Method for detecting the methylation of colorectal-cancer-specific methylation marker genes for colorectal cancer diagnosis

Abstract

The present disclosure relates to a method for detecting CpG methylation of SDC2 (Syndecan 2) gene, a kit for detecting CpG methylation of SDC2 (Syndecan 2) gene, and a method for detecting CpG methylation of SDC2 (Syndecan 2) gene for a colorectal cancer diagnosis.

What is claimed is: 
     
         1 . A method for detecting CpG methylation of SDC2 (Syndecan 2) gene, the method comprising the steps of:
 (a) isolating genomic DNA from a clinical sample;   (b) treating the genomic DNA from step (a) with bisulfite; and   (c) determining hypermethylation of a CpG of the SDC2 gene in the genomic DNA treated with bisulfite according the step (b) by using primer(s) to amplify a methylated CpG of the bisulfite-treated SDC2 gene.   
     
     
         2 . The method according to  claim 1 , wherein step (c) is performed by a method selected from the group consisting of PCR, methylation specific PCR, real-time methylation specific PCR, PCR using a methylated DNA-specific binding protein, quantitative PCR, pyrosequencing, and bisulfite sequencing. 
     
     
         3 . The method according to  claim 1 , wherein step (c) comprises measuring a CpG methylation of a regulatory region or intron region of SDC2 gene in the clinical sample. 
     
     
         4 . The method of  claim 1 , wherein the primer(s) of step (c) comprises at least one or more CpG dinucleotide in a region which hybridizes to the methylated CpG of SDC2. 
     
     
         5 . The method of  claim 1 , wherein the primer(s) of step (c) comprises sequence(s) having a homology of 80% or more with sequence(s) selected from the group consisting of SEQ ID NOs: 3, 4, 6-67, 69-100, 102-153, 155-216, 218-279, 281-342, 344-395, 397-448, 450-511, 513-572, 636, 637, 639-700, 702-763, 765-826, 828-839. 
     
     
         6 . The method according to  claim 1 , further comprising probe(s) capable of hybridizing with a methylated CpG of SDC2 comprising at least one or more CpG dinucleotide in a region which hybridizes to the methylated CpG of SDC2. 
     
     
         7 . The method according to  claim 6 , wherein the probe(s) comprises sequence(s) having a homology of 80% or more with sequence(s) selected from the group consisting of SEQ ID NOs: 5, 68, 101, 154, 217, 280, 343, 396, 449, 512, 638, 701, 764 and 827. 
     
     
         8 . A kit for detecting CpG methylation of SDC2 (Syndecan 2) gene, comprising primer(s) to amplify a methylated CpG of the SDC2 gene, wherein the primer(s) comprises sequence(s) having a homology of 80% or more with sequence(s) selected from the group consisting of SEQ ID NOs: 3, 4, 6-67, 69-100, 102-153, 155-216, 218-279, 281-342, 344-395, 397-448, 450-511, 513-572, 636, 637, 639-700, 702-763, 765-826, 828-839. 
     
     
         9 . The kit of  claim 8 , further comprising probe(s) capable of hybridizing with a methylated CpG of SDC2 comprising at least one or more CpG dinucleotide in a region which hybridizes to the methylated CpG of SDC2. 
     
     
         10 . The kit of  claim 9 , wherein the probe(s) comprises sequence(s) having a homology of 80% or more with sequence(s) selected from the group consisting of SEQ ID NOs: 5, 68, 101, 154, 217, 280, 343, 396, 449, 512, 638, 701, 764, and 827. 
     
     
         11 . A method for detecting CpG methylation of SDC2 (Syndecan 2) gene for a colorectal cancer diagnosis, the method comprising the steps of:
 (a) isolating genomic DNA from a clinical sample;   (b) treating the genomic DNA from step (a) with bisulfite; and   (c) determining hypermethylation of a CpG of the SDC2 gene in the genomic DNA treated with bisulfite according the step (b) by using primer(s) to amplify a methylated CpG of the bisulfite-treated SDC2 gene, wherein a colorectal cancer is detected in human subject based on increased CpG methylation of the SDC2 gene relative to that of a control.   
     
     
         12 . The method according to  claim 11 , wherein step (c) is performed by a method selected from the group consisting of PCR, methylation specific PCR, real-time methylation specific PCR, PCR using a methylated DNA-specific binding protein, quantitative PCR, pyrosequencing, and bisulfite sequencing. 
     
     
         13 . The method according to  claim 11 , wherein step (c) comprises measuring a CpG methylation of a regulatory region or intron region of SDC2 gene in the clinical sample. 
     
     
         14 . The method of  claim 11 , wherein the primer(s) of step (c) comprises at least one or more CpG dinucleotide in a region which hybridizes to the methylated CpG of SDC2. 
     
     
         15 . The method of  claim 11 , wherein the primer(s) of step (c) comprises sequence(s) having a homology of 80% or more with sequence(s) selected from the group consisting of SEQ ID NOs: 3, 4, 6-67, 69-100, 102-153, 155-216, 218-279, 281-342, 344-395, 397-448, 450-511, 513-572, 636, 637, 639-700, 702-763, 765-826, 828-839. 
     
     
         16 . The method according to  claim 11 , further comprising probe(s) capable of hybridizing with a methylated CpG of SDC2 comprising at least one or more CpG dinucleotide in a region which hybridizes to the methylated CpG of SDC2. 
     
     
         17 . The method according to  claim 16 , wherein the probe(s) comprises sequence(s) having a homology of 80% or more with sequence(s) selected from the group consisting of SEQ ID NOs: 5, 68, 101, 154, 217, 280, 343, 396, 449, 512, 638, 701, 764, and 827.