Granted Patent B2

US 12,662,697 · App. 17/701,165 · Granted Jun 23, 2026

Inventors: AmirAli Talasaz (Atherton, CA); Stefanie Ann Ward Mortimer (Morgan Hill, CA)

Assignee: GUARDANT HEALTH, INC.

C12Q1/6827C12Q1/6806G16B30/00C12Q1/6869

Abstract

Claims (29)

1 . A method for detecting a presence or an absence of one or more somatic genetic variants in polynucleotides from a sample of a subject, comprising:

(a) tagging a plurality of polynucleotides from a population of polynucleotides obtained or derived from the sample with molecular barcodes to produce tagged parent polynucleotides,

wherein said tagging comprises ligating molecular barcodes to the ends of a polynucleotide molecule from the population of polynucleotides using more than a 10× molar excess of molecular barcodes relative to the polynucleotides in the population of polynucleotides,

wherein at least 20% of the polynucleotides from the population of polynucleotides are attached to molecular barcodes,

wherein the polynucleotides in the population are tagged with n different molecular barcodes, wherein n is at least 2 and no more than 100,000*z, wherein z is a mean of an expected number of duplicate molecules in the population of polynucleotides that map to identical start and stop positions on a reference sequence;

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

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

(d) grouping a plurality of the sequencing reads into a plurality of families using sequence information from at least the molecular barcodes;

(e) generating, from among the sequencing reads in a family, a consensus sequence for each family from among the plurality of families; and

(f) detecting, from among one or more consensus sequences, the presence or the absence of the one or more somatic genetic variants as compared to the reference sequence.

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

3 . The method of claim 1 , wherein the sample is blood, plasma, serum, tissue or a tumor biopsy.

4 . The method of claim 1 , wherein the polynucleotides comprise deoxyribonucleic acid (DNA) molecules, ribonucleic acid (RNA) molecules, complementary DNA (cDNA) molecules, or any combination thereof.

5 . The method of claim 1 , wherein the population of polynucleotides comprises 100 to 100,000 haploid human genome equivalents of polynucleotides.

6 . The method of claim 1 , wherein n different molecular barcodes is no more than 10,000*z.

7 . The method of claim 1 , wherein n different molecular barcodes is no more than 1,000*z.

8 . The method of claim 1 , wherein n different molecular barcodes is no more than 100*z.

9 . The method of claim 1 , wherein the molecular barcode sequences are from 5 to 20 nucleotides in length.

10 . The method of claim 6 , wherein the molecular barcode sequences are from 5 to 20 nucleotides in length.

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

12 . The method of claim 1 , wherein the ligating comprises using more than an 80× molar excess of molecular barcodes relative to the polynucleotides in the population of polynucleotides.

13 . The method of claim 1 , wherein the ligating comprises using more than a 100× molar excess of molecular barcodes relative to the polynucleotides in the population of polynucleotides.

14 . The method of claim 1 , wherein at least 40% of the polynucleotides in the population of polynucleotides are attached to molecular barcodes.

15 . The method of claim 1 , further comprising selectively enriching the progeny polynucleotides for target regions associated with cancer prior to the sequencing in (c).

16 . The method of claim 1 , further comprising filtering out sequencing reads that fail to meet a quality threshold prior to the grouping in (d).

17 . The method of claim 1 , further comprising mapping a plurality of the sequencing reads to the reference sequence.

18 . The method of claim 17 , wherein the grouping in (d) is further based on at least (1) a start base position of a given sequencing read from among the sequencing reads at which the given sequencing read is determined to start mapping to the reference sequence and/or (2) a stop base position of the given sequencing read at which the given sequencing read is determined to stop mapping to the reference sequence.

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 . The method of claim 1 , wherein the one or more somatic genetic variants is an SNV.

Assignments (1)

Continuity (9)

References Cited (400)