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

A. Toland,A. Forman,F. Couch,Julie O. Culver,D. Eccles,W. Foulkes,F. Hogervorst,C. Houdayer,E. Levy-Lahad,A. Monteiro,S. Neuhausen,S. Plon,S. K. Sharan,A. Spurdle,C. Szabo,L. Brody

Published 2018 in npj Genomic Medicine

ABSTRACT

Clinical testing of BRCA1 and BRCA2 began over 20 years ago. With the expiration and overturning of the BRCA patents, limitations on which laboratories could offer commercial testing were lifted. These legal changes occurred approximately the same time as the widespread adoption of massively parallel sequencing (MPS) technologies. Little is known about how these changes impacted laboratory practices for detecting genetic alterations in hereditary breast and ovarian cancer genes. Therefore, we sought to examine current laboratory genetic testing practices for BRCA1/BRCA2. We employed an online survey of 65 questions covering four areas: laboratory characteristics, details on technological methods, variant classification, and client-support information. Eight United States (US) laboratories and 78 non-US laboratories completed the survey. Most laboratories (93%; 80/86) used MPS platforms to identify variants. Laboratories differed widely on: (1) technologies used for large rearrangement detection; (2) criteria for minimum read depths; (3) non-coding regions sequenced; (4) variant classification criteria and approaches; (5) testing volume ranging from 2 to 2.5 × 105 tests annually; and (6) deposition of variants into public databases. These data may be useful for national and international agencies to set recommendations for quality standards for BRCA1/BRCA2 clinical testing. These standards could also be applied to testing of other disease genes. Global protocols and standards differ widely when it comes to analyzing variants in the BRCA1 and BRCA2 cancer susceptibility genes. A team led by Amanda Toland from the Ohio State University Comprehensive Cancer Center in Columbus, Ohio, USA, surveyed 86 laboratories around the world about their testing practices for BRCA1/2, genes linked to hereditary cases of breast and ovarian cancer. The vast majority of responding labs—93%—used next-generation sequencing technologies; only 6 relied on traditional Sanger sequencing methods. But otherwise, the researchers found, laboratories differed widely in their approach to analyzing BRCA—including in the extent of variant confirmation, whether non-coding DNA regions were sequenced, and the techniques used to detect large genomic rearrangements. The survey results now provide a baseline dataset for organizations to formulate global best-practice guidelines for BRCA testing.

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