An Optimized BRCA1/2 Next-Generation Sequencing for Different Clinical Sample Types

Authors
Yoonjung KimChi-Heum ChoJung-Sook HaDo-Hoon KimSun Young KwonSeoung Chul OhKyung-A Lee
Department
Dept. of Obstetrics & Gynecology (산부인과학); Dept. of Laboratory Medicine (진단검사의학); Dept. of Pathology (병리학)
Issue Date
2020
Citation
Journal of gynecologic oncology, Vol.31(1) : e9-e9, 2020
ISSN
2005-0399
Abstract
Objective: A simultaneous detection of germline and somatic mutations in ovarian cancer (OC) using tumor materials is considered to be cost-effective for BRCA1/2 testing. However, there are limited studies of the analytical performances according to various sample types. The aim of this study is to propose a strategy for routine BRCA1/2 next-generation sequencing (NGS) screening based on analytical performance according to different sample types. Methods: We compared BRCA1/2 NGS screening assay using buffy coat, fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) from 130 samples. Results: The rate of repeated tests in a total of buffy coat, FF and FFPE was 0%, 8%, and 34%, respectively. The accuracy of BRCA1/2 NGS testing was 100.0%, 99.9% and 99.9% in buffy coat, FFPE and FF, respectively. However, due to the presence of variant allele frequency (VAF) shifted heterozygous variants, tumor materials (FFPE and FF) showed lower sensitivity (95.5%–99.0%) than buffy coat (100%). Furthermore, FFPE showed 51.4% of the positive predictive value (PPV) on account of sequence artifacts. When performed in the post-filtration process, PPV was increased by approximately 20% in FFPE. Buffy coat showed 100% of sensitivity, specificity and accuracy in BRCA1/2 NGS test. Conclusions: On the comparison of the analytical performance according to different sample types, the buffy coat was not affected by sequencing artifacts and VAF shifted variants. Therefore, the blood test should be given priority in detecting germline BRCA1/2 mutation, and tumor materials could be suitable to detect somatic mutations in OC patients without identifying germline BRCA1/2 mutation.
Keywords
BRCA1BRCA2Blood Buffy CoatTissue PreservationHigh-Throughput Nucleotide Sequencing
URI
http://kumel.medlib.dsmc.or.kr/handle/2015.oak/42367
Appears in Collections:
1. Journal Papers (연구논문) > 1. School of Medicine (의과대학) > Dept. of Obstetrics & Gynecology (산부인과학)
1. Journal Papers (연구논문) > 1. School of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학)
1. Journal Papers (연구논문) > 1. School of Medicine (의과대학) > Dept. of Pathology (병리학)
Keimyung Author(s)
조치흠; 하정숙; 김도훈; 권선영
Full Text
https://www.ejgo.org/DOIx.php?id=10.3802/jgo.2020.31.e9
File in this Item
oak-2019-0343.pdf(1.77 MB)Download
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