Targeted Sequencing of Cancer-Related Genes in Colorectal Cancer Using Next-Generation Sequencing

Recent advance in sequencing technology has enabled comprehensive genome-wide study of genetic alterations in cancer. We have established a targeted sequencing platform using NGS technology, which comprises of 183 cancer-related genes. We analyzed the gene set in normal and tumor tissue pairs of 60 colorectal adenocarcinoma patients. A total of 532 somatic non-synonymous sequence variations were found in 113 genes. Among these, 278 single nucleotide variations (SNV) were 233 point mutations not found in the normal tissues. 216 SNV were 79 known single nucleotide polymorphisms in the dbSNP. 38 variations were 29 indel mutations. Among the 232 somatic mutations, 166 mutations were previously unreported novel mutations. Median number of mutated gene per tumor was 4 (range 1 – 23). Using the coverage data, we could also analyze copy number variations. Copy number gain (> X2 fold) was found in 65 genes in 40 patients, whereas copy number loss (< X0.5 fold) was found in 103 genes in 39 patients. The most frequently altered (mutation and CNV) genes were APC in 35 patients (58%), TP53 in 34 (57%), and KRAS in 24 (40%). Mutated gene list revealed ErbB signaling pathway as the most commonly involved pathway (25 patients, 42%). Targeted sequencing platform using NGS technology is feasible for clinical use and provides comprehensive genetic alteration data.