative distributions in heterogeneous mixtures of polynucleotides and methods and enabling reagents related thereto. In certain embodiments this method relates to the complete full length sequencing and quantitative profiling of mRNAs present in the transcriptomes of cells or tissues of but not limited to, higher multicellular organisms that possess interrupted genes subject to complex post-transcriptional RNA processing | 02-18-2016 |
20160046985 | MULTIPLE TAGGING OF LONG DNA FRAGMENTS - The present invention 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. | 02-18-2016 |
20160053253 | NUCLEIC ACID SEQUENCE ANALYSIS FROM SINGLE CELLS - Presented herein are methods and compositions for multiplexed single cell gene expression analysis. Some methods and compositions include the use of droplets and/or beads bearing unique barcodes such as unique molecular barcodes (UMI). | 02-25-2016 |
20160060621 | DIGITAL PCR BARCODING - Methods, compositions, and kits are provided for nucleic acid analysis, including single cell analysis. | 03-03-2016 |
20160060622 | METHODS AND KIT FOR CHARACTERIZING THE MODIFIED BASE STATUS OF A TRANSCRIPTOME - This invention relates to a method of characterizing the modified base status of a transcriptome, which involves contacting a transcriptome comprising one or more modified bases with an antibody specific to the modified bases under conditions effective to bind the antibody to the modified bases; isolating, from the transcriptome, a pool of RNA transcripts to which the antibody binds; and identifying isolated RNA transcripts that are present in a higher abundance in the isolated pool relative to the transcriptome, where each of said isolated RNA transcripts that are present in a higher abundance in the isolated pool together characterize the modified base status of the transcriptome. Also disclosed are a method of diagnosis or prognosis of a disease, a method of determining the effect of a treatment on modified base levels in RNA, and a kit for characterizing the modified base status of a transcriptome. | 03-03-2016 |
20160061738 | APPARATUS AND METHOD FOR PERFORMING NUCLEIC ACID ANALYSIS - The present invention relates to optical confinements, methods of preparing and methods of using them for analyzing molecules and/or monitoring chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost single-molecular analysis. | 03-03-2016 |
20160068886 | ATTENUATORS - Methods for detecting nucleic acid sequences, where attenuator oligonucleotides are provided to reduce the number of detection products resulting from highly abundant sequences. | 03-10-2016 |
20160068902 | SEQUENCING NUCLEIC ACIDS BY ENZYME ACTIVATION - Provided herein are methods of nucleic acid sequencing using nucleotides with labels attached to the phosphate group so that incorporation of such nucleotides into a primed template results in formation of a phospho-label. Treatment of the phospho-label with a phophatase generates a free label which can be detected in a variety of ways. The labels can include, e.g., chemiluminescent labels, chemiluminescent substrates and enzyme activators. Also provided are reagents such as nucleotides phospholinked to labels such as enzyme activators. | 03-10-2016 |
20160076023 | METHOD FOR GENERATING EXTENDED SEQUENCE READS - The present invention provides an approach to increase the effective read length of commercially available sequencing platforms to several kilobases and be broadly applied to obtain long sequence reads from mixed template populations. A method for generating extended sequence reads of long DNA molecules in a sample, comprising the steps of: assigning a specific barcode sequence to each template DNA molecule in a sample to obtain barcode-tagged molecules; amplifying the barcode-tagged molecules; fragmenting the amplified barcode-tagged molecules to obtain barcode-containing fragments; juxtaposing the barcode-containing fragments to random short segments of the original DNA template molecule during the process of generating a sequencing library to obtain demultiplexed reads; and assembling the demultiplexed reads to obtain extended sequence reads for each DNA template molecule, is disclosed. Also disclosed are methods systems and software for assembling paired end sequence reads to produce extended reads. | 03-17-2016 |
20160076081 | Targeted Chromosome Conformation Capture - The invention relates to a method which enables the possibility to capture chromosome conformation as well as a kit containing components useful to be used the method, such as to detect promoter and enhancer relations. The method comprises the following steps: i) providing cross-linked genomic DNA, wherein the DNA comprises a first and a second set of regions, ii) fragmenting the cross-linked genome, thus creating a plurality of fragments with junctions, iii) adding a labelled junction marker such as biotin and ligating the fragments to the marker, iv) purifying the marked fragments, v) adding labelled capture probes and selectively purifying the hybridised fragments, and vi) analysing the fragments captured by hybridisation and identify the fragments. | 03-17-2016 |
20160076095 | METHODS AND SYSTEMS FOR NUCLEIC ACID SEQUENCING VALIDATION,CALIBRATION AND NORMALIZATION - A system for performing quality control for nucleic acid sample sequencing is disclosed. The system comprises a set of solid supports, each solid support having attached thereto a plurality of nucleic acid sequences, wherein the set comprises plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived, and the nucleic acids sequences are designed such that the nucleic acid sequences produce a predefined pattern of detectable signals during a sequencing run. A method of preparing a quality control for performing nucleic acid sample sequencing, a method of validating a nucleic acid sequencing instrument during a nucleic acid sequencing experiment, and a method of processing nucleic acid sequencing data during a nucleic acid sequencing experiment are also disclosed. | 03-17-2016 |
20160076096 | Methods and Systems for Nucleic Acid Sequencing Validation, Calibration and Normalization - A system for performing quality control for nucleic acid sample sequencing is disclosed. The system comprises a set of solid supports, each solid support having attached thereto a plurality of nucleic acid sequences, wherein the set comprises plural groups of solid supports and each group contains solid supports having the same nucleic acid sequences attached thereto. The nucleic acid sequences of each group differ from each other. The nucleic acid sequences are synthetically derived, and the nucleic acids sequences are designed such that the nucleic acid sequences produce a predefined pattern of detectable signals during a sequencing run. A method of preparing a quality control for performing nucleic acid sample sequencing, a method of validating a nucleic acid sequencing instrument during a nucleic acid sequencing experiment, and a method of processing nucleic acid sequencing data during a nucleic acid sequencing experiment are also disclosed. | 03-17-2016 |
20160083718 | EXPANDED RADIX FOR POLYMERIC TAGS - A method having steps of (a) providing nucleic acids having a tag sequence (N | 03-24-2016 |
20160083724 | METHODS FOR SAMPLE PREPARATION - The disclosure provides for single amplification and double amplification methods for preparing nucleic acid samples for sequencing. | 03-24-2016 |
20160083786 | IN SITU INTERACTION DETERMINATION - Methods, reagents, compositions, and kits for in situ interaction determination (ISID) via interaction-dependent polymerase chain reaction (ID-PCR) are provided herein. ISID technology is useful for rapidly evaluating potential small molecule-target interactions from mixtures in a single solution. ISID is compatible with unpurified targets in biological samples and can be used to evaluate ligand-binding in DNA-encoded chemical libraries in cell lysates. ISID is also useful to screen ligand interactions of proteins or other molecules in their native state, including their native post-translational modifications and any interactions with accessory proteins and metabolites, in ways that better reflect their relevant biological environment. Because ISID is compatible with crude cell lysates, difficult-to-purify, poorly soluble, intrinsically unstable, and aggregation-prone targets may also be compatible with this method, without requiring truncation or other strategies used to promote heterologous expression. | 03-24-2016 |
20160084761 | INTEGRATED DEVICE WITH EXTERNAL LIGHT SOURCE FOR PROBING DETECTING AND ANALYZING MOLECULES - System and methods for analyzing single molecules and performing nucleic acid sequencing. An integrated device includes multiple pixels with sample wells configured to receive a sample, which when excited, emits radiation. The integrated device includes at least one waveguide configured to propagate excitation energy to the sample wells from a region of the integrated device configured to couple with an excitation energy source. A pixel may also include at least one element for directing the emission energy towards a sensor within the pixel. The system also includes an instrument that interfaces with the integrated device. The instrument may include an excitation energy source for providing excitation energy to the integrated device by coupling to an excitation energy coupling region of the integrated device. One of multiple markers distinguishable by temporal parameters of the emission energy may label the sample and configuration of the sensor within a pixel may allow for detection of a temporal parameter associated with the marker labeling the sample. | 03-24-2016 |
20160090621 | DESIGN AND SYNTHESIS OF CLEAVABLE FLUORESCENT NUCLEOTIDES AS REVERSIBLE TERMINATORS FOR DNA SEQUENCING BY SYNTHESIS - This invention provides novel azido linkers for deoxynucleotide analogues having a detectable marker attached thereto. | 03-31-2016 |
20160090623 | 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. | 03-31-2016 |
20160090624 | Phased Genome Sequencing - The present disclosure provides methods for determining phased nucleic acid sequence for a single chromosome of interest and/or a single chromosomal fragment of interest. The present disclosure also provides methods for determining phased nucleic acid sequence for a plurality of single chromosomes of interest and/or a plurality of single chromosomal fragments of interest. The plurality of single chromosomes of interest may be of one chromosome type or of two or more chromosome types. The present disclosure also provides a method for isolating a plurality of chromosomal fragments of a specified size range, where the chromosomal fragments are from one or more specified regions of the genome. The plurality of chromosomal fragments may be separated into single chromosomal fragments and sequenced to provide phased nucleic acid sequence for the single chromosomal fragments. Alternatively, the plurality of chromosomal fragments may be sequenced together to provide unphased nucleic acid sequence for the chromosomal fragments. | 03-31-2016 |
20160108394 | MOLECULAR IDENTITY TAGS AND USES THEREOF IN IDENTIFYING INTERMOLECULAR LIGATION PRODUCTS - Molecular identity tags and methods of marking target nucleic acids with molecular identity tags for identifying intermolecular ligation products. Terminal regions of linear target nucleic acids are marked with pairs of distinguishable molecular identity tags. Each linear target nucleic acid is marked with only one distinguishable pair. The terminal ends of the marked target nucleic acids are joined to generate circularized nucleic acids, thereby juxtaposing two molecular identity tags across the joined terminal ends. Circularized nucleic acids or downstream products thereof comprising juxtaposed unpaired molecular identity tags constitute intermolecular nucleic acid products that can be identified and eliminated from subsequent analyses of the nucleic acids. The molecular identity tags may comprise physically linked and non-physically linked pairs. Physically linked molecular identity tags designed for production and analysis of mate-pair libraries with next-generation sequencing platforms are provided. | 04-21-2016 |
20160108468 | Isothermal Amplification of Nucleic Acid, and Library Preparation and Clone Generation in Sequencing - An amplification system that provides methods and reaction components that allow for isothermal amplification for detection of target nucleic acid | 04-21-2016 |
20160115474 | TARGETED TRANSPOSITION FOR USE IN EPIGENETIC STUDIES - Disclosed herein are compositions, methods and kits useful for epigenetic analysis based on the use of transposons that are targeted to specific regions of chromatin based on DNA-DNA interactions, protein-protein interactions, RNA-RNA interactions, and nucleic acid-protein interactions. | 04-28-2016 |
20160115525 | DETECTION OF HYDROXYMETHYLCYTOSINE BASES - Methodologies for labeling the epigenetic modification 5-hydroxymethyl-cytosine (5hmC) along a DNA molecule, and for imaging this epigenetic modification along a DNA molecule are disclosed. Related compositions and reagents, and methods of preparing same are also disclosed. | 04-28-2016 |
20160115530 | DETERMINATION OF METHYLATION STATE AND CHROMATIN STRUCTURE OF TARGET GENETIC LOCI - The subject invention pertains to a method of determining methylation state and chromatin structure of target loci. The method comprises treating the genetic material obtained from the cells with DNA methyltransferase, capturing target genetic loci using a set of oligonucleotides, ligating the target loci with oligonucleotide patches that flank the target loci, treating the target loci flanked by oligonucleotide patches with bisulfite, optionally amplifying the target loci by polymerase chain reaction, sequencing the PCR products, and analyzing the sequences to determine methylation state and chromatin structure of the target loci. The current invention also provides a method to identify genes associated with a disease. The invention also provides a method to detect cells suffering from a disease in a group of cells. The current invention also provides kits suitable for carrying out the method of determining methylation state and chromatin structure of the target loci. | 04-28-2016 |
20160115531 | EFFICIENT OPTICAL ANALYSIS OF POLYMERS USING ARRAYS OF NANOSTRUCTURES - The invention is directed to methods and apparatus for detecting sequences of optical signals from parallel reactions on an array of nanostructures, such as nanopores, nanowells, or nanoparticles. In accordance with the invention, an array of nanostructures is provided, each nanostructure comprising a reaction site and each capable of confining a reaction that generates a sequence of optical signals, and the nanostructures of the array being arranged in clusters each comprising a number of nanostructures. Each different cluster is disposed within a different resolution limited area and the number of nanostructures in each cluster is either greater than one or a random variable with an average value greater than zero. Optical signals from reactions in the nanostructures are detected by an optical system operatively associated with the array. | 04-28-2016 |
20160115532 | HIGH SENSITIVITY MUTATION DETECTION USING SEQUENCE TAGS - The invention is directed to methods for increasing the sensitivity of high throughput sequencing, particularly for distinguishing true rare mutations from amplification, sequencing and other sample processing errors that occur in sequencing techniques. In one aspect, methods of the invention includes steps of (a) preparing templates from nucleic acids in a sample; (b) labeling by sampling the templates to form tag-template conjugates, wherein substantially every template of a tag-template conjugate has a unique sequence tag; (c) linearly amplifying the tag-template conjugates; (d) generating a plurality of sequence reads from the linearly amplified tag-template conjugates; and (e) determining a nucleotide sequence of each of the nucleic acids based on the frequencies, or numbers, of each type of nucleotide at each nucleotide position of each plurality of sequence reads having identical sequence tags. | 04-28-2016 |
20160115534 | 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. | 04-28-2016 |
20160115544 | MOLECULAR BARCODING FOR MULTIPLEX SEQUENCING - Described herein are methods, compositions and kits for preparing samples for multiplex next generation nucleic acid sequencing. The methods entail the use of in-line barcodes that minimize barcode-confusing chimeras, purification procedures with low cost, and/or a quantitative amplification to generate a desired amount of polynucleotides for sequencing. | 04-28-2016 |
20160122751 | NUCLEIC ACID-TAGGED COMPOSITIONS AND METHODS FOR MULTIPLEXED PROTEIN-PROTEIN INTERACTION PROFILING - Methods and compositions for multiplexed protein-protein interaction profiling (e.g., immunoprofiling), based on nucleic acid tagging of polypeptides (e.g., by RNA display) are described. In some embodiments the described compositions and methods utilize a library of prey polypeptide targets linked to prey RNAs encoding them, and a population of bait polypeptides, e.g., a mixture of antibodies, that bind to one or more of the prey polypeptide targets and are used to isolate and identify the bound prey polypeptide targets by amplification of their associated prey RNAs and sequencing of the corresponding cDNAs. In other embodiments the prey polypeptide targets are linked to DNA Bar Codes, which serve as unique identifiers of the tagged polypeptide. | 05-05-2016 |
20160122753 | HIGH-THROUGHPUT RNA-SEQ - The present invention relates generally to methods for single-cell nucleic acid profiling, and nucleic acids useful in those methods. For example, it concerns using barcode sequences to track individual nucleic acids at single-cell resolution, utilizing template switching and sequencing reactions to generate the nucleic acid profiles. These methods and compositions are also applicable to other starting materials, such as cell and tissue lysates or extracted/purified RNA. | 05-05-2016 |
20160122812 | NANOPORE-BASED POLYMER ANALYSIS WITH MUTALLY-QUENCHING FLUORESCENT LABELS - The invention is directed to a method for determining a monomer sequence of a polymer that is translocated through a nanopore. Monomers of the polymer are labeled with fluorescent labels such that in free solution fluorescent labels of adjacent monomers substantially quench each other and wherein the nanopore constrains fluorescent labels within its bore into a constrained state wherein no detectable fluorescent signal can be generated. By exciting the fluorescent label of each monomer as it exits the nanopore and transitions from a constrained state to a quenched state with an adjacent fluorescent label, a fluorescent signal can be generated by the exiting fluorescent label that allows its monomer to be identified, thereby permitting a monomer sequence to be determined from a sequence of fluorescent signals as the polymer translocates through the nanopore. | 05-05-2016 |
20160122817 | METHODS AND COMPOSITIONS FOR TARGETED NUCLEIC ACID SEQUENCING - The present invention is directed to methods, compositions and systems for capturing and analyzing sequence information contained in targeted regions of a genome. Such targeted regions may include exomes, partial exomes, introns, combinations of exonic and intronic regions, genes, panels of genes, and any other subsets of a whole genome that may be of interest. | 05-05-2016 |
20160122818 | GENE EXPRESSION ANALYSIS - The present invention is directed to methods and kits for gene analysis. The methods of the invention comprise the steps of providing nucleic acid; synthesis of a single-stranded DNA that is complementary to said nucleic acid molecule by contacting the nucleic acid with a DNA polymerase, a primer and a mixture of dNTPs under conditions that allow the generation of the DNA, wherein the primer comprises a target-complementary region and wherein the dNTP mixture comprises dATP, dGTP, dCTP, dTTP and dUTP; cleaving the DNA 5′ to dU sites by (i) contacting the DNA with an uracil deglycosylase to generate a basic sites at positions of dUTP incorporation in the DNA; and (ii) contacting the DNA with an apurinic/apyrimidinic (AP) endonuclease; contacting the DNA comprising at its 5′-end the nucleotide sequence of the primer with a ssDNA ligase to circularize the DNA; and sequencing the circularized cDNA. The kits comprise the components necessary to perform the methods of the invention. | 05-05-2016 |
20160123987 | ASSAY METHOD USING ENCODED PARTICLE-BASED PLATFORM - Provided is an assay method using an encoded particle-based platform. In the assay method, first, a plurality of encoded particles having codes distinguishable from one another according to kinds of included target materials are prepared. The plurality of encoded particles are provided onto a plate including a plurality of wells by pipetting, and disposed in the plurality of wells by a self-assembly method. An analyte is provided into the plurality of wells. The codes of the plurality of encoded particles disposed in the plurality of wells are decoded. The target materials of the plurality of encoded particles are released to cause a reaction between the target materials and the analyte. | 05-05-2016 |
20160130576 | 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. | 05-12-2016 |
20160130645 | ULTRAFAST SEQUENCING OF BIOLOGICAL POLYMERS USING A LABELED NANOPORE - Methods and systems for sequencing a biological molecule or polymer, e.g., a nucleic acid, are provided. One or more donor labels, which are attached to a pore or nanopore, may be illuminated or otherwise excited. A polymer having a monomer labeled with one or more acceptor labels, may be translocated through the pore. Either before, after or while the labeled monomer of the polymer passes through, exits or enters the pore, energy may be transferred from the excited donor label to the acceptor label of the monomer. As a result of the energy transfer, the acceptor label emits energy, and the emitted energy is detected in order to identify the labeled monomer of the translocated polymer and to thereby sequence the polymer. | 05-12-2016 |
20160130649 | Single Cell Nucleic Acid Detection and Analysis - Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided. | 05-12-2016 |
20160138011 | MULTIPLEXED DIGITAL QUANTITATION OF REARRANGED LYMPHOID RECEPTORS IN A COMPLEX MIXTURE - The invention relates to methods and compositions for estimating the absolute abundance individually for each unique rearranged lymphocyte receptor in a mixed sample. | 05-19-2016 |
20160138012 | RNA Tagging - Methods, kits, and compositions of matter suitable for use in RNA Tagging are disclosed. In one embodiment, a method includes: expressing a fusion protein within the cellular environment, the fusion protein including at least part of the protein of interest and a tagging domain, the tagging domain introducing a selective tag to an RNA to which the fusion protein selectively binds, the selective tag including a selective tag sequence or a selective covalent modification; allowing the tagging domain to tag the RNA to which the protein of interest selectively binds by waiting for about 1 minute to about 28 days; and identifying the tagged RNA. | 05-19-2016 |
20160139140 | MASS LABELS - The present invention provides set of two or more mass labels, wherein each mass label in the set has the same integer mass as every other label in the set, and each mass label in the set has an exact mass which is different to the mass of all other mass labels in the set such that all the mass labels in the set are distinguishable from each other by mass spectrometry. | 05-19-2016 |
20160145682 | METHODS OF MONITORING IMMUNOSUPPRESSIVE THERAPIES IN A TRANSPLANT RECIPIENT - The present disclosure relates to methods of monitoring the status of an allograft in a transplant recipient, as well as to methods of monitoring and adjusting immunosuppressive therapies being administered to the transplant recipient. | 05-26-2016 |
20160146799 | METAL COMPOSITES FOR ENHANCED IMAGING - Disclosed herein are compositions and systems that can be used for enhanced fluorescence-based imaging techniques and assays. The compositions and systems of the present disclosure can afford increased fluorescence for fluorescent molecules with excitation and emission in the visible and near-infrared, e.g. spanning from about 400 nm to about 2100 nm. Also provided herein are fluorescence detection based methods by utilizing the compositions and systems of the present disclosure. | 05-26-2016 |
20160152972 | METHODS FOR ASSEMBLING AND READING NUCLEIC ACID SEQUENCES FROM MIXED POPULATIONS | 06-02-2016 |
20160168564 | Methods for the Production of Long Length Clonal Sequence Verified Nucleic Acid Constructs | 06-16-2016 |
20160178609 | METHODS AND COMPOSITIONS FOR MARKING URINE SAMPLES TO IDENTIFY SOURCE | 06-23-2016 |
20160186255 | SUBSTRATES, SYSTEMS AND METHODS FOR ANALYZING MATERIALS - Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyses, cellular analyses and other molecular analyses. | 06-30-2016 |
20160187314 | METHODS FOR AUTHENTICATION AND IDENTIFICATION OF PETROLEUM PRODUCTS - A method is provided that associates a taggant with a product to produce a signature product. The taggant, when associated with the signature product, is visually undetectable; and comprises one or more amide compounds (e.g., a taggant array that comprises two or more amide compounds). The method also identifies the taggant in the signature product by an immunoassay specific for the taggant; maps the taggant of the signature product to a batch code of the signature product; obtains a test product to determine authenticity or identity of the test product; identifies the presence or absence of a taggant in the test product by an immunoassay specific for the taggant; and compares results of the immunoassay carried out on the test product with results of the immunoassay carried out on the signature product to determine authenticity or identity of the test product. Lubricating engine oils are provided containing the taggant. | 06-30-2016 |
20160187315 | METHODS FOR DETERMINING CONDITION AND QUALITY OF PETROLEUM PRODUCTS - A method is provided for determining the condition or quality of a product. The method involves adding to the product a taggant in which the taggant exhibits degradation in response to one or more stimuli; carrying out an immunoassay specific for the taggant to determine degradation of the taggant; and determining the condition of the product based on the degradation of the taggant. A method is provided for monitoring degradation or quality of a product. The method involves adding to the product a taggant in which the taggant exhibits degradation in response to one or more stimuli; and carrying out an immunoassay specific for the taggant to determine degradation of the taggant. The method further involves identifying the condition of the product based on the degradation of the taggant. Lubricating engine oils are provided containing the taggant. | 06-30-2016 |
20160194694 | MULTIPLEX TRANSCRIPTOME ANALYSIS | 07-07-2016 |
20160194697 | Apparatus, System, And Method Using Immiscible-Fluid-Discrete-Volumes | 07-07-2016 |
20160194699 | MOLECULAR CODING FOR ANALYSIS OF COMPOSITION OF MACROMOLECULES AND MOLECULAR COMPLEXES | 07-07-2016 |
20160194701 | ENZYME- AND AMPLIFICATION-FREE SEQUENCING | 07-07-2016 |
20160194704 | METHOD OF WHOLE-GENOME SEQUENCING | 07-07-2016 |
20160194710 | Methods of Determining Multiple Interactions Between Nucleic Acids in a Cell | 07-07-2016 |
20160194713 | CHROMOSOME CONFORMATION CAPTURE METHOD INCLUDING SELECTION AND ENRICHMENT STEPS | 07-07-2016 |
20160194726 | PRIMERS AND METHODS FOR DETECTING HUMAN HEPATITIS C VIRUS (HCV) VARIANTS IN AN ISOLATED SAMPLE | 07-07-2016 |
20160201054 | METHOD OF OBTAINING ANTIBODIES OF INTEREST AND NUCLEOTIDES ENCODING SAME | 07-14-2016 |
20160201124 | Targeted Sequencing and UID Filtering | 07-14-2016 |
20160201125 | COMPOSITIONS AND METHODS FOR MOLECULAR LABELING | 07-14-2016 |
20160201147 | ANALYSIS OF POLYNUCLEOTIDES | 07-14-2016 |
20160251650 | LINKING SEQUENCE READS USING PAIRED CODE TAGS | 09-01-2016 |
20160251713 | METHOD FOR GENOME SEQUENCING USING A SEQUENCE-BASED PHYSICAL MAP | 09-01-2016 |
20160251714 | SINGLE-CELL NUCLEIC ACIDS FOR HIGH-THROUGHPUT STUDIES | 09-01-2016 |
20160251715 | VARIETAL COUNTING OF NUCLEIC ACIDS FOR OBTAINING GENOMIC COPY NUMBER INFORMATION | 09-01-2016 |
20160376583 | 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. | 12-29-2016 |
20160376648 | 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. | 12-29-2016 |
20160376664 | Experimentally Validated Sets of Gene Specific Primers for Use in Multiplex Applications - Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications. | 12-29-2016 |
20160378916 | PROCESSING AND ANALYSIS OF COMPLEX NUCLEIC ACID SEQUENCE DATA - The present invention is directed to logic for analysis of nucleic acid sequence data that employs algorithms that lead to a substantial improvement in sequence accuracy and that can be used to phase sequence variations, e.g., in connection with the use of the long fragment read (LFR) process. | 12-29-2016 |
20170233724 | Partitioning of DNA Sequencing Libraries into Host and Microbial Components | 08-17-2017 |
20170233727 | METHODS FOR GENERATING AND DECODING BARCODES | 08-17-2017 |
20170233802 | CLASSIFICATION OF NUCLEIC ACID TEMPLATES | 08-17-2017 |
20170233805 | Additives to Improve Sequencing by Synthesis Performance | 08-17-2017 |
20170233829 | DETECTING CHROMOSOMAL ABERRATIONS ASSOCIATED WITH CANCER USING GENOMIC SEQUENCING | 08-17-2017 |
20170234868 | Detection of Neoantigens Using Peptide Arrays | 08-17-2017 |
20180023128 | SYSTEM AND METHOD FOR SINGLE CELL GENETIC ANALYSIS | 01-25-2018 |
20180024139 | QUANTITATIVE MASSIVELY PARALLEL PROTEOMICS | 01-25-2018 |
20180025109 | METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING | 01-25-2018 |
20180025111 | STRATEGIES FOR HIGH THROUGHPUT IDENTIFICATION AND DETECTION OF POLYMORPHISMS | 01-25-2018 |
20190144854 | METHODS AND SYSTEMS FOR PERFORMING SINGLE CELL ANALYSIS OF MOLECULES AND MOLECULAR COMPLEXES | 05-16-2019 |
20190144936 | SEMI-PERMEABLE ARRAYS FOR ANALYZING BIOLOGICAL SYSTEMS AND METHODS OF USING SAME | 05-16-2019 |
20190144938 | METHOD FOR HIGH-THROUGHPUT AFLP-BASED POLYMORPHISM DETECTION | 05-16-2019 |
20190147977 | STRATEGIES FOR HIGH THROUGHPUT IDENTIFICATION AND DETECTION OF POLYMORPHISMS | 05-16-2019 |
20220135965 | LIBRARIES FOR NEXT GENERATION SEQUENCING - Provided herein are compositions and methods for Next Generation Sequencing. Further provided herein are compositions and methods for uniquely labeling molecules. Further provided herein are compositions and methods for synthesizing unique molecular identifiers. | 05-05-2022 |