Detection of aberrant CpG island methylation in fecal DNA using an electrochemical DNA array chip as a molecular screening test for alimentary tract cancer

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As a preparation of samples, DNA has been extracted from the fresh frozen sections of the colorectal, the gastric, and the esophageal cancers that have been dissected in 1997. The fresh frozen sections of both of the colorectal cancer and normal mucosa and the stool samples before and after the cancer resection from the patients who had colorectal cancers and accepted oral and written informed consent were also collected and processed.Primers for methylation-specific PCR included the CpG islands of 24 genes (p16,TSP1,hMLH1,H-cad,RARbeta,XAF1,SLIT2,GATA5,TIMP3,RASSF1A,CACNA1G,DLC1,SFRP2,WIF1,HLTF,MGMT,SLC13A5,TSLC1,KIRREL2,HRK,LOX,CDH4,ID4,and RASSF4). We already studied colorectal cancers and normal colorectal mucosa for aberrant DNA methylation of 12 genes (p16,TSP1,hMLH1,HCAD,RARbeta,XAF1,SLIT2,GATA5,TIMP3,RASSF1A,CACNA1G,DLC1,and SFRP2), and we detected aberrant methylation of at least one gene in 88.1% of cancers. We have been detecting an aberrant methylation of the remaining 12 genes in colorectal cancers and of 24 genes in the gastric and esophageal cancers. We have been examining the combination of these genes thought to be useful for the diagnosis now. We already designed and established the gene chip for CpG island of p16,one of the candidate genes for detection of colorectal cancers, and the control experiment is under going. The nest examination schedule includes DNA extraction from the fecal sample, detection of an aberrant methylation in fecal DNA using an electrochemical chip, and verifying the sensitivity and the specificity of this molecular diagnostics.