Open AccessPerformance evaluation of an amplicon‐based next‐generation sequencing panel for BRCA1 and BRCA2 variant detection
Author(s) -
Park Kuenyoul,
Kim Min Kyu,
Lee Taegeun,
Hong Jinyoung,
Kim HyunKi,
Ahn Sunyoung,
Lee YoungJae,
Kim Jisun,
Lee ShinWha,
Lee Jong Won,
Lee Woochang,
Chun Sail,
Son Byung Ho,
Jung Kyung Hae,
Kim YongMan,
Min WonKi,
Ahn SeiHyun
Publication year - 2020
Publication title -
journal of clinical laboratory analysis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.536
H-Index - 50
eISSN - 1098-2825
pISSN - 0887-8013
DOI - 10.1002/jcla.23524
Subject(s) - amplicon , amplicon sequencing , computational biology , dna sequencing , computer science , genetics , biology , polymerase chain reaction , dna , gene , 16s ribosomal rna
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.