Methods and systems for genetic analysis

Patent metadata

Field	Value
Publication number	US-9745626-B2
Application number	US-201615222875-A
Country	US
Kind code	B2
Filing date	Jul 28, 2016
Priority date	Jan 17, 2013
Publication date	Aug 29, 2017
Grant date	Aug 29, 2017

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

First claim

What is claimed is:

1. A method for processing a nucleic acid sample of a subject, comprising:
(a) generating at least a first subset of nucleic acid molecules and a second subset of nucleic acid molecules from said nucleic acid sample of said subject, wherein said first subset of nucleic acid molecules is generated to differ from said second subset of nucleic acid molecules by genomic features selected from the group consisting of methylation state, GC content, insertion or deletion, single nucleotide variant (SNV) and molecular size with the aid of probes that selectively enrich for said genomic features as compared to other probes that do not selectively enrich for a difference in said genomic features;
(b) subjecting (i) said first subset of nucleic acid molecules to a first assay to yield a first result comprising a first nucleic acid sequence, and (ii) said second subset of nucleic acid molecules to a second assay to yield a second result comprising a second nucleic acid sequence; and
(c) combining, with the aid of a computer processor, said first result and said second result to generate an output comprising a consensus sequence from said first nucleic acid sequence and said second nucleic acid sequence.

2. The method of claim 1 , wherein said combining comprises producing a unified assessment of a genetic state of said nucleic acid sample at each locus addressed by said first assay and said second assay.

3. The method of claim 1 , wherein said first assay and/or said second assay comprises a nucleic acid amplification reaction.

4. The method of claim 1 , wherein said first subset of nucleic acid molecules and/or said second subset of nucleic acid molecules is generated with the aid of a hybridization reaction.

5. The method of claim 1 , wherein said first subset of nucleic acid molecules and/or said second subset of nucleic acid molecules is generated with the aid of differential amplification based on one or more genomic region features of said nucleic acid sample.

6. The method of claim 1 , wherein said combining in (c) comprises combining said first nucleic acid sequence and said second nucleic acid sequence using a precedence rule that uses one or more of genomic context(s) or assay(s) to resolve discordances between two or more sequencing data sets.

7. The method of claim 1 , wherein said combining in (c) comprises combining said first nucleic acid sequence and said second nucleic acid sequence using at least one of quality and read coverage metrics to resolve one or more discordant genotypes.

8. The method of claim 1 , wherein (c) comprises combining said first nucleic acid sequence and said second nucleic acid sequence using at least one of base read quality and allele frequency to yield a consensus call at one or more applicable loci.

9. The method of claim 1 , further comprising, subsequent to (c), generating a biomedical report that includes biomedical information of said subject, which biomedical information is indicative of said output.

10. The method of claim 9 , wherein said biomedical information of said subject is predictive, prognostics, or diagnostics of one or more biomedical features selected from the group consisting of disease state, genetic risk of a disease, reproductive risk, genetic risk to a fetus, risk of an adverse drug reaction, efficacy of a drug therapy, prediction of optimal drug dosage, and transplant tolerance.

11. The method of claim 1 , wherein said genomic features include GC content or molecular size.

12. The method of claim 1 , wherein said first subset and said second subset are complementary in at least one of GC content and molecular size.

13. The method of claim 1 , wherein said first assay and said second assay are different assays.

14. The method of claim 1 , wherein said first subset or said second subset of nucleic acid molecules is generated by a protocol that is selective for said genomic features.

15. The method of claim 1 , wherein said first subset of nucleic acid molecules and said second subset of nucleic acid molecules are subjected to said first assay and said second assay, respectively, in separate pools.

16. The method of claim 1 , wherein said first subset of nucleic acid molecules and said second subset of nucleic acid molecules are subjected to said first assay and said second assay, respectively, in a combined pool.

17. The method of claim 1 , wherein said genomic features include GC content or molecular size, and wherein nucleic acid molecules of said first subset of nucleic acid molecules and nucleic acid molecules of said second subset of nucleic acid molecules are prepared to differ by GC content or molecular size from a given genomic region of said nucleic acid sample.

18. The method of claim 17 , wherein said given genomic region includes high GC content, low GC content, low complexity, low mappability, a single nucleotide variation (SNV), an insertion or deletion, an alternative sequence, an entire exome, a set of genes, a set of regulatory elements, or methylated nucleotide(s).

19. The method of claim 18 , wherein said given genomic region includes said set of genes, and wherein said set of genes is selected from the group consisting of a set of genes with Mendelian traits, set of genes with disease traits, a set of genes with drug traits, and a set of genes with biomedically interpretable variants.

20. The method of claim 18 , wherein said given genomic region includes said alternative sequence, and wherein said alternative sequences is selected from the group consisting of one or more small insertions, small deletions, structural variant junctions, variable length tandem repeats, and flanking sequences.

21. The method of claim 1 , wherein said first assay and/or said second assay includes nucleic acid sequencing.

22. The method of claim 1 , wherein (c) comprises combining said first result and said second result to produce a combined data set, and generating said output from at least a portion of said combined data set.

Assignees

• Personalis Inc

Inventors

• Bartha Gabor T
• Chandratillake Gemma
• Chen Richard
• Garcia Sarah
• Lam Hugo Yu Kor
• Luo Shujun
• Pratt Mark R
• West John

Classifications

• G16C20/60

  In silico combinatorial chemistry · CPC title

• C12Q1/6806

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title

• C12Q1/6869

  Methods for sequencing · CPC title

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• G16B35/00

  ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides · CPC title