NRAS germline variant G138R and multiple rare somatic mutations on APC in colorectal cancer patients in Taiwan by next generation sequencing.
Colorectal cancer (CRC) arises from mutations in a subset of genes. We investigated the germline and somatic mutation spectrum of patients with CRC in Taiwan by using the AmpliSeq Cancer Hotspot Panel V2. Fifty paired freshly frozen stage 0-IV CRC tumors and adjacent normal tissue were collected. Blood DNA from 20 healthy donors were used for comparison of germline mutations. Variants were identified using an ion-torrent personal genomic machine and subsequently confirmed by Sanger sequencing or pyrosequencing. Five nonsynonymous germline variants on 4 cancer susceptible genes, CDH1, APC, MLH1, and NRAS, were observed in 6 patients with CRC (12%). Among them, oncogene NRAS G138R variant was identified as having a predicted damaging effect on protein function, which has never been reported by other laboratories. CDH1 T340A variants were presented in 3 patients. The germline variants in the cancer patients differed completely from those found in asymptomatic controls. Furthermore, a total of 56 COSMIC and 21 novel somatic variants distributed in 20 genes were detected in 44 (88%) of the CRC samples. High inter- and intra-tumor heterogeneity levels were observed. Nine rare variants located in the β-catenin binding region of the APC gene were discovered, 7 of which could cause amino acid frameshift and might have a pathogenic effect. In conclusion, panel-based mutation detection by using a high-throughput sequencing platform can elucidate race-dependent cancer genomes. This approach facilitates identifying individuals at high risk and aiding the recognition of novel mutations as targets for drug development.
Department of Laboratory Medicine, Chang Gung Memorial Hospital at LinKou Taoyuan, Taoyuan, Taiwan.|Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.|Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.
Pi-Yueh
PY
Chang
Department of Colorectal Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.
Jinn-Shiun
JS
Chen
Department of Laboratory Medicine, Chang Gung Memorial Hospital at LinKou Taoyuan, Taoyuan, Taiwan.
Nai-Chung
NC
Chang
Department of Laboratory Medicine, Chang Gung Memorial Hospital at LinKou Taoyuan, Taoyuan, Taiwan.|Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.
Shih-Cheng
SC
Chang
Department of Laboratory Medicine, Chang Gung Memorial Hospital at LinKou Taoyuan, Taoyuan, Taiwan.|Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.
Mei-Chia
MC
Wang
Department of Laboratory Medicine, Chang Gung Memorial Hospital at LinKou Taoyuan, Taoyuan, Taiwan.
Shu-Hui
SH
Tsai
Department of Laboratory Medicine, Chang Gung Memorial Hospital at LinKou Taoyuan, Taoyuan, Taiwan.
Ying-Hao
YH
Wen
Department of Colorectal Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan.
Wen-Sy
WS
Tsai
Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.|Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan.
Err-Cheng
EC
Chan
Department of Laboratory Medicine, Chang Gung Memorial Hospital at LinKou Taoyuan, Taoyuan, Taiwan.|Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.
Jang-Jih
JJ
Lu
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D016022:Case-Control Studies; D015179:Colorectal Neoplasms / Q000235:genetics*; D005260:Female; D020558:GTP Phosphohydrolases / Q000235:genetics*; D017491:Genes, APC; D011905:Genes, ras; D020022:Genetic Predisposition to Disease; D018095:Germ-Line Mutation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008565:Membrane Proteins / Q000235:genetics*; D008875:Middle Aged; D013624:Taiwan
D008565:Membrane Proteins; D020558:GTP Phosphohydrolases; C579846:NRAS protein, human
APC; NRAS; ampliSeq cancer hotspot panel; colorectal cancer; next-generation sequencing