IP Library › Granted Patent US 12,270,082
Granted Patent B2
US 12,270,082 · App. 17/678,829 · Granted Apr 8, 2025

Methods of detecting DNA in a sample

Inventors: Jared Robert Maguire (San Francisco, CA); Clement S. Chu (San Francisco, CA); Imran Saeedul Haque (San Francisco, CA); Eric Andrew Evans (San Bruno, CA); Noah Welker (Half Moon Bay, CA)
Assignee: Myriad Women's Health, Inc.
C12Q1/6886C12Q1/6818C12Q1/6874C12Q2600/156
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Quick Facts
Patent No.
US 12,270,082
App. No.
17/678,829
Granted
Apr 8, 2025
Kind
B2
Abstract

The present disclosure relates to methods for detecting unique genetic signatures derived from markers such as, for example, mutations, somatic or germ-line, in nucleic acids obtained from biological samples. The sensitivity of the methods provides for detection of mutations associated with a disease, e.g., cancer mutations, or with inherited disease, e.g., an autosomal recessive disease, in a noninvasive manner at ultra-low proportions of sequences carrying mutations to sequences carrying normal, e.g., non-cancer sequences, or a reference sequence, e.g., a human reference genome.

Claims (28)

1. A method of detecting deoxyribonucleic acid (DNA) in a sample, comprising:

(a) obtaining a tumor sample and a non-tumor sample from a subject with a history of cancer;

(b) sequencing DNA from the tumor sample and sequencing DNA from the non-tumor sample, thereby obtaining sequences of DNA from the tumor sample and sequences of genomic DNA from the non-tumor sample;

(c) aligning the sequences of DNA from the tumor sample to a reference human genome that is not from the subject, thereby obtaining a set of tumor-specific mutations and further obtaining from the set of tumor-specific mutations a set of tumor-specific somatic mutation sequences that are present in the sequences of DNA from the tumor sample but not present in the sequences of DNA from the non-tumor sample; and

at one or more timepoints subsequent to obtaining the set of tumor-specific mutation sequences:

(d) obtaining a fluid sample of whole blood, plasma, or serum from the subject;

(e) extracting cell-free DNA (cfDNA) from the fluid sample;

(f) enriching, from the extracted cfDNA, a DNA fraction of fragments comprising one or more of the set of tumor-specific somatic mutations wherein enriching comprises:

(i) hybrid capture-based enrichment,

(ii) PCR-target enrichment, or

(iii) on-sequencer enrichment;

(g) sequencing the DNA fraction, thereby obtaining a plurality of sequence reads; and

(h) detecting the presence or absence of a DNA fragment comprising any one of the set of tumor-specific somatic mutations, wherein the presence of a sequence read in the plurality of sequence reads corresponding to one or more of the tumor-specific somatic mutation sequences indicates the presence of the DNA fragment;

wherein (d)-(h) are performed after the subject has received a treatment for cancer or while the subject is in remission.

2. The method of claim 1 , wherein the method comprises a detection sensitivity of about 20 to about 50 DNA fragments comprising one or more of the set of tumor-specific somatic mutations per a total background of about 500,000 cfDNA fragments.

3. 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 set of tumor-specific somatic mutations.

4. The method of claim 3 , wherein hybrid capture-based enrichment comprises:

(i) contacting the extracted cfDNA from (e) with a plurality of oligonucleotides that each comprise a nucleic acid sequence that is capable of hybridizing to one of the set of tumor-specific somatic mutations or a corresponding unmutated sequence, and

(ii) selectively enriching cfDNA fragments that hybridize to the plurality of oligonucleotides.

5. The method of claim 4 , wherein the plurality of oligonucleotides is capable of detecting at least 10 different tumor-specific somatic mutations.

6. The method of claim 1 , wherein PCR-target enrichment is used to enrich the DNA fraction of fragments comprising one or more of the set of tumor-specific somatic mutations.

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

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

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

10. The method of claim 1 , wherein the fluid sample is a whole blood sample.

11. The method of claim 1 , wherein the fluid sample is a plasma sample.

12. The method of claim 1 , wherein the fluid sample is a serum sample.

13. The method of claim 1 , wherein (d)-(h) of the method are repeated at 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.

Assignments (5)
SECURITY INTEREST Recorded Aug 1, 2025
From: MYRIAD GENETICS, INC.; MYRIAD GENETIC LABORATORIES, INC.; MYRIAD WOMEN’S HEALTH, INC.; ASSUREX HEALTH, INC.; GATEWAY GENOMICS, LLC
To: ORBIMED ROYALTY & CREDIT OPPORTUNITIES IV, LP, AS ADMINISTRATIVE AGENT FOR SECURED PARTIES
Reel/Frame 072309/0932 →
RELEASE OF SECURITY INTEREST IN PATENTS PREVIOUSLY RECORDED AT REEL/FRAME (064235/0032) Recorded Aug 1, 2025
From: JPMORGAN CHASE BANK, N.A., AS ADMINISTRATIVE AGENT
To: MYRIAD GENETICS, INC.; MYRIAD WOMEN’S HEALTH, INC.; GATEWAY GENOMICS, LLC; ASSUREX HEALTH, INC.
Reel/Frame 072331/0215 →
PATENT SECURITY AGREEMENT Recorded Jul 7, 2023
From: MYRIAD GENETICS, INC.; MYRIAD WOMEN'S HEALTH, INC.; GATEWAY GENOMICS, LLC; ASSUREX HEALTH, INC.
To: JPMORGAN CHASE BANK, N.A.
Reel/Frame 064235/0032 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jun 29, 2023
From: MAGUIRE, JARED ROBERT; CHU, CLEMENT; HAQUE, IMRAN SAEEDUL; EVANS, ERIC ANDREW; WELKER, NOAH
To: COUNSYL, INC.
Reel/Frame 064109/0373 →
CHANGE OF NAME Recorded Jun 29, 2023
From: COUNSYL, INC.
To: MYRIAD WOMEN'S HEALTH, INC.
Reel/Frame 064163/0011 →
Continuity (5)
Continuation 17383273 · Jul 22, 2021
Continuation 16784761 · Feb 7, 2020
Continuation 15465553 · Mar 21, 2017
Provisional Application 62311899 · Mar 22, 2016
Related Publication 20220290229A1 · Sep 15, 2022
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