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1. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Author: Milne, Roger L, Kuchenbaecker, Karoline B, Michailidou, Kyriaki, Beesley, Jonathan, Kar, Siddhartha, Lindström, Sara, Hui, Shirley, Lemaçon, Audrey, Soucy, Penny, Dennis, Joe, Jiang, Xia, Rostamianfar, Asha, Finucane, Hilary, Bolla, Manjeet K, McGuffog, Lesley, Wang, Qin, Aalfs, Cora M, Adams, Marcia, Adlard, Julian, Agata, Simona, Ahmed, Shahana, Ahsan, Habibul, Aittomäki, Kristiina, Al-Ejeh, Fares, Allen, Jamie, Ambrosone, Christine B, Amos, Christopher I, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Arnold, Norbert, Aronson, Kristan J, Auber, Bernd, Auer, Paul L, Ausems, Margreet GEM, Azzollini, Jacopo, Bacot, François, Balmaña, Judith, Barile, Monica, Barjhoux, Laure, Barkardottir, Rosa B, Barrdahl, Myrto, Barnes, Daniel, Barrowdale, Daniel, Baynes, Caroline, Beckmann, Matthias W, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Bignon, Yves-Jean, Blazer, Kathleen R, Blok, Marinus J, Blomqvist, Carl, Blot, William, Bobolis, Kristie, Boeckx, Bram, Bogdanova, Natalia V, Bojesen, Anders, Bojesen, Stig E, Bonanni, Bernardo, Børresen-Dale, Anne-Lise, Bozsik, Aniko, Bradbury, Angela R, Brand, Judith S, Brauch, Hiltrud, Brenner, Hermann, Bressac-de Paillerets, Brigitte, Brewer, Carole, Brinton, Louise, Broberg, Per, Brooks-Wilson, Angela, Brunet, Joan, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S, Byun, Jinyoung, Cai, Qiuyin, Caldés, Trinidad, Caligo, Maria A, Campbell, Ian, Canzian, Federico, Caron, Olivier, Carracedo, Angel, Carter, Brian D, Castelao, J Esteban, Castera, Laurent, Caux-Moncoutier, Virginie, Chan, Salina B, Chang-Claude, Jenny, Chanock, Stephen J, Chen, Xiaoqing, Cheng, Ting-Yuan David, Chiquette, Jocelyne, Christiansen, Hans, Claes, Kathleen BM, Clarke, Christine L, Conner, Thomas, Conroy, Don M, and Cook, Jackie
Subjects: Biological Sciences, Genetics, Cancer, Human Genome, Prevention, Breast Cancer, Aging, Estrogen, 2.1 Biological and endogenous factors, Aetiology, BRCA1 Protein, Breast Neoplasms, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Heterozygote, Humans, Mutation, Polymorphism, Single Nucleotide, Receptors, Estrogen, Risk Factors, White People, ABCTB Investigators, EMBRACE, GEMO Study Collaborators, HEBON, kConFab/AOCS Investigators, NBSC Collaborators, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract: Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10-8 with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.
Published: 2017

2. Association analysis identifies 65 new breast cancer risk loci

Author: Michailidou, Kyriaki, Lindström, Sara, Dennis, Joe, Beesley, Jonathan, Hui, Shirley, Kar, Siddhartha, Lemaçon, Audrey, Soucy, Penny, Glubb, Dylan, Rostamianfar, Asha, Bolla, Manjeet K, Wang, Qin, Tyrer, Jonathan, Dicks, Ed, Lee, Andrew, Wang, Zhaoming, Allen, Jamie, Keeman, Renske, Eilber, Ursula, French, Juliet D, Qing Chen, Xiao, Fachal, Laura, McCue, Karen, McCart Reed, Amy E, Ghoussaini, Maya, Carroll, Jason S, Jiang, Xia, Finucane, Hilary, Adams, Marcia, Adank, Muriel A, Ahsan, Habibul, Aittomäki, Kristiina, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Aronson, Kristan J, Arun, Banu, Auer, Paul L, Bacot, François, Barrdahl, Myrto, Baynes, Caroline, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Bonanni, Bernardo, Børresen-Dale, Anne-Lise, Brand, Judith S, Brauch, Hiltrud, Brennan, Paul, Brenner, Hermann, Brinton, Louise, Broberg, Per, Brock, Ian W, Broeks, Annegien, Brooks-Wilson, Angela, Brucker, Sara Y, Brüning, Thomas, Burwinkel, Barbara, Butterbach, Katja, Cai, Qiuyin, Cai, Hui, Caldés, Trinidad, Canzian, Federico, Carracedo, Angel, Carter, Brian D, Castelao, Jose E, Chan, Tsun L, David Cheng, Ting-Yuan, Seng Chia, Kee, Choi, Ji-Yeob, Christiansen, Hans, Clarke, Christine L, Collée, Margriet, Conroy, Don M, Cordina-Duverger, Emilie, Cornelissen, Sten, Cox, David G, Cox, Angela, Cross, Simon S, Cunningham, Julie M, Czene, Kamila, Daly, Mary B, Devilee, Peter, Doheny, Kimberly F, Dörk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M, Ekici, Arif B, Eliassen, A Heather, Ellberg, Carolina, Elvira, Mingajeva, and Engel, Christoph
Subjects: Cancer, Asia, Asian People, Binding Sites, Breast Neoplasms, Computer Simulation, Europe, Female, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, Risk Assessment, Transcription Factors, White People, NBCS Collaborators, ABCTB Investigators, ConFab/AOCS Investigators, General Science & Technology
Abstract: Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry. We identified 65 new loci that are associated with overall breast cancer risk at P
Published: 2017

3. Large-scale genotyping identifies 41 new loci associated with breast cancer risk

Author: Michailidou, Kyriaki, Hall, Per, Gonzalez-Neira, Anna, Ghoussaini, Maya, Dennis, Joe, Milne, Roger L, Schmidt, Marjanka K, Chang-Claude, Jenny, Bojesen, Stig E, Bolla, Manjeet K, Wang, Qin, Dicks, Ed, Lee, Andrew, Turnbull, Clare, Rahman, Nazneen, Fletcher, Olivia, Peto, Julian, Gibson, Lorna, dos Santos Silva, Isabel, Nevanlinna, Heli, Muranen, Taru A, Aittomäki, Kristiina, Blomqvist, Carl, Czene, Kamila, Irwanto, Astrid, Liu, Jianjun, Waisfisz, Quinten, Meijers-Heijboer, Hanne, Adank, Muriel, van der Luijt, Rob B, Hein, Rebecca, Dahmen, Norbert, Beckman, Lars, Meindl, Alfons, Schmutzler, Rita K, Müller-Myhsok, Bertram, Lichtner, Peter, Hopper, John L, Southey, Melissa C, Makalic, Enes, Schmidt, Daniel F, Uitterlinden, Andre G, Hofman, Albert, Hunter, David J, Chanock, Stephen J, Vincent, Daniel, Bacot, François, Tessier, Daniel C, Canisius, Sander, Wessels, Lodewyk FA, Haiman, Christopher A, Shah, Mitul, Luben, Robert, Brown, Judith, Luccarini, Craig, Schoof, Nils, Humphreys, Keith, Li, Jingmei, Nordestgaard, Børge G, Nielsen, Sune F, Flyger, Henrik, Couch, Fergus J, Wang, Xianshu, Vachon, Celine, Stevens, Kristen N, Lambrechts, Diether, Moisse, Matthieu, Paridaens, Robert, Christiaens, Marie-Rose, Rudolph, Anja, Nickels, Stefan, Flesch-Janys, Dieter, Johnson, Nichola, Aitken, Zoe, Aaltonen, Kirsimari, Heikkinen, Tuomas, Broeks, Annegien, Veer, Laura J Van't, van der Schoot, C Ellen, Guénel, Pascal, Truong, Thérèse, Laurent-Puig, Pierre, Menegaux, Florence, Marme, Frederik, Schneeweiss, Andreas, Sohn, Christof, Burwinkel, Barbara, Zamora, M Pilar, Perez, Jose Ignacio Arias, Pita, Guillermo, Alonso, M Rosario, Cox, Angela, Brock, Ian W, Cross, Simon S, Reed, Malcolm WR, Sawyer, Elinor J, Tomlinson, Ian, Kerin, Michael J, Miller, Nicola, and Henderson, Brian E
Subjects: Biological Sciences, Genetics, Human Genome, Prevention, Breast Cancer, Cancer, Breast Neoplasms, Case-Control Studies, Cooperative Behavior, Female, Gene-Environment Interaction, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Meta-Analysis as Topic, Polymorphism, Single Nucleotide, Risk Factors, Breast and Ovarian Cancer Susceptibility Collaboration, Hereditary Breast and Ovarian Cancer Research Group Netherlands, kConFab Investigators, Australian Ovarian Cancer Study Group, GENICA (Gene Environment Interaction and Breast Cancer in Germany) Network, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract: Breast cancer is the most common cancer among women. Common variants at 27 loci have been identified as associated with susceptibility to breast cancer, and these account for ∼9% of the familial risk of the disease. We report here a meta-analysis of 9 genome-wide association studies, including 10,052 breast cancer cases and 12,575 controls of European ancestry, from which we selected 29,807 SNPs for further genotyping. These SNPs were genotyped in 45,290 cases and 41,880 controls of European ancestry from 41 studies in the Breast Cancer Association Consortium (BCAC). The SNPs were genotyped as part of a collaborative genotyping experiment involving four consortia (Collaborative Oncological Gene-environment Study, COGS) and used a custom Illumina iSelect genotyping array, iCOGS, comprising more than 200,000 SNPs. We identified SNPs at 41 new breast cancer susceptibility loci at genome-wide significance (P < 5 × 10(-8)). Further analyses suggest that more than 1,000 additional loci are involved in breast cancer susceptibility.
Published: 2013

4. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer.

Author: Pharoah, Paul DP, Tsai, Ya-Yu, Ramus, Susan J, Phelan, Catherine M, Goode, Ellen L, Lawrenson, Kate, Buckley, Melissa, Fridley, Brooke L, Tyrer, Jonathan P, Shen, Howard, Weber, Rachel, Karevan, Rod, Larson, Melissa C, Song, Honglin, Tessier, Daniel C, Bacot, François, Vincent, Daniel, Cunningham, Julie M, Dennis, Joe, Dicks, Ed, Australian Cancer Study, Australian Ovarian Cancer Study Group, Aben, Katja K, Anton-Culver, Hoda, Antonenkova, Natalia, Armasu, Sebastian M, Baglietto, Laura, Bandera, Elisa V, Beckmann, Matthias W, Birrer, Michael J, Bloom, Greg, Bogdanova, Natalia, Brenton, James D, Brinton, Louise A, Brooks-Wilson, Angela, Brown, Robert, Butzow, Ralf, Campbell, Ian, Carney, Michael E, Carvalho, Renato S, Chang-Claude, Jenny, Chen, Y Anne, Chen, Zhihua, Chow, Wong-Ho, Cicek, Mine S, Coetzee, Gerhard, Cook, Linda S, Cramer, Daniel W, Cybulski, Cezary, Dansonka-Mieszkowska, Agnieszka, Despierre, Evelyn, Doherty, Jennifer A, Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Eccles, Diana, Edwards, Robert, Ekici, Arif B, Fasching, Peter A, Fenstermacher, David, Flanagan, James, Gao, Yu-Tang, Garcia-Closas, Montserrat, Gentry-Maharaj, Aleksandra, Giles, Graham, Gjyshi, Anxhela, Gore, Martin, Gronwald, Jacek, Guo, Qi, Halle, Mari K, Harter, Philipp, Hein, Alexander, Heitz, Florian, Hillemanns, Peter, Hoatlin, Maureen, Høgdall, Estrid, Høgdall, Claus K, Hosono, Satoyo, Jakubowska, Anna, Jensen, Allan, Kalli, Kimberly R, Karlan, Beth Y, Kelemen, Linda E, Kiemeney, Lambertus A, Kjaer, Susanne Krüger, Konecny, Gottfried E, Krakstad, Camilla, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Le, Nhu D, Lee, Nathan, Lee, Janet, Leminen, Arto, Lim, Boon Kiong, Lissowska, Jolanta, Lubiński, Jan, Lundvall, Lene, Lurie, Galina, and Massuger, Leon FAG
Subjects: Australian Cancer Study, Australian Ovarian Cancer Study Group, Humans, Cystadenocarcinoma, Serous, Ovarian Neoplasms, Neoplasm Invasiveness, Genetic Predisposition to Disease, Risk Factors, Case-Control Studies, Cooperative Behavior, Genotype, Polymorphism, Single Nucleotide, Female, Meta-Analysis as Topic, Genome-Wide Association Study, Genetic Loci, Gene-Environment Interaction, Cancer, Human Genome, Prevention, Genetics, Rare Diseases, Ovarian Cancer, Aetiology, 2.1 Biological and endogenous factors, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract: Genome-wide association studies (GWAS) have identified four susceptibility loci for epithelial ovarian cancer (EOC), with another two suggestive loci reaching near genome-wide significance. We pooled data from a GWAS conducted in North America with another GWAS from the UK. We selected the top 24,551 SNPs for inclusion on the iCOGS custom genotyping array. We performed follow-up genotyping in 18,174 individuals with EOC (cases) and 26,134 controls from 43 studies from the Ovarian Cancer Association Consortium. We validated the two loci at 3q25 and 17q21 that were previously found to have associations close to genome-wide significance and identified three loci newly associated with risk: two loci associated with all EOC subtypes at 8q21 (rs11782652, P = 5.5 × 10(-9)) and 10p12 (rs1243180, P = 1.8 × 10(-8)) and another locus specific to the serous subtype at 17q12 (rs757210, P = 8.1 × 10(-10)). An integrated molecular analysis of genes and regulatory regions at these loci provided evidence for functional mechanisms underlying susceptibility and implicated CHMP4C in the pathogenesis of ovarian cancer.
Published: 2013

5. Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk.

Author: Couch, Fergus J, Wang, Xianshu, McGuffog, Lesley, Lee, Andrew, Olswold, Curtis, Kuchenbaecker, Karoline B, Soucy, Penny, Fredericksen, Zachary, Barrowdale, Daniel, Dennis, Joe, Gaudet, Mia M, Dicks, Ed, Kosel, Matthew, Healey, Sue, Sinilnikova, Olga M, Lee, Adam, Bacot, François, Vincent, Daniel, Hogervorst, Frans BL, Peock, Susan, Stoppa-Lyonnet, Dominique, Jakubowska, Anna, kConFab Investigators, Radice, Paolo, Schmutzler, Rita Katharina, SWE-BRCA, Domchek, Susan M, Piedmonte, Marion, Singer, Christian F, Friedman, Eitan, Thomassen, Mads, Ontario Cancer Genetics Network, Hansen, Thomas VO, Neuhausen, Susan L, Szabo, Csilla I, Blanco, Ignacio, Greene, Mark H, Karlan, Beth Y, Garber, Judy, Phelan, Catherine M, Weitzel, Jeffrey N, Montagna, Marco, Olah, Edith, Andrulis, Irene L, Godwin, Andrew K, Yannoukakos, Drakoulis, Goldgar, David E, Caldes, Trinidad, Nevanlinna, Heli, Osorio, Ana, Terry, Mary Beth, Daly, Mary B, van Rensburg, Elizabeth J, Hamann, Ute, Ramus, Susan J, Toland, Amanda Ewart, Caligo, Maria A, Olopade, Olufunmilayo I, Tung, Nadine, Claes, Kathleen, Beattie, Mary S, Southey, Melissa C, Imyanitov, Evgeny N, Tischkowitz, Marc, Janavicius, Ramunas, John, Esther M, Kwong, Ava, Diez, Orland, Balmaña, Judith, Barkardottir, Rosa B, Arun, Banu K, Rennert, Gad, Teo, Soo-Hwang, Ganz, Patricia A, Campbell, Ian, van der Hout, Annemarie H, van Deurzen, Carolien HM, Seynaeve, Caroline, Gómez Garcia, Encarna B, van Leeuwen, Flora E, Meijers-Heijboer, Hanne EJ, Gille, Johannes JP, Ausems, Margreet GEM, Blok, Marinus J, Ligtenberg, Marjolijn JL, Rookus, Matti A, Devilee, Peter, Verhoef, Senno, van Os, Theo AM, Wijnen, Juul T, HEBON, EMBRACE, Frost, Debra, Ellis, Steve, Fineberg, Elena, Platte, Radka, Evans, D Gareth, Izatt, Louise, Eeles, Rosalind A, and Adlard, Julian
Subjects: kConFab Investigators, SWE-BRCA, Ontario Cancer Genetics Network, HEBON, EMBRACE, GEMO Study Collaborators, BCFR, CIMBA, Humans, Breast Neoplasms, Ovarian Neoplasms, Genetic Predisposition to Disease, BRCA1 Protein, BRCA2 Protein, Prognosis, Risk Factors, Genotype, Heterozygote, Mutation, Polymorphism, Single Nucleotide, Middle Aged, Female, Genome-Wide Association Study, Polymorphism, Single Nucleotide, Developmental Biology, Genetics
Abstract: BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7 × 10(-8), HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4 × 10(-8), HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4 × 10(-8), HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific association. The 17q21.31 locus was also associated with ovarian cancer risk in 8,211 BRCA2 carriers (P = 2×10(-4)). These loci may lead to an improved understanding of the etiology of breast and ovarian tumors in BRCA1 carriers. Based on the joint distribution of the known BRCA1 breast cancer risk-modifying loci, we estimated that the breast cancer lifetime risks for the 5% of BRCA1 carriers at lowest risk are 28%-50% compared to 81%-100% for the 5% at highest risk. Similarly, based on the known ovarian cancer risk-modifying loci, the 5% of BRCA1 carriers at lowest risk have an estimated lifetime risk of developing ovarian cancer of 28% or lower, whereas the 5% at highest risk will have a risk of 63% or higher. Such differences in risk may have important implications for risk prediction and clinical management for BRCA1 carriers.
Published: 2013

6. Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31

Author: Permuth-Wey, Jennifer, Lawrenson, Kate, Shen, Howard C, Velkova, Aneliya, Tyrer, Jonathan P, Chen, Zhihua, Lin, Hui-Yi, Ann Chen, Y, Tsai, Ya-Yu, Qu, Xiaotao, Ramus, Susan J, Karevan, Rod, Lee, Janet, Lee, Nathan, Larson, Melissa C, Aben, Katja K, Anton-Culver, Hoda, Antonenkova, Natalia, Antoniou, Antonis C, Armasu, Sebastian M, Bacot, François, Baglietto, Laura, Bandera, Elisa V, Barnholtz-Sloan, Jill, Beckmann, Matthias W, Birrer, Michael J, Bloom, Greg, Bogdanova, Natalia, Brinton, Louise A, Brooks-Wilson, Angela, Brown, Robert, Butzow, Ralf, Cai, Qiuyin, Campbell, Ian, Chang-Claude, Jenny, Chanock, Stephen, Chenevix-Trench, Georgia, Cheng, Jin Q, Cicek, Mine S, Coetzee, Gerhard A, Cook, Linda S, Couch, Fergus J, Cramer, Daniel W, Cunningham, Julie M, Dansonka-Mieszkowska, Agnieszka, Despierre, Evelyn, Doherty, Jennifer A, Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Easton, Douglas F, Eccles, Diana, Edwards, Robert, Ekici, Arif B, Fasching, Peter A, Fenstermacher, David A, Flanagan, James M, Garcia-Closas, Montserrat, Gentry-Maharaj, Aleksandra, Giles, Graham G, Glasspool, Rosalind M, Gonzalez-Bosquet, Jesus, Goodman, Marc T, Gore, Martin, Górski, Bohdan, Gronwald, Jacek, Hall, Per, Halle, Mari K, Harter, Philipp, Heitz, Florian, Hillemanns, Peter, Hoatlin, Maureen, Høgdall, Claus K, Høgdall, Estrid, Hosono, Satoyo, Jakubowska, Anna, Jensen, Allan, Jim, Heather, Kalli, Kimberly R, Karlan, Beth Y, Kaye, Stanley B, Kelemen, Linda E, Kiemeney, Lambertus A, Kikkawa, Fumitaka, Konecny, Gottfried E, Krakstad, Camilla, Krüger Kjaer, Susanne, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Lancaster, Johnathan M, Le, Nhu D, Leminen, Arto, Levine, Douglas A, Liang, Dong, Kiong Lim, Boon, Lin, Jie, Lissowska, Jolanta, Lu, Karen H, and Lubiński, Jan
Subjects: Biological Sciences, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Biotechnology, Ovarian Cancer, Cancer, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Carcinoma, Ovarian Epithelial, Chromosomes, Human, Pair 17, Female, Genetic Predisposition to Disease, Humans, Neoplasms, Glandular and Epithelial, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Australian Cancer Study, Australian Ovarian Cancer Study, Consortium of Investigators of Modifiers of BRCA1/2
Abstract: Epithelial ovarian cancer (EOC) has a heritable component that remains to be fully characterized. Most identified common susceptibility variants lie in non-protein-coding sequences. We hypothesized that variants in the 3' untranslated region at putative microRNA (miRNA)-binding sites represent functional targets that influence EOC susceptibility. Here, we evaluate the association between 767 miRNA-related single-nucleotide polymorphisms (miRSNPs) and EOC risk in 18,174 EOC cases and 26,134 controls from 43 studies genotyped through the Collaborative Oncological Gene-environment Study. We identify several miRSNPs associated with invasive serous EOC risk (odds ratio=1.12, P=10(-8)) mapping to an inversion polymorphism at 17q21.31. Additional genotyping of non-miRSNPs at 17q21.31 reveals stronger signals outside the inversion (P=10(-10)). Variation at 17q21.31 is associated with neurological diseases, and our collaboration is the first to report an association with EOC susceptibility. An integrated molecular analysis in this region provides evidence for ARHGAP27 and PLEKHM1 as candidate EOC susceptibility genes.
Published: 2013

7. Supplementary Methods and Tables from The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers

Author: Amos, Christopher I., primary, Dennis, Joe, primary, Wang, Zhaoming, primary, Byun, Jinyoung, primary, Schumacher, Fredrick R., primary, Gayther, Simon A., primary, Casey, Graham, primary, Hunter, David J., primary, Sellers, Thomas A., primary, Gruber, Stephen B., primary, Dunning, Alison M., primary, Michailidou, Kyriaki, primary, Fachal, Laura, primary, Doheny, Kimberly, primary, Spurdle, Amanda B., primary, Li, Yafang, primary, Xiao, Xiangjun, primary, Romm, Jane, primary, Pugh, Elizabeth, primary, Coetzee, Gerhard A., primary, Hazelett, Dennis J., primary, Bojesen, Stig E., primary, Caga-Anan, Charlisse, primary, Haiman, Christopher A., primary, Kamal, Ahsan, primary, Luccarini, Craig, primary, Tessier, Daniel, primary, Vincent, Daniel, primary, Bacot, François, primary, Van Den Berg, David J., primary, Nelson, Stefanie, primary, Demetriades, Stephen, primary, Goldgar, David E., primary, Couch, Fergus J., primary, Forman, Judith L., primary, Giles, Graham G., primary, Conti, David V., primary, Bickeböller, Heike, primary, Risch, Angela, primary, Waldenberger, Melanie, primary, Brüske-Hohlfeld, Irene, primary, Hicks, Belynda D., primary, Ling, Hua, primary, McGuffog, Lesley, primary, Lee, Andrew, primary, Kuchenbaecker, Karoline, primary, Soucy, Penny, primary, Manz, Judith, primary, Cunningham, Julie M., primary, Butterbach, Katja, primary, Kote-Jarai, Zsofia, primary, Kraft, Peter, primary, FitzGerald, Liesel, primary, Lindström, Sara, primary, Adams, Marcia, primary, McKay, James D., primary, Phelan, Catherine M., primary, Benlloch, Sara, primary, Kelemen, Linda E., primary, Brennan, Paul, primary, Riggan, Marjorie, primary, O'Mara, Tracy A., primary, Shen, Hongbing, primary, Shi, Yongyong, primary, Thompson, Deborah J., primary, Goodman, Marc T., primary, Nielsen, Sune F., primary, Berchuck, Andrew, primary, Laboissiere, Sylvie, primary, Schmit, Stephanie L., primary, Shelford, Tameka, primary, Edlund, Christopher K., primary, Taylor, Jack A., primary, Field, John K., primary, Park, Sue K., primary, Offit, Kenneth, primary, Thomassen, Mads, primary, Schmutzler, Rita, primary, Ottini, Laura, primary, Hung, Rayjean J., primary, Marchini, Jonathan, primary, Amin Al Olama, Ali, primary, Peters, Ulrike, primary, Eeles, Rosalind A., primary, Seldin, Michael F., primary, Gillanders, Elizabeth, primary, Seminara, Daniela, primary, Antoniou, Antonis C., primary, Pharoah, Paul D.P., primary, Chenevix-Trench, Georgia, primary, Chanock, Stephen J., primary, Simard, Jacques, primary, and Easton, Douglas F., primary
Published: 2023
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8. A full molecular picture of F8 intron 1 inversion created with optical genome mapping

Author: Fahiminiya, Somayyeh, primary, Rivard, Georges‐Etienne, additional, Scott, Patrick, additional, Montpetit, Alexandre, additional, Bacot, François, additional, St‐Louis, Jean, additional, Mitchell, Grant A., additional, Foulkes, William D., additional, Soucy, Jean‐Francois, additional, and Gauthier, Julie, additional
Published: 2021
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9. Inherited variants in the inner centromere protein (INCENP) gene of the chromosomal passenger complex contribute to the susceptibility of ER-negative breast cancer

Author: Kabisch, Maria, Lorenzo Bermejo, Justo, Dünnebier, Thomas, Ying, Shibo, Michailidou, Kyriaki, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Shah, Mitul, Perkins, Barbara J., Czene, Kamila, Darabi, Hatef, Eriksson, Mikael, Bojesen, Stig E., Nordestgaard, Børge G., Nielsen, Sune F., Flyger, Henrik, Lambrechts, Diether, Neven, Patrick, Peeters, Stephanie, Weltens, Caroline, Couch, Fergus J., Olson, Janet E., Wang, Xianshu, Purrington, Kristen, Chang-Claude, Jenny, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Peto, Julian, dos-Santos-Silva, Isabel, Johnson, Nichola, Fletcher, Olivia, Nevanlinna, Heli, Muranen, Taru A., Aittomäki, Kristiina, Blomqvist, Carl, Schmidt, Marjanka K., Broeks, Annegien, Cornelissen, Sten, Hogervorst, Frans B.L., Li, Jingmei, Brand, Judith S., Humphreys, Keith, Guénel, Pascal, Truong, Thérèse, Menegaux, Florence, Sanchez, Marie, Burwinkel, Barbara, Marmé, Frederik, Yang, Rongxi, Bugert, Peter, González-Neira, Anna, Benitez, Javier, Pilar Zamora, M., Arias Perez, Jose I., Cox, Angela, Cross, Simon S., Reed, Malcolm W.R., Andrulis, Irene L., Knight, Julia A., Glendon, Gord, Tchatchou, Sandrine, Sawyer, Elinor J., Tomlinson, Ian, Kerin, Michael J., Miller, Nicola, Haiman, Christopher A., Schumacher, Fredrick, Henderson, Brian E., Le Marchand, Loic, Lindblom, Annika, Margolin, Sara, Hooning, Maartje J., Hollestelle, Antoinette, Kriege, Mieke, Koppert, Linetta B., Hopper, John L., Southey, Melissa C., Tsimiklis, Helen, Apicella, Carmel, Slettedahl, Seth, Toland, Amanda E., Vachon, Celine, Yannoukakos, Drakoulis, Giles, Graham G., Milne, Roger L., McLean, Catriona, Fasching, Peter A., Ruebner, Matthias, Ekici, Arif B., Beckmann, Matthias W., Brenner, Hermann, Dieffenbach, Aida K., Arndt, Volker, Stegmaier, Christa, Ashworth, Alan, Orr, Nicholas, Schoemaker, Minouk J., Swerdlow, Anthony, García-Closas, Montserrat, Figueroa, Jonine, Chanock, Stephen J., Lissowska, Jolanta, Goldberg, Mark S., Labrèche, France, Dumont, Martine, Winqvist, Robert, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Grip, Mervi, Brauch, Hiltrud, Brüning, Thomas, Ko, Yon-Dschun, Radice, Paolo, Peterlongo, Paolo, Scuvera, Giulietta, Fortuzzi, Stefano, Bogdanova, Natalia, Dörk, Thilo, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M., Devilee, Peter, Tollenaar, Robert A.E.M., Seynaeve, Caroline, Van Asperen, Christi J., Jakubowska, Anna, Lubinski, Jan, Jaworska-Bieniek, Katarzyna, Durda, Katarzyna, Zheng, Wei, Shrubsole, Martha J., Cai, Qiuyin, Torres, Diana, Anton-Culver, Hoda, Kristensen, Vessela, Bacot, François, Tessier, Daniel C., Vincent, Daniel, Luccarini, Craig, Baynes, Caroline, Ahmed, Shahana, Maranian, Mel, Simard, Jacques, Chenevix-Trench, Georgia, Hall, Per, Pharoah, Paul D.P., Dunning, Alison M., Easton, Douglas F., and Hamann, Ute
Published: 2015
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10. Improving and accelerating clinical molecular diagnosis of severe hemophilia A with optical genome mapping technology

Author: Fahiminiya, Somayyeh, primary, Rivard, Georges-Etienne, additional, Scott, Patrick, additional, Montpetit, Alexandre, additional, Bacot, François, additional, St-Louis, Jean, additional, Mitchell, Grant A., additional, Foulkes, William, additional, Soucy, Jean-Francois, additional, and Gauthier, Julie, additional
Published: 2021
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11. Identification of susceptibility genes for complex diseases using pooling-based genome-wide association scans

Author: Bossé, Yohan, Bacot, François, Montpetit, Alexandre, Rung, Johan, Qu, Hui-Qi, Engert, James C., Polychronakos, Constantin, Hudson, Thomas J., Froguel, Philippe, Sladek, Robert, and Desrosiers, Martin
Published: 2009
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12. Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression

Author: Kote-Jarai, Zsofia, Saunders, Edward J., Leongamornlert, Daniel A., Tymrakiewicz, Malgorzata, Dadaev, Tokhir, Jugurnauth-Little, Sarah, Ross-Adams, Helen, Al Olama, Ali Amin, Benlloch, Sara, Halim, Silvia, Russel, Roslin, Dunning, Alison M., Luccarini, Craig, Dennis, Joe, Neal, David E., Hamdy, Freddie C., Donovan, Jenny L., Muir, Ken, Giles, Graham G., Severi, Gianluca, Wiklund, Fredrik, Gronberg, Henrik, Haiman, Christopher A., Schumacher, Fredrick, Henderson, Brian E., Le Marchand, Loic, Lindstrom, Sara, Kraft, Peter, Hunter, David J., Gapstur, Susan, Chanock, Stephen, Berndt, Sonja I., Albanes, Demetrius, Andriole, Gerald, Schleutker, Johanna, Weischer, Maren, Canzian, Federico, Riboli, Elio, Key, Tim J., Travis, Ruth C., Campa, Daniele, Ingles, Sue A., John, Esther M., Hayes, Richard B., Pharoah, Paul, Khaw, Kay-Tee, Stanford, Janet L., Ostrander, Elaine A., Signorello, Lisa B., Thibodeau, Stephen N., Schaid, Dan, Maier, Christiane, Vogel, Walther, Kibel, Adam S., Cybulski, Cezary, Lubinski, Jan, Cannon-Albright, Lisa, Brenner, Hermann, Park, Jong Y., Kaneva, Radka, Batra, Jyotsna, Spurdle, Amanda, Clements, Judith A., Teixeira, Manuel R., Govindasami, Koveela, Guy, Michelle, Wilkinson, Rosemary A., Sawyer, Emma J., Morgan, Angela, Dicks, Ed, Baynes, Caroline, Conroy, Don, Bojesen, Stig E., Kaaks, Rudolf, Vincent, Daniel, Bacot, François, Tessier, Daniel C., Easton, Douglas F., and Eeles, Rosalind A.
Published: 2013
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13. No association of type 1 diabetes with a functional polymorphism of the LRAP gene

Author: Qu, Hui-Qi, Marchand, Luc, Fréchette, Rosalie, Bacot, François, Lu, Yang, and Polychronakos, Constantin
Published: 2007
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14. Genetic Control of Alternative Splicing in the TAP2 Gene: Possible Implication in the Genetics of Type 1 Diabetes

Author: Qu, Hui-Qi, Lu, Yang, Marchand, Luc, Bacot, François, Fréchette, Rosalie, Tessier, Marie-Catherine, Montpetit, Alexandre, and Polychronakos, Constantin
Published: 2007

15. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Author: Milne, Roger L., Kuchenbaecker, Karoline B., Michailidou, Kyriaki, Beesley, Jonathan, Kar, Siddhartha, Lindström, Sara, Hui, Shirley, Lemaçon, Audrey, Soucy, Penny, Dennis, Joe, Jiang, Xia, Rostamianfar, Asha, Finucane, Hilary K, Bolla, Manjeet K., McGuffog, Lesley, Wang, Qin, Aalfs, Cora M., Adams, Marcia, Adlard, Julian, Agata, Simona, Ahmed, Shahana, Ahsan, Habibul, Aittomäki, Kristiina, Al-Ejeh, Fares, Allen, Jamie, Ambrosone, Christine B., Amos, Christopher I, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Arnold, Norbert, Aronson, Kristan J, Auber, Bernd, Auer, Paul L., Ausems, Margreet G E M, Azzollini, Jacopo, Bacot, François, Balmaña, Judith, Barile, Monica, Barjhoux, Laure, Barkardottir, Rosa B., Barrdahl, Myrto, Barnes, Daniel R, Barrowdale, Daniel, Baynes, Caroline, Beckmann, Matthias W., Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, and ABCTB Investigators
Subjects: Heterozygote, Receptors, Estrogen, BRCA1 Protein, Risk Factors, European Continental Ancestry Group, Mutation, Journal Article, Humans, Breast Neoplasms, Female, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genome-Wide Association Study
Abstract: Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10-8 with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.
Published: 2017

16. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers

Author: Amos, Christopher I., primary, Dennis, Joe, additional, Wang, Zhaoming, additional, Byun, Jinyoung, additional, Schumacher, Fredrick R., additional, Gayther, Simon A., additional, Casey, Graham, additional, Hunter, David J., additional, Sellers, Thomas A., additional, Gruber, Stephen B., additional, Dunning, Alison M., additional, Michailidou, Kyriaki, additional, Fachal, Laura, additional, Doheny, Kimberly, additional, Spurdle, Amanda B., additional, Li, Yafang, additional, Xiao, Xiangjun, additional, Romm, Jane, additional, Pugh, Elizabeth, additional, Coetzee, Gerhard A., additional, Hazelett, Dennis J., additional, Bojesen, Stig E., additional, Caga-Anan, Charlisse, additional, Haiman, Christopher A., additional, Kamal, Ahsan, additional, Luccarini, Craig, additional, Tessier, Daniel, additional, Vincent, Daniel, additional, Bacot, François, additional, Van Den Berg, David J., additional, Nelson, Stefanie, additional, Demetriades, Stephen, additional, Goldgar, David E., additional, Couch, Fergus J., additional, Forman, Judith L., additional, Giles, Graham G., additional, Conti, David V., additional, Bickeböller, Heike, additional, Risch, Angela, additional, Waldenberger, Melanie, additional, Brüske-Hohlfeld, Irene, additional, Hicks, Belynda D., additional, Ling, Hua, additional, McGuffog, Lesley, additional, Lee, Andrew, additional, Kuchenbaecker, Karoline, additional, Soucy, Penny, additional, Manz, Judith, additional, Cunningham, Julie M., additional, Butterbach, Katja, additional, Kote-Jarai, Zsofia, additional, Kraft, Peter, additional, FitzGerald, Liesel, additional, Lindström, Sara, additional, Adams, Marcia, additional, McKay, James D., additional, Phelan, Catherine M., additional, Benlloch, Sara, additional, Kelemen, Linda E., additional, Brennan, Paul, additional, Riggan, Marjorie, additional, O'Mara, Tracy A., additional, Shen, Hongbing, additional, Shi, Yongyong, additional, Thompson, Deborah J., additional, Goodman, Marc T., additional, Nielsen, Sune F., additional, Berchuck, Andrew, additional, Laboissiere, Sylvie, additional, Schmit, Stephanie L., additional, Shelford, Tameka, additional, Edlund, Christopher K., additional, Taylor, Jack A., additional, Field, John K., additional, Park, Sue K., additional, Offit, Kenneth, additional, Thomassen, Mads, additional, Schmutzler, Rita, additional, Ottini, Laura, additional, Hung, Rayjean J., additional, Marchini, Jonathan, additional, Amin Al Olama, Ali, additional, Peters, Ulrike, additional, Eeles, Rosalind A., additional, Seldin, Michael F., additional, Gillanders, Elizabeth, additional, Seminara, Daniela, additional, Antoniou, Antonis C., additional, Pharoah, Paul D.P., additional, Chenevix-Trench, Georgia, additional, Chanock, Stephen J., additional, Simard, Jacques, additional, and Easton, Douglas F., additional
Published: 2017
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17. Variations in 5-methylcytosine and 5-hydroxymethylcytosine among human brain, blood, and saliva using oxBS and the Infinium MethylationEPIC array

Author: Gross, Jeffrey A., primary, Lefebvre, François, primary, Lutz, Pierre-Eric, primary, Bacot, François, primary, Vincent, Daniel, primary, Bourque, Guillaume, primary, and Turecki, Gustavo, primary
Published: 2016
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18. Erratum: Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia

Author: Rung, Johan, primary, Cauchi, Stéphane, additional, Albrechtsen, Anders, additional, Shen, Lishuang, additional, Rocheleau, Ghislain, additional, Cavalcanti-Proença, Christine, additional, Bacot, François, additional, Balkau, Beverley, additional, Belisle, Alexandre, additional, Borch-Johnsen, Knut, additional, Charpentier, Guillaume, additional, Dina, Christian, additional, Durand, Emmanuelle, additional, Elliott, Paul, additional, Hadjadj, Samy, additional, Järvelin, Marjo-Riitta, additional, Laitinen, Jaana, additional, Lauritzen, Torsten, additional, Marre, Michel, additional, Mazur, Alexander, additional, Meyre, David, additional, Montpetit, Alexandre, additional, Pisinger, Charlotta, additional, Posner, Barry, additional, Poulsen, Pernille, additional, Pouta, Anneli, additional, Prentki, Marc, additional, Ribel-Madsen, Rasmus, additional, Ruokonen, Aimo, additional, Sandbaek, Anelli, additional, Serre, David, additional, Tichet, Jean, additional, Vaxillaire, Martine, additional, Wojtaszewski, Jørgen F P, additional, Vaag, Allan, additional, Hansen, Torben, additional, Polychronakos, Constantin, additional, Pedersen, Oluf, additional, Froguel, Philippe, additional, and Sladek, Robert, additional
Published: 2009
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19. Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia

Author: Rung, Johan, primary, Cauchi, Stéphane, additional, Albrechtsen, Anders, additional, Shen, Lishuang, additional, Rocheleau, Ghislain, additional, Cavalcanti-Proença, Christine, additional, Bacot, François, additional, Balkau, Beverley, additional, Belisle, Alexandre, additional, Borch-Johnsen, Knut, additional, Charpentier, Guillaume, additional, Dina, Christian, additional, Durand, Emmanuelle, additional, Elliott, Paul, additional, Hadjadj, Samy, additional, Järvelin, Marjo-Riitta, additional, Laitinen, Jaana, additional, Lauritzen, Torsten, additional, Marre, Michel, additional, Mazur, Alexander, additional, Meyre, David, additional, Montpetit, Alexandre, additional, Pisinger, Charlotta, additional, Posner, Barry, additional, Poulsen, Pernille, additional, Pouta, Anneli, additional, Prentki, Marc, additional, Ribel-Madsen, Rasmus, additional, Ruokonen, Aimo, additional, Sandbaek, Anelli, additional, Serre, David, additional, Tichet, Jean, additional, Vaxillaire, Martine, additional, Wojtaszewski, Jørgen F P, additional, Vaag, Allan, additional, Hansen, Torben, additional, Polychronakos, Constantin, additional, Pedersen, Oluf, additional, Froguel, Philippe, additional, and Sladek, Robert, additional
Published: 2009
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20. PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS

Author: Southey, Melissa C, Goldgar, David E, Winqvist, Robert, Pylkäs, Katri, Couch, Fergus, Tischkowitz, Marc, Foulkes, William D, Dennis, Joe, Michailidou, Kyriaki, van Rensburg, Elizabeth J, Heikkinen, Tuomas, Nevanlinna, Heli, Hopper, John L, Dörk, Thilo, Claes, Kathleen BM, Reis-Filho, Jorge, Teo, Zhi Ling, Radice, Paolo, Catucci, Irene, Peterlongo, Paolo, Tsimiklis, Helen, Odefrey, Fabrice A, Dowty, James G, Schmidt, Marjanka K, Broeks, Annegien, Hogervorst, Frans B, Verhoef, Senno, Carpenter, Jane, Clarke, Christine, Scott, Rodney J, Fasching, Peter A, Haeberle, Lothar, Ekici, Arif B, Beckmann, Matthias W, Peto, Julian, dos-Santos-Silva, Isabel, Fletcher, Olivia, Johnson, Nichola, Bolla, Manjeet K, Sawyer, Elinor J, Tomlinson, Ian, Kerin, Michael J, Miller, Nicola, Marme, Federik, Burwinkel, Barbara, Yang, Rongxi, Guénel, Pascal, Truong, Thérèse, Menegaux, Florence, Sanchez, Marie, Bojesen, Stig, Nielsen, Sune F, Flyger, Henrik, Benitez, Javier, Zamora, M Pilar, Arias Perez, Jose Ignacio, Menéndez, Primitiva, Anton-Culver, Hoda, Neuhausen, Susan, Ziogas, Argyrios, Clarke, Christina A, Brenner, Hermann, Arndt, Volker, Stegmaier, Christa, Brauch, Hiltrud, Brüning, Thomas, Ko, Yon-Dschun, Muranen, Taru A, Aittomäki, Kristiina, Blomqvist, Carl, Bogdanova, Natalia V, Antonenkova, Natalia N, Lindblom, Annika, Margolin, Sara, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M, Spurdle, Amanda B, Wauters, Els, Smeets, Dominiek, Beuselinck, Benoit, Floris, Giuseppe, Chang-Claude, Jenny, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Olson, Janet E, Vachon, Celine, Pankratz, Vernon S, McLean, Catriona, Haiman, Christopher A, Henderson, Brian E, Schumacher, Fredrick, Le Marchand, Loic, Kristensen, Vessela, Alnæs, Grethe Grenaker, Zheng, Wei, Hunter, David J, Lindstrom, Sara, Hankinson, Susan E, Kraft, Peter, Andrulis, Irene, Knight, Julia A, Glendon, Gord, Mulligan, Anna Marie, Jukkola-Vuorinen, Arja, Grip, Mervi, Kauppila, Saila, Devilee, Peter, Tollenaar, Robert A E M, Seynaeve, Caroline, Hollestelle, Antoinette, Garcia-Closas, Montserrat, Figueroa, Jonine, Chanock, Stephen J, Lissowska, Jolanta, Czene, Kamila, Darabi, Hatef, Eriksson, Mikael, Eccles, Diana M, Rafiq, Sajjad, Tapper, William J, Gerty, Sue M, Hooning, Maartje J, Martens, John W M, Collée, J Margriet, Tilanus-Linthorst, Madeleine, Hall, Per, Li, Jingmei, Brand, Judith S, Humphreys, Keith, Cox, Angela, Reed, Malcolm W R, Luccarini, Craig, Baynes, Caroline, Dunning, Alison M, Hamann, Ute, Torres, Diana, Ulmer, Hans Ulrich, Rüdiger, Thomas, Jakubowska, Anna, Lubinski, Jan, Jaworska, Katarzyna, Durda, Katarzyna, Slager, Susan, Toland, Amanda E, Ambrosone, Christine B, Yannoukakos, Drakoulis, Swerdlow, Anthony, Ashworth, Alan, Orr, Nick, Jones, Michael, González-Neira, Anna, Pita, Guillermo, Alonso, M Rosario, Álvarez, Nuria, Herrero, Daniel, Tessier, Daniel C, Vincent, Daniel, Bacot, Francois, Simard, Jacques, Dumont, Martine, Soucy, Penny, Eeles, Rosalind, Muir, Kenneth, Wiklund, Fredrik, Gronberg, Henrik, Schleutker, Johanna, Nordestgaard, Børge G, Weischer, Maren, Travis, Ruth C, Neal, David, Donovan, Jenny L, Hamdy, Freddie C, Khaw, Kay-Tee, Stanford, Janet L, Blot, William J, Thibodeau, Stephen, Schaid, Daniel J, Kelley, Joseph L, Maier, Christiane, Kibel, Adam S, Cybulski, Cezary, Cannon-Albright, Lisa, Butterbach, Katja, Park, Jong, Kaneva, Radka, Batra, Jyotsna, Teixeira, Manuel R, Kote-Jarai, Zsofia, Al Olama, Ali Amin, Benlloch, Sara, Renner, Stefan P, Hartmann, Arndt, Hein, Alexander, Ruebner, Matthias, Lambrechts, Diether, Van Nieuwenhuysen, Els, Vergote, Ignace, Lambretchs, Sandrina, Doherty, Jennifer A, Rossing, Mary Anne, Nickels, Stefan, Eilber, Ursula, Wang-Gohrke, Shan, Odunsi, Kunle, Sucheston-Campbell, Lara E, Friel, Grace, Lurie, Galina, Killeen, Jeffrey L, Wilkens, Lynne R, Goodman, Marc T, Runnebaum, Ingo, Hillemanns, Peter A, Pelttari, Liisa M, Butzow, Ralf, Modugno, Francesmary, Edwards, Robert P, Ness, Roberta B, Moysich, Kirsten B, du Bois, Andreas, Heitz, Florian, Harter, Philipp, Kommoss, Stefan, Karlan, Beth Y, Walsh, Christine, Lester, Jenny, Jensen, Allan, Kjaer, Susanne Krüger, Høgdall, Estrid, Peissel, Bernard, Bonanni, Bernardo, Bernard, Loris, Goode, Ellen L, Fridley, Brooke L, Vierkant, Robert A, Cunningham, Julie M, Larson, Melissa C, Fogarty, Zachary C, Kalli, Kimberly R, Liang, Dong, Lu, Karen H, Hildebrandt, Michelle A T, Wu, Xifeng, Levine, Douglas A, Dao, Fanny, Bisogna, Maria, Berchuck, Andrew, Iversen, Edwin S, Marks, Jeffrey R, Akushevich, Lucy, Cramer, Daniel W, Schildkraut, Joellen, Terry, Kathryn L, Poole, Elizabeth M, Stampfer, Meir, Tworoger, Shelley S, Bandera, Elisa V, Orlow, Irene, Olson, Sara H, Bjorge, Line, Salvesen, Helga B, van Altena, Anne M, Aben, Katja K H, Kiemeney, Lambertus A, Massuger, Leon F A G, Pejovic, Tanja, Bean, Yukie, Brooks-Wilson, Angela, Kelemen, Linda E, Cook, Linda S, Le, Nhu D, Górski, Bohdan, Gronwald, Jacek, Menkiszak, Janusz, Høgdall, Claus K, Lundvall, Lene, Nedergaard, Lotte, Engelholm, Svend Aage, Dicks, Ed, Tyrer, Jonathan, Campbell, Ian, McNeish, Iain, Paul, James, Siddiqui, Nadeem, Glasspool, Rosalind, Whittemore, Alice S, Rothstein, Joseph H, McGuire, Valerie, Sieh, Weiva, Cai, Hui, Shu, Xiao-Ou, Teten, Rachel T, Sutphen, Rebecca, McLaughlin, John R, Narod, Steven A, Phelan, Catherine M, Monteiro, Alvaro N, Fenstermacher, David, Lin, Hui-Yi, Permuth, Jennifer B, Sellers, Thomas A, Chen, Y Ann, Tsai, Ya-Yu, Chen, Zhihua, Gentry-Maharaj, Aleksandra, Gayther, Simon A, Ramus, Susan J, Menon, Usha, Wu, Anna H, Pearce, Celeste L, Van Den Berg, David, Pike, Malcolm C, Dansonka-Mieszkowska, Agnieszka, Plisiecka-Halasa, Joanna, Moes-Sosnowska, Joanna, Kupryjanczyk, Jolanta, Pharoah, Paul DP, Song, Honglin, Winship, Ingrid, Chenevix-Trench, Georgia, Giles, Graham G, Tavtigian, Sean V, Easton, Doug F, and Milne, Roger L
Abstract: Background: The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study. Methods: We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant. Results: For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10−5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10−8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants. Conclusions: This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.
Published: 2016
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21. Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

Author: Zeng, Chenjie, Guo, Xingyi, Long, Jirong, Kuchenbaecker, Karoline B., Droit, Arnaud, Michailidou, Kyriaki, Ghoussaini, Maya, Kar, Siddhartha, Freeman, Adam, Hopper, John L., Milne, Roger L., Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Agata, Simona, Ahmed, Shahana, Aittomäki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arason, Adalgeir, Arndt, Volker, Arun, Banu K., Arver, Brita, Bacot, Francois, Barrowdale, Daniel, Baynes, Caroline, Beeghly-Fadiel, Alicia, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Blot, William J., Bogdanova, Natalia V., Bojesen, Stig E., Bonanni, Bernardo, Borresen-Dale, Anne-Lise, Brand, Judith S., Brauch, Hiltrud, Brennan, Paul, Brenner, Hermann, Broeks, Annegien, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S., Cai, Qiuyin, Caldes, Trinidad, Campbell, Ian, Carpenter, Jane, Chang-Claude, Jenny, Choi, Ji-Yeob, Claes, Kathleen B. M., Clarke, Christine, Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., de la Hoya, Miguel, De Leeneer, Kim, Devilee, Peter, Diez, Orland, Domchek, Susan M., Doody, Michele, Dorfling, Cecilia M., Dörk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Dwek, Miriam, Dworniczak, Bernd, Egan, Kathleen, Eilber, Ursula, Einbeigi, Zakaria, Ejlertsen, Bent, Ellis, Steve, Frost, Debra, Lalloo, Fiona, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Friedlander, Michael, Friedman, Eitan, Gambino, Gaetana, Gao, Yu-Tang, Garber, Judy, García-Closas, Montserrat, Gehrig, Andrea, Damiola, Francesca, Lesueur, Fabienne, Mazoyer, Sylvie, Stoppa-Lyonnet, Dominique, Giles, Graham G., Godwin, Andrew K., Goldgar, David E., González-Neira, Anna, Greene, Mark H., Guénel, Pascal, Haeberle, Lothar, Haiman, Christopher A., Hallberg, Emily, Hamann, Ute, Hansen, Thomas V. O., Hart, Steven, Hartikainen, Jaana M., Hartman, Mikael, Hassan, Norhashimah, Healey, Sue, Hogervorst, Frans B. L., Verhoef, Senno, Hendricks, Carolyn B., Hillemanns, Peter, Hollestelle, Antoinette, Hulick, Peter J., Hunter, David J., Imyanitov, Evgeny N., Isaacs, Claudine, Ito, Hidemi, Jakubowska, Anna, Janavicius, Ramunas, Jaworska-Bieniek, Katarzyna, Jensen, Uffe Birk, John, Esther M., Joly Beauparlant, Charles, Jones, Michael, Kabisch, Maria, Kang, Daehee, Karlan, Beth Y., Kauppila, Saila, Kerin, Michael J., Khan, Sofia, Khusnutdinova, Elza, Knight, Julia A., Konstantopoulou, Irene, Kraft, Peter, Kwong, Ava, Laitman, Yael, Lambrechts, Diether, Lazaro, Conxi, Le Marchand, Loic, Lee, Chuen Neng, Lee, Min Hyuk, Lester, Jenny, Li, Jingmei, Liljegren, Annelie, Lindblom, Annika, Lophatananon, Artitaya, Lubinski, Jan, Mai, Phuong L., Mannermaa, Arto, Manoukian, Siranoush, Margolin, Sara, Marme, Frederik, Matsuo, Keitaro, McGuffog, Lesley, Meindl, Alfons, Menegaux, Florence, Montagna, Marco, Muir, Kenneth, Mulligan, Anna Marie, Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Newcomb, Polly A., Nord, Silje, Nussbaum, Robert L., Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo I., Olswold, Curtis, Osorio, Ana, Papi, Laura, Park-Simon, Tjoung-Won, Paulsson-Karlsson, Ylva, Peeters, Stephanie, Peissel, Bernard, Peterlongo, Paolo, Peto, Julian, Pfeiler, Georg, Phelan, Catherine M., Presneau, Nadege, Radice, Paolo, Rahman, Nazneen, Ramus, Susan J., Rashid, Muhammad Usman, Rennert, Gad, Rhiem, Kerstin, Rudolph, Anja, Salani, Ritu, Sangrajrang, Suleeporn, Sawyer, Elinor J., Schmidt, Marjanka K, Schmutzler, Rita K., Schoemaker, Minouk J., Schürmann, Peter, Seynaeve, Caroline, Shen, Chen-Yang, Shrubsole, Martha J., Shu, Xiao-Ou, Sigurdson, Alice, Singer, Christian F., Slager, Susan, Soucy, Penny, Southey, Melissa, Steinemann, Doris, Swerdlow, Anthony, Szabo, Csilla I., Tchatchou, Sandrine, Teixeira, Manuel R., Teo, Soo H., Terry, Mary Beth, Tessier, Daniel C., Teulé, Alex, Thomassen, Mads, Tihomirova, Laima, Tischkowitz, Marc, Toland, Amanda E., Tung, Nadine, Turnbull, Clare, van den Ouweland, Ans M. W., van Rensburg, Elizabeth J., ven den Berg, David, Vijai, Joseph, Wang-Gohrke, Shan, Weitzel, Jeffrey N., Whittemore, Alice S., Winqvist, Robert, Wong, Tien Y., Wu, Anna H., Yannoukakos, Drakoulis, Yu, Jyh-Cherng, Pharoah, Paul D. P., Hall, Per, Chenevix-Trench, Georgia, Dunning, Alison M., Simard, Jacques, Couch, Fergus J., Antoniou, Antonis C., Easton, Douglas F., and Zheng, Wei
Subjects: Fine-scale mapping, Genetic risk factor, Breast cancer
Abstract: Background: Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk. Method We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation. Results: Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06–1.12; P = 3 × 10-9), rs805510 (OR = 1.08, 95 % CI = 1.04–1.12, P = 2 × 10-5), and rs1871152 (OR = 1.04, 95 % CI = 1.02–1.06; P = 2 × 10-4) identified in the general populations, and rs113824616 (P = 7 × 10-5) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05. Conclusion: This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0718-0) contains supplementary material, which is available to authorized users.
Published: 2016
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22. Genetic Control of Alternative Splicing in the TAP2 Gene.

Author: Hui-Qi Qu, Yang Lu, Marchand, Luc, Bacot, François, Fréchette, Rosalie, Tessier, Marie-Catherine, Montpetit, Alexandre, and Polychronakos, Constantin
Subjects: DIABETES, GENETIC engineering, GENETIC polymorphisms, PEPTIDES, RNA, LYMPHOBLASTOID cell lines
Abstract: The transporter 2, ATP-binding cassette, subfamily B (TAP2) is involved in the transport of antigenic peptides to HLA molecules. Coding TAP2 polymorphisms shows a strong association with type 1 diabetes, but it is not clear whether this association may be entirely due to linkage disequilibrium with HLA DR and DQ. Functionally, rat Tap2 nonsynonymous single-nucleotide polymorphisms (nsSNPs) confer differential selectivity for antigenic peptides, but this was not shown to be the case for human TAP2 nsSNPs. In the human, differential peptide selectivity is rather conferred by two splicing isoforms with alternative carboxy terminals. Here, we tested the hypothesis that alleles at the coding SNPs favor different splicing isoforms, thus determining peptide selectivity indirectly. This may be the basis for independent contribution to the type 1 diabetes association. In RNA from heterozygous lymphoblastoid lines, we measured the relative abundance of each SNP haplotype in each isoform. In isoform NM_000544, the G (Ala) allele at 665 Thr>Ala (rs241447) is more than twice as abundant as A (Thr) (GA = 2.2 ± 0.4, P = 1.5 x 10-4), while isoform NM_018833 is derived almost exclusively from chromosomes carrying A (AG = 18.1 ± 5.6, P = 2.04 x 10-7). In 889 Canadian children with type 1 diabetes, differential transmission of parental TAP2 alleles persisted (P -- 0.011) when analysis was confined to chromosomes carrying only DQ*02 alleles, which mark a conserved DR-DQ haplotype, thus eliminating most of the variation at DR-DQ. Thus, we present evidence of TAP2 association with type 1 diabetes that is independent of HLA DR-DQ and describe a plausible functional mechanism based on allele dependence of splicing into isoforms known to have differential peptide selectivities. Diabetes 56: 270-275, 2007 [ABSTRACT FROM AUTHOR]
Published: 2007
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23. Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

Author: Michailidou, Kyriaki, Beesley, Jonathan, Lindstrom, Sara, Canisius, Sander, Dennis, Joe, Lush, Michael, Maranian, Mel J, Bolla, Manjeet K, Wang, Qin, Shah, Mitul, Perkins, Barbara J, Czene, Kamila, Eriksson, Mikael, Darabi, Hatef, Brand, Judith S, Bojesen, Stig E, Nordestgaard, Børge G, Flyger, Henrik, Nielsen, Sune F, Rahman, Nazneen, Turnbull, Clare, Fletcher, Olivia, Peto, Julian, Gibson, Lorna, dos-Santos-Silva, Isabel, Chang-Claude, Jenny, Flesch-Janys, Dieter, Rudolph, Anja, Eilber, Ursula, Behrens, Sabine, Nevanlinna, Heli, Muranen, Taru A, Aittomäki, Kristiina, Blomqvist, Carl, Khan, Sofia, Aaltonen, Kirsimari, Ahsan, Habibul, Kibriya, Muhammad G, Whittemore, Alice S, John, Esther M, Malone, Kathleen E, Gammon, Marilie D, Santella, Regina M, Ursin, Giske, Makalic, Enes, Schmidt, Daniel F, Casey, Graham, Hunter, David J, Gapstur, Susan M, Gaudet, Mia M, Diver, W Ryan, Haiman, Christopher A, Schumacher, Fredrick, Henderson, Brian E, Le Marchand, Loic, Berg, Christine D, Chanock, Stephen, Figueroa, Jonine, Hoover, Robert N, Lambrechts, Diether, Neven, Patrick, Wildiers, Hans, van Limbergen, Erik, Schmidt, Marjanka K, Broeks, Annegien, Verhoef, Senno, Cornelissen, Sten, Couch, Fergus J, Olson, Janet E, Hallberg, Emily, Vachon, Celine, Waisfisz, Quinten, Meijers-Heijboer, Hanne, Adank, Muriel A, van der Luijt, Rob B, Li, Jingmei, Liu, Jianjun, Humphreys, Keith, Kang, Daehee, Choi, Ji-Yeob, Park, Sue K, Yoo, Keun-Young, Matsuo, Keitaro, Ito, Hidemi, Iwata, Hiroji, Tajima, Kazuo, Guénel, Pascal, Truong, Thérèse, Mulot, Claire, Sanchez, Marie, Burwinkel, Barbara, Marme, Frederik, Surowy, Harald, Sohn, Christof, Wu, Anna H, Tseng, Chiu-chen, Van Den Berg, David, Stram, Daniel O, González-Neira, Anna, Benitez, Javier, Zamora, M Pilar, Perez, Jose Ignacio Arias, Shu, Xiao-Ou, Lu, Wei, Gao, Yu-Tang, Cai, Hui, Cox, Angela, Cross, Simon S, Reed, Malcolm WR, Andrulis, Irene L, Knight, Julia A, Glendon, Gord, Mulligan, Anna Marie, Sawyer, Elinor J, Tomlinson, Ian, Kerin, Michael J, Miller, Nicola, Lindblom, Annika, Margolin, Sara, Teo, Soo Hwang, Yip, Cheng Har, Taib, Nur Aishah Mohd, TAN, Gie-Hooi, Hooning, Maartje J, Hollestelle, Antoinette, Martens, John WM, Collée, J Margriet, Blot, William, Signorello, Lisa B, Cai, Qiuyin, Hopper, John L, Southey, Melissa C, Tsimiklis, Helen, Apicella, Carmel, Shen, Chen-Yang, Hsiung, Chia-Ni, Wu, Pei-Ei, Hou, Ming-Feng, Kristensen, Vessela N, Nord, Silje, Alnaes, Grethe I Grenaker, Giles, Graham G, Milne, Roger L, McLean, Catriona, Canzian, Federico, Trichopoulos, Dmitrios, Peeters, Petra, Lund, Eiliv, Sund, Malin, Khaw, Kay-Tee, Gunter, Marc J, Palli, Domenico, Mortensen, Lotte Maxild, Dossus, Laure, Huerta, Jose-Maria, Meindl, Alfons, Schmutzler, Rita K, Sutter, Christian, Yang, Rongxi, Muir, Kenneth, Lophatananon, Artitaya, Stewart-Brown, Sarah, Siriwanarangsan, Pornthep, Hartman, Mikael, Miao, Hui, Chia, Kee Seng, Chan, Ching Wan, Fasching, Peter A, Hein, Alexander, Beckmann, Matthias W, Haeberle, Lothar, Brenner, Hermann, Dieffenbach, Aida Karina, Arndt, Volker, Stegmaier, Christa, Ashworth, Alan, Orr, Nick, Schoemaker, Minouk J, Swerdlow, Anthony J, Brinton, Louise, Garcia-Closas, Montserrat, Zheng, Wei, Halverson, Sandra L, Shrubsole, Martha, Long, Jirong, Goldberg, Mark S, Labrèche, France, Dumont, Martine, Winqvist, Robert, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Grip, Mervi, Brauch, Hiltrud, Hamann, Ute, Brüning, Thomas, Radice, Paolo, Peterlongo, Paolo, Manoukian, Siranoush, Bernard, Loris, Bogdanova, Natalia V, Dörk, Thilo, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M, Devilee, Peter, Tollenaar, Robert AEM, Seynaeve, Caroline, Van Asperen, Christi J, Jakubowska, Anna, Lubinski, Jan, Jaworska, Katarzyna, Huzarski, Tomasz, Sangrajrang, Suleeporn, Gaborieau, Valerie, Brennan, Paul, McKay, James, Slager, Susan, Toland, Amanda E, Ambrosone, Christine B, Yannoukakos, Drakoulis, Kabisch, Maria, Torres, Diana, Neuhausen, Susan L, Anton-Culver, Hoda, Luccarini, Craig, Baynes, Caroline, Ahmed, Shahana, Healey, Catherine S, Tessier, Daniel C, Vincent, Daniel, Bacot, Francois, Pita, Guillermo, Alonso, M Rosario, Álvarez, Nuria, Herrero, Daniel, Simard, Jacques, Pharoah, Paul PDP, Kraft, Peter, Dunning, Alison M, Chenevix-Trench, Georgia, Hall, Per, and Easton, Douglas F
Abstract: Genome wide association studies (GWAS) and large scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ~14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS comprising of 15,748 breast cancer cases and 18,084 controls, and 46,785 cases and 42,892 controls from 41 studies genotyped on a 200K custom array (iCOGS). Analyses were restricted to women of European ancestry. Genotypes for more than 11M SNPs were generated by imputation using the 1000 Genomes Project reference panel. We identified 15 novel loci associated with breast cancer at P<5×10−8. Combining association analysis with ChIP-Seq data in mammary cell lines and ChIA-PET chromatin interaction data in ENCODE, we identified likely target genes in two regions: SETBP1 on 18q12.3 and RNF115 and PDZK1 on 1q21.1. One association appears to be driven by an amino-acid substitution in EXO1.
Published: 2015
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24. Prediction of Breast Cancer Risk Based on Profiling With Common Genetic Variants

Author: Mavaddat, Nasim, Pharoah, Paul D. P., Michailidou, Kyriaki, Tyrer, Jonathan, Brook, Mark N., Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Dunning, Alison M., Shah, Mitul, Luben, Robert, Brown, Judith, Bojesen, Stig E., Nordestgaard, Børge G., Nielsen, Sune F., Flyger, Henrik, Czene, Kamila, Darabi, Hatef, Eriksson, Mikael, Peto, Julian, dos-Santos-Silva, Isabel, Dudbridge, Frank, Johnson, Nichola, Schmidt, Marjanka K., Broeks, Annegien, Verhoef, Senno, Rutgers, Emiel J., Swerdlow, Anthony, Ashworth, Alan, Orr, Nick, Schoemaker, Minouk J., Figueroa, Jonine, Chanock, Stephen J., Brinton, Louise, Lissowska, Jolanta, Couch, Fergus J., Olson, Janet E., Vachon, Celine, Pankratz, Vernon S., Lambrechts, Diether, Wildiers, Hans, Van Ongeval, Chantal, van Limbergen, Erik, Kristensen, Vessela, Grenaker Alnæs, Grethe, Nord, Silje, Borresen-Dale, Anne-Lise, Nevanlinna, Heli, Muranen, Taru A., Aittomäki, Kristiina, Blomqvist, Carl, Chang-Claude, Jenny, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Fasching, Peter A., Haeberle, Lothar, Ekici, Arif B., Beckmann, Matthias W., Burwinkel, Barbara, Marme, Frederik, Schneeweiss, Andreas, Sohn, Christof, Trentham-Dietz, Amy, Newcomb, Polly, Titus, Linda, Egan, Kathleen M., Hunter, David J., Lindstrom, Sara, Tamimi, Rulla M., Kraft, Peter, Rahman, Nazneen, Turnbull, Clare, Renwick, Anthony, Seal, Sheila, Li, Jingmei, Liu, Jianjun, Humphreys, Keith, Benitez, Javier, Pilar Zamora, M., Arias Perez, Jose Ignacio, Menéndez, Primitiva, Jakubowska, Anna, Lubinski, Jan, Jaworska-Bieniek, Katarzyna, Durda, Katarzyna, Bogdanova, Natalia V., Antonenkova, Natalia N., Dörk, Thilo, Anton-Culver, Hoda, Neuhausen, Susan L., Ziogas, Argyrios, Bernstein, Leslie, Devilee, Peter, Tollenaar, Robert A. E. M., Seynaeve, Caroline, van Asperen, Christi J., Cox, Angela, Cross, Simon S., Reed, Malcolm W. R., Khusnutdinova, Elza, Bermisheva, Marina, Prokofyeva, Darya, Takhirova, Zalina, Meindl, Alfons, Schmutzler, Rita K., Sutter, Christian, Yang, Rongxi, Schürmann, Peter, Bremer, Michael, Christiansen, Hans, Park-Simon, Tjoung-Won, Hillemanns, Peter, Guénel, Pascal, Truong, Thérèse, Menegaux, Florence, Sanchez, Marie, Radice, Paolo, Peterlongo, Paolo, Manoukian, Siranoush, Pensotti, Valeria, Hopper, John L., Tsimiklis, Helen, Apicella, Carmel, Southey, Melissa C., Brauch, Hiltrud, Brüning, Thomas, Ko, Yon-Dschun, Sigurdson, Alice J., Doody, Michele M., Hamann, Ute, Torres, Diana, Ulmer, Hans-Ulrich, Försti, Asta, Sawyer, Elinor J., Tomlinson, Ian, Kerin, Michael J., Miller, Nicola, Andrulis, Irene L., Knight, Julia A., Glendon, Gord, Marie Mulligan, Anna, Chenevix-Trench, Georgia, Balleine, Rosemary, Giles, Graham G., Milne, Roger L., McLean, Catriona, Lindblom, Annika, Margolin, Sara, Haiman, Christopher A., Henderson, Brian E., Schumacher, Fredrick, Le Marchand, Loic, Eilber, Ursula, Wang-Gohrke, Shan, Hooning, Maartje J., Hollestelle, Antoinette, van den Ouweland, Ans M. W., Koppert, Linetta B., Carpenter, Jane, Clarke, Christine, Scott, Rodney, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M., Brenner, Hermann, Arndt, Volker, Stegmaier, Christa, Karina Dieffenbach, Aida, Winqvist, Robert, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Grip, Mervi, Offit, Kenneth, Vijai, Joseph, Robson, Mark, Rau-Murthy, Rohini, Dwek, Miriam, Swann, Ruth, Annie Perkins, Katherine, Goldberg, Mark S., Labrèche, France, Dumont, Martine, Eccles, Diana M., Tapper, William J., Rafiq, Sajjad, John, Esther M., Whittemore, Alice S., Slager, Susan, Yannoukakos, Drakoulis, Toland, Amanda E., Yao, Song, Zheng, Wei, Halverson, Sandra L., González-Neira, Anna, Pita, Guillermo, Rosario Alonso, M., Álvarez, Nuria, Herrero, Daniel, Tessier, Daniel C., Vincent, Daniel, Bacot, Francois, Luccarini, Craig, Baynes, Caroline, Ahmed, Shahana, Maranian, Mel, Healey, Catherine S., Simard, Jacques, Hall, Per, Easton, Douglas F., and Garcia-Closas, Montserrat
Abstract: Background: Data for multiple common susceptibility alleles for breast cancer may be combined to identify women at different levels of breast cancer risk. Such stratification could guide preventive and screening strategies. However, empirical evidence for genetic risk stratification is lacking. Methods: We investigated the value of using 77 breast cancer-associated single nucleotide polymorphisms (SNPs) for risk stratification, in a study of 33 673 breast cancer cases and 33 381 control women of European origin. We tested all possible pair-wise multiplicative interactions and constructed a 77-SNP polygenic risk score (PRS) for breast cancer overall and by estrogen receptor (ER) status. Absolute risks of breast cancer by PRS were derived from relative risk estimates and UK incidence and mortality rates. Results: There was no strong evidence for departure from a multiplicative model for any SNP pair. Women in the highest 1% of the PRS had a three-fold increased risk of developing breast cancer compared with women in the middle quintile (odds ratio [OR] = 3.36, 95% confidence interval [CI] = 2.95 to 3.83). The ORs for ER-positive and ER-negative disease were 3.73 (95% CI = 3.24 to 4.30) and 2.80 (95% CI = 2.26 to 3.46), respectively. Lifetime risk of breast cancer for women in the lowest and highest quintiles of the PRS were 5.2% and 16.6% for a woman without family history, and 8.6% and 24.4% for a woman with a first-degree family history of breast cancer. Conclusions: The PRS stratifies breast cancer risk in women both with and without a family history of breast cancer. The observed level of risk discrimination could inform targeted screening and prevention strategies. Further discrimination may be achievable through combining the PRS with lifestyle/environmental factors, although these were not considered in this report.
Published: 2015
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25. Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2

Author: Orr, Nick, Dudbridge, Frank, Dryden, Nicola, Maguire, Sarah, Novo, Daniela, Perrakis, Eleni, Johnson, Nichola, Ghoussaini, Maya, Hopper, John L., Southey, Melissa C., Apicella, Carmel, Stone, Jennifer, Schmidt, Marjanka K., Broeks, Annegien, Van't Veer, Laura J., Hogervorst, Frans B., Fasching, Peter A., Haeberle, Lothar, Ekici, Arif B., Beckmann, Matthias W., Gibson, Lorna, Aitken, Zoe, Warren, Helen, Sawyer, Elinor, Tomlinson, Ian, Kerin, Michael J., Miller, Nicola, Burwinkel, Barbara, Marme, Frederik, Schneeweiss, Andreas, Sohn, Chistof, Guénel, Pascal, Truong, Thérèse, Cordina-Duverger, Emilie, Sanchez, Marie, Bojesen, Stig E., Nordestgaard, Børge G., Nielsen, Sune F., Flyger, Henrik, Benitez, Javier, Zamora, Maria Pilar, Arias Perez, Jose Ignacio, Menéndez, Primitiva, Anton-Culver, Hoda, Neuhausen, Susan L., Brenner, Hermann, Dieffenbach, Aida Karina, Arndt, Volker, Stegmaier, Christa, Hamann, Ute, Brauch, Hiltrud, Justenhoven, Christina, Brüning, Thomas, Ko, Yon-Dschun, Nevanlinna, Heli, Aittomäki, Kristiina, Blomqvist, Carl, Khan, Sofia, Bogdanova, Natalia, Dörk, Thilo, Lindblom, Annika, Margolin, Sara, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M., Chenevix-Trench, Georgia, Beesley, Jonathan, Lambrechts, Diether, Moisse, Matthieu, Floris, Guiseppe, Beuselinck, Benoit, Chang-Claude, Jenny, Rudolph, Anja, Seibold, Petra, Flesch-Janys, Dieter, Radice, Paolo, Peterlongo, Paolo, Peissel, Bernard, Pensotti, Valeria, Couch, Fergus J., Olson, Janet E., Slettedahl, Seth, Vachon, Celine, Giles, Graham G., Milne, Roger L., McLean, Catriona, Haiman, Christopher A., Henderson, Brian E., Schumacher, Fredrick, Le Marchand, Loic, Simard, Jacques, Goldberg, Mark S., Labrèche, France, Dumont, Martine, Kristensen, Vessela, Alnæs, Grethe Grenaker, Nord, Silje, Borresen-Dale, Anne-Lise, Zheng, Wei, Deming-Halverson, Sandra, Shrubsole, Martha, Long, Jirong, Winqvist, Robert, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Grip, Mervi, Andrulis, Irene L., Knight, Julia A., Glendon, Gord, Tchatchou, Sandrine, Devilee, Peter, Tollenaar, Robertus A. E. M., Seynaeve, Caroline M., Van Asperen, Christi J., Garcia-Closas, Montserrat, Figueroa, Jonine, Chanock, Stephen J., Lissowska, Jolanta, Czene, Kamila, Darabi, Hatef, Eriksson, Mikael, Klevebring, Daniel, Hooning, Maartje J., Hollestelle, Antoinette, van Deurzen, Carolien H. M., Kriege, Mieke, Hall, Per, Li, Jingmei, Liu, Jianjun, Humphreys, Keith, Cox, Angela, Cross, Simon S., Reed, Malcolm W. R., Pharoah, Paul D. P., Dunning, Alison M., Shah, Mitul, Perkins, Barbara J., Jakubowska, Anna, Lubinski, Jan, Jaworska-Bieniek, Katarzyna, Durda, Katarzyna, Ashworth, Alan, Swerdlow, Anthony, Jones, Michael, Schoemaker, Minouk J., Meindl, Alfons, Schmutzler, Rita K., Olswold, Curtis, Slager, Susan, Toland, Amanda E., Yannoukakos, Drakoulis, Muir, Kenneth, Lophatananon, Artitaya, Stewart-Brown, Sarah, Siriwanarangsan, Pornthep, Matsuo, Keitaro, Ito, Hidema, Iwata, Hiroji, Ishiguro, Junko, Wu, Anna H., Tseng, Chiu-chen, Van Den Berg, David, Stram, Daniel O., Teo, Soo Hwang, Yip, Cheng Har, Kang, Peter, Ikram, Mohammad Kamran, Shu, Xiao-Ou, Lu, Wei, Gao, Yu-Tang, Cai, Hui, Kang, Daehee, Choi, Ji-Yeob, Park, Sue K., Noh, Dong-Young, Hartman, Mikael, Miao, Hui, Lim, Wei Yen, Lee, Soo Chin, Sangrajrang, Suleeporn, Gaborieau, Valerie, Brennan, Paul, Mckay, James, Wu, Pei-Ei, Hou, Ming-Feng, Yu, Jyh-Cherng, Shen, Chen-Yang, Blot, William, Cai, Qiuyin, Signorello, Lisa B., Luccarini, Craig, Bayes, Caroline, Ahmed, Shahana, Maranian, Mel, Healey, Catherine S., González-Neira, Anna, Pita, Guillermo, Alonso, M. Rosario, Álvarez, Nuria, Herrero, Daniel, Tessier, Daniel C., Vincent, Daniel, Bacot, Francois, Hunter, David J., Lindstrom, Sara, Dennis, Joe, Michailidou, Kyriaki, Bolla, Manjeet K., Easton, Douglas F., dos Santos Silva, Isabel, Fletcher, Olivia, and Peto, Julian
Abstract: We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88–0.92]; P-value = 1.58 × 10−25). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08–1.17]; P-value = 7.89 × 10−09) and rs13294895 (OR = 1.09 [1.06–1.12]; P-value = 2.97 × 10−11). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06–1.18]; P-value = 2.77 × 10−05). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis.
Published: 2015
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26. Genetic variation at CYP3A is associated with age at menarche and breast cancer risk: a case-control study

Author: Johnson, Nichola, Dudbridge, Frank, Orr, Nick, Gibson, Lorna, Jones, Michael E, Schoemaker, Minouk J, Folkerd, Elizabeth J, Haynes, Ben P, Hopper, John L, Southey, Melissa C, Dite, Gillian S, Apicella, Carmel, Schmidt, Marjanka K, Broeks, Annegien, Van’t Veer, Laura J, Atsma, Femke, Muir, Kenneth, Lophatananon, Artitaya, Fasching, Peter A, Beckmann, Matthias W, Ekici, Arif B, Renner, Stefan P, Sawyer, Elinor, Tomlinson, Ian, Kerin, Michael, Miller, Nicola, Burwinkel, Barbara, Marme, Frederik, Schneeweiss, Andreas, Sohn, Christof, Guénel, Pascal, Truong, Therese, Cordina, Emilie, Menegaux, Florence, Bojesen, Stig E, Nordestgaard, Børge G, Flyger, Henrik, Milne, Roger, Zamora, M Pilar, Arias Perez, Jose Ignacio, Benitez, Javier, Bernstein, Leslie, Anton-Culver, Hoda, Ziogas, Argyrios, Clarke Dur, Christina, Brenner, Hermann, Müller, Heiko, Arndt, Volker, Dieffenbach, Aida Karina, Meindl, Alfons, Heil, Joerg, Bartram, Claus R, Schmutzler, Rita K, Brauch, Hiltrud, Justenhoven, Christina, Ko, Yon-Dschun, Nevanlinna, Heli, Muranen, Taru A, Aittomäki, Kristiina, Blomqvist, Carl, Matsuo, Keitaro, Dörk, Thilo, Bogdanova, Natalia V, Antonenkova, Natalia N, Lindblom, Annika, Mannermaa, Arto, Kataja, Vesa, Kosma, Veli-Matti, Hartikainen, Jaana M, Chenevix-Trench, Georgia, Beesley, Jonathan, Wu, Anna H, Van den Berg, David, Tseng, Chiu-Chen, Lambrechts, Diether, Smeets, Dominiek, Neven, Patrick, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Nickels, Stefan, Flesch-Janys, Dieter, Radice, Paolo, Peterlongo, Paolo, Bonanni, Bernardo, Pensotti, Valeria, Couch, Fergus J, Olson, Janet E, Wang, Xianshu, Fredericksen, Zachary, Pankratz, Vernon S, Giles, Graham G, Severi, Gianluca, Baglietto, Laura, Haiman, Chris, Simard, Jacques, Goldberg, Mark S, Labrèche, France, Dumont, Martine, Soucy, Penny, Teo, Soo, Yip, Cheng Har, Phuah, Sze Yee, Cornes, Belinda K, Kristensen, Vessela N, Grenaker Alnæs, Grethe, Børresen-Dale, Anne-Lise, Zheng, Wei, Winqvist, Robert, Pylkäs, Katri, Jukkola-Vuorinen, Arja, Grip, Mervi, Andrulis, Irene L, Knight, Julia A, Glendon, Gord, Mulligan, Anna Marie, Devillee, Peter, Figueroa, Jonine, Chanock, Stephen J, Lissowska, Jolanta, Sherman, Mark E, Hall, Per, Schoof, Nils, Hooning, Maartje, Hollestelle, Antoinette, Oldenburg, Rogier A, Tilanus-Linthorst, Madeleine, Liu, Jianjun, Cox, Angie, Brock, Ian W, Reed, Malcolm WR, Cross, Simon S, Blot, William, Signorello, Lisa B, Pharoah, Paul DP, Dunning, Alison M, Shah, Mitul, Kang, Daehee, Noh, Dong-Young, Park, Sue K, Choi, Ji-Yeob, Hartman, Mikael, Miao, Hui, Lim, Wei Yen, Tang, Anthony, Hamann, Ute, Försti, Asta, Rüdiger, Thomas, Ulmer, Hans Ulrich, Jakubowska, Anna, Lubinski, Jan, Jaworska-Bieniek, Katarzyna, Durda, Katarzyna, Sangrajrang, Suleeporn, Gaborieau, Valerie, Brennan, Paul, McKay, James, Slager, Susan, Toland, Amanda E, Vachon, Celine, Yannoukakos, Drakoulis, Shen, Chen-Yang, Yu, Jyh-Cherng, Huang, Chiun-Sheng, Hou, Ming-Feng, González-Neira, Anna, Tessier, Daniel C, Vincent, Daniel, Bacot, Francois, Luccarini, Craig, Dennis, Joe, Michailidou, Kyriaki, Bolla, Manjeet K, Wang, Jean, Easton, Douglas F, García-Closas, Montserrat, Dowsett, Mitch, Ashworth, Alan, Swerdlow, Anthony J, Peto, Julian, dos Santos Silva, Isabel, and Fletcher, Olivia
Abstract: Introduction: We have previously shown that a tag single nucleotide polymorphism (rs10235235), which maps to the CYP3A locus (7q22.1), was associated with a reduction in premenopausal urinary estrone glucuronide levels and a modest reduction in risk of breast cancer in women age ≤50 years. Methods: We further investigated the association of rs10235235 with breast cancer risk in a large case control study of 47,346 cases and 47,570 controls from 52 studies participating in the Breast Cancer Association Consortium. Genotyping of rs10235235 was conducted using a custom Illumina Infinium array. Stratified analyses were conducted to determine whether this association was modified by age at diagnosis, ethnicity, age at menarche or tumor characteristics. Results: We confirmed the association of rs10235235 with breast cancer risk for women of European ancestry but found no evidence that this association differed with age at diagnosis. Heterozygote and homozygote odds ratios (ORs) were OR = 0.98 (95% CI 0.94, 1.01; P = 0.2) and OR = 0.80 (95% CI 0.69, 0.93; P = 0.004), respectively (Ptrend = 0.02). There was no evidence of effect modification by tumor characteristics. rs10235235 was, however, associated with age at menarche in controls (Ptrend = 0.005) but not cases (Ptrend = 0.97). Consequently the association between rs10235235 and breast cancer risk differed according to age at menarche (Phet = 0.02); the rare allele of rs10235235 was associated with a reduction in breast cancer risk for women who had their menarche age ≥15 years (ORhet = 0.84, 95% CI 0.75, 0.94; ORhom = 0.81, 95% CI 0.51, 1.30; Ptrend = 0.002) but not for those who had their menarche age ≤11 years (ORhet = 1.06, 95% CI 0.95, 1.19, ORhom = 1.07, 95% CI 0.67, 1.72; Ptrend = 0.29). Conclusions: To our knowledge rs10235235 is the first single nucleotide polymorphism to be associated with both breast cancer risk and age at menarche consistent with the well-documented association between later age at menarche and a reduction in breast cancer risk. These associations are likely mediated via an effect on circulating hormone levels.
Published: 2014
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27. Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer

Author: Shen, Hui, Fridley, Brooke L., Song, Honglin, Lawrenson, Kate, Cunningham, Julie M., Ramus, Susan J., Cicek, Mine S., Tyrer, Jonathan, Stram, Douglas, Larson, Melissa C., Köbel, Martin, Ziogas, Argyrios, Zheng, Wei, Yang, Hannah P., Wu, Anna H., Wozniak, Eva L., Ling Woo, Yin, Winterhoff, Boris, Wik, Elisabeth, Whittemore, Alice S., Wentzensen, Nicolas, Palmieri Weber, Rachel, Vitonis, Allison F., Vincent, Daniel, Vierkant, Robert A., Vergote, Ignace, Van Den Berg, David, Van Altena, Anne M., Tworoger, Shelley Slate, Thompson, Pamela J., Tessier, Daniel C., Terry, Kathryn Lynne, Teo, Soo-Hwang, Templeman, Claire, Stram, Daniel O., Southey, Melissa C., Sieh, Weiva, Siddiqui, Nadeem, Shvetsov, Yurii B., Shu, Xiao-Ou, Shridhar, Viji, Wang-Gohrke, Shan, Severi, Gianluca, Schwaab, Ira, Salvesen, Helga B., Rzepecka, Iwona K., Runnebaum, Ingo B., Anne Rossing, Mary, Rodriguez-Rodriguez, Lorna, Risch, Harvey A., Renner, Stefan P., Poole, Elizabeth M., Pike, Malcolm C., Phelan, Catherine M., Pelttari, Liisa M., Pejovic, Tanja, Paul, James, Orlow, Irene, Zawiah Omar, Siti, Olson, Sara H., Odunsi, Kunle, Nickels, Stefan, Nevanlinna, Heli, Ness, Roberta B., Narod, Steven A., Nakanishi, Toru, Moysich, Kirsten B., Monteiro, Alvaro N.A., Moes-Sosnowska, Joanna, Modugno, Francesmary, Menon, Usha, McLaughlin, John R., McGuire, Valerie, Matsuo, Keitaro, Mat Adenan, Noor Azmi, Massuger, Leon F.A.G, Lurie, Galina, Lundvall, Lene, Lubiński, Jan, Lissowska, Jolanta, Levine, Douglas A., Leminen, Arto, Lee, Alice W., Le, Nhu D., Lambrechts, Sandrina, Lambrechts, Diether, Kupryjanczyk, Jolanta, Krakstad, Camilla, Konecny, Gottfried E., Krüger Kjaer, Susanne, Kiemeney, Lambertus A., Kelemen, Linda E., Keeney, Gary L., Karlan, Beth Y., Karevan, Rod, Kalli, Kimberly R., Kajiyama, Hiroaki, Ji, Bu-Tian, Jensen, Allan, Jakubowska, Anna, Iversen, Edwin, Hosono, Satoyo, Høgdall, Claus K., Høgdall, Estrid, Hoatlin, Maureen, Hillemanns, Peter, Heitz, Florian, Hein, Rebecca, Harter, Philipp, Halle, Mari K., Hall, Per, Gronwald, Jacek, Gore, Martin, Goodman, Marc T., Giles, Graham G., Gentry-Maharaj, Aleksandra, Garcia-Closas, Montserrat, Flanagan, James M., Fasching, Peter A., Ekici, Arif B., Edwards, Robert, Eccles, Diana, Easton, Douglas F., Dürst, Matthias, du Bois, Andreas, Dörk, Thilo, Doherty, Jennifer A., Despierre, Evelyn, Dansonka-Mieszkowska, Agnieszka, Cybulski, Cezary, Cramer, Daniel William, Cook, Linda S., Chen, Xiaoqing, Charbonneau, Bridget, Chang-Claude, Jenny, Campbell, Ian, Butzow, Ralf, Bunker, Clareann H., Brueggmann, Doerthe, Brown, Robert, Brooks-Wilson, Angela, Brinton, Louise A., Bogdanova, Natalia, Block, Matthew S., Benjamin, Elizabeth, Beesley, Jonathan, Beckmann, Matthias W., Bandera, Elisa V., Baglietto, Laura, Bacot, François, Armasu, Sebastian M., Antonenkova, Natalia, Anton-Culver, Hoda, Aben, Katja K., Liang, Dong, Wu, Xifeng, Lu, Karen, Hildebrandt, Michelle A.T., Schildkraut, Joellen M., Sellers, Thomas A., Huntsman, David, Berchuck, Andrew, Chenevix-Trench, Georgia, Gayther, Simon A., Pharoah, Paul D.P., Laird, Peter W., Goode, Ellen L., and Leigh Pearce, Celeste
Abstract: HNF1B is overexpressed in clear cell epithelial ovarian cancer, and we observed epigenetic silencing in serous epithelial ovarian cancer, leading us to hypothesize that variation in this gene differentially associates with epithelial ovarian cancer risk according to histological subtype. Here we comprehensively map variation in HNF1B with respect to epithelial ovarian cancer risk and analyse DNA methylation and expression profiles across histological subtypes. Different single-nucleotide polymorphisms associate with invasive serous (rs7405776 odds ratio (OR) = 1.13, P = 3.1 × 10−10) and clear cell (rs11651755 OR = 0.77, P = 1.6 × 10−8) epithelial ovarian cancer. Risk alleles for the serous subtype associate with higher HNF1B-promoter methylation in these tumours. Unmethylated, expressed HNF1B, primarily present in clear cell tumours, coincides with a CpG island methylator phenotype affecting numerous other promoters throughout the genome. Different variants in HNF1B associate with risk of serous and clear cell epithelial ovarian cancer; DNA methylation and expression patterns are also notably distinct between these subtypes. These findings underscore distinct mechanisms driving different epithelial ovarian cancer histological subtypes.
Published: 2013
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28. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer

Author: Pharoah, Paul D. P., Tsai, Ya-Yu, Ramus, Susan J., Phelan, Catherine M., Goode, Ellen L., Lawrenson, Kate, Price, Melissa, Fridley, Brooke L., Tyrer, Jonathan P., Shen, Howard, Weber, Rachel, Karevan, Rod, Larson, Melissa C., Song, Honglin, Tessier, Daniel C., Bacot, François, Vincent, Daniel, Cunningham, Julie M., Dennis, Joe, Dicks, Ed, Aben, Katja K., Anton-Culver, Hoda, Antonenkova, Natalia, Armasu, Sebastian M., Baglietto, Laura, Bandera, Elisa V., Beckmann, Matthias W., Birrer, Michael J., Bloom, Greg, Bogdanova, Natalia, Brenton, James D., Brinton, Louise A., Brooks-Wilson, Angela, Brown, Robert, Butzow, Ralf, Campbell, Ian, Carney, Michael E, Carvalho, Renato S., Chang-Claude, Jenny, Chen, Y. Anne, Chen, Zhihua, Chow, Wong-Ho, Cicek, Mine S., Coetzee, Gerhard, Cook, Linda S., Cramer, Daniel W., Cybulski, Cezary, Dansonka-Mieszkowska, Agnieszka, Despierre, Evelyn, Doherty, Jennifer A, Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Eccles, Diana, Edwards, Robert, Ekici, Arif B., Fasching, Peter A., Fenstermacher, David, Flanagan, James, Gao, Yu-Tang, Garcia-Closas, Montserrat, Gentry-Maharaj, Aleksandra, Giles, Graham, Gjyshi, Anxhela, Gore, Martin, Gronwald, Jacek, Guo, Qi, Halle, Mari K, Harter, Philipp, Hein, Alexander, Heitz, Florian, Hillemanns, Peter, Hoatlin, Maureen, Høgdall, Estrid, Høgdall, Claus K., Hosono, Satoyo, Jakubowska, Anna, Jensen, Allan, Kalli, Kimberly R., Karlan, Beth Y., Kelemen, Linda E., Kiemeney, Lambertus A., Kjaer, Susanne Krüger, Konecny, Gottfried E., Krakstad, Camilla, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Le, Nhu D., Lee, Nathan, Lee, Janet, Leminen, Arto, Lim, Boon Kiong, Lissowska, Jolanta, Lubiński, Jan, Lundvall, Lene, Lurie, Galina, Massuger, Leon F.A.G., Matsuo, Keitaro, McGuire, Valerie, McLaughlin, John R, Menon, Usha, Modugno, Francesmary, Moysich, Kirsten B., Nakanishi, Toru, Narod, Steven A., Ness, Roberta B., Nevanlinna, Heli, Nickels, Stefan, Noushmehr, Houtan, Odunsi, Kunle, Olson, Sara, Orlow, Irene, Paul, James, Pejovic, Tanja, Pelttari, Liisa M, Permuth-Wey, Jenny, Pike, Malcolm C, Poole, Elizabeth M, Qu, Xiaotao, Risch, Harvey A., Rodriguez-Rodriguez, Lorna, Rossing, Mary Anne, Rudolph, Anja, Runnebaum, Ingo, Rzepecka, Iwona K, Salvesen, Helga B., Schwaab, Ira, Severi, Gianluca, Shen, Hui, Shridhar, Vijayalakshmi, Shu, Xiao-Ou, Sieh, Weiva, Southey, Melissa C., Spellman, Paul, Tajima, Kazuo, Teo, Soo-Hwang, Terry, Kathryn L., Thompson, Pamela J, Timorek, Agnieszka, Tworoger, Shelley S., van Altena, Anne M., Berg, David Van Den, Vergote, Ignace, Vierkant, Robert A., Vitonis, Allison F., Wang-Gohrke, Shan, Wentzensen, Nicolas, Whittemore, Alice S., Wik, Elisabeth, Winterhoff, Boris, Woo, Yin Ling, Wu, Anna H, Yang, Hannah P., Zheng, Wei, Ziogas, Argyrios, Zulkifli, Famida, Goodman, Marc T., Hall, Per, Easton, Douglas F, Pearce, Celeste L, Berchuck, Andrew, Chenevix-Trench, Georgia, Iversen, Edwin, Monteiro, Alvaro N.A., Gayther, Simon A., Schildkraut, Joellen M., and Sellers, Thomas A.
Abstract: Genome wide association studies (GWAS) have identified four susceptibility loci for epithelial ovarian cancer (EOC) with another two loci being close to genome-wide significance. We pooled data from a GWAS conducted in North America with another GWAS from the United Kingdom. We selected the top 24,551 SNPs for inclusion on the iCOGS custom genotyping array. Follow-up genotyping was carried out in 18,174 cases and 26,134 controls from 43 studies from the Ovarian Cancer Association Consortium. We validated the two loci at 3q25 and 17q21 previously near genome-wide significance and identified three novel loci associated with risk; two loci associated with all EOC subtypes, at 8q21 (rs11782652, P=5.5×10-9) and 10p12 (rs1243180; P=1.8×10-8), and another locus specific to the serous subtype at 17q12 (rs757210; P=8.1×10-10). An integrated molecular analysis of genes and regulatory regions at these loci provided evidence for functional mechanisms underlying susceptibility that implicates CHMP4C in the pathogenesis of ovarian cancer.
Published: 2013
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29. Identification of a BRCA2-Specific Modifier Locus at 6p24 Related to Breast Cancer Risk

Author: Gaudet, Mia M., Kuchenbaecker, Karoline B., Vijai, Joseph, Klein, Robert J., Kirchhoff, Tomas, McGuffog, Lesley, Barrowdale, Daniel, Dunning, Alison M., Dennis, Joe, Healey, Sue, Dicks, Ed, Soucy, Penny, Sinilnikova, Olga M., Pankratz, Vernon S., Wang, Xianshu, Eldridge, Ronald C., Tessier, Daniel C., Vincent, Daniel, Bacot, Francois, Hogervorst, Frans B. L., Peock, Susan, Stoppa-Lyonnet, Dominique, Peterlongo, Paolo, Schmutzler, Rita K., Nathanson, Katherine L., Piedmonte, Marion, Singer, Christian F., Thomassen, Mads, Hansen, Thomas v. O., Neuhausen, Susan L., Blanco, Ignacio, Greene, Mark H., Weitzel, Jeffrey N., Andrulis, Irene L., Goldgar, David E., D'Andrea, Emma, Caldes, Trinidad, Nevanlinna, Heli, Osorio, Ana, van Rensburg, Elizabeth J., Arason, Adalgeir, Rennert, Gad, van den Ouweland, Ans M. W., van der Hout, Annemarie H., Kets, Carolien M., Aalfs, Cora M., Wijnen, Juul T., Ausems, Margreet G. E. M., Frost, Debra, Ellis, Steve, Fineberg, Elena, Platte, Radka, Adlard, Julian, Tischkowitz, Marc, Porteous, Mary E., Damiola, Francesca, Golmard, Lisa, Barjhoux, Laure, Longy, Michel, Belotti, Muriel, Ferrer, Sandra Fert, Mazoyer, Sylvie, Spurdle, Amanda B., Manoukian, Siranoush, Barile, Monica, Genuardi, Maurizio, Arnold, Norbert, Meindl, Alfons, Sutter, Christian, Wappenschmidt, Barbara, Domchek, Susan M., Pfeiler, Georg, Friedman, Eitan, Jensen, Uffe Birk, Robson, Mark, Shah, Sohela, Lazaro, Conxi, Benitez, Javier, Southey, Melissa C., Schmidt, Marjanka K., Fasching, Peter A., Peto, Julian, Humphreys, Manjeet K., Michailidou, Kyriaki, Sawyer, Elinor J., Burwinkel, Barbara, Guénel, Pascal, Bojesen, Stig E., Milne, Roger L., Brenner, Hermann, Lochmann, Magdalena, Aittomäki, Kristiina, Dörk, Thilo, Margolin, Sara, Mannermaa, Arto, Lambrechts, Diether, Chang-Claude, Jenny, Radice, Paolo, Giles, Graham G., Haiman, Christopher A., Winqvist, Robert, Devillee, Peter, García-Closas, Montserrat, Schoof, Nils, Hooning, Maartje J., Cox, Angela, Pharoah, Paul D. P., Jakubowska, Anna, Orr, Nick, González-Neira, Anna, Pita, Guillermo, Alonso, M. Rosario, Hall, Per, Couch, Fergus J., Simard, Jacques, Easton, Douglas F., Chenevix-Trench, Georgia, Antoniou, Antonis C., Offit, Kenneth, Lee, Andrew, Evans, D. Gareth, Jacobs, Chris, Mai, Phuong L., Wang, Qin, Altshuler, David Matthew, and Garber, Judy Ellen
Subjects: Biology, Genetics, Cancer Genetics, Genome-Wide Association Studies
Abstract: Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80–0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer.
Published: 2013
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30. Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

Author: Couch, Fergus J., Wang, Xianshu, McGuffog, Lesley, Lee, Andrew, Olswold, Curtis, Kuchenbaecker, Karoline B., Soucy, Penny, Fredericksen, Zachary, Barrowdale, Daniel, Dennis, Joe, Gaudet, Mia M., Dicks, Ed, Kosel, Matthew, Healey, Sue, Sinilnikova, Olga M., Lee, Adam, Bacot, François, Vincent, Daniel, Hogervorst, Frans B. L., Peock, Susan, Stoppa-Lyonnet, Dominique, Jakubowska, Anna, Radice, Paolo, Schmutzler, Rita Katharina, Domchek, Susan M., Piedmonte, Marion, Singer, Christian F., Friedman, Eitan, Thomassen, Mads, Hansen, Thomas V. O., Neuhausen, Susan L., Szabo, Csilla I., Blanco, Ignacio, Greene, Mark H., Karlan, Beth Y., Garber, Judy, Phelan, Catherine M., Weitzel, Jeffrey N., Montagna, Marco, Olah, Edith, Andrulis, Irene L., Godwin, Andrew K., Yannoukakos, Drakoulis, Goldgar, David E., Caldes, Trinidad, Nevanlinna, Heli, Osorio, Ana, Terry, Mary Beth, Daly, Mary B., Van Rensburg, Elizabeth J., Hamann, Ute, Ramus, Susan J., Toland, Amanda Ewart, Caligo, Maria A., Olopade, Olufunmilayo I., Tung, Nadine, Claes, Kathleen, Beattie, Mary S., Southey, Melissa C., Imyanitov, Evgeny N., Tischkowitz, Marc, Janavicius, Ramunas, John, Esther M., Kwong, Ava, Diez, Orland, Balmaña, Judith, Barkardottir, Rosa B., Arun, Banu K., Rennert, Gad, Teo, Soo-Hwang, Ganz, Patricia A., Campbell, Ian, Van Der Hout, Annemarie H., Van Deurzen, Carolien H. M., Seynaeve, Caroline, Gómez Garcia, Encarna B., Van Leeuwen, Flora E., Meijers-Heijboer, Hanne E. J., Gille, Johannes J. P., Ausems, Margaret G. E. M., Blok, Marinus J., Ligtenberg, Marjolijn J. L., Rookus, Matti A., Devilee, Peter, Verhoef, Senno, Van Os, Theo A. M., Wijnen, Juul T., Frost, Debra, Ellis, Steve, Fineberg, Elena, Izatt, Louise, Platte, Radka, Evans, D. Gareth, Eeles, Rosalind A., Adlard, Julian, Eccles, Diana M., Cook, Jackie, Brewer, Carole, Douglas, Fiona, Hodgson, Shirley, Murray, Alex, Morrison, Patrick J., Side, Lucy E., Gregory, Helen, Donaldson, Alan, Dorkins, Huw, Houghton, Catherine, Rogers, Mark T., McCann, Emma, Eason, Jacqueline, Calender, Alain, Hardouin, Agnès, Berthet, Pascaline, Delnatte, Capucine, Nogues, Catherine, Lasset, Christine, Houdayer, Claude, Leroux, Dominique, Rouleau, Etienne, Prieur, Fabienne, Damiola, Francesca, Sobol, Hagay, Coupier, Isabelle, Venat-Bouvet, Laurence, Castera, Laurent, Gauthier-Villars, Marion, Léoné, Mélanie, Pujol, Pascal, Mazoyer, Sylvie, Bignon, Yves-Jean, GEMO Study Collaborators, Złowocka-Perłowska, Elżbieta, Gronwald, Jacek, Lubinski, Jan, Durda, Katarzyna, Jaworska, Katarzyna, Huzarski, Tomasz, Spurdle, Amanda B., Viel, Alessandra, Peissel, Bernard, Bonanni, Bernardo, Melloni, Giulia, Ottini, Laura, Papi, Laura, Varesco, Liliana, Tibiletti, Maria Grazia, Peterlongo, Paolo, Volorio, Sara, Manoukian, Siranoush, Pensotti, Valeria, Arnold, Norbert, Engel, Chrisoph, Deissler, Helmut, Gadzicki, Dorothea, Gehrig, Andrea, Kast, Karin, Rhiem, Kerstin, Meindl, Alfons, Niederacher, Dieter, Ditsch, Nina, Plendl, Hansjoerg, Preisler-Adams, Sabine, Engert, Stefanie, Sutter, Christian, Varon-Mateeva, Raymonda, Wappenschmidt, Barbara, Weber, Bernhard H. F., Arver, Brita, Stenmark-Askmalm, Marie, Loman, Niklas, Rosenquist, Richard, Einbeigi, Zakaria, Nathanson, Katherine L., Rebbeck, Timothy R., Blank, Stephanie V., Cohn, David E., Friedlander, Michael, Small, Laurie, Rodriguez, Gustavo C., Bae-Jump, Victoria L., Fink-Retter, Anneliese, Rappaport, Christine, Gschwantler-Kaulich, Daphne, Pfeiler, Georg, Tea, Muy-Kheng, Lindor, Noralane M., Kaufman, Bella, Paluch, Shani Shimon, Skytte, Anne-Bine, Laitman, Yael, Kruse, Torben A., Pedersen, Inge Sokilde, Gerdes, Anne-Marie, Moeller, Sanne Traasdahl, Jensen, Uffe Birk, Vijai, Joseph, Sarrel, Kara, Robson, Mark, Kauff, Noah, Mulligan, Anna Marie, Glendon, Gord, Ejlertsen, Bent, Ozcelik, Hilmi, Nielsen, Finn C., Jønson, Lars, Andersen, Mette K., Ding, Yuan Chun, Steele, Linda, Foretova, Lenka, Lazaro, Conxi, Teule, Alex, Brunet, Joan, Pujana, Miquel Angel, Mai, Phuong L., Loud, Jennifer T., Walsh, Christine, Lester, Jenny, Orsulic, Sandra, Narod, Steven A., Herzog, Josef, Tognazzo, Silvia, Sand, Sharon R., Weaver, Joellen, Agata, Simona, Vaszko, Tibor, Stavropoulou, Alexandra V., Buys, Saundra S., Romero, Atocha, De La Hoya, Miguel, Aittomäki, Kristiina, Muranen, Taru A., Duran, Mercedes, Chung, Wendy K., Lasa, Adriana, Dorfling, Cecilia M., Miron, Alexander, BCFR, Benitez, Javier, Senter, Leigha, Chan, Salina B., Huo, Dezheng, Sokolenko, Anna P., Chiquette, Jocelyne, Tihomirova, Laima, Friebel, Tara M., Agnarsson, Bjarni A., Lu, Karen H., James, Paul A., Lejbkowicz, Flavio, Hall, Per, Dunning, Alison M., Tessier, Daniel, Cunningham, Julie, Slager, Susan L., Wang, Chen, Hart, Steven, Stevens, Kristen, Simard, Jacques, Pastinen, Tomi, Pankratz, Vernon S., Offit, Kenneth, Easton, Douglas F., Chenevix-Trench, Georgia, and Antoniou, Antonis C.
Subjects: Breast--Cancer--Genetic aspects, Ovaries--Cancer--Risk factors, Breast--Cancer--Epidemiology, endocrine system diseases, Epidemiology, Ovaries--Cancer--Genetic aspects, skin and connective tissue diseases, 3. Good health, Breast--Cancer--Risk factors
Abstract: BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10⁻⁸, HR = 1.14, 95% CI: 1.09–1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10⁻⁸, HR = 1.27, 95% CI: 1.17–1.38) and 4q32.3 (rs4691139, P = 3.4×10⁻⁸, HR = 1.20, 95% CI: 1.17–1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific association. The 17q21.31 locus was also associated with ovarian cancer risk in 8,211 BRCA2 carriers (P = 2×10⁻⁴). These loci may lead to an improved understanding of the etiology of breast and ovarian tumors in BRCA1 carriers. Based on the joint distribution of the known BRCA1 breast cancer risk-modifying loci, we estimated that the breast cancer lifetime risks for the 5% of BRCA1 carriers at lowest risk are 28%–50% compared to 81%–100% for the 5% at highest risk. Similarly, based on the known ovarian cancer risk-modifying loci, the 5% of BRCA1 carriers at lowest risk have an estimated lifetime risk of developing ovarian cancer of 28% or lower, whereas the 5% at highest risk will have a risk of 63% or higher. Such differences in risk may have important implications for risk prediction and clinical management for BRCA1 carriers.

31. Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

Author: Bacot, François, Soucy, Penny, Jakubowska, Anna, Wang, Xianshu, Domchek, Susan M., Radice, Paolo, Friedman, Eitan, Kosel, Matthew, Dennis, Joe, Piedmonte, Marion, Healey, Sue, Barrowdale, Daniel, Sinilnikova, Olga M., Fredericksen, Zachary, Vincent, Daniel, Lee, Andrew, Peock, Susan, Neuhausen, Susan L., Dicks, Ed, Couch, Fergus J., Lee, Adam, Schmutzler, Rita Katharina, Gaudet, Mia M., Singer, Christian F., McGuffog, Lesley, Thomassen, Mads, Kuchenbaecker, Karoline B., Hogervorst, Frans B. L., Hansen, Thomas V. O., Investigators, kConFab, Olswold, Curtis, and Stoppa-Lyonnet, Dominique
Subjects: endocrine system diseases, skin and connective tissue diseases, 3. Good health
Abstract: BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10−8, HR = 1.14, 95% CI: 1.09–1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10−8, HR = 1.27, 95% CI: 1.17–1.38) and 4q32.3 (rs4691139, P = 3.4×10−8, HR = 1.20, 95% CI: 1.17–1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific association. The 17q21.31 locus was also associated with ovarian cancer risk in 8,211 BRCA2 carriers (P = 2×10−4). These loci may lead to an improved understanding of the etiology of breast and ovarian tumors in BRCA1 carriers. Based on the joint distribution of the known BRCA1 breast cancer risk-modifying loci, we estimated that the breast cancer lifetime risks for the 5% of BRCA1 carriers at lowest risk are 28%–50% compared to 81%–100% for the 5% at highest risk. Similarly, based on the known ovarian cancer risk-modifying loci, the 5% of BRCA1 carriers at lowest risk have an estimated lifetime risk of developing ovarian cancer of 28% or lower, whereas the 5% at highest risk will have a risk of 63% or higher. Such differences in risk may have important implications for risk prediction and clinical management for BRCA1 carriers.

32. Erratum: Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia.

Author: Johan Rung, Cauchi, Stéphane, Albrechtsen, Anders, Lishuang Shen, Rocheleau, Ghislain, Cavalcanti-Proença, Christine, Bacot, François, Balkau, Beverley, Belisle, Alexandre, Borch-Johnsen, Knut, Charpentier, Guillaume, Dina, Christian, Durand, Emmanuelle, Elliott, Paul, Hadjadj, Samy, Järvelin, Marjo-Riitta, Laitinen, Jaana, Lauritzen, Torsten, Marre, Michel, and Mazur, Alexander
Subjects: TYPE 2 diabetes
Abstract: A correction to the article "Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia" that was published in the September 6, 2009 issue is presented.
Published: 2009
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33. eP447 - Improving and accelerating clinical molecular diagnosis of severe hemophilia A with optical genome mapping technology.

Author: Fahiminiya, Somayyeh, Rivard, Georges-Etienne, Scott, Patrick, Montpetit, Alexandre, Bacot, François, St-Louis, Jean, Mitchell, Grant A., Foulkes, William, Soucy, Jean-Francois, and Gauthier, Julie
Subjects: *GENE mapping, *HEMOPHILIA, *MOLECULAR diagnosis
Published: 2021
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34. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.

Author: Eeles RA, Olama AA, Benlloch S, Saunders EJ, Leongamornlert DA, Tymrakiewicz M, Ghoussaini M, Luccarini C, Dennis J, Jugurnauth-Little S, Dadaev T, Neal DE, Hamdy FC, Donovan JL, Muir K, Giles GG, Severi G, Wiklund F, Gronberg H, Haiman CA, Schumacher F, Henderson BE, Le Marchand L, Lindstrom S, Kraft P, Hunter DJ, Gapstur S, Chanock SJ, Berndt SI, Albanes D, Andriole G, Schleutker J, Weischer M, Canzian F, Riboli E, Key TJ, Travis RC, Campa D, Ingles SA, John EM, Hayes RB, Pharoah PD, Pashayan N, Khaw KT, Stanford JL, Ostrander EA, Signorello LB, Thibodeau SN, Schaid D, Maier C, Vogel W, Kibel AS, Cybulski C, Lubinski J, Cannon-Albright L, Brenner H, Park JY, Kaneva R, Batra J, Spurdle AB, Clements JA, Teixeira MR, Dicks E, Lee A, Dunning AM, Baynes C, Conroy D, Maranian MJ, Ahmed S, Govindasami K, Guy M, Wilkinson RA, Sawyer EJ, Morgan A, Dearnaley DP, Horwich A, Huddart RA, Khoo VS, Parker CC, Van As NJ, Woodhouse CJ, Thompson A, Dudderidge T, Ogden C, Cooper CS, Lophatananon A, Cox A, Southey MC, Hopper JL, English DR, Aly M, Adolfsson J, Xu J, Zheng SL, Yeager M, Kaaks R, Diver WR, Gaudet MM, Stern MC, Corral R, Joshi AD, Shahabi A, Wahlfors T, Tammela TL, Auvinen A, Virtamo J, Klarskov P, Nordestgaard BG, Røder MA, Nielsen SF, Bojesen SE, Siddiq A, Fitzgerald LM, Kolb S, Kwon EM, Karyadi DM, Blot WJ, Zheng W, Cai Q, McDonnell SK, Rinckleb AE, Drake B, Colditz G, Wokolorczyk D, Stephenson RA, Teerlink C, Muller H, Rothenbacher D, Sellers TA, Lin HY, Slavov C, Mitev V, Lose F, Srinivasan S, Maia S, Paulo P, Lange E, Cooney KA, Antoniou AC, Vincent D, Bacot F, Tessier DC, Kote-Jarai Z, and Easton DF
Subjects: Case-Control Studies, Cooperative Behavior, Genome-Wide Association Study, Genotype, Humans, Male, Meta-Analysis as Topic, Oligonucleotide Array Sequence Analysis, Prostatic Neoplasms pathology, Risk Factors, Genetic Loci genetics, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide genetics, Prostatic Neoplasms etiology
Abstract: Prostate cancer is the most frequently diagnosed cancer in males in developed countries. To identify common prostate cancer susceptibility alleles, we genotyped 211,155 SNPs on a custom Illumina array (iCOGS) in blood DNA from 25,074 prostate cancer cases and 24,272 controls from the international PRACTICAL Consortium. Twenty-three new prostate cancer susceptibility loci were identified at genome-wide significance (P < 5 × 10(-8)). More than 70 prostate cancer susceptibility loci, explaining ∼30% of the familial risk for this disease, have now been identified. On the basis of combined risks conferred by the new and previously known risk loci, the top 1% of the risk distribution has a 4.7-fold higher risk than the average of the population being profiled. These results will facilitate population risk stratification for clinical studies.
Published: 2013
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34 results on '"Bacot, François"'

1. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

2. Association analysis identifies 65 new breast cancer risk loci

3. Large-scale genotyping identifies 41 new loci associated with breast cancer risk

4. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer.

5. Genome-wide association study in BRCA1 mutation carriers identifies novel loci associated with breast and ovarian cancer risk.

6. Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31

7. Supplementary Methods and Tables from The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers

8. A full molecular picture of F8 intron 1 inversion created with optical genome mapping

9. Inherited variants in the inner centromere protein (INCENP) gene of the chromosomal passenger complex contribute to the susceptibility of ER-negative breast cancer

10. Improving and accelerating clinical molecular diagnosis of severe hemophilia A with optical genome mapping technology

11. Identification of susceptibility genes for complex diseases using pooling-based genome-wide association scans

12. Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression

13. No association of type 1 diabetes with a functional polymorphism of the LRAP gene

14. Genetic Control of Alternative Splicing in the TAP2 Gene: Possible Implication in the Genetics of Type 1 Diabetes

15. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

16. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers

17. Variations in 5-methylcytosine and 5-hydroxymethylcytosine among human brain, blood, and saliva using oxBS and the Infinium MethylationEPIC array

18. Erratum: Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia

19. Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia

20. PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS

21. Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

22. Genetic Control of Alternative Splicing in the TAP2 Gene.

23. Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

24. Prediction of Breast Cancer Risk Based on Profiling With Common Genetic Variants

25. Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2

26. Genetic variation at CYP3A is associated with age at menarche and breast cancer risk: a case-control study

27. Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer

28. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer

29. Identification of a BRCA2-Specific Modifier Locus at 6p24 Related to Breast Cancer Risk

30. Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

31. Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

32. Erratum: Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia.

33. eP447 - Improving and accelerating clinical molecular diagnosis of severe hemophilia A with optical genome mapping technology.

34. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.

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34 results on '"Bacot, François"'

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