A comparative study of germline BRCA1 and BRCA2 mutation screening methods in use in 20 European clinical diagnostic laboratories

Abstract

Background:Thousands of clinically relevant variations in BRCA1 and BRCA2 have been discovered and this poses a significant challenge with respect to the accurate detection, analysis turn-around time, characterisation and interpretation of these sequence variants.Methods:We evaluated the performance of different BRCA1/2 gene testing practices in routine diagnostic use in 20 European laboratories, with a focus on next-generation sequencing-based strategies as this is the technical approach implemented by or under adoption by most European clinical laboratories. Participant laboratories, selected on expertise and diagnostic service quality, tested 10 identical DNA samples containing a range of challenging pathogenic variants.Results:A small number of errors in the detection of pathogenic and significant variants were identified (2.6% diagnostic error rate). There was a high degree of concordance (>97%) across all laboratories for all variants detected. No systematic technical flaw was identified in the strategies employed across the participating laboratories.Conclusions:The discrepancies identified are most likely due to human error or the way the methodology has been implemented locally, for example, next-generation sequencing bioinformatics pipelines, rather than technical limitations of the methods. The choice of BRCA1/2 testing method will therefore depend on multiple factors including required throughput and turn-around times, access to equipment, expertise and budget.

Clinical testing of BRCA1 and BRCA2: a worldwide snapshot of technological practices

“…Laboratories reported VUS at varying rates, but also calculated rates of VUS differently. Based on these results and two recent studies, one showing a 2.6% diagnostic error rate for detection of pathogenic and significant variants using MPS approaches, 11 and a second study suggesting that only two of seven MPS workflows could detect all 23 “challenging variants” in a blinded study 12 , we suggest points for consideration for laboratories performing or contemplating BRCA or panel testing (Fig. 5 ).…”

Fertility preservation in BRCA mutation carriers—efficacy and safety issues: a review

“…It is of significance that the result of the BRCA mutation test is accurate, as important clinical decisions are being made based on the results. A comparative study of germline BRCA mutation screening methods in use in European clinical diagnostic laboratories compared the accuracy of NGS, Sanger sequencing, denaturing high-performance liquid chromatography (dHPLC) and high-resolution melting (HRM), the concordance was high (> 97%) across all laboratories using different techniques [50]. Besides genetic testing methods, The Breast Cancer Genetics Referral Screening Tool (B-RST™) was created and validated to identify individuals at increased risk for hereditary breast and ovarian cancer for referral to cancer genetics services easily [51].…”

Germline BRCA 1-2 status prediction through ovarian ultrasound images radiogenomics: a hypothesis generating study (PROBE study)

“…Although this strategy is currently considered as the most cost-effective option, the available tools (such as BOADICEA, Myriad, BRCAPRO, etc.) combined with pre-test genetic counselling, showed a moderate to high diagnostic accuracy (around 2.6% diagnostic error rate) in predicting gBRCA1/2 mutations, however, a number of individuals, potentially at risk, might not be identified 20 – 25 .…”