Methods of detecting and enriching circulating tumor DNA

Patent metadata

Field	Value
Publication number	US-12351880-B2
Application number	US-202519029541-A
Country	US
Kind code	B2
Filing date	Jan 17, 2025
Priority date	Mar 22, 2016
Publication date	Jul 8, 2025
Grant date	Jul 8, 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 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.

2. The method of claim 1 , wherein the set of tumor-specific somatic mutations comprises at least 10 different tumor-specific somatic mutations.

3. The method of claim 1 , wherein sequencing DNA from the tumor sample and sequencing DNA from the non-tumor sample comprises whole genome sequencing or whole exome sequencing.

4. The method of claim 1 , wherein the cfDNA sample is extracted from a fluid sample from the subject.

5. The method of claim 4 , wherein the fluid sample is a whole blood sample, a plasma sample, or a serum sample.

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

7. The method of claim 1 , the cfDNA sample is obtained one or more times during a cancer treatment, following completion of a cancer treatment, while the subject is in remission, or coinciding with or prior to surgery.

8. A method of enriching a sample comprising circulating tumor DNA (ctDNA), comprising:
extracting cell-free DNA (cfDNA) from a fluid sample obtained from a subject with a history of cancer;
enriching, from the extracted cfDNA, fragments comprising one or more of a set of tumor-specific somatic mutations via
(i) hybrid capture-based enrichment,
(ii) PCR-target enrichment, or
(iii) on-sequencer enrichment,
thereby obtaining a DNA fraction comprising ctDNA;
wherein the set of tumor-specific somatic mutations is specific to the subject based on a comparison of sequence reads from sequencing DNA from a tumor sample from the subject and sequence reads from sequencing DNA from a non-tumor sample from the subject.

9. The method of claim 8 , wherein the set of tumor-specific somatic mutations comprises at least 10 different tumor-specific somatic mutations.

10. The method of claim 8 , wherein sequencing DNA from the tumor sample and sequencing DNA from the non-tumor sample comprises whole genome sequencing or whole exome sequencing.

11. The method of claim 8 , wherein the fluid sample is a whole blood sample, a plasma sample, or a serum sample.

12. The method of claim 8 , wherein enriching comprises hybrid capture-based enrichment.

13. The method of claim 8 , wherein enriching comprises PCR-target enrichment.

14. The method of claim 8 , the fluid sample is obtained one or more times during a cancer treatment, following completion of a cancer treatment, while the subject is in remission, or coinciding with or prior to surgery.

15. The method of claim 8 , further comprising 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.

16. 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;
determining a set of tumor-specific somatic mutations based on the sequence reads from the tumor sample and the sequence reads from the non-tumor sample, and selecting a subset of tumor-specific somatic mutations that are specific to the subject;
enriching, from a cell free DNA (cfDNA) sample from the subject, a DNA fraction of fragments comprising one or more of the subset of tumor-specific somatic mutations;
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 subset of tumor-specific somatic mutations, wherein the presence of a sequence read comprising any one of the subset of tumor-specific somatic mutations indicates the presence of ctDNA in the fluid sample.

17. The method of claim 16 , wherein the subset of tumor-specific somatic mutations comprises at least 10 different tumor-specific somatic mutations.

18. The method of claim 16 , wherein sequencing DNA from the tumor sample and sequencing DNA from the non-tumor sample comprises whole genome sequencing or whole exome sequencing.

19. The method of claim 16 , wherein the cfDNA sample is extracted from a fluid sample from the subject.

20. The method of claim 19 , wherein the fluid sample is a whole blood sample, a plasma sample, or a serum sample.

21. The method of claim 16 , wherein enriching the DNA fraction comprises hybrid capture-based enrichment, PCR-target enrichment, or on-sequencer enrichment.

22. The method of claim 16 , the cfDNA sample is obtained one or more times during a cancer treatment, following completion of a cancer treatment, while the subject is in remission, or coinciding with or prior to surgery.

23. A method of enriching a sample comprising circulating tumor DNA (ctDNA), comprising:
extracting cell-free DNA (cfDNA) from a fluid sample obtained from a subject with a history of cancer;
enriching, from the extracted cfDNA, fragments comprising one or more of a subset of tumor-specific somatic mutations via
(i) hybrid capture-based enrichment,
(ii) PCR-target enrichment, or
(iii) on-sequencer enrichment,
thereby obtaining a DNA fraction comprising ctDNA;
wherein the subset of tumor-specific somatic mutations is specific to the subject and selected from a set of somatic mutations determined from sequence reads from sequencing DNA from a tumor sample from the subject and sequence reads from sequencing DNA from a non-tumor sample from the subject.

24. The method of claim 23 , wherein the subset of tumor-specific somatic mutations comprises at least 10 different tumor-specific somatic mutations.

25. The method of claim 23 , wherein sequencing DNA from the tumor sample and sequencing DNA from the non-tumor sample comprises whole genome sequencing or whole exome sequencing.

26. The method of claim 23 , wherein the fluid sample is a whole blood sample, a plasma sample, or a serum sample.

27. The method of claim 23 , wherein enriching comprises hybrid capture-based en

Assignees

• Myriad Womens Health Inc

Inventors

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

Classifications

• 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

• C12Q1/6806

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