title: Comparison between two amplicon-based sequencing panels of different scales in the detection of somatic mutations associated with gastric cancer.
abstract: Sequencing data from The Cancer Genome Atlas (TGCA), the International Cancer Genome Consortium and other research institutes have revealed the presence of genetic alterations in several tumor types, including gastric cancer. These data have been combined into a catalog of significantly mutated genes for each cancer type. However, it is unclear to what extent significantly mutated genes need to be examined for detecting genetic alterations in gastric cancer patients. Here, we constructed two custom-made sequencing panels of different scales, the Selective ﻿hotspot﻿ Panel and the Comprehensive Panel, to analyze genetic alterations in 21 resected specimens endoscopically obtained from 20 gastric cancer patients, and we assessed how many mutations were detectable using these different panels.
  
  
  
  A total of 21 somatic mutations were identified by the Selective hotspot Panel and 70 mutations were detected by the Comprehensive Panel. All mutations identified by the Selective hotspot Panel were detected by the Comprehensive Panel, with high concordant values of the variant allelic fraction of each mutation (correlation coefficient, R = 0.92). At least one mutation was identified in 13 patients (65 %) by the Selective hotspot Panel, whereas the Comprehensive Panel detected mutations in 19 (95 %) patients. Library preparation and sequencing costs were comparable between the two panels.
  
  
  
  Our results indicate the utility of comprehensive panel-based targeted sequencing in gastric cancer.
authors: Genome Analysis Center, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, 400-8506, Japan. hirotsu-bdyu@ych.pref.yamanashi.jp.
authors: Yosuke
authors: Y
authors: Hirotsu
authors: Department of Gastroenterology, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, 400-8506, Japan.
authors: Yuichiro
authors: Y
authors: Kojima
authors: Genome Analysis Center, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, 400-8506, Japan.|Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8677, Japan.
authors: Kenichiro
authors: K
authors: Okimoto
authors: Genome Analysis Center, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, 400-8506, Japan.
authors: Kenji
authors: K
authors: Amemiya
authors: Genome Analysis Center, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, 400-8506, Japan.|Department of Gastroenterology, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, 400-8506, Japan.
authors: Hitoshi
authors: H
authors: Mochizuki
authors: Genome Analysis Center, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, 400-8506, Japan.|Department of Gastroenterology, Yamanashi Prefectural Central Hospital, 1-1-1 Fujimi, Kofu, Yamanashi, 400-8506, Japan.|The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
authors: Masao
authors: M
authors: Omata
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000483:Alleles; D014408:Biomarkers, Tumor; D004252:DNA Mutational Analysis; D005260:Female; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D013274:Stomach Neoplasms / Q000175:diagnosis / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor
keywords: Endoscopic submucosal dissection; Endoscopy; Gastric cancer; Ion PGM; Ion Proton; Mutation; Next-generation sequencing; Targeted sequencing; Tumor