Performance evaluation of an amplicon-based next-generation sequencing panel for BRCA1 and BRCA2 variant detection - PubMed

Performance evaluation of an amplicon-based next-generation sequencing panel for BRCA1 and BRCA2 variant detection - PubMed

Performance evaluation of an amplicon-based next-generation sequencing panel for BRCA1 and BRCA2 variant detection

Kuenyoul Park 1, Min Kyu Kim 2, Taegeun Lee 1, Jinyoung Hong 1, Hyun-Ki Kim 1, Sunyoung Ahn 3, Young-Jae Lee 4, Jisun Kim 5, Shin-Wha Lee 4, Jong Won Lee 5, Woochang Lee 1, Sail Chun 1, Byung Ho Son 5, Kyung Hae Jung 6, Yong-Man Kim 4, Won-Ki Min 1, Sei-Hyun Ahn 5

Affiliations 

• PMID: 32812259
 
• DOI: 10.1002/jcla.23524

Abstract

Background: As next-generation sequencing (NGS) technology matures, various amplicon-based NGS tests for BRCA1/2 genotyping have been introduced. This study was designed to evaluate an NGS test using a newly released amplicon-based panel, AmpliSeq for Illumina BRCA Panel (AmpliSeq panel), for detection of clinically significant BRCA variants, and to compare it to another amplicon-based NGS test confirmed by Sanger sequencing.

Methods: We reviewed BRCA test results done by NGS using the TruSeq Custom Amplicon kit from patients suspected of hereditary breast/ovarian cancer syndrome (HBOC) in 2018. Of those, 96 residual samples with 100 clinically significant variants were included in this study using predefined criteria: 100 variants were distributed throughout the BRCA1 and BRCA2 genes. All target variants were confirmed by Sanger sequencing. Duplicate NGS testing of these samples was performed using the AmpliSeq panel, and the concordance of results from the two amplicon-based NGS tests was assessed.

Results: Ninety-nine of 100 variants were detected in duplicate BRCA1/2 genotyping using the AmpliSeq panel (sensitivity, 99%; specificity, 100%). In the discordant case, one variant (BRCA1 c.3627dupA) was found only in repeat 1, but not in repeat 2. Automated nomenclature of all variants, except for two indel variants, was in consensus with Human Genome Variation Society nomenclature.

Conclusion: Our findings confirm that the analytic performance of the AmpliSeq panel is satisfactory, with high sensitivity and specificity.

Keywords: BRCA1; BRCA2; amplicon-based panel; evaluation; next-generation sequencing.

© 2020 The Authors. Journal of Clinical Laboratory Analysis published by Wiley Periodicals LLC.

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