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Breast cancer risks associated with missense variants in breast cancer susceptibility genes.

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cam.issuedOnline2022-05-18
datacite.isderivedfrom.doi10.1101/2021.09.02.21262369
dc.contributor.authorDorling, Leila
dc.contributor.authorCarvalho, Sara
dc.contributor.authorAllen, Jamie
dc.contributor.authorParsons, Michael T
dc.contributor.authorFortuno, Cristina
dc.contributor.authorGonzález-Neira, Anna
dc.contributor.authorHeijl, Stephan M
dc.contributor.authorAdank, Muriel A
dc.contributor.authorAhearn, Thomas U
dc.contributor.authorAndrulis, Irene L
dc.contributor.authorAuvinen, Päivi
dc.contributor.authorBecher, Heiko
dc.contributor.authorBeckmann, Matthias W
dc.contributor.authorBehrens, Sabine
dc.contributor.authorBermisheva, Marina
dc.contributor.authorBogdanova, Natalia V
dc.contributor.authorBojesen, Stig E
dc.contributor.authorBolla, Manjeet K
dc.contributor.authorBremer, Michael
dc.contributor.authorBriceno, Ignacio
dc.contributor.authorCamp, Nicola J
dc.contributor.authorCampbell, Archie
dc.contributor.authorCastelao, Jose E
dc.contributor.authorChang-Claude, Jenny
dc.contributor.authorChanock, Stephen J
dc.contributor.authorChenevix-Trench, Georgia
dc.contributor.authorNBCS Collaborators
dc.contributor.authorCollée, J Margriet
dc.contributor.authorCzene, Kamila
dc.contributor.authorDennis, Joe
dc.contributor.authorDörk, Thilo
dc.contributor.authorEriksson, Mikael
dc.contributor.authorEvans, D Gareth
dc.contributor.authorFasching, Peter A
dc.contributor.authorFigueroa, Jonine
dc.contributor.authorFlyger, Henrik
dc.contributor.authorGabrielson, Marike
dc.contributor.authorGago-Dominguez, Manuela
dc.contributor.authorGarcía-Closas, Montserrat
dc.contributor.authorGiles, Graham G
dc.contributor.authorGlendon, Gord
dc.contributor.authorGuénel, Pascal
dc.contributor.authorGündert, Melanie
dc.contributor.authorHadjisavvas, Andreas
dc.contributor.authorHahnen, Eric
dc.contributor.authorHall, Per
dc.contributor.authorHamann, Ute
dc.contributor.authorHarkness, Elaine F
dc.contributor.authorHartman, Mikael
dc.contributor.authorHogervorst, Frans BL
dc.contributor.authorHollestelle, Antoinette
dc.contributor.authorHoppe, Reiner
dc.contributor.authorHowell, Anthony
dc.contributor.authorkConFab Investigators
dc.contributor.authorSGBCC Investigators
dc.contributor.authorJakubowska, Anna
dc.contributor.authorJung, Audrey
dc.contributor.authorKhusnutdinova, Elza
dc.contributor.authorKim, Sung-Won
dc.contributor.authorKo, Yon-Dschun
dc.contributor.authorKristensen, Vessela N
dc.contributor.authorLakeman, Inge MM
dc.contributor.authorLi, Jingmei
dc.contributor.authorLindblom, Annika
dc.contributor.authorLoizidou, Maria A
dc.contributor.authorLophatananon, Artitaya
dc.contributor.authorLubiński, Jan
dc.contributor.authorLuccarini, Craig
dc.contributor.authorMadsen, Michael J
dc.contributor.authorMannermaa, Arto
dc.contributor.authorManoochehri, Mehdi
dc.contributor.authorMargolin, Sara
dc.contributor.authorMavroudis, Dimitrios
dc.contributor.authorMilne, Roger L
dc.contributor.authorMohd Taib, Nur Aishah
dc.contributor.authorMuir, Kenneth
dc.contributor.authorNevanlinna, Heli
dc.contributor.authorNewman, William G
dc.contributor.authorOosterwijk, Jan C
dc.contributor.authorPark, Sue K
dc.contributor.authorPeterlongo, Paolo
dc.contributor.authorRadice, Paolo
dc.contributor.authorSaloustros, Emmanouil
dc.contributor.authorSawyer, Elinor J
dc.contributor.authorSchmutzler, Rita K
dc.contributor.authorShah, Mitul
dc.contributor.authorSim, Xueling
dc.contributor.authorSouthey, Melissa C
dc.contributor.authorSurowy, Harald
dc.contributor.authorSuvanto, Maija
dc.contributor.authorTomlinson, Ian
dc.contributor.authorTorres, Diana
dc.contributor.authorTruong, Thérèse
dc.contributor.authorvan Asperen, Christi J
dc.contributor.authorWaltes, Regina
dc.contributor.authorWang, Qin
dc.contributor.authorYang, Xiaohong R
dc.contributor.authorPharoah, Paul DP
dc.contributor.authorSchmidt, Marjanka K
dc.contributor.authorBenitez, Javier
dc.contributor.authorVroling, Bas
dc.contributor.authorDunning, Alison M
dc.contributor.authorTeo, Soo Hwang
dc.contributor.authorKvist, Anders
dc.contributor.authorde la Hoya, Miguel
dc.contributor.authorDevilee, Peter
dc.contributor.authorSpurdle, Amanda B
dc.contributor.authorVreeswijk, Maaike PG
dc.contributor.authorEaston, Douglas F
dc.contributor.orcidDennis, Joe [0000-0003-4591-1214]
dc.contributor.orcidPharoah, Paul [0000-0001-8494-732X]
dc.contributor.orcidEaston, Douglas [0000-0003-2444-3247]
dc.date.accessioned2022-06-29T19:42:04Z
dc.date.available2022-06-29T19:42:04Z
dc.date.issued2022-05-18
dc.date.updated2022-06-29T19:42:04Z
dc.description.abstractBACKGROUND: Protein truncating variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 are associated with increased breast cancer risk, but risks associated with missense variants in these genes are uncertain. METHODS: We analyzed data on 59,639 breast cancer cases and 53,165 controls from studies participating in the Breast Cancer Association Consortium BRIDGES project. We sampled training (80%) and validation (20%) sets to analyze rare missense variants in ATM (1146 training variants), BRCA1 (644), BRCA2 (1425), CHEK2 (325), and PALB2 (472). We evaluated breast cancer risks according to five in silico prediction-of-deleteriousness algorithms, functional protein domain, and frequency, using logistic regression models and also mixture models in which a subset of variants was assumed to be risk-associated. RESULTS: The most predictive in silico algorithms were Helix (BRCA1, BRCA2 and CHEK2) and CADD (ATM). Increased risks appeared restricted to functional protein domains for ATM (FAT and PIK domains) and BRCA1 (RING and BRCT domains). For ATM, BRCA1, and BRCA2, data were compatible with small subsets (approximately 7%, 2%, and 0.6%, respectively) of rare missense variants giving similar risk to those of protein truncating variants in the same gene. For CHEK2, data were more consistent with a large fraction (approximately 60%) of rare missense variants giving a lower risk (OR 1.75, 95% CI (1.47-2.08)) than CHEK2 protein truncating variants. There was little evidence for an association with risk for missense variants in PALB2. The best fitting models were well calibrated in the validation set. CONCLUSIONS: These results will inform risk prediction models and the selection of candidate variants for functional assays and could contribute to the clinical reporting of gene panel testing for breast cancer susceptibility.
dc.identifier.doi10.17863/CAM.85841
dc.identifier.eissn1756-994X
dc.identifier.issn1756-994X
dc.identifier.other35585550
dc.identifier.otherPMC9116026
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/338428
dc.languageeng
dc.language.isoeng
dc.publisherSpringer Science and Business Media LLC
dc.publisher.urlhttp://dx.doi.org/10.1186/s13073-022-01052-8
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.sourceessn: 1756-994X
dc.sourcenlmid: 101475844
dc.subjectBreast cancer
dc.subjectGenetic epidemiology
dc.subjectMissense variants
dc.subjectRisk prediction
dc.subjectBreast Neoplasms
dc.subjectCase-Control Studies
dc.subjectFemale
dc.subjectGenetic Predisposition to Disease
dc.subjectHumans
dc.subjectMutation, Missense
dc.titleBreast cancer risks associated with missense variants in breast cancer susceptibility genes.
dc.typeArticle
dcterms.dateAccepted2022-05-04
prism.issueIdentifier1
prism.publicationNameGenome Med
prism.volume14
pubs.funder-project-idWellcome Trust (203477/Z/16/Z)
pubs.funder-project-idEuropean Commission Horizon 2020 (H2020) Societal Challenges (634935)
pubs.funder-project-idEuropean Commission Horizon 2020 (H2020) Societal Challenges (633784)
pubs.funder-project-idCancer Research UK (16563)
rioxxterms.licenseref.urihttps://creativecommons.org/licenses/by/4.0/
rioxxterms.versionVoR
rioxxterms.versionofrecord10.1186/s13073-022-01052-8

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