Automated methods of detecting cell free DNA

Patent metadata

Field	Value
Publication number	US-12215391-B1
Application number	US-202318357799-A
Country	US
Kind code	B1
Filing date	Jul 24, 2023
Priority date	Mar 22, 2016
Publication date	Feb 4, 2025
Grant date	Feb 4, 2025

Abstract

The present disclosure relates to a laboratory execution system that provides for automation of laboratory processes. A centralized data management system may be dynamically updated and used to facilitate management of components of the laboratory execution system, such as an automation system and an analytics results management system that may facilitate complex analytical functions, such as synthesizing raw test data. Potential workflows include the detection of specific molecules of interest.

First claim

The invention claimed is:

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.

2. The method of claim 1 , wherein the cfDNA is extracted from the sample using a liquid handling apparatus configured for extraction of components of samples.

3. The method of claim 1 , further comprising providing, by the application module, the report to a user device.

4. The method of claim 1 , wherein the result is presence or absence of a molecule in the sample.

5. The method of claim 1 , further comprising positioning, by the automation system, the container at a destination location prior to performing the one or more operations.

6. The method of claim 1 , wherein the automation system is configured to interface with the laboratory equipment using one or more robotics units, and wherein the computer module is configured to perform the one or more operations on the sample using the one or more robotics units.

7. The method of claim 1 , wherein the sample is plasma.

8. The method of claim 1 , wherein enriching comprises hybrid capture-based enrichment, PCR-target enrichment, or on-sequencer enrichment.

9. The method of claim 1 , wherein the method comprises a detection sensitivity of 20 to 50 ctDNA fragments comprising one or more of the plurality of somatic mutations in fluid sample per a total background of 500,000 cfDNA fragments.

10. The method of claim 1 , wherein hybrid capture-based enrichment is used to enrich the DNA fraction of fragments comprising one or more of the plurality of tumor-specific somatic mutations.

11. The method of claim 10 , wherein hybrid capture-based enrichment comprises:
(i) contacting the extracted cfDNA with a plurality of oligonucleotides that each comprise a nucleic acid sequence that is capable of hybridizing to one of the plurality of tumor-specific somatic mutations; and
(ii) selectively enriching cfDNA fragments that hybridize to the plurality of oligonucleotides.

12. The method of claim 11 , wherein the plurality of oligonucleotides is capable of detecting at least 50 different tumor-specific somatic mutations.

13. The method of claim 1 , wherein sequencing comprises whole genome sequencing.

14. The method of claim 1 , wherein sequencing comprises targeted sequencing.

15. The method of claim 1 , further comprising determining a fraction of the cfDNA fragments that are circulating tumor DNA (ctDNA) fragments.

16. The method of claim 1 , wherein the mutations in the plurality of tumor-specific somatic mutations comprise one or more mutations selected from SNPs, insertions, deletions, and translocations.

Assignees

• Myriad Womens Health Inc

Inventors

• Maguire Jared Robert
• Chu Clement S
• Haque Imran Saeedul
• Evans Eric Andrew
• Welker Noah

Classifications

• C12Q1/6806

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title

• G01N35/0099

  comprising robots or similar manipulators (robots per se B25J) · CPC title

• C12Q1/6818 Primary

  involving interaction of two or more labels, e.g. resonant energy transfer · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q1/6874

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title