Systems and methods to detect rare mutations and copy number variation

• US 10,704,086 B2
• Filed: 10/04/2019
• Issued: 07/07/2020
• Est. Priority Date: 03/05/2014
• Status: Active Grant

• Current Assignee: Guardant Health Inc.
• Original Assignee: Guardant Health Inc.
• Inventors: Talasaz, AmirAli, Mortimer, Stefanie Ann Ward
• Primary Examiner(s): Horlick, Kenneth R
• Application Number:
  US16/593,653
• Publication Number:
  US 20200115739A1
• Time in Patent Office: 277 Days
• Field of Search: None
• 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 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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
• CPC Class Codes: G16B 30/20 Sequence assembly

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 cell-free deoxyribonucleic acid (cfDNA) molecules from a bodily fluid sample of a subject, comprising:

(a) non-uniquely tagging a plurality of cfDNA molecules from a population of cfDNA molecules obtained from the bodily fluid sample with molecular barcodes from a set of molecular barcodes to produce non-uniquely tagged parent polynucleotides,

wherein the non-uniquely tagging comprises ligating molecular barcodes from the set of molecular barcodes to both ends of a cfDNA molecule from the plurality of cfDNA molecules using more than a 10×

molar excess of molecular barcodes relative to the population of cfDNA molecules,

wherein the cfDNA molecules that map to a mappable base position of a reference sequence are tagged with a number of diffrent molecular barcodes ranging from at least 2 and fewer than a number of cfDNA molecules that map to the mappable base position, and

wherein at least 20% of the cfDNA molecules from the population of cfDNA molecules are attached to molecular barcodes;

(b) amplifying a plurality of the non-uniquely tagged parent polynucleotides to produce progeny polynucleotides with associated molecular barcodes;

(c) sequencing a plurality of the progeny polynucleotides to produce sequencing reads of the progeny polynucleotides with associated molecular barcodes;

(d) mapping a plurality of the sequencing reads to the reference sequence to generate mapped sequencing reads;

(e) grouping a plurality of the mapped sequencing reads into a plurality of families based on sequence information from the molecular barcodes and at least (1) a start base position of a given mapped sequencing read from among the mapped sequencing reads at which the given mapped sequencing read is determined to start mapping to the reference sequence and/or (2) a stop base position of the given mapped sequencing read at which the given mapped sequencing read is determined to stop mapping to the reference sequence; and

(f) detecting, from among the mapped sequencing reads in a plurality of the families, the presence or absence of the one or more somatic genetic variants.

2. The method of claim 1, wherein the bodily fluid sample is blood, plasma, or serum.

3. The method of claim 1, wherein the population comprises 1 nanogram (ng) to 100 ng of cfDNA molecules.

4. The method of claim 1, wherein the ligating is performed using blunt-end ligation or sticky-end ligation.

5. The method of claim 1, wherein a given molecular barcode is a member of the set of molecular barcodes having 2 to 1,000 different molecular barcode sequences.

6. The method of claim 1, wherein a given molecular barcode is a member of the set of molecular barcodes having 5 to 100 different molecular barcode sequences.

7. The method of claim 6, wherein the set of molecular barcodes comprises sequences from 5 to 20 nucleotides in length.

8. The method of claim 1, wherein the ligating comprises using more than an 80×

molar excess of molecular barcodes relative to the population of cfDNA molecules.

9. The method of claim 1, wherein the ligating comprises using more than a 100×

molar excess of molecular barcodes relative to the population of cfDNA molecules.

10. The method of claim 1, wherein at least 30% of the cfDNA molecules from the population of cfDNA molecules are attached to molecular barcodes.

11. The method of claim 1, wherein at least 40% of the cfDNA molecules from the population of cfDNA molecules are attached to molecular barcodes.

12. The method of claim 1, further comprising selectively enriching the progeny polynucleotides for target regions associated with cancer.

13. The method of claim 1, further comprising filtering out one or more of the sequencing reads that fail to meet a quality threshold.

14. The method of claim 1, further comprising generating a consensus sequence for each family from among the plurality of families.

15. The method of claim 14, further comprising identifying a subset of the plurality of consensus sequences comprising a somatic genetic variant as compared to the reference sequence.

16. The method of claim 1, further comprising generating a base call for at least one of the plurality of families at a genetic locus of a plurality of genetic locus of the reference sequence.

17. The method of claim 1, further comprising detecting cancer in the subject when the presence of the one or more somatic genetic variants is detected.

18. The method of claim 17, further comprising administering a therapy to the subject to treat the cancer.

19. The method of claim 1, wherein the one or more somatic genetic variants comprise a single nucleotide variation (SNV), an insertion or deletion (indel), a copy number variation (CNV), or a gene fusion.

20. A method for quantifying single nucleotide variant tumor markers in cell-free deoxyribonucleic acid (cfDNA) molecules from a bodily fluid sample of a subject, comprising:

(a) non-uniquely tagging a plurality of cfDNA molecules from a population of cfDNA molecules obtained from the bodily fluid sample with molecular barcodes from a set of molecular barcodes to produce non-uniquely tagged parent polynucleotides,

wherein the non-uniquely tagging comprises ligating molecular barcodes from the set of molecular barcodes to both ends of a cfDNA molecule from the plurality of cfDNA molecules using more than a 10×

molar excess of molecular barcodes relative to the population of cfDNA molecules,

wherein the cfDNA molecules that map to a mappable base position of a reference sequence are tagged with a number of diffrent molecular barcodes ranging from at least 2 and fewer than a number of cfDNA molecules that map to the mappable base position, and

wherein at least 20% of the cfDNA molecules from the population of cfDNA molecules are attached to molecular barcodes;

(b) amplifying a plurality of the non-uniquely tagged parent polynucleotides to produce progeny polynucleotides with associated molecular barcodes;

(c) sequencing at least a subset of the progeny polynucleotides to produce sequencing reads of the progeny polynucleotides with associated molecular barcodes;

(d) mapping a plurality of the sequencing reads to the reference sequence to generate mapped sequencing reads;

(e) grouping a plurality of the mapped sequencing reads into a plurality of families based on sequence information from the molecular barcodes and at least (1) a start base position of a given mapped sequencing read from among the mapped sequencing reads at which the given mapped sequencing read is determined to start mapping to the reference sequence and/or (2) a stop base position of the given mapped sequencing read at which the given mapped sequencing read is determined to stop mapping to the reference sequence;

(f) generating a consensus sequence for each family from among the plurality of families;

(g) identifying a subset of the plurality of consensus sequences comprising a single nucleotide variant as compared to the reference sequence; and

(h) calculating a number of the subset of the plurality of consensus sequences comprising the single nucleotide variant, thereby quantifying single nucleotide variant tumor markers in the cfDNA molecules from the bodily fluid sample of the subject.

21. The method of claim 20, wherein the bodily fluid sample is blood, plasma, or serum.

22. The method of claim 20, wherein the population comprises 1 nanogram (ng) to 100 ng of cfDNA molecules.

23. The method of claim 20, wherein the ligating is performed using blunt-end ligation or sticky-end ligation.

24. The method of claim 20, wherein a given molecular barcode is a member of the set of molecular barcodes having 5 to 1,000 different molecular barcode sequences.

25. The method of claim 24, wherein the set of molecular barcodes comprises sequences from 5 to 20 nucleotides in length.

26. The method of claim 20, wherein the ligating comprises using more than an 80×

molar excess of molecular barcodes relative to the population of cfDNA molecules.

27. The method of claim 20, wherein at least 30% of the cfDNA molecules from the population of cfDNA molecules are attached to molecular barcodes.

28. The method of claim 20, further comprising selectively enriching the progeny polynucleotides for target regions associated with cancer.

29. The method of claim 20, further comprising filtering out one or more of sequencing reads that fail to meet a quality threshold.

30. The method of claim 20, wherein consensus sequences of the plurality of consensus sequences are representative of cfDNA molecules from the bodily fluid sample comprising a sequence of 140 to 180 nucleotides in length.