EPIGENOMIC DNA MODIFICATIONS FOR TISSUE TYPING, EARLY CANCER DETECTION, AND DISEASE MANAGEMENT
Provided herein is a suitable method for detecting the presence or absence of a cancer in an individual, by determining the level of methylation of the sense strand of a selected regulatory region of a tumor suppressor gene. Also provided herein is a method of detecting the presence or absence a cancer in an individual by determining if there is an apparent 100% methylation by assay of the CpG sites in the anti-sense strand of a selected regulatory region of a tumor suppressor gene. Also provided herein is a method of tissue typing by determining the level of methylation of the anti-sense strand of a selected regulatory region of a tumor suppressor gene indicating an enhanced likelihood that a tissue is liver.
1 . A method for detecting the presence or absence of a cancer in an individual, the method comprising:
determining the level of methylation of the sense strand of a selected regulatory region of a tumor suppressor gene from said individual;
comparing said level of methylation with the level of methylation found in one or more control samples from individuals known not to have said cancer; and
correlating a finding of elevated methylation in said individual as compared to the level of methylation in said one or more controls with an enhanced likelihood that said individual has said cancer.
2 . The method of claim 1 wherein the cancer is hepatocellular carcinoma (HCC).
3 . The method of claim 2 wherein the control is matched adjacent non-HCC sample.
4 . The method of claim 1 wherein the tumor suppressor gene is adenomatous polypsis coli (APC).
5 . The method of claim 1 wherein the regulatory region is the promoter of the APC gene.
6 . The method of claim 1 wherein the regulatory region is the first exon of the APC gene.
7 . The method of claim 1 wherein the regulatory region is the promoter and first exon of the APC gene.
8 . The method of claim 1 wherein the individual is a human.
9 . The method of claim 1 wherein determining the level of methylation of the sense strand is determining by methylation specific PCR (MSP).
10 . The method of claim 9 wherein the methylation specific PCR (MSP) uses primers of the nucleotide sequences as set forth in SEQ ID NO: 15 and SEQ ID NO:16 and is probed by a probe of the nucleotide sequence as set forth in SEQ ID NO:17.
11 . The method of claim 1 wherein determining the level of methylation of the sense strand is determining by bisulfite specific PCR (BSP) and sequencing.
12 . The method of claim 11 wherein the bisulfite specific PCR (BSP) uses primers of the nucleotide sequences as set forth in SEQ ID NO: 1 and SEQ ID NO:2.
13 . A method for detecting the presence or absence of a cancer in an individual, the method comprising:
determining if there is an apparent 100% methylation by assay of CpG sites in the anti-sense strand of a selected regulatory region of a tumor suppressor gene from said individual; and
correlating a finding of an apparent 100% methylation by assay in said individual with an enhanced likelihood that said individual has said cancer.
14 . The method of claim 13 wherein the cancer is hepatocellular carcinoma (HCC).
15 . The method of claim 13 wherein the tumor suppressor gene is adenomatous polypsis coli (APC).
16 . The method of claim 13 wherein the regulatory region is the promoter and first exon of the APC gene.
17 . The method of claim 13 wherein the individual is a human.
18 . The method of claim 13 wherein determining the level of methylation of the sense strand is determining by bisulfite specific PCR (BSP) and sequencing.
19 . The method of claim 18 wherein the bisulfite specific PCR (BSP) and sequencing uses primers of the nucleotide sequences as set forth in SEQ ID NO: 3 and SEQ ID NO: 4.
20 . The method of claim 18 wherein the bisulfite specific PCR (BSP) and sequencing uses primers of the nucleotide sequences as set forth in SEQ ID NO: 5 and SEQ ID NO: 6.
21 . A method for tissue typing, the method comprising:
determining the level of methylation of the anti-sense strand of a selected regulatory region of a tumor suppressor gene from said individual;
comparing said level of methylation with the level of methylation found in one or more control samples; and
correlating a finding of elevated methylation as compared to the level of methylation in said one or more controls with an enhanced likelihood that a tissue is liver.
22 . The method of claim 21 wherein the tumor suppressor gene is adenomatous polypsis coli (APC).