# US 10,501,804 B2 · Differential methylation level of CPG loci that are determinative of a biochemical reoccurrence of prostate cancer

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- Number: US 10,501,804 B2
- Document ID: US10501804B2
- Status: Granted
- Kind: B2
- Application number: 14/977,779
- Filed: 2015-12-22
- Published: 2016-09-08
- Granted: 2019-12-10
- Earliest claimed: 2013-03-14
- Assignees: HudsonAlpha Institute for Biotechnology; The Board of Trustees of the Leland Stanford Junior University
- Applicants: HudsonAlpha Institute for Biotechnology; Board of Directors of the Leland Stanford Junior University
- Inventors: Richard M. Myers; James D. Brooks; Marie K. Kirby
- Web page: https://patentgrep.com/patent/US10501804B2

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
- C12Q 2600/112: Disease subtyping, staging or classification
- C12Q 2600/154: Methylation markers
- 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

The present disclosure provides for and relates to the identification of novel biomarkers for diagnosis and prognosis of prostate cancer or the biochemical reoccurrence of prostate cancer. The biomarkers of the invention show altered methylation levels of certain CpG loci relative to normal prostate tissue, as set forth.

## Claims

### Claim 1

A method for treating a biochemical reoccurrence of prostate cancer in an individual, the method comprising:
(a) identifying an individual who has undergone a previous treatment for prostate cancer, wherein said previous treatment comprises a radical prostatectomy, and may be in need of treatment of the biochemical reoccurrence of prostate cancer;
(b) obtaining a sample from the individual and isolating the DNA therefrom;
(c) contacting the isolated DNA with sodium bisulfite;
(d) determining the methylation level of at least one cytosine within a DNA region in the isolated DNA where the DNA region is at least 90% identical to SEQ ID NO: 2 and determining the methylation level of at least one cytosine within a DNA region in a sample from the individual where the DNA region is at least 90% identical to SEQ ID NO: 1, wherein said determining step comprises performing a molecular assay to determine the methylation level of the at least one cytosine, wherein said determining of the methylation level of the at least one cytosine also comprises contacting the DNA region with a primer that hybridizes to the DNA region;
(e) comparing the methylation level of the at least one cytosine to a threshold value for the at least one cytosine, wherein the threshold value distinguishes between individuals with and without a biochemical reoccurrence of prostate cancer, wherein the comparison of the methylation level to the threshold value is predictive of the presence or absence a biochemical reoccurrence of prostate cancer in the individual;
(f) determining that the individual has a biochemical reoccurrence of prostate cancer based on the compared methylation levels in step (e); and
(g) administering one or both of radiation therapy and androgen deprivation therapy to the individual determined to have the biochemical reoccurrence of prostate cancer in step (f), to thereby treat the biochemical reoccurrence of prostate cancer.

### Claim 2 (depends on 1)

The method of claim 1 wherein said sample is a biopsy sample.

### Claim 3 (depends on 1)

The method of claim 1 wherein said sample is a blood sample.

### Claim 4 (depends on 1)

The method of claim 1 wherein said sample is a urine sample.

### Claim 5 (depends on 1)

The method of claim 1 wherein the DNA region is at least 95% identical to SEQ ID. NO. 2.

### Claim 6 (depends on 1)

The method of claim 1 wherein step (d) comprises determining whether cytosine residue at position 61 of SEQ ID NO: 2 is methylated.

### Claim 7 (depends on 1)

The method of claim 1 further comprising determining the methylation level of cytosine in at least one of SEQ ID NOS: 3-32.

### Claim 8 (depends on 1)

The method of claim 1 further comprising determining the methylation level of cytosine in at least four of SEQ ID NOS: 3-32.

### Claim 9 (depends on 1)

The method of claim 1 further comprising determining the methylation level of cytosine in at least nine of SEQ ID NOS: 3-32.

### Claim 10 (depends on 6)

The method of claim 6 wherein said sample is a biopsy sample.

### Claim 11 (depends on 6)

The method of claim 6 wherein said sample is a blood sample.

### Claim 12 (depends on 6)

The method of claim 6 wherein said sample is a urine sample.