Profiling cancer-related gene mutations in oral squamous cell carcinoma from Japanese patients by targeted amplicon sequencing
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Takafumi Nakagaki1,2, Miyuki Tamura1, Kenta Kobashi1, Ryota Koyama1, Hisayo Fukushima1, Tomoko Ohashi1, Masashi Idogawa1, Kazuhiro Ogi2, Hiroyoshi Hiratsuka2, Takashi Tokino1 and Yasushi Sasaki1
1Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
2Department of Oral Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
Takashi Tokino, email: firstname.lastname@example.org
Yasushi Sasaki, email: email@example.com
Keywords: OSCC, next-generation sequencing, Ion Torrent, somatic mutations, copy number variations
Received: January 23, 2017 Accepted: June 20, 2017 Published: July 15, 2017
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95.4% of total, 1.69 megabases of target sequence). The number of somatic mutations in 47 patients with OSCC ranged from 1 to 20 with a mean of 7.60. The most frequent mutations were in TP53 (61.7%), NOTCH1 (25.5%), CDKN2A (19.1%), SYNE1 (14.9%), PIK3CA (10.6%), ROS1 (10.6%), and TAF1L (10.6%). We also detected copy number variations (CNVs) in the segments of the genome that could be duplicated or deleted from deep sequencing data. Pathway assessment showed that the somatic aberrations within OSCC genomes are mainly involved in several important pathways, including cell cycle regulation and RTK–MAPK-PI3K. This study may enable better selection of therapies and deliver improved outcomes for OSCC patients when combined with clinical diagnostics.
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