Comparison between two amplicon-based sequencing panels of different scales in the detection of somatic mutations associated with gastric cancer. (December 2016)

• Record Type: Journal Article
• Authors: Hirotsu, Yosuke; Kojima, Yuichiro; Okimoto, Kenichiro; Amemiya, Kenji; Mochizuki, Hitoshi; Omata, Masao
• Is Part Of: BMC genomics. Volume 17:Number 1(2016)
• Page Start: 1
• Page End: 9
• Publication Date: 2016-12
• Subjects: Endoscopic submucosal dissection -- Endoscopy -- Gastric cancer -- Ion PGM -- Ion Proton -- Mutation -- Next-generation sequencing -- Targeted sequencing -- Tumor; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-3166-4
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background 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. Results 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. Conclusions Our results indicate the utility of comprehensive panel-based targeted sequencing in gastric cancer.