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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.
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1 Departments of Cancer Biology and Genetics and Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
2 Fox Chase Cancer Center, Philadelphia, PA, USA
3 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
4 USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
5 Faculty of Medicine, University of Southampton, Southampton, UK
6 Departments of Human Genetics, Medicine and Oncology, McGill University, Montreal, QC, Canada
7 Family Cancer Clinic, Netherlands Cancer Institute, Amsterdam, Netherlands
8 Oncogenetics and INSERM U830, Institut Curie, Paris and Paris Descartes University, Paris, France
9 Faculty of Medicine, Shaare Zedek Medical Center, Hebrew University of Jerusalem and Medical Genetics Institute, Jerusalem, Israel
10 Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
11 Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
12 Baylor College of Medicine, Houston, TX, USA
13 Mouse Cancer Genetics Program, Center for Cancer Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
14 Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, Australia
15 National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA