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

Yoonjung Kim, Chi Heum Cho, Jung Sook Ha, Do Hoon Kim, Sun Young Kwon, Seoung Chul Oh, Kyung A. Lee

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


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.

Original languageEnglish
Article numbere9
JournalJournal of Gynecologic Oncology
Issue number1
Publication statusPublished - 2020 Jan

Bibliographical note

Funding Information:
This research was conducted with support from AstraZeneca Korea Ltd. (ESR-16-12150).

Funding Information:
The biospecimens for this study were provided by Keimyung University Dongsan Hospital Korea Regional Biobank, a member of the National Biobank of Korea, which is supported by the Ministry of Health and Welfare.

Publisher Copyright:
© 2020. Asian Society of Gynecologic Oncology, Korean Society of Gynecologic Oncology.

All Science Journal Classification (ASJC) codes

  • Oncology
  • Obstetrics and Gynaecology


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