Granted Patent B2

US 12,252,749 · App. 18/426,665 · Granted Mar 18, 2025

Inventor: AmirAli Talasaz (Atherton, CA)

Assignee: Guardant Health, Inc.

C12Q1/6886C12N15/1065C12Q1/6806C12Q1/6869C12Q1/6874G16B30/00G16B30/10C12Q2600/118C12Q2600/156C12Q2600/158C12Q2600/16

Abstract

Claims (30)

1. A method, comprising:

(a) providing at least one set of tagged parent polynucleotides, wherein different sets map to different mappable positions in a reference sequence in one or more genomes, and, for the at least one set of tagged parent polynucleotides:

i) amplifying the tagged parent polynucleotides to produce a set of amplified polynucleotides,

ii) sequencing at least a subset of the set of amplified polynucleotides, to produce a set of sequencing reads,

iii) grouping sequences reads sequenced from the amplified polynucleotides into families, wherein a family is amplified from the same tagged parent polynucleotide,

iv) determining a quantitative measure of sequence reads in the individual families;

(b) determining a quantitative measure of unique families; and

(c) based on (1) the quantitative measure of unique families and (2) the quantitative measure of sequence reads in the individual families, inferring a measure of unique tagged parent polynucleotides in the set.

2. The method of claim 1 , wherein the inferring is performed using statistical or probabilistic models.

3. The method of claim 1 , wherein the at least one set is a plurality of sets.

4. The method of claim 3 , further comprising correcting for amplification or representational bias between at least two sets of the plurality of sets.

5. The method of claim 4 , further comprising using a control or set of control samples to correct for amplification or representational biases between the at least two sets.

6. The method of claim 3 , further comprising determining copy number variation between the sets.

7. The method of claim 1 , further comprising:

(d) determining a quantitative measure of polymorphic forms among the families; and

(e) based on the determined quantitative measure of polymorphic forms, inferring a quantitative measure of polymorphic forms in the number of inferred unique tagged parent polynucleotides.

8. The method of claim 7 , wherein polymorphic forms are selected from: substitutions, insertions, deletions, inversions, microsatellite changes, transversions, translocations, fusions, methylation, hypermethylation, and hydroxymethylation.

9. The method claim 1 , wherein the sets derive from a common sample, and the method further comprises:

(d) inferring copy number variation for the plurality of sets based on a comparison of the inferred number of tagged parent polynucleotides in each set mapping to each of a plurality of mappable positions in a reference sequence.

10. The method of claim 9 , wherein the original number of polynucleotides in each set is further inferred.

11. The method of claim 1 , wherein at least a subset of the tagged parent polynucleotides in each set are non-uniquely tagged.

12. The method of claim 1 , wherein the tagged parent polynucleotides are uniquely tagged.

13. The method of claim 1 , wherein the sequence reads are grouped based on sequence information at the beginning (start) and end (stop) regions of the sequence read and the length of the sequence read.

14. The method of claim 1 , wherein the sequence reads are grouped based on sequence information at the beginning (start) and end (stop) regions of the sequence read, the length of the sequence read and attachment of a barcode.

15. The method of claim 1 , wherein the parent polynucleotides are cell free polynucleotides.

16. The method of claim 15 , wherein the parent polynucleotides are extracted from blood, plasma, or serum.

17. The method of claim 1 , wherein the parent polynucleotides are tagged with from 25 to 100,000 different identifiers.

18. The method of claim 1 , wherein the method comprises detection and monitoring of an abnormality or disease within an individual.

19. The method of claim 1 , further comprising tagging no more than 100 ng of cfDNA molecules with molecular barcodes to generate the at least one set of tagged parent polynucleotides.

20. The method of claim 19 , wherein the molecular barcodes are pre-determined sequences of at least 5 nucleotides in length.

Assignments (1)

Continuity (18)

References Cited (400)