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PLoS Genet. 2018 Dec 26;14(12):e1007752. doi: 10.1371/journal.pgen.1007752. eCollection 2018 Dec.

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2.

Author information

1
University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America.
2
Broad Institute, Cambridge, Massachusetts, United States of America.
3
Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
4
Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.
5
Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland.
6
Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland.
7
Biocybernetics Laboratory, Computer Science Department, University of California, Los Angeles, California, United States of America.
8
Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom.
9
Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America.
10
School for the Future of Innovation in Society, and Consortium for Science, Policy & Outcomes, Arizona State University, Tempe, Arizona, United States of America.
11
Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.
12
The Global Alliance for Genomics and Health, Toronto, Ontario, Canada.
13
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
14
Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
15
Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
16
Program in Cancer Genetics, Department of Oncology and Human Genetics, McGill University, Montréal, Quebec, Canada.
17
Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America.
18
Huntsman Cancer Institute and Department of Dermatology, University of Utah, Salt Lake City, Utah, United States of America.
19
Partners HealthCare Laboratory for Molecular Medicine and Harvard Medical School, Boston, Massachusetts, United States of America.
20
Graduate School of Medicine, Osaka University, Osaka, Japan.
21
Centre of Genomics and Policy, Faculty of Medicine, Human Genetics, McGill University, Montreal, Québec, Canada.
22
Center for Biomolecular Science & Engineering, University of California, Santa Cruz, California, United States of America.
23
Invitae, San Francisco, California, United States of America.
24
Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.
25
Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America.
26
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
27
National Disease Registration, National Cancer Registration and Analysis Service, Public Health England, London, United Kingdom.
28
Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, United States of America.
29
Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
30
CancerLinQ at American Society of Clinical Oncology (ASCO), Alexandria, Virginia, United States of America.
31
Institut Curie, Cancer Genetic Clinic, Paris, France.
32
Department of Oncological Sciences, The University of Utah, Salt Lake City, Utah, United States of America.
33
Centre of Genomics and Policy, McGill University, Montreal, Canada.
34
Department of Computer Science, University of California, Santa Cruz, Santa Cruz, California, United States of America.
35
Institute of Genetic Medicine, Newcastle University, Centre for Life, Newcastle upon Tyne, United Kingdom.
36
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America.
37
Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.
38
Swiss Institute for Bioinformatics, Lausanne, Switzerland.
39
Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia.

Abstract

The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org. The purpose of the BRCA Exchange is to provide the community with a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. More than 20,000 variants have been aggregated, three times the number found in the next-largest public database at the project's outset, of which approximately 7,250 have expert classifications. The data set is based on shared information from existing clinical databases-Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)-as well as population databases, all linked to a single point of access. The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. Ongoing work includes direct contact with national centers with access to BRCA1 and BRCA2 diagnostic data to encourage data sharing, development of methods suitable for extraction of genetic variation at the level of individual laboratory reports, and engagement with participant communities to enable a more comprehensive understanding of the clinical significance of genetic variation in BRCA1 and BRCA2.

PMID:
30586411
PMCID:
PMC6324924
DOI:
10.1371/journal.pgen.1007752
[Indexed for MEDLINE]
Free PMC Article

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