Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women.
Breast Cancer Association Consortium None., Dorling L., Carvalho S., Allen J., González-Neira A., Luccarini C., Wahlström C., Pooley KA., Parsons MT., Fortuno C., Wang Q., Bolla MK., Dennis J., Keeman R., Alonso MR., Álvarez N., Herraez B., Fernandez V., Núñez-Torres R., Osorio A., Valcich J., Li M., Törngren T., Harrington PA., Baynes C., Conroy DM., Decker B., Fachal L., Mavaddat N., Ahearn T., Aittomäki K., Antonenkova NN., Arnold N., Arveux P., Ausems MGEM., Auvinen P., Becher H., Beckmann MW., Behrens S., Bermisheva M., Białkowska K., Blomqvist C., Bogdanova NV., Bogdanova-Markov N., Bojesen SE., Bonanni B., Børresen-Dale A-L., Brauch H., Bremer M., Briceno I., Brüning T., Burwinkel B., Cameron DA., Camp NJ., Campbell A., Carracedo A., Castelao JE., Cessna MH., Chanock SJ., Christiansen H., Collée JM., Cordina-Duverger E., Cornelissen S., Czene K., Dörk T., Ekici AB., Engel C., Eriksson M., Fasching PA., Figueroa J., Flyger H., Försti A., Gabrielson M., Gago-Dominguez M., Georgoulias V., Gil F., Giles GG., Glendon G., Garcia EBG., Alnæs GIG., Guénel P., Hadjisavvas A., Haeberle L., Hahnen E., Hall P., Hamann U., Harkness EF., Hartikainen JM., Hartman M., He W., Heemskerk-Gerritsen BAM., Hillemanns P., Hogervorst FBL., Hollestelle A., Ho WK., Hooning MJ., Howell A., Humphreys K., Idris F., Jakubowska A., Jung A., Kapoor PM., Kerin MJ., Khusnutdinova E., Kim S-W., Ko Y-D., Kosma V-M., Kristensen VN., Kyriacou K., Lakeman IMM., Lee JW., Lee MH., Li J., Lindblom A., Lo W-Y., Loizidou MA., Lophatananon A., Lubiński J., MacInnis RJ., Madsen MJ., Mannermaa A., Manoochehri M., Manoukian S., Margolin S., Martinez ME., Maurer T., Mavroudis D., McLean C., Meindl A., Mensenkamp AR., Michailidou K., Miller N., Mohd Taib NA., Muir K., Mulligan AM., Nevanlinna H., Newman WG., Nordestgaard BG., Ng P-S., Oosterwijk JC., Park SK., Park-Simon T-W., Perez JIA., Peterlongo P., Porteous DJ., Prajzendanc K., Prokofyeva D., Radice P., Rashid MU., Rhenius V., Rookus MA., Rüdiger T., Saloustros E., Sawyer EJ., Schmutzler RK., Schneeweiss A., Schürmann P., Shah M., Sohn C., Southey MC., Surowy H., Suvanto M., Thanasitthichai S., Tomlinson I., Torres D., Truong T., Tzardi M., Valova Y., van Asperen CJ., Van Dam RM., van den Ouweland AMW., van der Kolk LE., van Veen EM., Wendt C., Williams JA., Yang XR., Yoon S-Y., Zamora MP., Evans DG., de la Hoya M., Simard J., Antoniou AC., Borg Å., Andrulis IL., Chang-Claude J., García-Closas M., Chenevix-Trench G., Milne RL., Pharoah PDP., Schmidt MK., Spurdle AB., Vreeswijk MPG., Benitez J., Dunning AM., Kvist A., Teo SH., Devilee P., Easton DF.
BACKGROUND: Genetic testing for breast cancer susceptibility is widely used, but for many genes, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are lacking. METHODS: We used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 women with breast cancer and 53,461 controls. In separate analyses for protein-truncating variants and rare missense variants in these genes, we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluated missense-variant associations according to domain and classification of pathogenicity. RESULTS: Protein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2) were associated with a risk of breast cancer overall with a P value of less than 0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D, and TP53) were associated with a risk of breast cancer overall with a P value of less than 0.05 and a Bayesian false-discovery probability of less than 0.05. For protein-truncating variants in 19 of the remaining 25 genes, the upper limit of the 95% confidence interval of the odds ratio for breast cancer overall was less than 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios were higher for estrogen receptor (ER)-positive disease than for ER-negative disease; for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, odds ratios were higher for ER-negative disease than for ER-positive disease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 were associated with a risk of breast cancer overall with a P value of less than 0.001. For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a risk of breast cancer overall, with the risk being similar to that of protein-truncating variants. CONCLUSIONS: The results of this study define the genes that are most clinically useful for inclusion on panels for the prediction of breast cancer risk, as well as provide estimates of the risks associated with protein-truncating variants, to guide genetic counseling. (Funded by European Union Horizon 2020 programs and others.).