Global dna hypomethylation and biomarkers for clinical indications in cancer

Abstract

The present invention provides methods of determination of a global DNA methylation index (GDMI) in a sample from a subject, using a variety of methods which can detect global, genome-wide, and gene-specific DNA methylation to create methylation portraits that can be used for early detection, diagnosis, and clinical management in the personalized medicine space. Further, the invention provides methods of diagnosis of cancer, including gastric cancer and hepatocellular cancer in a subject, by comparing the GDMI in a sample obtained from a subject to the methylation index of standard controls. These methods allow diagnosis of gastric carcinoma and liver cancer in patients who may be asymptomatic or have inconclusive pathology, and allowing earlier treatment of the subject.

1 . A method for obtaining a global DNA methylation index (GDMI) in a sample comprising:
 a) obtaining a biological sample comprising DNA from a subject;   b) determining the amount of 2′-deoxycytidine (2dc) and 5-methyl-2′-deoxycytidine (5mdc) in the DNA sample;   c) generating a GDMI for the sample by comparing the amount of 5mdc relative to the amount of 5mdc+2dc in the sample and generating a ratio.   
     
     
         2 . The method of  claim 1 , wherein the method of for making the determination of b) is selected from the group consisting of quantitative methylation specific PCR (qMSP), oligonucleotide methylation tiling arrays, methylation BeadChip assays, ELISA, and the use of HPLC/MS. 
     
     
         3 . A method for identifying whether a subject has an increased risk of hepatocellular carcinoma (HCC) comprising:
 a) obtaining a biological sample of hepatocytes comprising DNA from a subject;   b) determining the amount of 2′-deoxycytidine (2dc) and 5-methyl-2′-deoxycytidine (5mdc) in the DNA sample;   c) generating a global DNA methylation index (GDMI) for the sample by comparing the amount of 5mdc relative to the amount of 5mdc+2dc in the sample and generating a ratio; and   d) comparing the GDMI of the sample to the GDMI of a control,   wherein when the GDMI of the sample is less than the GDMI of the control, then the subject has an increased risk of HCC; and   e) identifying the appropriate treatment regimen for the subject.   
     
     
         4 . The method of  claim 3 , wherein the method of for making the determination of b) is selected from the group consisting of quantitative methylation specific PCR (qMSP), oligonucleotide methylation tiling arrays, methylation BeadChip assays, ELISA, and the use of HPLC/MS. 
     
     
         5 . The method of  claim 3 , wherein the subject is infected with HBV or HCV. 
     
     
         6 .- 8 . (canceled) 
     
     
         9 . A method for identifying whether a subject has an increased risk of gastric carcinoma (GC) comprising:
 a) obtaining a biological sample of the gastric mucosa comprising DNA from a subject;   b) determining the amount of 2′-deoxycytidine (2dc) and 5-methyl-2′-deoxycytidine (5mdc) in the DNA sample;   c) generating a global DNA methylation index (GDMI) for the sample by comparing the amount of 5mdc relative to the amount of Smdc+2dc in the sample and generating a ratio; and   d) comparing the GDMI of the sample to the GDMI of a control,   wherein when the GDMI of the sample is less than the GDMI of the control, then the subject has an increased risk of GC; and   e) identifying the appropriate treatment regimen for the subject.   
     
     
         10 . The method of  claim 9 , wherein the method of for making the determination of b) is selected from the group consisting of quantitative methylation specific PCR (qMSP), oligonucleotide methylation tiling arrays, methylation BeadChip assays, ELISA, and the use of HPLC/MS. 
     
     
         11 . A method for differentiating whether a subject has a high risk of developing GC or a low risk of developing GC in a subject who is diagnosed with deep gastric inflammation comprising:
 a) obtaining a biological sample of gastric tissue comprising DNA from the subject;   b) determining the amount of 2′-deoxycytidine (2dc) and 5-methyl-2′-deoxycytidine (5mdc) in the DNA sample;   c) generating a GDMI for the sample by comparing the amount of 5mdc relative to the amount of Smdc+2dc in the sample and generating a ratio; and   d) comparing the GDMI of the sample to the GDMI of a control,   wherein when the GDMI of the sample is less than the GDMI of the control, then the subject has a high risk of GC; and   e) identifying the appropriate treatment regimen for the subject.   
     
     
         12 . The method of  claim 11 , wherein the method of for making the determination of b) is selected from the group consisting of quantitative methylation specific PCR (qMSP), oligonucleotide methylation tiling arrays, methylation BeadChip assays, ELISA, and the use of HPLC/MS. 
     
     
         13 . The method of  claim 11 , wherein the subject is ambulatory. 
     
     
         14 . The method of  claim 11 , wherein the sample is obtained or assessed with an endoscope.