NRAS germline variant G138R and multiple rare somatic mutations on APC in colorectal cancer patients in Taiwan by next generation sequencing
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Pi-Yueh Chang1,2,4, Jinn-Shiun Chen3, Nai-Chung Chang1, Shih-Cheng Chang1,2, Mei-Chia Wang1,2, Shu-Hui Tsai1, Ying-Hao Wen1, Wen-Sy Tsai3, Err-Cheng Chan2,4,*, Jang-Jih Lu1,2,*
1Department of Laboratory Medicine, Chang Gung Memorial Hospital at LinKou Taoyuan, Taoyuan, Taiwan
2Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
3Department of Colorectal Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
4Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
*Co-corresponding authors with equal contribution to this manuscript
Jang-Jih Lu, e-mail: [email protected]
Keywords: next-generation sequencing, colorectal cancer, ampliSeq cancer hotspot panel, NRAS, APC
Received: October 25, 2015 Accepted: March 28, 2016 Published: April 21, 2016
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.
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