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.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Hirotsu Y,Kojima Y,Okimoto K,Amemiya K,Mochizuki H,Omata Mdoi
10.1186/s12864-016-3166-4subject
Has Abstractpub_date
2016-10-26 00:00:00pages
833issue
1issn
1471-2164pii
10.1186/s12864-016-3166-4journal_volume
17pub_type
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