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Reliable assessment of BRCA1 and BRCA2 germline variants by next-generation sequencing: a multicenter study

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Abstract

Background

BRCA1/2 gene mutation testing, based on next-generation sequencing (NGS), has been gradually applied in the clinic to serve as preventive early screening for predisposed individuals or to provide treatment options for patients with hereditary breast or ovarian cancers. Here, we evaluated the accuracy of NGS-based mutation detection in BRCA1/2 and the consistency in variant interpretation among clinical laboratories to find the possible reasons underlying inaccurate results and discrepant variant interpretation.

Methods

Laboratories were asked to use their routine procedures to detect six mimetic DNA samples with different BRCA1/2 germline variants. The results of variant detection were required to be submitted via a web-based evaluation system and were automatically scored, according to predefined criteria. The variant interpretation report, including the detailed clinical evidence, was summarized and analyzed for reasons underlying inconsistent results.

Results

Overall, only 55.2% (16/29) of laboratories, whose detection score was higher than 90 points, was found to be an acceptable detection capability level. 82.9% (29/35) of the errors were genotype errors. The variant classification results were generally consistent, and 77.8% (7/9) of the variants were given the consistent classification answer. Only two single nucleotide variants (SNVs) had a discrepant classification opinion across laboratories.

Conclusions

The BRCA1/2 variant detection performance should be further improved, especially in reporting the correct genome coordinates. Inconsistent variant classification may be a result of the different clinical pieces of evidence collected by the laboratories. However, discordant clinical evidence also appeared within the same classification results. Therefore, our study provided clear clinical evidence assessment strategies for BRCA1/2 variants, which was aimed at obtaining a consistent variant classification strategy for providing accurate clinical reports to the clinicians.

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Funding

This work was supported by the Fund for Beijing Dongcheng District Outstanding Talents Team Program 2019DCT-M-01(Rui Zhang), National Key R&D Program of China 2018YFE0201604 (Jinming Li), National Natural Science Foundation of China Grant 81974319 (Jinming Li), Beijing Hospital Nova Project BJ-2018-136 (Rui Zhang).

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Author notes

  1. Rui Zhang and Peng Gao contributed equally to the work.

Authors and Affiliations

  1. National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China

    Rui Zhang, Peng Gao, Yanxi Han, Runling Zhang, Ping Tan, Li Zhou, Jiawei Zhang, Jiehong Xie & Jinming Li

  2. Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China

    Peng Gao, Runling Zhang, Ping Tan, Li Zhou, Jiawei Zhang & Jinming Li

  3. Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China

    Rui Zhang, Peng Gao, Yanxi Han, Runling Zhang, Ping Tan, Li Zhou, Jiawei Zhang, Jiehong Xie & Jinming Li

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  1. Rui Zhang
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Correspondence to Jinming Li.

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Zhang, R., Gao, P., Han, Y. et al. Reliable assessment of BRCA1 and BRCA2 germline variants by next-generation sequencing: a multicenter study. Breast Cancer 28, 672–683 (2021). https://doi.org/10.1007/s12282-020-01204-x

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  • DOI: https://doi.org/10.1007/s12282-020-01204-x

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