# US 12,601,011 B2 · Detecting gastric neoplasm

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- Number: US 12,601,011 B2
- Document ID: US12601011B2
- Status: Granted
- Kind: B2
- Application number: 18/508,945
- Filed: 2023-11-14
- Published: 2024-06-13
- Granted: 2026-04-14
- Earliest claimed: 2015-08-31
- Assignees: Mayo Foundation for Medical Education and Research; Exact Sciences Corporation
- Applicants: Mayo Foundation for Medical Education and Research; Exact Sciences Corporation
- Inventors: David A. Ahlquist; William R. Taylor; John B. Kisiel; Tracy C. Yab; Douglas W. Mahoney; Hatim T. Allawi
- Web page: https://patentgrep.com/patent/US12601011B2

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- C12Q 2600/154: Methylation markers
- C12Q 2600/16: Primer sets for multiplex assays
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as gastric cancer.

## Claims

### Claim 1

A method of characterizing a biological sample, the method comprising:
treating DNA in the biological sample with a reagent that modifies DNA in a methylation-specific manner, wherein the biological sample is from a human subject having or suspected of having a gastric neoplasm;
amplifying the treated DNA using primers specific for FAIM2; and
determining a methylation level for FAIM2, using methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, and/or bisulfite genomic sequencing PCR.

### Claim 2 (depends on 1)

The method of claim 1, wherein the biological sample is a tissue sample, a stool sample, a urine sample, a blood sample, a plasma sample, and/or a serum sample.

### Claim 3 (depends on 2)

The method of claim 2, wherein the tissue sample is a gastric tissue sample.

### Claim 4 (depends on 1)

The method of claim 1, wherein the method further comprises extracting DNA from the biological sample.

### Claim 5 (depends on 1)

The method of claim 1, wherein determining the methylation level comprises determining a methylation score for at least one CpG site, and/or determining a methylation frequency for at least one CpG site.

### Claim 6 (depends on 5)

The method of claim 5, wherein the at least one CpG site is present in a coding region or a regulatory region.

### Claim 7 (depends on 1)

The method of claim 1, wherein the reagent that modifies DNA in a methylation-specific manner comprises a methylation-sensitive restriction enzyme, a methylation-dependent restriction enzyme, and/or a bisulfite reagent.

### Claim 8 (depends on 1)

The method of claim 1, wherein the method further comprises amplifying the treated DNA using primers specific for ARHGEF4, and determining a methylation level for ARHGEF4.

### Claim 9 (depends on 8)

The method of claim 8, wherein the primers specific for ARHGEF4 are capable of binding an amplicon bound by SEQ ID NOs: 17 and 18, SEQ ID NOs: 23 and 24, or SEQ ID NOs: 95 and 96.

### Claim 10 (depends on 1)

The method of claim 1, wherein the method further comprises amplifying the treated DNA using primers specific for MAX.chr1.110, and determining a methylation level for MAX.chr1.110.

### Claim 11 (depends on 1)

The method of claim 1, wherein the method further comprises amplifying the treated DNA using primers specific for ARHGEF4 and MAX.chr1.110, and determining a methylation level for ARHGEF4 and MAX.chr1.110.