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학술연구/단체지원/교육 등 연구자 활동을 지속하도록 DBpia가 지원하고 있어요.
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연구자들이 자신의 연구와 전문성을 널리 알리고, 새로운 협력의 기회를 만들 수 있는 네트워킹 공간이에요.
논문 기본 정보
- 자료유형
- 학술저널
- 저자정보
- 발행연도
- 2018.1
- 수록면
- 255 - 264 (10page)
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Purpose Transition to next generation sequencing (NGS) for BRCA1/BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1/2. Materials and Methods The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1/BRCA2. Ten clinical samples and 14 reference DNA samples were additionally sequenced by Ion PGM Dx with Torrent Suite. Results Fifty types of variants including 18 pathogenic or variants of unknown significance were identified from 75 clinical samples and known variants of the reference samples were confirmed by Sanger sequencing and/or NGS. One false-negative results were present for Ion PGM/OTG-snpcaller for an indel variant misidentified as a single nucleotide variant. However, eight discordant results were present for Ion PGM Dx/Torrent Suite with both falsepositive and -negative results. A 40-bp deletion, a 4-bp deletion and a 1-bp deletion variant was not called and a false-positive deletion was identified. Four other variants were misidentified as another variant. Conclusion Ion PGM/OTG-snpcaller showed acceptable performance with good concordance with Sanger sequencing. However, Ion PGM Dx/Torrent Suite showed many discrepant results not suitable for use in a clinical laboratory, requiring further optimization of the data analysis for calling variants.
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참고문헌 (27)
참고문헌 신청
Ford D / 1998 / Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium / Am J Hum Genet 62:676~689
King MC / 2003 / Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2 / Science 302:643~646
Hartmann LC / 2016 / The role of risk-reducing surgery in hereditary breast and ovarian cancer / N Engl J Med 374:454~468
National Comprehensive Cancer Network / 2016 / NCCN guidelines, version 2. 2016. Breast and/or ovarian cancer genetic assessment
Tafe LJ / 2015 / Molecular testing for the BRCA1 and BRCA2 Ashkenazi Jewish founder mutations: a report on the College of American Pathologists proficiency testing surveys / Genet Med 17:58~62
King MC / 2003 / Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2 / Science 302:643~646
Hartmann LC / 2016 / The role of risk-reducing surgery in hereditary breast and ovarian cancer / N Engl J Med 374:454~468
National Comprehensive Cancer Network / 2016 / NCCN guidelines, version 2. 2016. Breast and/or ovarian cancer genetic assessment
Tafe LJ / 2015 / Molecular testing for the BRCA1 and BRCA2 Ashkenazi Jewish founder mutations: a report on the College of American Pathologists proficiency testing surveys / Genet Med 17:58~62
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