US 12,344,901 B2
Automated methods of detecting cell free 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 Aug. 8, 2022, as Appl. No. 17/883,414.
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 2023/0295716 A1, Sep. 21, 2023
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)] 15 Claims
 
1. An automated method of detecting a DNA fragment, comprising:
(i) receiving, via an application module configured to receive commands from at least one of a user computing device or a script server, a workflow process corresponding to a result to be obtained based on operations on a sample selected from whole blood, plasma, or serum from a subject with a history of cancer;
(ii) obtaining, via an automation system configured to interface with laboratory equipment, based on the workflow process, a container with the sample from an origin location;
(iii) performing, by the automated system,
(a) extracting cell free DNA (cfDNA) from the sample;
(b) enriching, from the extracted cfDNA, a DNA fraction of fragments comprising one or more of a plurality of tumor-specific somatic mutations that are specific to the subject and that were determined prior to obtaining the sample by sequencing genomic DNA from a solid tumor sample previously obtained from the subject and genomic DNA from a non-tumor sample previously obtained from the subject;
(c) sequencing the enriched fraction of fragments; and
(d) detecting a presence or absence of a DNA fragment comprising any one of the plurality of tumor-specific somatic mutations in the enriched DNA fraction of fragments; and
(iv) generating a report comprising the result of the detection of the presence or absence of the DNA fragment.