The Journal of Medical Investigation
Online ISSN : 1349-6867
Print ISSN : 1343-1420
ISSN-L : 1343-1420
Construction of a combinatorial pipeline using two somatic variant  calling  methods  for whole exome sequence data of gastric cancer
Tomohiro KohmotoKiyoshi MasudaTakuya NarutoShoichiro TangeKatsutoshi ShodaJunichi HamadaMasako SaitoDaisuke IchikawaAtsushi TajimaEigo OtsujiIssei Imoto
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2017 Volume 64 Issue 3.4 Pages 233-240


High-throughput next-generation sequencing is a powerful tool to identify the genotypic landscapes of somatic variants and therapeutic targets in various cancers including gastric cancer, forming the basis for personalized medicine in the clinical setting. Although the advent of many computational algorithms leads to higher accuracy in somatic variant calling, no standard method exists due to the limitations of each method. Here, we constructed a new pipeline. We combined two different somatic variant callers with different algorithms, Strelka and VarScan 2, and evaluated performance using whole exome sequencing data obtained from 19 Japanese cases with gastric cancer (GC); then, we characterized these tumors based on identified driver molecular alterations. More single nucleotide variants (SNVs) and small insertions/deletions were detected by Strelka and VarScan 2, respectively. SNVs detected by both tools showed higher accuracy for estimating somatic variants compared with those detected by only one of the two tools and accurately showed the mutation signature and mutations of driver genes reported for GC. Our combinatorial pipeline may have an advantage in detection of somatic mutations in GC and may be useful for further genomic characterization of Japanese patients with GC to improve the efficacy of GC treatments. J. Med. Invest. 64: 233-240, August, 2017

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© 2017 by The University of Tokushima Faculty of Medicine
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