US 12,286,672 B2
Methods and systems for detecting genetic variants
AmirAli Talasaz, Atherton, CA (US); Helmy Eltoukhy, Atherton, CA (US); and Stefanie Ann Ward Mortimer, Morgan Hill, CA (US)
Assigned to Guardant Health, Inc., Palo Alto, CA (US)
Filed by GUARDANT HEALTH, INC., Palo Alto, CA (US)
Filed on Aug. 23, 2024, as Appl. No. 18/813,477.
Application 18/813,477 is a continuation of application No. 18/812,385, filed on Aug. 22, 2024.
Application 18/812,385 is a continuation of application No. 18/538,986, filed on Dec. 13, 2023, granted, now 12,098,422.
Application 18/538,986 is a continuation of application No. 18/535,485, filed on Dec. 11, 2023, granted, now 12,024,746, issued on Jul. 2, 2024.
Application 18/535,485 is a continuation of application No. 18/491,071, filed on Oct. 20, 2023, granted, now 12,024,745, issued on Jul. 2, 2024.
Application 18/491,071 is a continuation of application No. 18/317,550, filed on May 15, 2023, granted, now 12,098,421.
Application 18/317,550 is a continuation of application No. 17/512,587, filed on Oct. 27, 2021, granted, now 11,767,556, issued on Sep. 26, 2023.
Application 17/512,587 is a continuation of application No. 17/410,903, filed on Aug. 24, 2021, granted, now 11,434,531, issued on Sep. 6, 2022.
Application 17/410,903 is a continuation of application No. 17/167,974, filed on Feb. 4, 2021, granted, now 11,149,307, issued on Oct. 19, 2021.
Application 17/167,974 is a continuation of application No. 16/945,124, filed on Jul. 31, 2020, granted, now 11,149,306, issued on Oct. 19, 2021.
Application 16/945,124 is a continuation of application No. 16/601,168, filed on Oct. 14, 2019, granted, now 10,801,063, issued on Oct. 13, 2020.
Application 16/601,168 is a continuation of application No. 15/892,178, filed on Feb. 8, 2018, granted, now 10,883,139, issued on Jan. 5, 2021.
Application 15/892,178 is a continuation of application No. 14/861,989, filed on Sep. 22, 2015, granted, now 9,920,366, issued on Mar. 20, 2018.
Prior Publication US 2024/0425915 A1, Dec. 26, 2024
This patent is subject to a terminal disclaimer.
Int. Cl. C12P 19/34 (2006.01); C12Q 1/6869 (2018.01); C12Q 1/6886 (2018.01); G16B 15/00 (2019.01)
CPC C12Q 1/6869 (2013.01) [C12Q 1/6886 (2013.01); C12Q 2535/122 (2013.01); C12Q 2600/158 (2013.01); G16B 15/00 (2019.02)] 30 Claims
 
1. A method for treating a subject having a cancer associated with one or more genetic variants, comprising:
(a) selecting the subject having the cancer, comprising:
(i) providing a sample of cell-free deoxyribonucleic acid (cfDNA) molecules from the subject having the cancer;
(ii) ligating adapters to a plurality of the cfDNA molecules to produce tagged parent polynucleotides;
(iii) amplifying the tagged polynucleotides to produce tagged progeny polynucleotides;
(iv) enriching the tagged progeny polynucleotides with a sequencing panel to produce enriched polynucleotides, wherein the sequencing panel comprises oligonucleotide probes comprising genomic regions from each of the following genes:
ALK, APC, BRAF, CDKN2A, EGFR, ERBB2, FBXW7, KRAS, MYC, NOTCH1, NRAS, PIK3CA, PTEN, RB1, TP53, MET, AR, ABL1, AKT1, ATM, CDH1, CSF1R, CTNNB1, ERBB4, EZH2, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, MLH1, MPL, NPM1, PDGFRA, PTPN11, RET, SMAD4, SMARCB1, SMO, SRC, STK11, VHL, TERT, CCND1, CDK4, CDKN2B, RAF1, BRCA1, CCND2, CDK6, NF1, ARIDIA, BRCA2, CCNE1, ESR1, RIT1, GATA3, MAP2K1, RHEB, ROS1, ARAF, MAP2K2, NFE2L2, RHOA, and NTRK1;
(v) sequencing one or more genomic regions from each gene of the sequencing panel from a plurality of enriched polynucleotides to generate sequence reads;
(vi) determining, from a plurality of the sequence reads, a presence of one or more genetic variants from the one or more genomic regions; and
(b) treating the subject with a therapy based on determining the presence of the one or more genetic variants.