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基于扩增子的新一代测序 panel 用于 BRCA1 和 BRCA2 变异检测的性能评估。

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

机构信息

Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.

Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon-Si, Korea.

出版信息

J Clin Lab Anal. 2020 Dec;34(12):e23524. doi: 10.1002/jcla.23524. Epub 2020 Aug 19.

DOI:10.1002/jcla.23524
PMID:32812259
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7755770/
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.

摘要

背景

随着下一代测序（NGS）技术的成熟，各种基于扩增子的 BRCA1/2 基因分型 NGS 检测已被引入。本研究旨在评估一种使用新发布的基于扩增子的 panel，AmpliSeq for Illumina BRCA Panel（AmpliSeq 面板）进行临床显著 BRCA 变体检测的 NGS 检测，并将其与另一种经 Sanger 测序确认的基于扩增子的 NGS 检测进行比较。

方法

我们回顾了 2018 年使用 TruSeq Custom Amplicon 试剂盒进行 NGS 的 BRCA 检测结果，这些结果来自疑似遗传性乳腺癌/卵巢癌综合征（HBOC）的患者。其中，根据预设标准，有 96 个残留样本，包含 100 个具有临床意义的变体，包括在此项研究中：100 个变体分布在 BRCA1 和 BRCA2 基因中。所有目标变体均通过 Sanger 测序确认。对这些样本进行了两次基于扩增子的 NGS 测试，使用的是 AmpliSeq 面板，评估了两种基于扩增子的 NGS 测试结果的一致性。

结果

在使用 AmpliSeq 面板进行的 BRCA1/2 基因重复分型中，检测到 100 个变体中的 99 个（灵敏度，99%；特异性，100%）。在不一致的病例中，一个变体（BRCA1 c.3627dupA）仅在重复 1 中发现，而不在重复 2 中发现。除了两个插入缺失变体外，所有变体的自动命名均与人类基因组变异协会命名法一致。

结论

我们的研究结果证实，AmpliSeq 面板的分析性能令人满意，具有高灵敏度和特异性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/814f/7755770/b389d0b8226f/JCLA-34-e23524-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/814f/7755770/9ab5c85739d5/JCLA-34-e23524-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/814f/7755770/eabbe8a45ece/JCLA-34-e23524-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/814f/7755770/b389d0b8226f/JCLA-34-e23524-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/814f/7755770/9ab5c85739d5/JCLA-34-e23524-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/814f/7755770/eabbe8a45ece/JCLA-34-e23524-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/814f/7755770/b389d0b8226f/JCLA-34-e23524-g003.jpg

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