US 12,215,391 B1
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 Jul. 24, 2023, as Appl. No. 18/357,799.
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.
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.
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); G01N 35/00 (2006.01)
CPC C12Q 1/6886 (2013.01) [G01N 35/0099 (2013.01); C12Q 2600/156 (2013.01)] 16 Claims
 
1. A method of using a laboratory control system,
(A) the laboratory control system comprising:
(i) an application module configured to receive commands from at least one of a user computing device or a script server;
(ii) an automation system configured to interface with laboratory equipment to perform movements related to testing laboratory samples;
(iii) a computer module configured to perform operations on components extracted from samples; and
(iv) an analytics results management system (ARMS) configured to dynamically render laboratory information;
(B) the method comprising:
(i) receiving, via the application module, a workflow process corresponding to a result to be obtained based on operations on a sample comprising whole blood, plasma, or serum from a subject with a history of cancer;
(ii) obtaining, via the automation system, based on the workflow process, a container with the sample from an origin location;
(iii) performing, by the computer module, operations comprising (a) extracting cell-free DNA (cfDNA) from the sample in the container, (b) enriching, from the extracted cfDNA, a DNA fraction of DNA comprising at least 10 tumor-specific somatic mutations that are specific to the subject, (c) sequencing the enriched fraction of DNA, thereby obtaining a plurality of sequence reads, and (d) determining a presence or absence of circulating tumor DNA (ctDNA), wherein the presence of one or more sequence reads in the plurality of sequence reads corresponding to one or more of the tumor-specific mutation sequences indicates the presence of ctDNA in the plasma sample; and
(iv) generating, by the ARMS, a report comprising the result based on the one or more operations;
wherein the method is repeated one or more times during a treatment of the subject, following completion of a treatment of the subject, while the subject is in remission, or coinciding with or prior to surgery.