Identification Of SNPs Of APC Gene In Colorectal Cancer Patients By Next-generation Sequencing

We described an approach for identifying single nucleotide polymorphisms(SNPs), and used adenomatous polyposis coli(APC) gene as an example. We used long-range PCR or NimbleGen sequence capture technique to capture the genomic regions of APC gene including upstream and downstream sequences in order to be sequenced by Solexa sequencing. Using analysis program Samtools, we indentified 210 potential SNPs, of which 69 were novel. Only 11 SNPs we identified were in the exonic region, and one of them have not reported yet. These SNPs were predicted to affect splicing by creating or removing exonic splicing enhancers or exonic splicing silencers by FASTSNP & ployphen software.7 SNPs were found in the upstream region.6 out of 7 SNPs were predicted to affect transcription factor binding by using PROMO software. The left of the SNPs were in the inronic regions.4 of the 37 SNPs which were only found in the cancer tissue were predicted to related with colorectal cancer. Allele specific PCR were used to confirm the SNPs,10 SNPs were randomly selected, and 8 high-quality SNPs were confirmed.