Dna markers for management of cancer

Abstract

A method is provided for assessing allelic losses and hypermethylation of genes in CpG tumor promotor region on specific chromosomal regions in cancer patients, including melanoma, neuroblastoma breast, colorectal, and prostate cancer patients. The method relies on the evidence that free DNA and hypermethylation of genes in CpG tumor promotor region may be identified in the bone marrow, serum, plasma, and tumor tissue samples of cancer patients. Methods of melanoma, neuroblastoma, colorectal cancer, breast cancer and prostate cancer detection, staging, and prognosis are also provided.

1 . A method of detecting DNA markers in a sample, comprising: providing a blood sample from a subject; and detecting one or more DNA markers in the sample, wherein the DNA markers are indicative of LOH or DNA hypermethylation, or the DNA markers are indicative of DNA mutation in KRAS or BRAF gene. 
     
     
         2 . The method of  claim 1 , wherein the DNA markers are in the 1p, 3p, 6p, 6q, 8p, 10q, 11q, 14q, 16q, or 17p region. 
     
     
         3 . The method of  claim 1 , wherein the DNA markers include D1S228, D8S321, D4S175, D4S1586, D5S299, D8S133, D8S261, D8S262, D8S264, D9S171, D10S197, D10S591, D10S532, D14S51, D14S62, D15S127, D16S421, D16S422, D17S796, D17S849, D17S855, D18S58, D18S61, or D18S70. 
     
     
         4 . The method of  claim 1 , wherein the DNA markers are indicative of hypermethylation in RASSF1A, MGMT, GSTP1, RAR-.beta., TWIST, APC, DAPK, P16, or Cyclin D2 promoter. 
     
     
         5 . A method of detecting cancer, comprising providing a blood sample from a subject; and detecting the presence or absence of LOH, DNA hypermethylation, mutation or a combination thereof of one or more DNA markers in the sample; and determining that the presence of LOH, DNA hypermethylation, mutation or a combination thereof of the one or more DNA markers is indicative of cancer in the subject. 
     
     
         6 . The method of  claim 5 , wherein the markers include KRAS or BRAF, and mutation of the markers is indicative of cancer in the subject. 
     
     
         7 . The method of  claim 6 , wherein the cancer is melanoma, neuroblastoma, colorectal, breast, or prostate cancer. 
     
     
         8 . The method of  claim 5 , wherein a combination of LOH and DNA hypermethylation of the markers is indicative of melanoma, neuroblastoma, colorectal or prostate cancer in the subject. 
     
     
         9 . The method of  claim 8 , wherein the presence of absence of LOH is indicated by one or more DNA markers that include D1S228, D8S321, D4S175, D4S1586, D5S299, D8S133, D8S261, D8S262, D8S264, D9S171, D10S591, D10S532, D14S51, D14S62, D15S127, D16S421, D16S422, D17S796, D17S849, D17S855, D18S58, D18S61, or D18S70. 
     
     
         10 . The method of  claim 8 , wherein the presence or absence of DNA hypermethylation is detected in RASSF1A, MGMT, GSTP1, RAR-.beta., TWIST, APC, DAPK, or Cyclin D2. 
     
     
         11 . A method of staging cancer, comprising providing a blood sample from a subject suffering from cancer; and detecting the presence or absence of LOH, DNA hypermethylation, mutation or a combination thereof of one or more DNA markers in the sample; and determining that the presence of LOH, DNA hypermethylation, mutation or a combination thereof of the one or more DNA markers is indicative of an advanced stage of the cancer in the subject. 
     
     
         12 . The method of  claim 11 , wherein the cancer is melanoma, neuroblastoma, colorectal, breast, or prostate cancer. 
     
     
         13 . The method of  claim 11 , wherein a combination of LOH and DNA hypermethylation of the markers is indicative of an advanced stage melanoma, neuroblastoma, colorectal or prostate cancer in the subject. 
     
     
         14 . The method of  claim 13 , wherein the presence or absence of LOH is indicated by one or more DNA markers that include D1S228, D8S321, D4S175, D4S1586, D5S299, D8S133, D8S261, D8S262, D8S264, D9S171, D10S591, D10S532, D14S51, D14S62, D15S127, D16S421, D16S422, D17S796, D17S849, D17S855, D18S58, D18S61, or D18S70. 
     
     
         15 . The method of  claim 13 , wherein the presence or absence of DNA hypermethylation is detected in RASSF1A, MGMT, GSTP1, RAR-.beta., TWIST, APC, DAPK, or Cyclin D2. 
     
     
         16 . A method of prognosing cancer, comprising providing a blood sample from a subject suffering from cancer; and detecting the presence or absence of LOH, DNA hypermethylation, mutation or a combination thereof of one or more DNA markers in the sample; and determining that the presence of LOH, DNA hypermethylation, mutation or a combination thereof of the one or more DNA markers is indicative of a poor prognosis of the cancer in the subject. 
     
     
         17 . The method of  claim 16 , wherein the cancer is melanoma, neuroblastoma, colorectal, breast, or prostate cancer. 
     
     
         18 . The method of  claim 16 , wherein a combination of LOH and DNA hypermethylation of the markers is indicative of a poor prognosis of the cancer in the subject. 
     
     
         19 . The method of  claim 18 , wherein the presence or absence of LOH is indicated by one or more DNA markers that include D1S228, D8S321, D4S175, D4S1586, D5S299, D8S133, D8S261, D8S262, D8S264, D9S171, D10S591, D10S532, D14S51, D14S62, D15S127, D16S421, D16S422, D17S796, D17S849, D17S855, D18S58, D18S61, or D18S70. 
     
     
         20 . The method of  claim 18 , wherein the presence or absence of DNA hypermethylation is detected in RASSF1A, MGMT, GSTP1, RAR-.beta., TWIST, APC, DAPK, or Cyclin D2.