US 12,258,626 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. 22, 2024, as Appl. No. 18/812,385.
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.
Application 14/861,989 is a continuation of application No. PCT/US2014/072383, filed on Dec. 24, 2014.
Claims priority of provisional application 61/948,509, filed on Mar. 5, 2014.
Claims priority of provisional application 61/921,456, filed on Dec. 28, 2013.
Prior Publication US 2025/0002993 A1, Jan. 2, 2025
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)] 27 Claims
 
1. A method for treating a subject having lung cancer, comprising:
(a) determining that a sample from the subject comprises a genetic variant associated with a T790M EGFR mutation, wherein the sample comprises double-stranded deoxyribonucleic acid (DNA) molecules from the subject, by:
performing or having performed a diagnostic assay on the sample to determine the presence of the genetic variant associated with the EGFR mutation, wherein the diagnostic assay comprises:
i) attaching adapters comprising molecular barcodes to a plurality of the double-strand DNA molecules from the sample to produce tagged parent polynucleotides;
ii) amplifying a plurality of the tagged parent polynucleotides to produce amplified progeny polynucleotides;
iii) sequencing a plurality of the amplified progeny polynucleotides to produce a set of sequencing reads;
iv) mapping a plurality of the sequencing reads from the set of sequencing reads to a reference sequence to generate mapped sequencing reads;
v) reducing or tracking redundancy in a plurality of the mapped sequencing reads using at least sequence information from the molecular barcodes to generate a plurality of consensus sequences representative of original DNA molecules from among the tagged parent polynucleotides, wherein the plurality of consensus sequences is generated from (i) paired reads corresponding to mapped sequencing reads generated from a first tagged strand and a second tagged complementary strand derived from a DNA molecule from among the tagged parent polynucleotides, and (ii) unpaired reads corresponding to sequence reads generated from a first tagged strand having no second tagged complementary strand derived from a DNA molecule from among the tagged parent polynucleotides;
vi) detecting the genetic variant associated with the T790M EGFR mutation from among the plurality of consensus sequences; and
(b) administering a therapy responsive to the T790M EGFR mutation to the subject to treat the lung cancer based on detecting the presence of the genetic variant associated with the T790M EGFR mutation.