Granted Patent E1

US 50,806 · App. 17/735,474 · Granted Feb 24, 2026

Inventors: David A. Ahlquist (Rochester, MN); William R. Taylor (Lake City, MN); Douglas W. Mahoney (Elgin, MN); Tracy C. Yab (Rochester, MN); John B. Kisiel (Rochester, MN); Hatim T. Allawi (Middleton, WI); Graham P. Lidgard (Middleton, WI); Michael W. Kaiser (Stoughton, WI)

Assignees: Mayo Foundation for Medical Education and Research; Exact Sciences Corporation

C12Q1/6886C12Q1/6806C12Q1/6809C12Q1/6811C12Q1/682C12Q1/6827C12Q1/6837C12Q1/6853G16H50/30C12Q2537/143C12Q2600/106C12Q2600/112C12Q2600/118C12Q2600/154C12Q2600/156C12Q2600/158C12Q2600/16

Abstract

Claims (20)

1 . A method, comprising:

measuring a methylation level for four genes in a biological sample of a human individual through

treating genomic DNA in the biological sample with a reagent that modifies DNA in a methylation-specific manner;

amplifying the treated genomic DNA using a specific set of primers for each of the four genes; and

determining the methylation level of the four genes by polymerase chain reaction, nucleic acid sequencing, mass spectrometry, methylation-specific nuclease, mass-based separation, and or target capture;

wherein the four genes are ITPRIPL1, FAM59B, TRH_A and c17orf64_B.

2 . The method of claim 1 , wherein the DNA is treated with a reagent that modifies DNA in a methylation-specific manner.

3 . The method of claim 2 1 , wherein the reagent comprises one or more of a methylation-sensitive restriction enzyme, a methylation-dependent restriction enzyme, and a bisulfite reagent.

4 . The method of claim 3 , wherein the DNA is treated with a the bisulfite reagent to produce bisulfite-treated DNA.

5 . The method of claim 1 , wherein the measuring comprises multiplex amplification.

6 . The method of claim 1 , wherein measuring the amount of at least one methylated marker gene determining the methylation level of the four genes comprises using one or more methods selected from the group consisting of methylation-specific PCR, quantitative methylation-specific PCR, methylation-specific DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, flap endonuclease assay, PCR-flap assay, and bisulfite genomic sequencing PCR.

7 . The method of claim 1 ,

wherein the specific set of primers for each of the selected four genes is selected from the group consisting of:

for TRH_A a set of primers consisting of SEQ ID NOS: 245 and 246, and SEQ ID NOS 447 and 448,

for ITPRIPL1 a set of primers selected from the group consisting of from SEQ ID NOS: 97 and 98, SEQ ID NOS: 99 and 100, SEQ ID NOS: 309 and 310, and SEQ ID NOS: 425 and 426,

for C17orf64_B a set of primers selected from the group consisting of SEQ ID NOS: 269 25 and 270 26, and SEQ ID NOS: 449 and 450, and

for FAM59_B a set of primers consisting of SEQ ID NOS: 427 and 428.

8 . The method of claim 1 , wherein the biological sample comprises tissue.

9 . The method of claim 8 , wherein the tissue is breast tissue.

10 . The method of claim 1 , wherein the biological sample is blood, serum, or plasma.

Assignments (3)

Continuity (2)

References Cited (381)