Gene methylation in cancer diagnosis

Abstract

The present invention provides DNA biomarker sequences that are differentially methylated in samples from normal individuals and individuals with cancer. The invention further provides methods of identifying differentially methylated DNA biomarker sequences and their use in detecting and diagnosing cancer.

1 . A method for determining the methylation status of an individual, the method comprising:
 obtaining a biological sample from an individual; and   determining the methylation status 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 a sequence selected from the group consisting of SEQ ID NOs: 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, and 265.   
     
     
         2 . The method of  claim 1 , wherein the determining step comprises determining the methylation status of at least one cytosine in the DNA region corresponding to a nucleotide in a biomarker in the DNA region, wherein the biomarker is a sequence selected from the group consisting of SEQ ID NOs:160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, and 212. 
     
     
         3 . The method of  claim 2 , wherein the determining step comprises determining the methylation status of the DNA region corresponding to the biomarker. 
     
     
         4 . The method of  claim 1 , wherein the sample is from blood serum, blood plasma, fine needle aspirate of the breast, biopsy of the breast, ductal fluid, or ductal lavage. 
     
     
         5 . The method of  claim 1 , wherein the methylation status of at least one cytosine is compared to the methylation status of a control locus. 
     
     
         6 . The method of  claim 5 , wherein the control locus is an endogenous control. 
     
     
         7 . The method of  claim 5 , wherein the control locus is an exogenous control. 
     
     
         8 . The method of  claim 1 , wherein the determining step comprises determining the methylation status of at least one cytosine in at least two DNA regions selected from the group consisting of SEQ ID NOs: 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, and 265. 
     
     
         9 . A method for determining the presence or absence of cancer in an individual, the method comprising:
 a) determining the methylation status of at least one cytosine within a DNA region in a sample from an individual where the DNA region is at least 90% identical to a sequence selected from the group consisting of SEQ ID NOs: 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, and 265;   b) comparing the methylation status 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 cancer, wherein the comparison of the methylation status to the threshold value is predictive of the presence or absence of cancer in the individual.   
     
     
         10 . The method of  claim 9 , wherein DNA region is a sequence selected from the group consisting of SEQ ID NOs: 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, and 265. 
     
     
         11 . The method of  claim 9 , wherein the determining step comprises determining the methylation status of at least one cytosine in the DNA region corresponding to a nucleotide in a biomarker, wherein the biomarker is at least 90% identical to a sequence selected from the group consisting of SEQ ID NOs: 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, and 212. 
     
     
         12 . The method of  claim 11 , wherein the determining step comprises determining the methylation status of the DNA region corresponding to the biomarker. 
     
     
         13 . The method of  claim 9 , wherein the sample is from blood serum, blood plasma, fine needle aspirate of the breast, biopsy of the breast, ductal fluid, or ductal lavage. 
     
     
         14 . The method of  claim 9 , wherein the methylation status of at least one biomarker from the list is compared to the methylation value of a control locus. 
     
     
         15 . The method of  claim 14 , wherein the control locus is an endogenous control. 
     
     
         16 . The method of  claim 14 , wherein the control locus is an exogenous control. 
     
     
         17 . The method of  claim 9 , wherein the determining step comprises determining the methylation status of at least one cytosine from at least two DNA regions. 
     
     
         18 . A computer-implemented method for determining the presence or absence of cancer in an individual, the method comprising:
 receiving, at a host computer, a methylation value representing the methylation status 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 a sequence selected from the group consisting of SEQ ID NOs: 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, and 265; and   comparing, in the host computer, the methylation value to a threshold value, wherein the threshold value distinguishes between individuals with and without cancer, wherein the comparison of the methylation value to the threshold value is predictive of the presence or absence of cancer in the individual.   
     
     
         19 . The method of  claim 18 , wherein the receiving step comprises receiving at least two methylation values, the two methylation values representing the methylation status of at least one cytosine biomarkers from two different DNA regions; and
 the comparing step comprises comparing the methylation values to one or more threshold value(s) wherein the threshold value distinguishes between individuals with and without cancer, wherein the comparison of the methylation value to the threshold value is predictive of the presence or absence of cancer in the individual.