Systems and methods to detect rare mutations and copy number variation

• US 10,501,810 B2
• Filed: 02/22/2019
• Issued: 12/10/2019
• Est. Priority Date: 09/04/2012
• Status: Active Grant

• Current Assignee: Guardant Health Inc.
• Original Assignee: Guardant Health Inc.
• Inventors: Talasaz, AmirAli
• Primary Examiner(s): Horlick, Kenneth R
• Application Number:
  US16/283,629
• Publication Number:
  US 20190185940A1
• Time in Patent Office: 291 Days
• Field of Search: None
• CPC Class Codes: C12N 15/1065 Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

Abstract

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.

Claims

1. A method for detecting somatic genetic variants of cell-free deoxyribonucleic acid (DNA) in a human subject, the method comprising:

a) obtaining 10 to 100 nanograms (ng) of double-stranded cell-free DNA from a blood sample from the human subject;

b) ligating adapters comprising molecular barcodes to ends of a plurality of molecules of the double-stranded cell-free DNA to produce tagged parent polynucleotides, wherein the molecular barcodes together constitute a set of 5-100 molecular barcodes from 5-20 nucleotides in length;

c) amplifying a plurality of the tagged parent polynucleotides to produce progeny polynucleotides with associated molecular barcodes;

d) selectively enriching the progeny polynucleotides for target regions associated with cancer, whereby enriched progeny polynucleotides are generated;

e) sequencing a portion of the enriched progeny polynucleotides to produce sequencing reads of the progeny polynucleotides with associated molecular barcodes;

f) aligning mappable portions of the sequencing reads to a human reference genome;

g) grouping a plurality of the sequencing reads into families based on the sequence information of the molecular barcodes and the beginning and end base positions of the mapped portion of the progeny polynucleotides; and

h) detecting, from among a plurality of the families, the presence or absence of one or more somatic genetic variants comprising a single nucleotide variant (SNV), a copy number variation (CNV), an insertion or deletion (indel), a gene fusion, or any combination thereof.

2. The method of claim 1, wherein the human subject has a cancer.

3. The method of claim 1, wherein ligating comprises blunt-end ligation.

4. The method of claim 1, wherein ligating comprises sticky-end ligation.

5. The method of claim 1, wherein at least 20% of the double-stranded cell-free DNA are ligated with adapters.

6. The method of claim 1, wherein at least 40% of the double-stranded cell-free DNA are ligated with adapters.

7. The method of claim 1, wherein the molecular barcodes have a predetermined sequence.

8. The method of claim 1, wherein the target regions comprise genomic sequences of actionable cancer-related genes.

9. The method of claim 1, wherein the target regions comprise a genomic sequence from one of TP53, KRAS, PIK3CA, APC, EGFR, BRAF, MET, and MYC.

10. The method of claim 1, wherein sequencing comprises next generation sequencing.

11. The method of claim 1, further comprising filtering out sequencing reads that fail to meet a quality control threshold.

12. The method of claim 1, wherein the number of sequencing reads in a family is between 2 and 10.

13. The method of claim 1, wherein detecting comprises generating a set of consensus sequences from among the sequence reads in the families.

14. The method of claim 13, wherein a consensus sequence within the set of consensus sequences corresponds to a mapped portion of the progeny polynucleotides.

15. The method of claim 13, further comprising determining the presence or absence of the one or more somatic genetic variants in the set of consensus sequences compared with the human reference genome.

16. The method of claim 1, wherein detecting comprises generating a base call at a genetic locus of the human reference genome for a family from among the plurality of families.

17. The method of claim 1, further comprising quantifying the number of families.

18. The method of claim 1, wherein the presence of at least one or more somatic genetic variants detected is an SNV.

19. The method of claim 1, wherein the presence of at least one or more somatic genetic variants detected is an indel.

20. The method of claim 1, wherein the presence of at least one or more somatic genetic variants detected is a CNV.

21. The method of claim 1, wherein the presence of at least one or more somatic genetic variants detected is a gene fusion.

22. The method of claim 1, wherein the presence of at least one or more somatic genetic variants detected is a SNV and CNV.

23. The method of claim 1, wherein the double-stranded cell-free DNA comprises circulating tumor DNA (ctDNA).

24. The method of claim 1, wherein less than 5% of the double-stranded cell-free DNA is from one or more cancer genomes.

25. The method of claim 1, wherein less than 1% of the double-stranded cell-free DNA is from one or more cancer genomes.

26. The method of claim 1, wherein less than 0.1% of the double-stranded cell-free DNA is from one or more cancer genomes.

27. The method of claim 1, further comprising generating a report that includes a cell-free tumor mutation profile of the human subject based on the detection of the presence or absence of the one or more somatic genetic variants.

28. The method of claim 27, wherein the report further includes a treatment recommendation for the human subject based on the cell-free tumor mutation profile.