IP Library › Granted Patent US 12,319,969
Granted Patent B2
US 12,319,969 · App. 17/410,383 · Granted Jun 3, 2025

Detecting esophageal disorders

Inventors: David A. Ahlquist (Rochester, MN); William R. Taylor (Lake City, MN); John B. Kisiel (Rochester, MN); Douglas W. Mahoney (Elgin, MN); Tracy C. Yab (Rochester, MN); Graham P. Lidgard (Middleton, WI); Hatim T. Allawi (Middleton, WI)
Assignees: Exact Sciences Corporation; Mayo Foundation for Medical Education and Research
C12Q1/6886C12Q1/6883G01N33/57407C12Q2600/112C12Q2600/154C12Q2600/166G01N2440/12G01N2800/14
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Quick Facts
Patent No.
US 12,319,969
App. No.
17/410,383
Granted
Jun 3, 2025
Kind
B2
Abstract

Provided herein is technology for esophageal disorder screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of esophageal disorders (e.g., Barrett's esophagus, Barrett's esophageal dysplasia, etc.). In addition, the technology provides methods, compositions and related uses for distinguishing between Barrett's esophagus and Barrett's esophageal dysplasia, and between Barrett's esophageal low-grade dysplasia, Barrett's esophageal high-grade dysplasia, and esophageal adenocarcinoma within samples obtained through endoscopic brushing or nonendoscopic whole esophageal brushing or swabbing using a tethered device (e.g. such as a capsule sponge, balloon, or other device).

Claims (19)

1. A method comprising:

extracting genomic DNA from a biological sample from a human individual suspected of having or having an esophageal disorder,

treating the extracted genomic DNA with bisulfite,

amplifying the bisulfite-treated genomic DNA using primers specific for each of ten or fewer markers, and

measuring a methylation level of at least one differentially methylated region (DMR) in each of the ten or fewer markers using methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, or bisulfite genomic sequencing PCR,

wherein the ten or fewer markers comprise VAV3.

2. The method of claim 1 , wherein the ten or fewer markers comprise one or both of NDRG4 and ZNF682.

3. The method of claim 2 , wherein the primers specific for NDRG4 are capable of binding an amplicon bound by a sequence comprising SEQ ID NOs: 15 and 16.

4. The method of claim 2 , wherein the primers specific for NDRG4 comprise SEQ ID NOs: 15 and 16.

5. The method of claim 2 , wherein the primers specific for ZNF682 are capable of binding an amplicon bound by a sequence comprising SEQ ID NOs: 31 and 32.

6. The method of claim 2 , wherein the primers specific for ZNF682 comprise SEQ ID NOs: 31 and 32.

7. The method of claim 1 , wherein the biological sample comprises cells, tissues, and/or secretions from the upper gastrointestinal tract and/or the lower gastrointestinal tract.

8. The method of claim 1 , wherein the biological sample is a stool sample, a tissue sample, a blood sample, or a urine sample.

9. The method of claim 8 , wherein the tissue sample comprise esophageal tissue.

10. The method of claim 1 , wherein the esophageal disorder is Barrett's esophagus (BE).

11. The method of claim 10 , wherein the methylation level of the at least one DMR in each of the ten or fewer markers distinguishes BE from normal tissue.

12. The method of claim 1 , wherein the primers specific for VAV3 are capable of binding an amplicon bound by a sequence comprising SEQ ID NOs: 39 and 40.

13. The method of claim 1 , wherein the primers specific for VAV3 comprise SEQ ID NOs: 39 and 40.

14. The method of claim 1 , wherein the ten or fewer markers comprise BMP3, SFMBT2, DIO3, HUNK, ELMO1, CD1D, CDKN2A, and/or OPLAH.

Assignments (5)
TERMINATION AND RELEASE OF SECURITY INTEREST IN PATENT RIGHTS (REEL/FRAME 72285/0393) Recorded Mar 27, 2026
From: JPMORGAN CHASE BANK, N.A.
To: EXACT SCIENCES CORPORATION
Reel/Frame 075288/0464 →
PATENT SECURITY AGREEMENT Recorded Jul 28, 2025
From: EXACT SCIENCES CORPORATION
To: JPMORGAN CHASE BANK, N.A.
Reel/Frame 072285/0393 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jan 26, 2022
From: LIDGARD, GRAHAM P.; ALLAWI, HATIM T.
To: EXACT SCIENCES CORPORATION
Reel/Frame 058777/0539 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jan 26, 2022
From: AHLQUIST, DAVID A.; TAYLOR, WILLIAM R.; KISIEL, JOHN B.; MAHONEY, DOUGLAS W.; YAB, TRACY C.
To: MAYO FOUNDATION FOR MEDICAL EDUCATION AND RESEARCH
Reel/Frame 058777/0615 →
MERGER Recorded Jan 24, 2022
From: EXACT SCIENCES DEVELOPMENT COMPANY, LLC
To: EXACT SCIENCES CORPORATION
Reel/Frame 058745/0739 →
Continuity (4)
Continuation 16570782 · Sep 13, 2019
Continuation 15550703
Provisional Application 62139243 · Mar 27, 2015
Related Publication 20210381066A1 · Dec 9, 2021
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