Systems and methods to detect rare mutations and copy number variation

• US 10,494,678 B2
• Filed: 02/22/2019
• Issued: 12/03/2019
• 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:
  US16/283,635
• Publication Number:
  US 20190185941A1
• Time in Patent Office: 284 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 a presence or absence of one or more somatic genetic variants in a sample comprising cell-free deoxyribonucleic acid (cfDNA) molecules from a subject having a cancer or suspected of having a cancer, the method comprising:

(a) contacting a set of molecular barcodes comprising 2 to 1,000 different molecular barcodes with a population of cfDNA molecules obtained from the sample to produce tagged parent polynucleotides,

wherein the tagged parent polynucleotides have a first molecular barcode from the set of molecular barcodes that is attached to a first end of a cfDNA molecule from among the population of cfDNA molecules and a second molecular barcode from the set of molecular barcodes that is attached to a second end of the cfDNA molecule, and

wherein a plurality of the tagged parent polynucleotides has identical first molecular barcodes and second molecular barcodes;

(b) amplifying a plurality of the tagged parent polynucleotides to produce amplified progeny polynucleotides;

(c) sequencing a plurality of the amplified progeny polynucleotides to produce a set of sequencing reads; and

(d) detecting, from among a plurality of the set of sequencing reads, 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), or a gene fusion.

2. The method of claim 1, wherein the sample is a bodily fluid sample selected from the group consisting of blood, plasma, and serum.

3. The method of claim 1, wherein an amount of cfDNA molecules in the population of cfDNA molecules is between 1 nanogram (ng) and 100 ng.

4. The method of claim 1, wherein an expected length distribution of the population of cfDNA molecules is 140 to 180 nucleotides.

5. The method of claim 1, wherein the molecular barcodes in the set of molecular barcodes have a length of 5 to 20 nucleotides.

6. The method of claim 1, wherein the set of molecular barcodes comprises 5 to 100 different molecular barcodes.

7. The method of claim 6, wherein the molecular barcodes in the set of molecular barcodes have a length of 5 to 20 nucleotides.

8. The method of claim 7, wherein the 5 to 20 nucleotides of the molecular barcodes in the set of molecular barcodes are a fixed sequence.

9. The method of claim 1, wherein the contacting comprises performing blunt-end ligation or sticky-end ligation.

10. The method of claim 1, wherein at least 20% of the cfDNA molecules in the population of cfDNA molecules are tagged with the molecular barcodes from the set of molecular barcodes.

11. The method of claim 1, wherein at least 30% of the cfDNA molecules in the population of cfDNA molecules are tagged with the molecular barcodes from the set of molecular barcodes.

12. The method of claim 1, wherein at least 40% of the cfDNA molecules in the population of cfDNA molecules are tagged with the molecular barcodes from the set of molecular barcodes.

13. The method of claim 1, wherein each of the molecular barcodes in the set of molecular barcodes is part of an adapter sequence.

14. The method of claim 1, further comprising, prior to sequencing, selectively enriching the amplified progeny polynucleotides for target regions associated with cancer.

15. The method of claim 14, wherein the target regions associated with cancer are selected from a panel of actionable cancer-related genes.

16. The method of claim 1, wherein the sequencing is performed by a next-generation sequencer.

17. The method of claim 1, further comprising filtering out sequencing reads from the set of sequencing reads that fail to meet a quality threshold.

18. The method of claim 1, wherein the detecting comprises aligning a plurality of sequencing reads from the set of sequencing reads to a reference sequence.

19. The method of claim 1 or 18, wherein the detecting further comprises grouping a plurality of sequencing reads from the set of sequencing reads into one or more families based at least on sequence information from the molecular barcodes.

20. The method of claim 19, further comprising generating one or more consensus sequences corresponding to the one or more families.

21. The method of claim 19, further comprising determining a base call for a family from among the one or more families at a genetic locus of the reference sequence.

22. The method of claim 1, further comprising detecting the presence or absence of two or more somatic genetic variants.

23. The method of claim 22, wherein the two or more somatic genetic variants comprise an SNV and a CNV.

24. The method of claim 19, further comprising quantifying a number of the one or more families mapping to predefined regions of the reference sequence.

25. The method of claim 24, further comprising detecting the presence or absence of a CNV in one or more of the predefined regions based on the number of the one or more families mapping to the predefined regions of the reference sequence.

26. The method of claim 25, further comprising normalizing the number of the one or more families mapping to the predefined regions to each other, and normalizing the numbers of the one or more families mapping to the predefined regions against numbers of families mapping to the predefined regions for at least one reference sample.

27. The method of claim 1, further comprising isolating or extracting the population of cfDNA molecules from the sample.

28. The method of claim 1, wherein the cfDNA molecules in the population of cfDNA molecules comprise between 0.1% and 1% of cfDNA molecules from a cancer genome.

29. The method of claim 1, wherein the cfDNA molecules in the population of cfDNA molecules comprise between 0.1% and 0.5% of cfDNA molecules from a cancer genome.

30. The method of claim 19, wherein the grouping is further based on aligned portions of the plurality of sequencing reads, wherein the aligned portions of the plurality of sequencing reads comprise a start base position of a given sequencing read from among the set of sequencing reads at which the given sequencing read starts aligning to the reference sequence, and a stop base position of the given sequencing read at which the given sequencing read stops aligning to the reference sequence.