Comparison between two amplicon-based sequencing panels of different scales in the detection of somatic mutations associated with gastric cancer View Full Text


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Article Info

DATE

2016-10-26

AUTHORS

Yosuke Hirotsu, Yuichiro Kojima, Kenichiro Okimoto, Kenji Amemiya, Hitoshi Mochizuki, Masao Omata

ABSTRACT

BackgroundSequencing 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.ResultsA 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.ConclusionsOur results indicate the utility of comprehensive panel-based targeted sequencing in gastric cancer. More... »

PAGES

833

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    40 schema:description BackgroundSequencing 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.ResultsA 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.ConclusionsOur results indicate the utility of comprehensive panel-based targeted sequencing in gastric cancer.
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    47 schema:keywords Cancer Genome Atlas
    48 ConclusionsOur results
    49 Genome Atlas
    50 Genome Consortium
    51 Institute
    52 International Cancer Genome Consortium
    53 Research Institute
    54 ResultsA total
    55 allelic fraction
    56 alterations
    57 atlas
    58 cancer
    59 cancer patients
    60 cancer types
    61 catalogue
    62 comparison
    63 comprehensive panel
    64 concordant values
    65 consortium
    66 cost
    67 data
    68 detected mutations
    69 detection
    70 different panels
    71 different scales
    72 extent
    73 fraction
    74 gastric cancer
    75 gastric cancer patients
    76 genes
    77 genetic alterations
    78 hotspot panel
    79 library preparation
    80 mutations
    81 panel
    82 patients
    83 preparation
    84 presence
    85 results
    86 scale
    87 selective
    88 sequencing
    89 sequencing costs
    90 sequencing panel
    91 somatic mutations
    92 specimens
    93 total
    94 tumor types
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    99 schema:name Comparison between two amplicon-based sequencing panels of different scales in the detection of somatic mutations associated with gastric cancer
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