APPLYING LOW COVERAGE WHOLE GENOME SEQUENCING FOR INTELLIGENT GENOMIC ROUTING
First Claim
1. A method, comprising:
- performing, at a processing system, a low coverage whole genome sequencing of a biological sample from a subject to obtain a set of reads;
evaluating, at a processing system, coverage of the set of reads;
performing, by the processing system, statistical association for loci of the set of reads having an observation;
determining, by the processing system, an inference of a phenotype from the set of reads based on the statistical association;
obtaining, by the processing system, self-reported data from the subject;
executing, by the processing system, a first query on eligibility criteria for a plurality of genomic routes to obtain a set of genomic routes that satisfy the first query, wherein the first query includes the phenotype;
executing, by the processing system, a second query on routing criteria for the set of genomic routes to obtain a subset of ranked genomic routes that satisfy the second query, wherein the second query includes the phenotype and at least one piece of information from the self-reported data; and
selecting, by the processing system, one or more genomic routes from the subset of ranked genomic routes based on the ranking of each of the one or more genomic routes.
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Accused Products
Abstract
Techniques for next generation sequencing (NGS), and more particularly, to techniques for applying low coverage whole genome sequencing (lcWGS) in genome wide association studies (GWAS). One aspect includes performing a lcWGS of a biological sample from a subject to obtain a set of reads, determining an inference of a phenotype from the set of reads, obtaining self-reported data from the subject, executing a first query on eligibility criteria for a plurality of genomic routes to obtain a set of genomic routes that satisfy the first query, executing a second query on routing criteria for the set of genomic routes to obtain a subset of ranked genomic routes that satisfy the second query, and selecting one or more genomic routes from the subset of ranked genomic routes based on the ranking of each of the one or more genomic routes.
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Citations
20 Claims
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1. A method, comprising:
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performing, at a processing system, a low coverage whole genome sequencing of a biological sample from a subject to obtain a set of reads; evaluating, at a processing system, coverage of the set of reads; performing, by the processing system, statistical association for loci of the set of reads having an observation; determining, by the processing system, an inference of a phenotype from the set of reads based on the statistical association; obtaining, by the processing system, self-reported data from the subject; executing, by the processing system, a first query on eligibility criteria for a plurality of genomic routes to obtain a set of genomic routes that satisfy the first query, wherein the first query includes the phenotype; executing, by the processing system, a second query on routing criteria for the set of genomic routes to obtain a subset of ranked genomic routes that satisfy the second query, wherein the second query includes the phenotype and at least one piece of information from the self-reported data; and selecting, by the processing system, one or more genomic routes from the subset of ranked genomic routes based on the ranking of each of the one or more genomic routes. - View Dependent Claims (2, 3, 4, 5, 6, 7)
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8. A system comprising:
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one or more processors; and memory coupled to the one or more processors, the memory encoded with a set of instructions configured to perform a process comprising; performing a low coverage whole genome sequencing of a biological sample from a subject to obtain a set of reads; evaluating coverage of the set of reads; performing statistical association for loci of the set of reads having an observation; determining an inference of a phenotype from the set of reads based on the statistical association; obtaining self-reported data from the subject; executing a first query on eligibility criteria for a plurality of genomic routes to obtain a set of genomic routes that satisfy the first query, wherein the first query includes the phenotype; executing a second query on routing criteria for the set of genomic routes to obtain a subset of ranked genomic routes that satisfy the second query, wherein the second query includes the phenotype and at least one piece of information from the self-reported data; and selecting one or more genomic routes from the subset of ranked genomic routes based on the ranking of each of the one or more genomic routes. - View Dependent Claims (9, 10, 11, 12, 13, 14)
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15. A non-transitory computer readable storage medium storing instructions that, when executed by one or more processors of a computing system, cause the computing system to perform a process comprising:
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performing a low coverage whole genome sequencing of a biological sample from a subject to obtain a set of reads; evaluating coverage of the set of reads; performing statistical association for loci of the set of reads having an observation; determining an inference of a phenotype from the set of reads based on the statistical association; obtaining self-reported data from the subject; executing a first query on eligibility criteria for a plurality of genomic routes to obtain a set of genomic routes that satisfy the first query, wherein the first query includes the phenotype; executing a second query on routing criteria for the set of genomic routes to obtain a subset of ranked genomic routes that satisfy the second query, wherein the second query includes the phenotype and at least one piece of information from the self-reported data; and selecting one or more genomic routes from the subset of ranked genomic routes based on the ranking of each of the one or more genomic routes. - View Dependent Claims (16, 17, 18, 19, 20)
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Specification