US 12,351,880 B2
Methods of detecting and enriching circulating tumor DNA
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 Jan. 17, 2025, as Appl. No. 19/029,541.
Application 19/029,541 is a continuation of application No. 18/357,799, filed on Jul. 24, 2023, granted, now 12,215,391.
Application 18/357,799 is a continuation of application No. 17/883,414, filed on Aug. 8, 2022.
Application 17/883,414 is a continuation of application No. 17/678,829, filed on Feb. 23, 2022, granted, now 12,270,082.
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.
Claims priority of provisional application 62/311,899, filed on Mar. 22, 2016.
Prior Publication US 2025/0154605 A1, May 15, 2025
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); G01N 35/00 (2006.01)
CPC C12Q 1/6886 (2013.01) [C12Q 1/6818 (2013.01); C12Q 1/6874 (2013.01); G01N 35/0099 (2013.01); C12Q 2600/156 (2013.01)] 30 Claims
 
1. A method of detecting circulating tumor DNA (ctDNA) in a sample, comprising:
sequencing DNA from a tumor sample obtained from a subject with a history of cancer and sequencing DNA from a non-tumor sample from the subject, thereby obtaining sequence reads from the tumor sample and sequence reads from the non-tumor sample;
obtaining a fluid sample from the subject;
enriching, from a cell free DNA (cfDNA) sample from the subject, a DNA fraction of fragments comprising one or more of a set of tumor-specific somatic mutations that are specific to the subject, wherein the set of tumor-specific somatic mutations are present in the sequence reads from the tumor sample but not present in the sequence reads from the non-tumor sample;
sequencing the DNA fraction, thereby obtaining a plurality of sequence reads; and
detecting in the plurality of sequence reads the presence of a sequence read comprising any one of the set of tumor-specific somatic mutations, wherein the presence of a sequence read comprising any one of the set of tumor-specific somatic mutations indicates the presence of ctDNA in the fluid sample.