US 12,270,082 B2
Methods of detecting DNA in a sample
Jared Robert Maguire, San Francisco, CA (US); Clement S. Chu, San Francisco, CA (US); Imran Saeedul Haque, San Francisco, CA (US); Eric Andrew Evans, San Bruno, CA (US); and Noah Welker, Half Moon Bay, CA (US)
Assigned to Myriad Women's Health, Inc., South San Francisco, CA (US)
Filed by MYRIAD WOMEN'S HEALTH, INC., South San Francisco, CA (US)
Filed on Feb. 23, 2022, as Appl. No. 17/678,829.
Application 17/678,829 is a continuation of application No. 17/383,273, filed on Jul. 22, 2021, granted, now 11,932,910.
Application 17/383,273 is a continuation of application No. 16/784,761, filed on Feb. 7, 2020, granted, now 12,024,749.
Application 16/784,761 is a continuation of application No. 15/465,553, filed on Mar. 21, 2017, granted, now 10,597,717, issued on Mar. 24, 2020.
Claims priority of provisional application 62/311,899, filed on Mar. 22, 2016.
Prior Publication US 2022/0290229 A1, Sep. 15, 2022
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); C12Q 1/6818 (2018.01); C12Q 1/6874 (2018.01)
CPC C12Q 1/6886 (2013.01) [C12Q 1/6818 (2013.01); C12Q 1/6874 (2013.01); C12Q 2600/156 (2013.01)] 13 Claims
 
1. A method of detecting deoxyribonucleic acid (DNA) in a sample, comprising:
(a) obtaining a tumor sample and a non-tumor sample from a subject with a history of cancer;
(b) sequencing DNA from the tumor sample and sequencing DNA from the non-tumor sample, thereby obtaining sequences of DNA from the tumor sample and sequences of genomic DNA from the non-tumor sample;
(c) aligning the sequences of DNA from the tumor sample to a reference human genome that is not from the subject, thereby obtaining a set of tumor-specific mutations and further obtaining from the set of tumor-specific mutations a set of tumor-specific somatic mutation sequences that are present in the sequences of DNA from the tumor sample but not present in the sequences of DNA from the non-tumor sample; and
at one or more timepoints subsequent to obtaining the set of tumor-specific mutation sequences:
(d) obtaining a fluid sample of whole blood, plasma, or serum from the subject;
(e) extracting cell-free DNA (cfDNA) from the fluid sample;
(f) enriching, from the extracted cfDNA, a DNA fraction of fragments comprising one or more of the set of tumor-specific somatic mutations wherein enriching comprises:
(i) hybrid capture-based enrichment,
(ii) PCR-target enrichment, or
(iii) on-sequencer enrichment;
(g) sequencing the DNA fraction, thereby obtaining a plurality of sequence reads; and
(h) detecting the presence or absence of a DNA fragment comprising any one of the set of tumor-specific somatic mutations, wherein the presence of a sequence read in the plurality of sequence reads corresponding to one or more of the tumor-specific somatic mutation sequences indicates the presence of the DNA fragment;
wherein (d)-(h) are performed after the subject has received a treatment for cancer or while the subject is in remission.