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An optimized BRCA1/2 next-generation sequencing for different clinical sample types

Authors
 Yoonjung Kim  ;  Chi-Heum Cho  ;  Jung-Sook Ha  ;  Do-Hoon Kim  ;  Sun Young Kwon  ;  Seoung Chul Oh  ;  Kyung-A Lee 
Citation
 JOURNAL OF GYNECOLOGIC ONCOLOGY, Vol.31(1) : e9, 2020 
Journal Title
 JOURNAL OF GYNECOLOGIC ONCOLOGY 
ISSN
 2005-0380 
Issue Date
2020
Keywords
BRCA1 ; BRCA2 ; Blood Buffy Coat ; High-Throughput Nucleotide Sequencing ; Tissue Preservation
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.
Files in This Item:
T202000436.pdf Download
DOI
10.3802/jgo.2020.31.e9
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
Yonsei Authors
Kim, Yoon Jung(김윤정) ORCID logo https://orcid.org/0000-0002-4370-4265
Lee, Kyung A(이경아) ORCID logo https://orcid.org/0000-0001-5320-6705
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/175496
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