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1. Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes

Author

Fachal, L., Aschard, H., Beesley, J., Barnes, D.R., Allen, J., Kar, S., Pooley, K.A., Dennis, J., Michailidou, K., Turman, C., Soucy, P., Lemaçon, A., Lush, M., Tyrer, J.P., Ghoussaini, M., Marjaneh, M.M., Jiang, X., Agata, S., Aittomäki, K., Alonso, M.R., Andrulis, I.L., Anton-Culver, H., Antonenkova, N.N., Arason, A., Arndt, V., Aronson, K.J., Arun, B.K., Auber, B., Auer, P.L., Azzollini, J., Balmaña, J., Barkardottir, R.B., Barrowdale, D., Beeghly-Fadiel, A., Benitez, J., Bermisheva, M., Białkowska, K., Blanco, A.M., Blomqvist, C., Blot, W., Bogdanova, N.V., Bojesen, S.E., Bolla, M.K., Bonanni, B., Borg, A., Bosse, K., Brauch, H., Brenner, H., Briceno, I., Brock, I.W., Brooks-Wilson, A., Brüning, T., Burwinkel, B., Buys, S.S., Cai, Q., Caldés, T., Caligo, M.A., Camp, N.J., Campbell, I., Canzian, F., Carroll, J.S., Carter, B.D., Castelao, J.E., Chiquette, J., Christiansen, H., Chung, W.K., Claes, K.B.M., Clarke, C.L., Mari, V., Berthet, P., Castera, L., Vaur, D., Lallaoui, H., Bignon, Y.-J., Uhrhammer, N., Bonadona, V., Lasset, C., Révillion, F., Vennin, P., Muller, D., Gomes, D.M., Ingster, O., Coupier, I., Pujol, P., Collonge-Rame, M.-A., Mortemousque, I., Bera, O., Rose, M., Baurand, A., Bertolone, G., Faivre, L., Dreyfus, H., Leroux, D., Venat-Bouvet, L., Bézieau, S., Delnatte, C., Chiesa, J., Gilbert-Dussardier, B., Gesta, P., Prieur, F.P., Bronner, M., Sokolowska, J., Coulet, F., Boutry-Kryza, N., Calender, A., Giraud, S., Leone, M., Fert-Ferrer, S., Stoppa-Lyonnet, D., Jiao, Y., Lesueur, F.L., Mebirouk, N., Barouk-Simonet, E., Bubien, V., Longy, M., Sevenet, N., Gladieff, L., Toulas, C., Reimineras, A., Sobol, H., Paillerets, B.B.-D., Cabaret, O., Caron, O., Guillaud-Bataille, M., Rouleau, E., Belotti, M., Buecher, B., Caputo, S., Colas, C., Pauw, A.D., Fourme, E., Gauthier-Villars, M., Golmard, L., Moncoutier, V., Saule, C., Donaldson, A., Murray, A., Brady, A., Brewer, C., Pottinger, C., Miller, C., Gallagher, D., Gregory, H., Cook, J., Eason, J., Adlard, J., Barwell, J., Ong, K.-R., Snape, K., Walker, L., Izatt, L., Side, L., Tischkowitz, M., Rogers, M.T., Porteous, M.E., Ahmed, M., Morrison, P.J., Brennan, P., Eeles, R., Davidson, R., Collée, M., Cornelissen, S., Couch, F.J., Cox, A., Cross, S.S., Cybulski, C., Czene, K., Daly, M.B., de la Hoya, M., Devilee, P., Diez, O., Ding, Y.C., Dite, G.S., Domchek, S.M., Dörk, T., dos-Santos-Silva, I., Droit, A., Dubois, S., Dumont, M., Duran, M., Durcan, L., Dwek, M., Eccles, D.M., Engel, C., Eriksson, M., Evans, D.G., Fasching, P.A., Fletcher, O., Floris, G., Flyger, H., Foretova, L., Foulkes, W.D., Friedman, E., Fritschi, L., Frost, D., Gabrielson, M., Gago-Dominguez, M., Gambino, G., Ganz, P.A., Gapstur, S.M., Garber, J., García-Sáenz, J.A., Gaudet, M.M., Georgoulias, V., Giles, G., Glendon, G., Godwin, A.K., Goldberg, M.S., Goldgar, D.E., González-Neira, A., Tibiletti, M.G., Greene, M.H., Grip, M., Gronwald, J., Grundy, A., Guénel, P., Hahnen, E., Haiman, C.A., Håkansson, N., Hall, P., Hamann, U., Harrington, P.A., Hartikainen, J.M., Hartman, M., He, W., Healey, C.S., Heemskerk-Gerritsen, B.A.M., Heyworth, J., Hillemanns, P., Hogervorst, F.B.L., Hollestelle, A., Hooning, M., Hopper, J., Howell, A., Huang, G., Hulick, P.J., Imyanitov, E.N., Sexton, A., Christian, A., Trainer, A., Spigelman, A., Fellows, A., Shelling, A., Fazio, A.D., Blackburn, A., Crook, A., Meiser, B., Patterson, B., Clarke, C., Saunders, C., Hunt, C., Scott, C., Amor, D., Marsh, D., Edkins, E., Salisbury, E., Haan, E., Neidermayr, E., Macrea, F., Farshid, G., Lindeman, G., Chenevix-Trench, G., Mann, G., Gill, G., Thorne, H., Hickie, I., Winship, I., Flanagan, J., Kollias, J., Visvader, J., Stone, J., Taylor, J., Burke, J., Saunus, J., Forbes, J., Kirk, J., French, J., Tucker, K., Wu, K., Phillips, K., Lipton, L., Andrews, L., Lobb, L., Kentwell, M., Spurdle, M., Cummings, M., Gleeson, M., Harris, M., Jenkins, M., Young, M.A., Delatycki, M., Wallis, M., Burgess, M., Price, M., Brown, M., Southey, M., Bogwitz, M., Field, M., Friedlander, M., Gattas, M., Saleh, M., Hayward, N., Pachter, N., Cohen, P., Duijf, P., James, P., Simpson, P., Fong, P., Butow, P., Williams, R., Kefford, R., Scott, R., Milne, R.L., Balleine, R., Dawson, S.–J., Lok, S., O’Connell, S., Greening, S., Nightingale, S., Edwards, S., Fox, S., McLachlan, S.-A., Lakhani, S., Antill, Y., Aalfs, C., Meijers-Heijboer, H., van Engelen, K., Gille, H., Boere, I., van Deurzen, C., Obdeijn, I.-M., van den Ouweland, A., Seynaeve, C., Siesling, S., Verloop, J., van Asperen, C.J., van Cronenburg, T., Blok, R., de Boer, M., Garcia, E.G., Adank, M., Hogervorst, F., Jenner, D., van Leeuwen, F., Rookus, M., Russell, N., Schmidt, M., van den Belt-Dusebout, S., Kets, C., Mensenkamp, A., de Bock, T., van der Hout, A., Mourits, M., Oosterwijk, J., Ausems, M., Koudijs, M., Baxter, R., Yip, D., Carpenter, J., Davis, A., Pathmanathan, N., Graham, D., Sachchithananthan, M., Isaacs, C., Iwasaki, M., Jager, A., Jakimovska, M., Jakubowska, A., James, P.A., Janavicius, R., Jankowitz, R.C., John, E.M., Johnson, N., Jones, M.E., Jukkola-Vuorinen, A., Jung, A., Kaaks, R., Kang, D., Kapoor, P.M., Karlan, B.Y., Keeman, R., Kerin, M.J., Khusnutdinova, E., Kiiski, J.I., Kitahara, C.M., Ko, Y.-D., Konstantopoulou, I., Kosma, V.-M., Koutros, S., Kubelka-Sabit, K., Kwong, A., Kyriacou, K., Laitman, Y., Lambrechts, D., Lee, E., Leslie, G., Lester, J., Lesueur, F., Lindblom, A., Lo, W.-Y., Long, J., Lophatananon, A., Loud, J.T., Lubiński, J., MacInnis, R.J., Maishman, T., Makalic, E., Mannermaa, A., Manoochehri, M., Manoukian, S., Margolin, S., Martinez, M.E., Matsuo, K., Maurer, T., Mavroudis, D., Mayes, R., McGuffog, L., McLean, C., Meindl, A., Miller, A., Miller, N., Montagna, M., Moreno, F., Muir, K., Mulligan, A.M., Muñoz-Garzon, V.M., Muranen, T.A., Narod, S.A., Nassir, R., Nathanson, K.L., Neuhausen, S.L., Nevanlinna, H., Neven, P., Nielsen, F.C., Nikitina-Zake, L., Norman, A., Offit, K., Olah, E., Olopade, O.I., Olsson, H., Orr, N., Osorio, A., Pankratz, V.S., Papp, J., Park, S.K., Park-Simon, T.-W., Parsons, M.T., Paul, J., Pedersen, I.S., Peissel, B., Peshkin, B., Peterlongo, P., Peto, J., Plaseska-Karanfilska, D., Prajzendanc, K., Prentice, R., Presneau, N., Prokofyeva, D., Pujana, M.A., Pylkäs, K., Radice, P., Ramus, S.J., Rantala, J., Rau-Murthy, R., Rennert, G., Risch, H.A., Robson, M., Romero, A., Rossing, M., Saloustros, E., Sánchez-Herrero, E., Sandler, D.P., Santamariña, M., Sawyer, E.J., Scheuner, M.T., Schmidt, D.F., Schmutzler, R.K., Schneeweiss, A., Schoemaker, M.J., Schöttker, B., Schürmann, P., Scott, R.J., Senter, L., Seynaeve, C.M., Shah, M., Sharma, P., Shen, C.-Y., Shu, X.-O., Singer, C.F., Slavin, T.P., Smichkoska, S., Southey, M.C., Spinelli, J.J., Spurdle, A.B., Sutter, C., Swerdlow, A.J., Tamimi, R.M., Tan, Y.Y., Tapper, W.J., Taylor, J.A., Teixeira, M.R., Tengström, M., Teo, S.H., Terry, M.B., Teulé, A., Thomassen, M., Thull, D.L., Toland, A.E., Tollenaar, R.A.E.M., Tomlinson, I., Torres, D., Torres-Mejía, G., Troester, M.A., Truong, T., Tung, N., Tzardi, M., Ulmer, H.-U., Vachon, C.M., van der Kolk, L.E., van Rensburg, E.J., Vega, A., Viel, A., Vijai, J., Vogel, M.J., Wang, Q., Wappenschmidt, B., Weinberg, C.R., Weitzel, J.N., Wendt, C., Wildiers, H., Winqvist, R., Wolk, A., Wu, A.H., Yannoukakos, D., Zhang, Y., Zheng, W., Hunter, D., Pharoah, P.D.P., Chang-Claude, J., García-Closas, M., Schmidt, M.K., Kristensen, V.N., French, J.D., Edwards, S.L., Antoniou, A.C., Simard, J., Easton, D.F., Kraft, P., Dunning, A.M., Collaborators, GEMO Study, Collaborators, EMBRACE, Investigators, KConFab, Investigators, HEBON, Investigators, ABCTB, Fachal, Laura, Aschard, Hugues, Beesley, Jonathan, Barnes, Daniel R, Duijf, Pascal, Dunning, Alison M, GEMO Study Collaborators, EMBRACE Collaborators, KConFab Investigators, HEBON Investigators, ABCTB Investigators, MUMC+: MA Medische Oncologie (9), RS: GROW - R3 - Innovative Cancer Diagnostics & Therapy, Klinische Genetica, MUMC+: DA KG Polikliniek (9), RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA KG Lab Centraal Lab (9), European Commission, Government of Canada, Canadian Institutes of Health Research, National Institutes of Health (US), Cancer Research UK, Département de Biologie Computationnelle - Department of Computational Biology, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), QIMR Berghofer Medical Research Institute, University of Cambridge [UK] (CAM), NSCAD, University of Cyprus [Nicosia], Harvard T.H. Chan School of Public Health, This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Sklodowska-Curie grant agreement number 656144. Genotyping of the OncoArray was principally funded from three sources: the PERSPECTIVE project (funded by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research, the ‘Ministère de l’Économie de la Science et de l’Innovation du Québec’ (through Genome Québec) and the Quebec Breast Cancer Foundation), the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) initiative and the Discovery, Biology and Risk of Inherited Variants in Breast Cancer (DRIVE) project (NIH grants U19 CA148065 and X01HG007492), and Cancer Research UK (C1287/A10118, C8197/A16565 and C1287/A16563). BCAC is funded by Cancer Research UK (C1287/A16563), by the European Community’s Seventh Framework Programme under grant agreement 223175 (HEALTH-F2-2009-223175) (COGS) and by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreements 633784 (B-CAST) and 634935 (BRIDGES). Genotyping of the iCOGS array was funded by the European Union (HEALTH-F2-2009-223175), Cancer Research UK (C1287/A10710), the Canadian Institutes of Health Research for the ‘CIHR Team in Familial Risks of Breast Cancer’ program, and the Ministry of Economic Development, Innovation and Export Trade of Quebec (grant PSR-SIIRI-701). Combining of the GWAS data was supported in part by NIH Cancer Post-Cancer GWAS initiative grant U19 CA 148065 (DRIVE, part of the GAME-ON initiative). For a full description of funding and acknowledgments, see the Supplementary Note., We thank all of the individuals who took part in these studies, as well as all of the researchers, clinicians, technicians and administrative staff who enabled this work to be carried out, European Project: 656144,H2020,H2020-MSCA-IF-2014,RADIOGENFF(2016), European Project: 223175,EC:FP7:HEALTH,FP7-HEALTH-2007-B,COGS(2009), European Project: 633784,H2020,H2020-PHC-2014-two-stage,B-CAST(2015), European Project: 634935,H2020,H2020-PHC-2014-two-stage,BRIDGES(2015), Clinical Genetics, Medical Oncology, Pathology, Radiology & Nuclear Medicine, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Cyprus [Nicosia] (UCY), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Damage and Repair in Cancer Development and Cancer Treatment (DARE), Life Course Epidemiology (LCE), Targeted Gynaecologic Oncology (TARGON), ​Basic and Translational Research and Imaging Methodology Development in Groningen (BRIDGE), Aschard, Hugues [0000-0002-7554-6783], Barnes, Daniel R [0000-0002-3781-7570], Dennis, Joe [0000-0003-4591-1214], Michailidou, Kyriaki [0000-0001-7065-1237], Lemaçon, Audrey [0000-0002-1817-7029], Andrulis, Irene L [0000-0002-4226-6435], Arason, Adalgeir [0000-0003-0480-886X], Arndt, Volker [0000-0001-9320-8684], Auber, Bernd [0000-0003-1880-291X], Azzollini, Jacopo [0000-0002-9364-9778], Bojesen, Stig E [0000-0002-4061-4133], Bonanni, Bernardo [0000-0003-3589-2128], Brauch, Hiltrud [0000-0001-7531-2736], Campbell, Ian [0000-0002-7773-4155], Carroll, Jason S [0000-0003-3643-0080], Claes, Kathleen BM [0000-0003-0841-7372], Collée, J Margriet [0000-0002-9272-9346], Devilee, Peter [0000-0002-8023-2009], Dörk, Thilo [0000-0002-9458-0282], Dwek, Miriam [0000-0001-7184-2932], Fletcher, Olivia [0000-0001-9387-7116], Floris, Giuseppe [0000-0003-2391-5425], Foulkes, William D [0000-0001-7427-4651], García-Sáenz, José A [0000-0001-6880-0301], Greene, Mark H [0000-0003-1852-9239], Guénel, Pascal [0000-0002-8359-518X], Heemskerk-Gerritsen, Bernadette AM [0000-0002-9724-6693], Hollestelle, Antoinette [0000-0003-1166-1966], Hulick, Peter J [0000-0001-8397-4078], Jakimovska, Milena [0000-0002-1506-0669], Jakubowska, Anna [0000-0002-5650-0501], James, Paul A [0000-0002-4361-4657], Jones, Michael E [0000-0001-7479-3451], Kapoor, Pooja Middha [0000-0001-5503-8215], Keeman, Renske [0000-0002-5452-9933], Konstantopoulou, Irene [0000-0002-0470-0309], Leslie, Goska [0000-0001-5756-6222], Lesueur, Fabienne [0000-0001-7404-4549], Matsuo, Keitaro [0000-0003-1761-6314], McLean, Catriona [0000-0002-0302-5727], Miller, Austin [0000-0001-9739-8462], Muir, Kenneth [0000-0001-6429-988X], Muranen, Taru A [0000-0002-5895-1808], Nathanson, Katherine L [0000-0002-6740-0901], Nevanlinna, Heli [0000-0002-0916-2976], Olopade, Olufunmilayo I [0000-0002-9936-1599], Orr, Nick [0000-0003-2866-942X], Pankratz, V Shane [0000-0002-3742-040X], Parsons, Michael T [0000-0003-3242-8477], Paul, James [0000-0001-7367-5816], Peshkin, Beth [0000-0002-2997-4701], Peterlongo, Paolo [0000-0001-6951-6855], Peto, Julian [0000-0002-1685-8912], Plaseska-Karanfilska, Dijana [0000-0001-8877-2416], Pylkäs, Katri [0000-0002-2449-0521], Radice, Paolo [0000-0001-6298-4111], Rennert, Gad [0000-0002-8512-068X], Robson, Mark [0000-0002-3109-1692], Romero, Atocha [0000-0002-1634-7397], Saloustros, Emmanouil [0000-0002-0485-0120], Scott, Christopher [0000-0003-1340-0647], Scott, Rodney J [0000-0001-7724-3404], Spurdle, Amanda B [0000-0003-1337-7897], Stone, Jennifer [0000-0001-5077-0124], Sutter, Christian [0000-0003-4051-5888], Tan, Yen Yen [0000-0003-1063-5352], Teixeira, Manuel R [0000-0002-4896-5982], Toland, Amanda E [0000-0002-0271-1792], Tomlinson, Ian [0000-0003-3037-1470], Viel, Alessandra [0000-0003-2804-0840], Vijai, Joseph [0000-0002-7933-151X], Wolk, Alicja [0000-0001-7387-6845], Yannoukakos, Drakoulis [0000-0001-7509-3510], Pharoah, Paul DP [0000-0001-8494-732X], Schmidt, Marjanka K [0000-0002-2228-429X], Milne, Roger L [0000-0001-5764-7268], Edwards, Stacey L [0000-0001-7428-4139], Simard, Jacques [0000-0001-6906-3390], Easton, Douglas F [0000-0003-2444-3247], Kraft, Peter [0000-0002-4472-8103], Dunning, Alison M [0000-0001-6651-7166], Apollo - University of Cambridge Repository, Academic Medical Center, ARD - Amsterdam Reproduction and Development, Human genetics, CCA - Cancer biology and immunology, Molecular cell biology and Immunology, Medicum, Kristiina Aittomäki / Principal Investigator, HUSLAB, Department of Medical and Clinical Genetics, University of Helsinki, HUS Comprehensive Cancer Center, Department of Oncology, Clinicum, Doctoral Programme in Clinical Research, Staff Services, INDIVIDRUG - Individualized Drug Therapy, HUS Gynecology and Obstetrics, and Department of Obstetrics and Gynecology

Subjects
CHROMATIN, Linkage disequilibrium, Genome-wide association study, Regulatory Sequences, Nucleic Acid, Genome-wide association studies, Linkage Disequilibrium, Basic medicine, 0302 clinical medicine, Breast cancer, MESH: Risk Factors, Risk Factors, COMPREHENSIVE MOLECULAR PORTRAITS, 11 Medical and Health Sciences, HEBON Investigators, Genetics & Heredity, 0303 health sciences, [STAT.AP]Statistics [stat]/Applications [stat.AP], PROTEIN FUNCTION, Tumor, breast tumor, MESH: Polymorphism, Single Nucleotide, 1184 Genetics, developmental biology, physiology, MESH: Genetic Predisposition to Disease, apoptosis, Chromosome Mapping, Single Nucleotide, 3. Good health, MESH: Linkage Disequilibrium, Female, MESH: Biomarkers, Tumor, Biomarkers, Tumor/genetics, [STAT.ME]Statistics [stat]/Methodology [stat.ME], Life Sciences & Biomedicine, SUSCEPTIBILITY LOCI, MESH: Bayes Theorem, Quantitative Trait Loci, ABCTB Investigators, INTEGRATIVE ANALYSIS, Breast Neoplasms, Computational biology, Biology, Quantitative trait locus, Breast Neoplasms/genetics, Polymorphism, Single Nucleotide, Article, ENHANCER, GEMO Study Collaborators, 03 medical and health sciences, breast cancer, SDG 3 - Good Health and Well-being, REVEALS, Genetics, Biomarkers, Tumor, MESH: Regulatory Sequences, Nucleic Acid, Humans, Genetic Predisposition to Disease, Polymorphism, GENOME-WIDE ASSOCIATION, FUNCTIONAL VARIANTS, EMBRACE Collaborators, Gene, 030304 developmental biology, Genetic association, Bayes Theorem, Genome-Wide Association Study, MESH: Humans, Science & Technology, Nucleic Acid, gene mapping, 06 Biological Sciences, MESH: Quantitative Trait Loci, DNA binding site, ESTROGEN-RECEPTOR, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Clinical medicine, Expression quantitative trait loci, MESH: Genome-Wide Association Study, Human genome, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, KConFab Investigators, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Chromosome Mapping, Chromosome Mapping/methods, Regulatory Sequences, MESH: Female, Biomarkers, 030217 neurology & neurosurgery, MESH: Breast Neoplasms, Developmental Biology
Abstract

Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes., This work was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Sklodowska-Curie grant agreement number 656144. Genotyping of the OncoArray was principally funded from three sources: the PERSPECTIVE project (funded by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research, the ‘Ministère de l’Économie de la Science et de l’Innovation du Québec’ (through Genome Québec) and the Quebec Breast Cancer Foundation); the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) initiative and the Discovery, Biology and Risk of Inherited Variants in Breast Cancer (DRIVE) project (NIH grants U19 CA148065 and X01HG007492); and Cancer Research UK (C1287/A10118, C8197/A16565 and C1287/A16563). BCAC is funded by Cancer Research UK (C1287/A16563), by the European Community’s Seventh Framework Programme under grant agreement 223175 (HEALTH-F2-2009-223175) (COGS) and by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreements 633784 (B-CAST) and 634935 (BRIDGES). Genotyping of the iCOGS array was funded by the European Union (HEALTH-F2-2009-223175), Cancer Research UK (C1287/A10710), the Canadian Institutes of Health Research for the ‘CIHR Team in Familial Risks of Breast Cancer’ program, and the Ministry of Economic Development, Innovation and Export Trade of Quebec (grant PSR-SIIRI-701). Combining of the GWAS data was supported in part by NIH Cancer Post-Cancer GWAS initiative grant U19 CA 148065 (DRIVE; part of the GAME-ON initiative).

Published
2020

2. Shared heritability and functional enrichment across six solid cancers (vol 10, 431, 2019)

Author

Jiang, X., Finucane, H.K., Schumacher, F.R., Schmit, S.L., Tyrer, J.P., Han, Y., Michailidou, K., Lesseur, C., Kuchenbaecker, K.B., Dennis, J., Conti, D.V., Casey, G., Gaudet, M.M., Huyghe, J.R., Albanes, D., Aldrich, M.C., Andrew, A.S., Andrulis, I.L., Anton-Culver, H., Antoniou, A.C., Antonenkova, N.N., Arnold, S.M., Aronson, K.J., Arun, B.K., Bandera, E.V., Barkardottir, R.B., Barnes, D.R., Batra, J., Beckmann, M.W., Benitez, J., Benlloch, S., Berchuck, A., Berndt, S.I., Bickeboller, H., Bien, S.A., Blomqvist, C., Boccia, S., Bogdanova, N.V., Bojesen, S.E., Bolla, M.K., Brauch, H., Brenner, H., Brenton, J.D., Brook, M.N., Brunet, J., Brunnstrom, H., Buchanan, D.D., Burwinkel, B., Butzow, R., Cadoni, G., Caldes, T., Caligo, M.A., Campbell, I., Campbell, P.T., Cancel-Tassin, G., Cannon-Albright, L., Campa, D., Caporaso, N., Carvalho, A.L., Chan, A.T., Chang-Claude, J., Chanock, S.J., Chen, C., Christiani, D.C., Claes, K.B.M., Claessens, F., Clements, J., Collee, J.M., Correa, M.C., Couch, F.J., Cox, A., Cunningham, J.M., Cybulski, C., Czene, K., Daly, M.B., deFazio, A., Devilee, P., Diez, O., Gago-Dominguez, M., Donovan, J.L., Dork, T., Duell, E.J., Dunning, A.M., Dwek, M., Eccles, D.M., Edlund, C.K., Edwards, D.R.V., Ellberg, C., Evans, D.G., Fasching, P.A., Ferris, R.L., Liloglou, T., Figueiredo, J.C., Fletcher, O., Fortner, R.T., Fostira, F., Franceschi, S., Friedman, E., Gallinger, S.J., Ganz, P.A., Garber, J., Garcia-Saenz, J.A., Gayther, S.A., Giles, G.G., Godwin, A.K., Goldberg, M.S., Goldgar, D.E., Goode, E.L., Goodman, M.T., Goodman, G., Grankvist, K., Greene, M.H., Gronberg, H., Gronwald, J., Guenel, P., Hakansson, N., Hall, P., Hamann, U., Hamdy, F.C., Hamilton, R.J., Hampe, J., Haugen, A., Heitz, F., Herrero, R., Hillemanns, P., Hoffmeister, M., Hogdall, E., Hong, Y.C., Hopper, J.L., Houlston, R., Hulick, P.J., Hunter, D.J., Huntsman, D.G., Idos, G., Imyanitov, E.N., Ingles, S.A., Isaacs, C., Jakubowska, A., James, P., Jenkins, M.A., Johansson, M., John, E.M., Joshi, A.D., Kaneva, R., Karlan, B.Y., Kelemen, L.E., Kuhl, T., Khaw, K.T., Khusnutdinova, E., Kibel, A.S., Kiemeney, L.A., Kim, J., Kjaer, S.K., Knight, J.A., Kogevinas, M., Kote-Jarai, Z., Koutros, S., Kristensen, V.N., Kupryjanczyk, J., Lacko, M., Lam, S., Lambrechts, D., Landi, M.T., Lazarus, P., N.D. le, Lee, E., Lejbkowicz, F., Lenz, H.J., Leslie, G., Lessel, D., Lester, J., Levine, D.A., Li, L., Li, C.I., Lindblom, A., Lindor, N.M., Liu, G., Loupakis, F., Lubinski, J., Maehle, L., Maier, C., Mannermaa, A., Marchand, L., Margolin, S., May, T., McGuffog, L., Meindl, A., Middha, P., Miller, A., Milne, R.L., MacInnis, R.J., Modugno, F., Montagna, M., Moreno, V., Moysich, K.B., Mucci, L., Muir, K., Mulligan, A.M., Nathanson, K.L., Neal, D.E., Ness, A.R., Neuhausen, S.L., Nevanlinna, H., Newcomb, P.A., Newcomb, L.F., Nielsen, F.C., Nikitina-Zake, L., Nordestgaard, B.G., Nussbaum, R.L., Offit, K., Olah, E., Olama, A.A. al, Olopade, O.I., Olshan, A.F., Olsson, H., Osorio, A., Pandha, H., Park, J.Y., Pashayan, N., Parsons, M.T., Pejovic, T., Penney, K.L., Peters, W.H.M., Phelan, C.M., Phipps, A.I., Plaseska-Karanfilska, D., Pring, M., Prokofyeva, D., Radice, P., Stefansson, K., Ramus, S.J., Raskin, L., Rennert, G., Rennert, H.S., Rensburg, E.J., Riggan, M.J., Risch, H.A., Risch, A., Roobol, M.J., Rosenstein, B.S., Rossing, M.A., Ruyck, K., Saloustros, E., Sandler, D.P., Sawyer, E.J., Schabath, M.B., Schleutker, J., Schmidt, M.K., Setiawan, V.W., Shen, H.B., Siegel, E.M., Sieh, W., Singer, C.F., Slattery, M.L., Sorensen, K.D., Southey, M.C., Spurdle, A.B., Stanford, J.L., Stevens, V.L., Stintzing, S., Stone, J., Sundfeldt, K., Sutphen, R., Swerdlow, A.J., Tajara, E.H., Tangen, C.M., Tardon, A., Taylor, J.A., Teare, M.D., Teixeira, M.R., Terry, M.B., Terry, K.L., Thibodeau, S.N., Thomassen, M., Bjorge, L., Tischkowitz, M., Toland, A.E., Torres, D., Townsend, P.A., Travis, R.C., Tung, N., and Tworoger

Published
2019

3. Two truncating variants in FANCC and breast cancer risk

Author

Dork, T., Peterlongo, P., Mannermaa, A., Bolla, M.K., Wang, Q., Dennis, J., Ahearn, T., Andrulis, I.L., Anton-Culver, H., Arndt, V., Aronson, K.J., Augustinsson, A., Freeman, L.E.B., Beckmann, M.W., Beeghly-Fadiel, A., Behrens, S., Bermisheva, M., Blomqvist, C., Bogdanova, N., Bojesen, S.E., Brauch, H., Brenner, H., Burwinkel, B., Canzian, F., Chan, T.L., Chang-Claude, J., Chanock, S.J., Choi, J.Y., Christiansen, H., Clarke, C.L., Couch, F.J., Czene, K., Daly, M.B., dos-Santos-Silva, I., Dwek, M., Eccles, D.M., Ekici, A.B., Eriksson, M., Evans, D.G., Fasching, P.A., Figueroa, J., Flyger, H., Fritschisl, L., Gabrielson, M., Gago-Dominguez, M., Gao, C., Gapstur, S.M., Garcia-Closas, M., Garcia-Saenz, J.A., Gaudet, M.M., Giles, G.G., Goldberg, M.S., Goldgar, D.E., Guenel, P., Haeberle, L., Haiman, C.A., Hakansson, N., Hall, P., Hamann, U., Hartman, M., Hauke, J., Hein, A., Hillemanns, P., Hogervorst, F.B.L., Hooning, M.J., Hopper, J.L., Howell, T., Huo, D.Z., Ito, H., Iwasaki, M., Jakubowska, A., Janni, W., John, E.M., Jung, A., Kaaks, R., Kang, D., Kapoor, P.M., Khusnutdinova, E., Kim, S.W., Kitahara, C.M., Koutros, S., Kraft, P., Kristensen, V.N., Kwon, A., Lambrechts, D., Marchand, L. le, Li, J.M., Lindstrom, S., Linet, M., W.Y. lo, Long, J.R., Lophatananon, A., Lubinski, J., Manoochehri, M., Manoukian, S., Margolin, S., Martinez, E., Matsuo, K., Mavroudis, D., Meindl, A., Menon, U., Milne, R.L., Taib, N.A.M., Muir, K., Mulligan, A.M., Neuhausen, S.L., Nevanlinna, H., Neven, P., Newman, W.G., Offit, K., Olopade, O.I., Olshan, A.F., Olson, J.E., Olsson, H., Park, S.K., Park-Simon, T.W., Peto, J., Plaseska-Karanfilska, D., Pohl-Rescigno, E., Presneau, N., Rack, B., Radice, P., Rashid, M.U., Rennert, G., Rennert, H.S., Romero, A., Ruebner, M., Saloustros, E., Schmidt, M.K., Schmutzler, R.K., Schneider, M.O., Schoemaker, M.J., Scott, C., Shen, C.Y., Shu, X.O., Simard, J., Slager, S., Smichkoska, S., Southey, M.C., Spinelli, J.J., Stone, J., Surowy, H., Swerdlow, A.J., Tamimi, R.M., Tapper, W.J., Teo, S.H., Terry, M.B., Toland, A.E., Tollenaar, R.A.E.M., Torres, D., Torres-Mejia, G., Troester, M.A., Truong, T., Tsugane, S., Untch, M., Vachon, C.M., Ouweland, A.M.W. van den, Veen, E.M. van, Vijai, J., Wendt, C., Wolk, A., Yu, J.C., Zheng, W., Ziogas, A., Ziv, E., Dunning, A.M., Pharoah, P.D.P., Schindler, D., Devilee, P., Easton, D.F., Balleine, R., Baxter, R., Braye, S., Carpenter, J., Dahlstrom, J., Forbes, J., Lee, C.S., Marsh, D., Morey, A., Pathmanathan, N., Scott, R., Simpson, P., Spigelman, A., Wilcken, N., Yip, D., Zeps, N., Borresen-Dale, A.L., Alnaes, G.I.G., Sahlberg, K.K., Ottestad, L., Karesen, R., Schlichting, E., Holmen, M.M., Sauer, T., Haakensen, V., Engebraten, O., Naume, B., Fossa, A., Kiserud, C.E., Reinertsen, K.V., Helland, A., Riis, M., Geisler, J., ABCTB Investigators, NBCS Collaborators, Andrulis, Irene L [0000-0002-4226-6435], Arndt, Volker [0000-0001-9320-8684], Brauch, Hiltrud [0000-0001-7531-2736], Dwek, Miriam [0000-0001-7184-2932], Ekici, Arif B [0000-0001-6099-7066], Fasching, Peter A [0000-0003-4885-8471], Figueroa, Jonine [0000-0002-5100-623X], Hein, Alexander [0000-0003-2601-3398], Ito, Hidemi [0000-0002-8023-4581], Matsuo, Keitaro [0000-0003-1761-6314], Menon, Usha [0000-0003-3708-1732], Milne, Roger L [0000-0001-5764-7268], Muir, Kenneth [0000-0001-6429-988X], Nevanlinna, Heli [0000-0002-0916-2976], Newman, William G [0000-0002-6382-4678], Peto, Julian [0000-0002-1685-8912], Rennert, Gad [0000-0002-8512-068X], Romero, Atocha [0000-0002-1634-7397], Schmidt, Marjanka K [0000-0002-2228-429X], Scott, Christopher [0000-0003-1340-0647], Stone, Jennifer [0000-0001-5077-0124], Truong, Thérèse [0000-0002-2943-6786], Tsugane, Shoichiro [0000-0003-4105-2774], Ziogas, Argyrios [0000-0003-4529-3727], Dunning, Alison M [0000-0001-6651-7166], Pharoah, Paul DP [0000-0001-8494-732X], Devilee, Peter [0000-0002-8023-2009], Easton, Douglas F [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Andrulis, Irene L. [0000-0002-4226-6435], Ekici, Arif B. [0000-0001-6099-7066], Fasching, Peter A. [0000-0003-4885-8471], Milne, Roger L. [0000-0001-5764-7268], Newman, William G. [0000-0002-6382-4678], Schmidt, Marjanka K. [0000-0002-2228-429X], Dunning, Alison M. [0000-0001-6651-7166], Pharoah, Paul D. P. [0000-0001-8494-732X], Easton, Douglas F. [0000-0003-2444-3247], HUS Comprehensive Cancer Center, Clinicum, University Management, Department of Oncology, University of Helsinki, Department of Obstetrics and Gynecology, HUS Gynecology and Obstetrics, Medical Oncology, and Clinical Genetics

Subjects
0301 basic medicine, Oncology, PROTEIN, lcsh:Medicine, 45/47, 0302 clinical medicine, Fanconi anemia, Genotype, lcsh:Science, Sequence Deletion, Multidisciplinary, BRCA1 Protein, Fanconi Anemia Complementation Group C Protein, 1184 Genetics, developmental biology, physiology, BRCA2 Protein, 3. Good health, BIALLELIC MUTATIONS, DNA-REPAIR, Female, 692/499, Medical Genetics, medicine.medical_specialty, PALB2, 3122 Cancers, ABCTB Investigators, Breast Neoplasms, FANCONIS ANEMIA, Article, 692/4028, NBCS Collaborators, 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Internal medicine, medicine, Humans, NONSENSE MUTATION, Genetic Predisposition to Disease, Medicinsk genetik, 45, business.industry, Genetic heterogeneity, lcsh:R, Case-control study, Genetic Variation, Odds ratio, medicine.disease, GENE, Fanconi Anemia, 030104 developmental biology, Risk factors, Case-Control Studies, lcsh:Q, 3111 Biomedicine, business, 030217 neurology & neurosurgery
Abstract

Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

Published
2019

4. Genome-wide association study of germline variants and breast cancer-specific mortality

Author

Escala-Garcia, M., Guo, Q., Dork, T., Canisius, S., Keeman, R., Dennis, J., Beesley, J., Lecarpentier, J., Bolla, M.K., Wang, Q., Abraham, J., Andrulis, I.L., Anton-Culver, H., Arndt, V., Auer, P.L., Beckmann, M.W., Behrens, S., Benitez, J., Bermisheva, M., Bernstein, L., Blomqvist, C., Boeckx, B., Bojesen, S.E., Bonanni, B., Borresen-Dale, A.L., Brauch, H., Brenner, H., Brentnall, A., Brinton, L., Broberg, P., Brock, I.W., Brucker, S.Y., Burwinkel, B., Caldas, C., Caldes, T., Campa, D., Canzian, F., Carracedo, A., Carter, B.D., Castelao, J.E., Chang-Claude, J., Chanock, S.J., Chenevix-Trench, G., Cheng, T.Y.D., Chin, S.F., Clarke, C.L., Cordina-Duverger, E., Couch, F.J., Cox, D.G., Cox, A., Cross, S.S., Czene, K., Daly, M.B., Devilee, P., Dunn, J.A., Dunning, A.M., Durcan, L., Dwek, M., Earl, H.M., Ekici, A.B., Eliassen, A.H., Ellberg, C., Engel, C., Eriksson, M., Evans, D.G., Figueroa, J., Flesch-Janys, D., Flyger, H., Gabrielson, M., Gago-Dominguez, M., Galle, E., Gapstur, S.M., Garcia-Closas, M., Garcia-Saenz, J.A., Gaudet, M.M., George, A., Georgoulias, V., Giles, G.G., Glendon, G., Goldgar, D.E., Gonzalez-Neira, A., Alnaes, G.I.G., Grip, M., Guenel, P., Haeberle, L., Hahnen, E., Haiman, C.A., Hakansson, N., Hall, P., Hamann, U., Hankinson, S., Harkness, E.F., Harrington, P.A., Hart, S.N., Hartikainen, J.M., Hein, A., Hillemanns, P., Hiller, L., Holleczek, B., Hollestelle, A., Hooning, M.J., Hoover, R.N., Hopper, J.L., Howell, A., Huang, G.M.Q., Humphreys, K., Hunter, D.J., Janni, W., John, E.M., Jones, M.E., Jukkola-Vuorinen, A., Jung, A., Kaaks, R., Kabisch, M., Kaczmarek, K., Kerin, M.J., Khan, S., Khusnutdinova, E., Kiiski, J.I., Kitahara, C.M., Knight, J.A., Ko, Y.D., Koppert, L.B., Kosma, V.M., Kraft, P., Kristensen, V.N., Kruger, U., Kuhl, T., Lambrechts, D., Marchand, L. le, Lee, E., Lejbkowicz, F., Li, L., Lindblom, A., Lindstrom, S., Linet, M., Lissowska, J., W.Y. lo, Loibl, S., Lubinski, J., Lux, M.P., MacInnis, R.J., Maierthaler, M., Maishman, T., Makalic, E., Mannermaa, A., Manoochehri, M., Manoukian, S., Margolin, S., Martinez, M.E., Mavroudis, D., McLean, C., Meindl, A., Middha, P., Miller, N., Milne, R.L., Moreno, F., Mulligan, A.M., Mulot, C., Nassir, R., Neuhausen, S.L., Newman, W.T., Nielsen, S.F., Nordestgaard, B.G., Norman, A., Olsson, H., Orr, N., Pankratz, V.S., Park-Simon, T.W., Perez, J.I.A., Perez-Barrios, C., Peterlongo, P., Petridis, C., Pinchev, M., Prajzendanc, K., Prentice, R., Presneau, N., Prokofieva, D., Pylkas, K., Rack, B., Radice, P., Ramachandran, D., Rennert, G., Rennert, H.S., Rhenius, V., Romero, A., Roylance, R., Saloustros, E., Sawyer, E.J., Schmidt, D.F., Schmutzler, R.K., Schneeweiss, A., Schoemaker, M.J., Schumacher, F., Schwentner, L., Scott, R.J., Scott, C., Seynaeve, C., Shah, M., Simard, J., Smeets, A., Sohn, C., Southey, M.C., Swerdlow, A.J., Talhouk, A., Tamimi, R.M., Tapper, W.J., Teixeira, M.R., Tengstrom, M., Terry, M.B., Thone, K., Tollenaar, R.A.E.M., Tomlinson, I., Torres, D., Truong, T., Turman, C., Turnbull, C., Ulmer, H.U., Untch, M., Vachon, C., Asperen, C.J. van, Ouweland, A.M.W. van den, Veen, E.M. van, Wendt, C., Whittemore, A.S., Willett, W., Winqvist, R., Wolk, A., Yang, X.R., Zhang, Y., Easton, D.F., Fasching, P.A., Nevanlinna, H., Eccles, D.M., Pharoah, P.D.P., Schmidt, M.K., and NBCS Collaborators

Abstract

BACKGROUND: We examined the associations between germline variants and breast cancer mortality using a large meta-analysis of women of European ancestry.METHODS: Meta-analyses included summary estimates based on Cox models of twelve datasets using similar to 10.4 million variants for 96,661 women with breast cancer and 7697 events (breast cancer-specific deaths). Oestrogen receptor (ER)-specific analyses were based on 64,171 ER-positive (4116) and 16,172 ER-negative (2125) patients. We evaluated the probability of a signal to be a true positive using the Bayesian false discovery probability (BFDP).RESULTS: We did not find any variant associated with breast cancer-specific mortality at P

Published
2019

5. Correction to: Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci (Nature Genetics, (2018), 50, 7, (928-936), 10.1038/s41588-018-0142-8).

Author

Xu J., Tyrer J., Truong T., Koudou Y.A., Khaw K.-T., Cannon-Albright L., Pandha H., Michael A., Thibodeau S.N., McDonnell S.K., Schaid D.J., Lindstrom S., Turman C., Ma J., Hunter D.J., Riboli E., Siddiq A., Canzian F., Kolonel L.N., Le Marchand L., Hoover R.N., Machiela M.J., Cui Z., Kraft P., Amos C.I., Conti D.V., Easton D.F., Wiklund F., Chanock S.J., Henderson B.E., Kote-Jarai Z., Haiman C.A., Eeles R.A., Schumacher F.R., Olama A.A.A., Berndt S.I., Benlloch S., Ahmed M., Saunders E.J., Dadaev T., Leongamornlert D., Anokian E., Cieza-Borrella C., Goh C., Brook M.N., Sheng X., Fachal L., Dennis J., Muir K., Lophatananon A., Stevens V.L., Gapstur S.M., Carter B.D., Tangen C.M., Goodman P.J., Thompson I.M., Batra J., Chambers S., Moya L., Clements J., Horvath L., Tilley W., Risbridger G.P., Gronberg H., Aly M., Nordstrom T., Pharoah P., Pashayan N., Schleutker J., Tammela T.L.J., Sipeky C., Auvinen A., Albanes D., Weinstein S., Wolk A., Hakansson N., West C.M.L., Dunning A.M., Burnet N., Mucci L.A., Giovannucci E., Andriole G.L., Cussenot O., Cancel-Tassin G., Koutros S., Beane Freeman L.E., Sorensen K.D., Orntoft T.F., Borre M., Maehle L., Grindedal E.M., Neal D.E., Donovan J.L., Hamdy F.C., Martin R.M., Travis R.C., Key T.J., Hamilton R.J., Fleshner N.E., Finelli A., Ingles S.A., Stern M.C., Rosenstein B.S., Kerns S.L., Ostrer H., Lu Y.-J., Zhang H.-W., Feng N., Mao X., Guo X., Wang G., Sun Z., Giles G.G., Southey M.C., MacInnis R.J., FitzGerald L.M., Kibel A.S., Drake B.F., Vega A., Gomez-Caamano A., Szulkin R., Eklund M., Kogevinas M., Llorca J., Castano-Vinyals G., Penney K.L., Stampfer M., Park J.Y., Sellers T.A., Lin H.-Y., Stanford J.L., Cybulski C., Wokolorczyk D., Lubinski J., Ostrander E.A., Geybels M.S., Nordestgaard B.G., Nielsen S.F., Weischer M., Bisbjerg R., Roder M.A., Iversen P., Brenner H., Cuk K., Holleczek B., Maier C., Luedeke M., Schnoeller T., Kim J., Logothetis C.J., John E.M., Teixeira M.R., Paulo P., Cardoso M., Neuhausen S.L., Steele L., Ding Y.C., De Ruyck K., De Meerleer G., Ost P., Razack A., Lim J., Teo S.-H., Lin D.W., Newcomb L.F., Lessel D., Gamulin M., Kulis T., Kaneva R., Usmani N., Singhal S., Slavov C., Mitev V., Parliament M., Claessens F., Joniau S., Van den Broeck T., Larkin S., Townsend P.A., Aukim-Hastie C., Gago-Dominguez M., Castelao J.E., Martinez M.E., Roobol M.J., Jenster G., van Schaik R.H.N., Menegaux F., Xu J., Tyrer J., Truong T., Koudou Y.A., Khaw K.-T., Cannon-Albright L., Pandha H., Michael A., Thibodeau S.N., McDonnell S.K., Schaid D.J., Lindstrom S., Turman C., Ma J., Hunter D.J., Riboli E., Siddiq A., Canzian F., Kolonel L.N., Le Marchand L., Hoover R.N., Machiela M.J., Cui Z., Kraft P., Amos C.I., Conti D.V., Easton D.F., Wiklund F., Chanock S.J., Henderson B.E., Kote-Jarai Z., Haiman C.A., Eeles R.A., Schumacher F.R., Olama A.A.A., Berndt S.I., Benlloch S., Ahmed M., Saunders E.J., Dadaev T., Leongamornlert D., Anokian E., Cieza-Borrella C., Goh C., Brook M.N., Sheng X., Fachal L., Dennis J., Muir K., Lophatananon A., Stevens V.L., Gapstur S.M., Carter B.D., Tangen C.M., Goodman P.J., Thompson I.M., Batra J., Chambers S., Moya L., Clements J., Horvath L., Tilley W., Risbridger G.P., Gronberg H., Aly M., Nordstrom T., Pharoah P., Pashayan N., Schleutker J., Tammela T.L.J., Sipeky C., Auvinen A., Albanes D., Weinstein S., Wolk A., Hakansson N., West C.M.L., Dunning A.M., Burnet N., Mucci L.A., Giovannucci E., Andriole G.L., Cussenot O., Cancel-Tassin G., Koutros S., Beane Freeman L.E., Sorensen K.D., Orntoft T.F., Borre M., Maehle L., Grindedal E.M., Neal D.E., Donovan J.L., Hamdy F.C., Martin R.M., Travis R.C., Key T.J., Hamilton R.J., Fleshner N.E., Finelli A., Ingles S.A., Stern M.C., Rosenstein B.S., Kerns S.L., Ostrer H., Lu Y.-J., Zhang H.-W., Feng N., Mao X., Guo X., Wang G., Sun Z., Giles G.G., Southey M.C., MacInnis R.J., FitzGerald L.M., Kibel A.S., Drake B.F., Vega A., Gomez-Caamano A., Szulkin R., Eklund M., Kogevinas M., Llorca J., Castano-Vinyals G., Penney K.L., Stampfer M., Park J.Y., Sellers T.A., Lin H.-Y., Stanford J.L., Cybulski C., Wokolorczyk D., Lubinski J., Ostrander E.A., Geybels M.S., Nordestgaard B.G., Nielsen S.F., Weischer M., Bisbjerg R., Roder M.A., Iversen P., Brenner H., Cuk K., Holleczek B., Maier C., Luedeke M., Schnoeller T., Kim J., Logothetis C.J., John E.M., Teixeira M.R., Paulo P., Cardoso M., Neuhausen S.L., Steele L., Ding Y.C., De Ruyck K., De Meerleer G., Ost P., Razack A., Lim J., Teo S.-H., Lin D.W., Newcomb L.F., Lessel D., Gamulin M., Kulis T., Kaneva R., Usmani N., Singhal S., Slavov C., Mitev V., Parliament M., Claessens F., Joniau S., Van den Broeck T., Larkin S., Townsend P.A., Aukim-Hastie C., Gago-Dominguez M., Castelao J.E., Martinez M.E., Roobol M.J., Jenster G., van Schaik R.H.N., and Menegaux F.

Abstract

In the version of this article initially published, the name of author Manuela Gago-Dominguez was misspelled as Manuela Gago Dominguez. The error has been corrected in the HTML and PDF version of the article.Copyright © 2018, The Author(s), under exclusive licence to Springer Nature America, Inc.

Published
2019

6. Author Correction: Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci (Nature Genetics, (2018), 50, 7, (928-936), 10.1038/s41588-018-0142-8).

Author

Truong T., Khaw K.-T., Cannon-Albright L., Pandha H., Michael A., Thibodeau S.N., McDonnell S.K., Schaid D.J., Lindstrom S., Turman C., Ma J., Hunter D.J., Riboli E., Siddiq A., Canzian F., Kolonel L.N., Le Marchand L., Hoover R.N., Machiela M.J., Cui Z., Kraft P., Amos C.I., Conti D.V., Easton D.F., Wiklund F., Chanock S.J., Henderson B.E., Kote-Jarai Z., Haiman C.A., Eeles R.A., Schumacher F.R., Olama A.A.A., Berndt S.I., Benlloch S., Ahmed M., Saunders E.J., Dadaev T., Leongamornlert D., Anokian E., Cieza-Borrella C., Goh C., Brook M.N., Sheng X., Fachal L., Dennis J., Tyrer J., Muir K., Lophatananon A., Stevens V.L., Gapstur S.M., Carter B.D., Tangen C.M., Goodman P.J., Thompson I.M., Batra J., Chambers S., Moya L., Clements J., Horvath L., Tilley W., Risbridger G.P., Gronberg H., Aly M., Nordstrom T., Pharoah P., Pashayan N., Schleutker J., Tammela T.L.J., Sipeky C., Auvinen A., Albanes D., Weinstein S., Wolk A., Hakansson N., West C.M.L., Dunning A.M., Burnet N., Mucci L.A., Giovannucci E., Andriole G.L., Cussenot O., Cancel-Tassin G., Koutros S., Beane Freeman L.E., Sorensen K.D., Orntoft T.F., Borre M., Maehle L., Grindedal E.M., Neal D.E., Donovan J.L., Hamdy F.C., Martin R.M., Travis R.C., Key T.J., Hamilton R.J., Fleshner N.E., Finelli A., Ingles S.A., Stern M.C., Rosenstein B.S., Kerns S.L., Ostrer H., Lu Y.-J., Zhang H.-W., Feng N., Mao X., Guo X., Wang G., Sun Z., Giles G.G., Southey M.C., MacInnis R.J., FitzGerald L.M., Kibel A.S., Drake B.F., Vega A., Gomez-Caamano A., Szulkin R., Eklund M., Kogevinas M., Llorca J., Castano-Vinyals G., Penney K.L., Stampfer M., Park J.Y., Sellers T.A., Lin H.-Y., Stanford J.L., Cybulski C., Wokolorczyk D., Lubinski J., Ostrander E.A., Geybels M.S., Nordestgaard B.G., Nielsen S.F., Weischer M., Bisbjerg R., Roder M.A., Iversen P., Brenner H., Cuk K., Holleczek B., Maier C., Luedeke M., Schnoeller T., Kim J., Logothetis C.J., John E.M., Teixeira M.R., Paulo P., Cardoso M., Neuhausen S.L., Steele L., Ding Y.C., De Ruyck K., De Meerleer G., Ost P., Razack A., Lim J., Teo S.-H., Lin D.W., Newcomb L.F., Lessel D., Gamulin M., Kulis T., Kaneva R., Usmani N., Singhal S., Slavov C., Mitev V., Parliament M., Claessens F., Joniau S., Van den Broeck T., Larkin S., Townsend P.A., Aukim-Hastie C., Gago-Dominguez M., Castelao J.E., Martinez M.E., Roobol M.J., Jenster G., van Schaik R.H.N., Menegaux F., Koudou Y.A., Xu J., Truong T., Khaw K.-T., Cannon-Albright L., Pandha H., Michael A., Thibodeau S.N., McDonnell S.K., Schaid D.J., Lindstrom S., Turman C., Ma J., Hunter D.J., Riboli E., Siddiq A., Canzian F., Kolonel L.N., Le Marchand L., Hoover R.N., Machiela M.J., Cui Z., Kraft P., Amos C.I., Conti D.V., Easton D.F., Wiklund F., Chanock S.J., Henderson B.E., Kote-Jarai Z., Haiman C.A., Eeles R.A., Schumacher F.R., Olama A.A.A., Berndt S.I., Benlloch S., Ahmed M., Saunders E.J., Dadaev T., Leongamornlert D., Anokian E., Cieza-Borrella C., Goh C., Brook M.N., Sheng X., Fachal L., Dennis J., Tyrer J., Muir K., Lophatananon A., Stevens V.L., Gapstur S.M., Carter B.D., Tangen C.M., Goodman P.J., Thompson I.M., Batra J., Chambers S., Moya L., Clements J., Horvath L., Tilley W., Risbridger G.P., Gronberg H., Aly M., Nordstrom T., Pharoah P., Pashayan N., Schleutker J., Tammela T.L.J., Sipeky C., Auvinen A., Albanes D., Weinstein S., Wolk A., Hakansson N., West C.M.L., Dunning A.M., Burnet N., Mucci L.A., Giovannucci E., Andriole G.L., Cussenot O., Cancel-Tassin G., Koutros S., Beane Freeman L.E., Sorensen K.D., Orntoft T.F., Borre M., Maehle L., Grindedal E.M., Neal D.E., Donovan J.L., Hamdy F.C., Martin R.M., Travis R.C., Key T.J., Hamilton R.J., Fleshner N.E., Finelli A., Ingles S.A., Stern M.C., Rosenstein B.S., Kerns S.L., Ostrer H., Lu Y.-J., Zhang H.-W., Feng N., Mao X., Guo X., Wang G., Sun Z., Giles G.G., Southey M.C., MacInnis R.J., FitzGerald L.M., Kibel A.S., Drake B.F., Vega A., Gomez-Caamano A., Szulkin R., Eklund M., Kogevinas M., Llorca J., Castano-Vinyals G., Penney K.L., Stampfer M., Park J.Y., Sellers T.A., Lin H.-Y., Stanford J.L., Cybulski C., Wokolorczyk D., Lubinski J., Ostrander E.A., Geybels M.S., Nordestgaard B.G., Nielsen S.F., Weischer M., Bisbjerg R., Roder M.A., Iversen P., Brenner H., Cuk K., Holleczek B., Maier C., Luedeke M., Schnoeller T., Kim J., Logothetis C.J., John E.M., Teixeira M.R., Paulo P., Cardoso M., Neuhausen S.L., Steele L., Ding Y.C., De Ruyck K., De Meerleer G., Ost P., Razack A., Lim J., Teo S.-H., Lin D.W., Newcomb L.F., Lessel D., Gamulin M., Kulis T., Kaneva R., Usmani N., Singhal S., Slavov C., Mitev V., Parliament M., Claessens F., Joniau S., Van den Broeck T., Larkin S., Townsend P.A., Aukim-Hastie C., Gago-Dominguez M., Castelao J.E., Martinez M.E., Roobol M.J., Jenster G., van Schaik R.H.N., Menegaux F., Koudou Y.A., and Xu J.

Abstract

In the version of this article initially published, the name of author Manuela Gago-Dominguez was misspelled as Manuela Gago Dominguez. The error has been corrected in the HTML and PDF version of the article.Copyright © 2018, The Author(s), under exclusive licence to Springer Nature America, Inc.

Published
2019

7. Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci.

Author

Grindedal E.M., Maier C., Luedeke M., Schnoeller T., Kim J., Logothetis C.J., John E.M., Teixeira M.R., Paulo P., Cardoso M., Neuhausen S.L., Steele L., Ding Y.C., De Ruyck K., De Meerleer G., Ost P., Razack A., Lim J., Teo S.-H., Lin D.W., Newcomb L.F., Lessel D., Gamulin M., Kulis T., Kaneva R., Usmani N., Singhal S., Slavov C., Mitev V., Parliament M., Claessens F., Joniau S., Van Den Broeck T., Larkin S., Townsend P.A., Aukim-Hastie C., Dominguez M.G., Castelao J.E., Martinez M.E., Roobol M.J., Jenster G., Van Schaik R.H.N., Menegaux F., Truong T., Koudou Y.A., Xu J., Khaw K.-T., Cannon-Albright L., Pandha H., Michael A., Thibodeau S.N., McDonnell S.K., Schaid D.J., Lindstrom S., Turman C., Ma J., Hunter D.J., Riboli E., Siddiq A., Canzian F., Kolonel L.N., Le Marchand L., Hoover R.N., Machiela M.J., Cui Z., Kraft P., Amos C.I., Conti D.V., Easton D.F., Wiklund F., Chanock S.J., Henderson B.E., Kote-Jarai Z., Haiman C.A., Eeles R.A., Schumacher F.R., Al Olama A.A., Berndt S.I., Benlloch S., Ahmed M., Saunders E.J., Dadaev T., Leongamornlert D., Anokian E., Cieza-Borrella C., Goh C., Brook M.N., Sheng X., Fachal L., Dennis J., Tyrer J., Muir K., Lophatananon A., Stevens V.L., Gapstur S.M., Carter B.D., Tangen C.M., Goodman P.J., Thompson I.M., Batra J., Chambers S., Moya L., Clements J., Horvath L., Tilley W., Risbridger G.P., Gronberg H., Aly M., Nordstrom T., Pharoah P., Pashayan N., Schleutker J., Tammela T.L.J., Sipeky C., Auvinen A., Albanes D., Weinstein S., Wolk A., Hakansson N., West C.M.L., Dunning A.M., Burnet N., Mucci L.A., Giovannucci E., Andriole G.L., Cussenot O., Cancel-Tassin G., Koutros S., Beane Freeman L.E., Sorensen K.D., Orntoft T.F., Borre M., Maehle L., Neal D.E., Donovan J.L., Hamdy F.C., Martin R.M., Travis R.C., Key T.J., Hamilton R.J., Fleshner N.E., Finelli A., Ingles S.A., Stern M.C., Rosenstein B.S., Kerns S.L., Ostrer H., Lu Y.-J., Zhang H.-W., Feng N., Mao X., Guo X., Wang G., Sun Z., Giles G.G., Southey M.C., MacInnis R.J., Fitzgerald L.M., Kibel A.S., Drake B.F., Vega A., Gomez-Caamano A., Szulkin R., Eklund M., Kogevinas M., Llorca J., Castano-Vinyals G., Penney K.L., Stampfer M., Park J.Y., Sellers T.A., Lin H.-Y., Stanford J.L., Cybulski C., Wokolorczyk D., Lubinski J., Ostrander E.A., Geybels M.S., Nordestgaard Bo.G., Nielsen S.F., Weischer M., Bisbjerg R., Roder M.A., Iversen P., Brenner H., Cuk K., Holleczek B., Grindedal E.M., Maier C., Luedeke M., Schnoeller T., Kim J., Logothetis C.J., John E.M., Teixeira M.R., Paulo P., Cardoso M., Neuhausen S.L., Steele L., Ding Y.C., De Ruyck K., De Meerleer G., Ost P., Razack A., Lim J., Teo S.-H., Lin D.W., Newcomb L.F., Lessel D., Gamulin M., Kulis T., Kaneva R., Usmani N., Singhal S., Slavov C., Mitev V., Parliament M., Claessens F., Joniau S., Van Den Broeck T., Larkin S., Townsend P.A., Aukim-Hastie C., Dominguez M.G., Castelao J.E., Martinez M.E., Roobol M.J., Jenster G., Van Schaik R.H.N., Menegaux F., Truong T., Koudou Y.A., Xu J., Khaw K.-T., Cannon-Albright L., Pandha H., Michael A., Thibodeau S.N., McDonnell S.K., Schaid D.J., Lindstrom S., Turman C., Ma J., Hunter D.J., Riboli E., Siddiq A., Canzian F., Kolonel L.N., Le Marchand L., Hoover R.N., Machiela M.J., Cui Z., Kraft P., Amos C.I., Conti D.V., Easton D.F., Wiklund F., Chanock S.J., Henderson B.E., Kote-Jarai Z., Haiman C.A., Eeles R.A., Schumacher F.R., Al Olama A.A., Berndt S.I., Benlloch S., Ahmed M., Saunders E.J., Dadaev T., Leongamornlert D., Anokian E., Cieza-Borrella C., Goh C., Brook M.N., Sheng X., Fachal L., Dennis J., Tyrer J., Muir K., Lophatananon A., Stevens V.L., Gapstur S.M., Carter B.D., Tangen C.M., Goodman P.J., Thompson I.M., Batra J., Chambers S., Moya L., Clements J., Horvath L., Tilley W., Risbridger G.P., Gronberg H., Aly M., Nordstrom T., Pharoah P., Pashayan N., Schleutker J., Tammela T.L.J., Sipeky C., Auvinen A., Albanes D., Weinstein S., Wolk A., Hakansson N., West C.M.L., Dunning A.M., Burnet N., Mucci L.A., Giovannucci E., Andriole G.L., Cussenot O., Cancel-Tassin G., Koutros S., Beane Freeman L.E., Sorensen K.D., Orntoft T.F., Borre M., Maehle L., Neal D.E., Donovan J.L., Hamdy F.C., Martin R.M., Travis R.C., Key T.J., Hamilton R.J., Fleshner N.E., Finelli A., Ingles S.A., Stern M.C., Rosenstein B.S., Kerns S.L., Ostrer H., Lu Y.-J., Zhang H.-W., Feng N., Mao X., Guo X., Wang G., Sun Z., Giles G.G., Southey M.C., MacInnis R.J., Fitzgerald L.M., Kibel A.S., Drake B.F., Vega A., Gomez-Caamano A., Szulkin R., Eklund M., Kogevinas M., Llorca J., Castano-Vinyals G., Penney K.L., Stampfer M., Park J.Y., Sellers T.A., Lin H.-Y., Stanford J.L., Cybulski C., Wokolorczyk D., Lubinski J., Ostrander E.A., Geybels M.S., Nordestgaard Bo.G., Nielsen S.F., Weischer M., Bisbjerg R., Roder M.A., Iversen P., Brenner H., Cuk K., and Holleczek B.

Abstract

Genome-wide association studies (GWAS) and fine-mapping efforts to date have identified more than 100 prostate cancer (PrCa)-susceptibility loci. We meta-analyzed genotype data from a custom high-density array of 46,939 PrCa cases and 27,910 controls of European ancestry with previously genotyped data of 32,255 PrCa cases and 33,202 controls of European ancestry. Our analysis identified 62 novel loci associated (P < 5.0 x 10-8) with PrCa and one locus significantly associated with early-onset PrCa (<=55 years). Our findings include missense variants rs1800057 (odds ratio (OR) = 1.16; P = 8.2 x 10-9; G>C, p.Pro1054Arg) in ATM and rs2066827 (OR = 1.06; P = 2.3 x 10-9; T>G, p.Val109Gly) in CDKN1B. The combination of all loci captured 28.4% of the PrCa familial relative risk, and a polygenic risk score conferred an elevated PrCa risk for men in the ninetieth to ninety-ninth percentiles (relative risk = 2.69; 95% confidence interval (CI): 2.55-2.82) and first percentile (relative risk = 5.71; 95% CI: 5.04-6.48) risk stratum compared with the population average. These findings improve risk prediction, enhance fine-mapping, and provide insight into the underlying biology of PrCa 1 .Copyright © 2018 The Author(s).

Published
2018

8. Genome-Wide Meta-Analyses of Smoking Behaviors in African Americans

Author

Hamidovic, A, Bergen, A W, Wessel, J, Kasberger, J L, Petruzella, S, Thacker, E L, Nalls, M A, Tranah, G J, Ambrosone, C B, Arnett, D, Bandera, E V, Becker, L, Berndt, S I, Blot, W J, Broeckel, U, Buxbaum, S G, Caporaso, N, Chanock, S J, Deming, S L, Diver, W R, Eaton, C B, Fornage, M, Franceschini, N, Hernandez, D G, Hitsman, B, Ingles, S A, Kittles, R, Kolb, S, Kolonel, L N, Le Marchand, L, Lohman, K K, McKnight, B, Millikan, R C, Neslund-Dudas, C, Nyante, S, Press, M, Psaty, B M, Rodriguez-Gil, J L, Rybicki, B A, Singleton, A B, Snively, B, Stanford, J L, Strom, S S, Swan, G E, Thun, M J, Yamamura, Y, Yanek, L R, Ziegler, R G, Zonderman, A B, Jorgenson, E, Haiman, C A, Furberg, H, David, S.P., Chen, G.K., Brown, W.M., Kim, Y., Sung, Y., Becker, D.M., Bernstein, L., Casey, G., Evans, D.S., Evans, M.K., Harris, T.B., Henderson, B.E., Hu, J.J., Hunt, S.C., John, E.M., Liu, Y., Murphy, A., Rao, D.C., Redline, Susan, Signorello, Lisa B., Smoller, Jordan W., Spring, B., Taylor, K.D., Wilson, A.F., Witte, J.S., Yu, K., and Zheng, W.

Abstract

The identification and exploration of genetic loci that influence smoking behaviors have been conducted primarily in populations of the European ancestry. Here we report results of the first genome-wide association study meta-analysis of smoking behavior in African Americans in the Study of Tobacco in Minority Populations Genetics Consortium (n=32 389). We identified one non-coding single-nucleotide polymorphism (SNP; rs2036527[A]) on chromosome 15q25.1 associated with smoking quantity (cigarettes per day), which exceeded genome-wide significance (\(\beta\)=0.040, s.e.=0.007, P=1.84 × 10\(^{−8}\)). This variant is present in the 5′-distal enhancer region of the CHRNA5 gene and defines the primary index signal reported in studies of the European ancestry. No other SNP reached genome-wide significance for smoking initiation (SI, ever vs never smoking), age of SI, or smoking cessation (SC, former vs current smoking). Informative associations that approached genome-wide significance included three modestly correlated variants, at 15q25.1 within PSMA4, CHRNA5 and CHRNA3 for smoking quantity, which are associated with a second signal previously reported in studies in European ancestry populations, and a signal represented by three SNPs in the SPOCK2 gene on chr10q22.1. The association at 15q25.1 confirms this region as an important susceptibility locus for smoking quantity in men and women of African ancestry. Larger studies will be needed to validate the suggestive loci that did not reach genome-wide significance and further elucidate the contribution of genetic variation to disparities in cigarette consumption, SC and smoking-attributable disease between African Americans and European Americans.

Published
2012
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