ID | 111123 |
Author |
Kohmoto, Tomohiro
Tokushima University
Shoda, Katsutoshi
Tokushima University|Kyoto Prefectural University of Medicine
Hamada, Junichi
Tokushima University|Kyoto Prefectural University of Medicine
Ichikawa, Daisuke
Kyoto Prefectural University of Medicine
Otsuji, Eigo
Kyoto Prefectural University of Medicine
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Keywords | Gastric cancer
exome
somatic mutations
variant calling algorithms
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Content Type |
Journal Article
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Description | 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 standardmethod 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 somaticmutations in GC andmay be useful for further genomic characterization of Japanese patients with GC to improve the efficacy of GC treatments.
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Journal Title |
The Journal of Medical Investigation
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ISSN | 13496867
13431420
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NCID | AA11166929
AA12022913
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Publisher | Faculty of Medicine Tokushima University
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Volume | 64
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Issue | 3-4
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Start Page | 233
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End Page | 240
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Sort Key | 233
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Published Date | 2017-08
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DOI (Published Version) | |
URL ( Publisher's Version ) | |
FullText File | |
language |
eng
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TextVersion |
Publisher
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departments |
Medical Sciences
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