Patent application number | Description | Published |
20150056613 | METHODS AND SYSTEMS FOR DETECTING SEQUENCE VARIANTS - The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer. | 02-26-2015 |
20150057946 | METHODS AND SYSTEMS FOR ALIGNING SEQUENCES - The invention includes methods for aligning reads (e.g., nucleic acid reads, amino acid reads) to a reference sequence construct, methods for building the reference sequence construct, and systems that use the alignment methods and constructs to produce sequences. The method is scalable, and can be used to align millions of reads to a construct thousands of bases or amino acids long. The invention additionally includes methods for identifying a disease or a genotype based upon alignment of nucleic acid reads to a location in the construct. | 02-26-2015 |
20150066381 | GENOMIC PIPELINE EDITOR WITH TOOL LOCALIZATION - The invention provides systems and methods for creating and using genomic analysis pipelines in which each analytical step within the pipeline can be independently set to run in a particular location. Steps that involve patient-identifying information or other sensitive research results can be restricted to running on a computer that is under the user's control, while steps that require a vast amount of processing power to sift through large amounts of raw data can be set to run on a powerful computer system such as a multi-processor server or cloud computer. The system provides a genomic pipeline editor with a plurality of genomic tools that can be arranging into pipelines. For one or more of the tools, the system receives a selection indicating execution by a particular computer. The system will cause genomic data to be analyzed according to the pipeline and the location selection. | 03-05-2015 |
20150112602 | SYSTEMS AND METHODS FOR USING PAIRED-END DATA IN DIRECTED ACYCLIC STRUCTURE - Methods of analyzing a transcriptome that involves obtaining at least one pair of paired-end reads from a transcriptome from an organism, finding an alignment with an optimal score between a first read of the pair and a node in a directed acyclic data structure (the data structure has nodes representing RNA sequences such as exons or transcripts and edges connecting pairs of nodes), identifying candidate paths that include the node connected to a downstream node by a path having a length substantially similar to an insert length of the pair of paired-end reads, and aligning the paired-end rends to the candidate paths to determine an optimal-scoring alignment. | 04-23-2015 |
20150112658 | SYSTEMS AND METHODS FOR TRANSCRIPTOME ANALYSIS - The invention generally provides systems and methods for analysis of RNA-Seq reads in which an annotated reference is represented as a directed acyclic graph (DAG) or similar data structure. Features such as exons and introns from the reference provide nodes in the DAG and those features are linked as pairs in their canonical genomic order by edges. The DAG can scale to any size and can in fact be populated in the first instance by import from an extrinsic annotated reference. | 04-23-2015 |
20150197815 | METHODS AND SYSTEMS FOR IDENTIFYING DISEASE-INDUCED MUTATIONS - The invention includes methods and systems for identifying diseased-induced mutations by producing multi-dimensional reference sequence constructs that account for variations between individuals, different diseases, and different stages of those diseases. Once constructed, these reference sequence constructs can be used to align sequence reads corresponding to genetic samples from patients suspected of having a disease, or who have had the disease and are in suspected remission. The reference sequence constructs also provide insight to the genetic progression of the disease. | 07-16-2015 |
20150199472 | METHODS AND SYSTEMS FOR GENOTYPING GENETIC SAMPLES - The invention provides methods and system for making specific base calls at specific loci using a reference sequence construct, e.g., a directed acyclic graph (DAG) that represents known variants at each locus of the genome. Because the sequence reads are aligned to the DAG during alignment, the subsequent step of comparing a mutation, vis-à-vis the reference genome, to a table of known mutations can be eliminated. The disclosed methods and systems are notably efficient in dealing with structural variations within a genome or mutations that are within a structural variation. | 07-16-2015 |
20150199473 | METHODS AND SYSTEMS FOR QUANTIFYING SEQUENCE ALIGNMENT - The invention includes methods for aligning reads (e.g., nucleic acid reads, amino acid reads) to a reference sequence construct, methods for building the reference sequence construct, and systems that use the alignment methods and constructs to produce sequences. The invention also includes methods and systems for evaluating the quality of the alignment between the reads and the reference sequence construct. The method is scalable, and can be used to align millions of reads to a construct thousands of bases or amino acids long. The invention additionally includes methods for identifying a disease or a genotype based upon alignment of nucleic acid reads to a location in the construct. | 07-16-2015 |
20150199474 | METHODS AND SYSTEMS FOR ALIGNING SEQUENCES IN THE PRESENCE OF REPEATING ELEMENTS - The invention includes methods for aligning reads (e.g., nucleic acid reads) comprising repeating sequences, methods for building reference sequence constructs comprising repeating sequences, and systems that can be used to align reads comprising repeating sequences. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long. The methods and systems can additionally account for variability within a repeating sequence, or near to a repeating sequence, due to genetic mutation. | 07-16-2015 |
20150199475 | SYSTEMS AND METHODS FOR USE OF KNOWN ALLELES IN READ MAPPING - The invention generally relates to genomic studies and specifically to improved methods for read mapping using identified nucleotides at known locations. The invention provides methods of using identified nucleotides at known places in a genome to guide the analysis of sequence reads from that genome by excluding potential mappings or assemblies that are not congruent with the identified nucleotides. Information about a plurality of SNPs in the subject's genome is used to identify candidate paths through a genomic directed acyclic graph (DAG). Sequence reads are mapped to the candidate paths. | 07-16-2015 |