Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification

Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification

Abstract Clinical genetic testing identifies variants causal for hereditary cancer, information that is used for risk assessment and clinical management. Unfortunately, some variants identified are of uncertain clinical significance (VUS), complicating patient management. Case-control data is one ev...

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Main Authors: Maria Zanti, Denise G. O’Mahony, Michael T. Parsons, Leila Dorling, Joe Dennis, Nicholas J. Boddicker, Wenan Chen, Chunling Hu, Marc Naven, Kristia Yiangou, Thomas U. Ahearn, Christine B. Ambrosone, Irene L. Andrulis, Antonis C. Antoniou, Paul L. Auer, Caroline Baynes, Clara Bodelon, Natalia V. Bogdanova, Stig E. Bojesen, Manjeet K. Bolla, Kristen D. Brantley, Nicola J. Camp, Archie Campbell, Jose E. Castelao, Melissa H. Cessna, Jenny Chang-Claude, Fei Chen, Georgia Chenevix-Trench, NBCS Collaborators, Don M. Conroy, Kamila Czene, Arcangela De Nicolo, Susan M. Domchek, Thilo Dörk, Alison M. Dunning, A. Heather Eliassen, D. Gareth Evans, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Manuela Gago-Dominguez, Montserrat García-Closas, Gord Glendon, Anna González-Neira, Felix Grassmann, Andreas Hadjisavvas, Christopher A. Haiman, Ute Hamann, Steven N. Hart, Mikael B. A. Hartman, Weang-Kee Ho, James M. Hodge, Reiner Hoppe, Sacha J. Howell, kConFab Investigators, Anna Jakubowska, Elza K. Khusnutdinova, Yon-Dschun Ko, Peter Kraft, Vessela N. Kristensen, James V. Lacey, Jingmei Li, Geok Hoon Lim, Sara Lindström, Artitaya Lophatananon, Craig Luccarini, Arto Mannermaa, Maria Elena Martinez, Dimitrios Mavroudis, Roger L. Milne, Kenneth Muir, Katherine L. Nathanson, Rocio Nuñez-Torres, Nadia Obi, Janet E. Olson, Julie R. Palmer, Mihalis I. Panayiotidis, Alpa V. Patel, Paul D. P. Pharoah, Eric C. Polley, Muhammad U. Rashid, Kathryn J. Ruddy, Emmanouil Saloustros, Elinor J. Sawyer, Marjanka K. Schmidt, Melissa C. Southey, Veronique Kiak-Mien Tan, Soo Hwang Teo, Lauren R. Teras, Diana Torres, Amy Trentham-Dietz, Thérèse Truong, Celine M. Vachon, Qin Wang, Jeffrey N. Weitzel, Siddhartha Yadav, Song Yao, Gary R. Zirpoli, Melissa S. Cline, Peter Devilee, Sean V. Tavtigian, David E. Goldgar, Fergus J. Couch, Douglas F. Easton, Amanda B. Spurdle, Kyriaki Michailidou
Format: Article
Language:English
Published: Nature Portfolio 2025-05-01
Series:Nature Communications
Online Access:https://doi.org/10.1038/s41467-025-59979-6
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Summary:Abstract Clinical genetic testing identifies variants causal for hereditary cancer, information that is used for risk assessment and clinical management. Unfortunately, some variants identified are of uncertain clinical significance (VUS), complicating patient management. Case-control data is one evidence type used to classify VUS. As an initiative of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Analytical Working Group we analyze germline sequencing data of BRCA1 and BRCA2 from 96,691 female breast cancer cases and 302,116 controls from three studies: the BRIDGES study of the Breast Cancer Association Consortium, the Cancer Risk Estimates Related to Susceptibility consortium, and the UK Biobank. We observe 11,207 BRCA1 and BRCA2 variants, with 6909 being coding, covering 23.4% of BRCA1 and BRCA2 VUS in ClinVar and 19.2% of ClinVar curated (likely) benign or pathogenic variants. Case-control likelihood ratio (ccLR) evidence is highly consistent with ClinVar assertions for (likely) benign or pathogenic variants; exhibiting 99.1% sensitivity and 95.3% specificity for BRCA1 and 93.3% sensitivity and 86.6% specificity for BRCA2. This approach provides case-control evidence for 787 unclassified variants; these include 579 with strong or moderate benign evidence and 10 with strong pathogenic evidence for which ccLR evidence is sufficient to alter clinical classification.
ISSN:2041-1723

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