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1. Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast–ovarian cancer susceptibility locus

Author: Kate Lawrenson, Siddhartha Kar, Karen McCue, Karoline Kuchenbaeker, Kyriaki Michailidou, Jonathan Tyrer, Jonathan Beesley, Susan J. Ramus, Qiyuan Li, Melissa K. Delgado, Janet M. Lee, Kristiina Aittomäki, Irene L. Andrulis, Hoda Anton-Culver, Volker Arndt, Banu K. Arun, Brita Arver, Elisa V. Bandera, Monica Barile, Rosa B. Barkardottir, Daniel Barrowdale, Matthias W. Beckmann, Javier Benitez, Andrew Berchuck, Maria Bisogna, Line Bjorge, Carl Blomqvist, William Blot, Natalia Bogdanova, Anders Bojesen, Stig E. Bojesen, Manjeet K. Bolla, Bernardo Bonanni, Anne-Lise Børresen-Dale, Hiltrud Brauch, Paul Brennan, Hermann Brenner, Fiona Bruinsma, Joan Brunet, Shaik Ahmad Buhari, Barbara Burwinkel, Ralf Butzow, Saundra S. Buys, Qiuyin Cai, Trinidad Caldes, Ian Campbell, Rikki Canniotto, Jenny Chang-Claude, Jocelyne Chiquette, Ji-Yeob Choi, Kathleen B. M. Claes, GEMO Study Collaborators, Linda S. Cook, Angela Cox, Daniel W. Cramer, Simon S. Cross, Cezary Cybulski, Kamila Czene, Mary B. Daly, Francesca Damiola, Agnieszka Dansonka-Mieszkowska, Hatef Darabi, Joe Dennis, Peter Devilee, Orland Diez, Jennifer A. Doherty, Susan M. Domchek, Cecilia M. Dorfling, Thilo Dörk, Martine Dumont, Hans Ehrencrona, Bent Ejlertsen, Steve Ellis, EMBRACE, Christoph Engel, Eunjung Lee, D. Gareth Evans, Peter A. Fasching, Lidia Feliubadalo, Jonine Figueroa, Dieter Flesch-Janys, Olivia Fletcher, Henrik Flyger, Lenka Foretova, Florentia Fostira, William D. Foulkes, Brooke L. Fridley, Eitan Friedman, Debra Frost, Gaetana Gambino, Patricia A. Ganz, Judy Garber, Montserrat García-Closas, Aleksandra Gentry-Maharaj, Maya Ghoussaini, Graham G. Giles, Rosalind Glasspool, Andrew K. Godwin, Mark S. Goldberg, David E. Goldgar, Anna González-Neira, Ellen L. Goode, Marc T. Goodman, Mark H. Greene, Jacek Gronwald, Pascal Guénel, Christopher A. Haiman, Per Hall, Emily Hallberg, Ute Hamann, Thomas V. O. Hansen, Patricia A. Harrington, Mikael Hartman, Norhashimah Hassan, Sue Healey, The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON), Florian Heitz, Josef Herzog, Estrid Høgdall, Claus K. Høgdall, Frans B. L. Hogervorst, Antoinette Hollestelle, John L. Hopper, Peter J. Hulick, Tomasz Huzarski, Evgeny N. Imyanitov, KConFab Investigators, Australian Ovarian Cancer Study Group, Claudine Isaacs, Hidemi Ito, Anna Jakubowska, Ramunas Janavicius, Allan Jensen, Esther M. John, Nichola Johnson, Maria Kabisch, Daehee Kang, Miroslav Kapuscinski, Beth Y. Karlan, Sofia Khan, Lambertus A. Kiemeney, Susanne Kruger Kjaer, Julia A. Knight, Irene Konstantopoulou, Veli-Matti Kosma, Vessela Kristensen, Jolanta Kupryjanczyk, Ava Kwong, Miguel de la Hoya, Yael Laitman, Diether Lambrechts, Nhu Le, Kim De Leeneer, Jenny Lester, Douglas A. Levine, Jingmei Li, Annika Lindblom, Jirong Long, Artitaya Lophatananon, Jennifer T. Loud, Karen Lu, Jan Lubinski, Arto Mannermaa, Siranoush Manoukian, Loic Le Marchand, Sara Margolin, Frederik Marme, Leon F. A. G. Massuger, Keitaro Matsuo, Sylvie Mazoyer, Lesley McGuffog, Catriona McLean, Iain McNeish, Alfons Meindl, Usha Menon, Arjen R. Mensenkamp, Roger L. Milne, Marco Montagna, Kirsten B. Moysich, Kenneth Muir, Anna Marie Mulligan, Katherine L. Nathanson, Roberta B. Ness, Susan L. Neuhausen, Heli Nevanlinna, Silje Nord, Robert L. Nussbaum, Kunle Odunsi, Kenneth Offit, Edith Olah, Olufunmilayo I. Olopade, Janet E. Olson, Curtis Olswold, David O’Malley, Irene Orlow, Nick Orr, Ana Osorio, Sue Kyung Park, Celeste L. Pearce, Tanja Pejovic, Paolo Peterlongo, Georg Pfeiler, Catherine M. Phelan, Elizabeth M. Poole, Katri Pylkäs, Paolo Radice, Johanna Rantala, Muhammad Usman Rashid, Gad Rennert, Valerie Rhenius, Kerstin Rhiem, Harvey A. Risch, Gus Rodriguez, Mary Anne Rossing, Anja Rudolph, Helga B. Salvesen, Suleeporn Sangrajrang, Elinor J. Sawyer, Joellen M. Schildkraut, Marjanka K. Schmidt, Rita K. Schmutzler, Thomas A. Sellers, Caroline Seynaeve, Mitul Shah, Chen-Yang Shen, Xiao-Ou Shu, Weiva Sieh, Christian F. Singer, Olga M. Sinilnikova, Susan Slager, Honglin Song, Penny Soucy, Melissa C. Southey, Marie Stenmark-Askmalm, Dominique Stoppa-Lyonnet, Christian Sutter, Anthony Swerdlow, Sandrine Tchatchou, Manuel R. Teixeira, Soo H. Teo, Kathryn L. Terry, Mary Beth Terry, Mads Thomassen, Maria Grazia Tibiletti, Laima Tihomirova, Silvia Tognazzo, Amanda Ewart Toland, Ian Tomlinson, Diana Torres, Thérèse Truong, Chiu-chen Tseng, Nadine Tung, Shelley S. Tworoger, Celine Vachon, Ans M. W. van den Ouweland, Helena C. van Doorn, Elizabeth J. van Rensburg, Laura J. Van't Veer, Adriaan Vanderstichele, Ignace Vergote, Joseph Vijai, Qin Wang, Shan Wang-Gohrke, Jeffrey N. Weitzel, Nicolas Wentzensen, Alice S. Whittemore, Hans Wildiers, Robert Winqvist, Anna H. Wu, Drakoulis Yannoukakos, Sook-Yee Yoon, Jyh-Cherng Yu, Wei Zheng, Ying Zheng, Kum Kum Khanna, Jacques Simard, Alvaro N. Monteiro, Juliet D. French, Fergus J. Couch, Matthew L. Freedman, Douglas F. Easton, Alison M. Dunning, Paul D. Pharoah, Stacey L. Edwards, Georgia Chenevix-Trench, Antonis C. Antoniou, and Simon A. Gayther
Subjects: Science
Abstract: A region on chromosome 19p13 is associated with the risk of developing ovarian and breast cancer. Here, the authors genotyped SNPs in this region in thousands of breast and ovarian cancer patients and identified SNPs associated with three genes, which were analysed with functional studies.
Published: 2016
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2. Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer

Author: Fergus J. Couch, Karoline B. Kuchenbaecker, Kyriaki Michailidou, Gustavo A. Mendoza-Fandino, Silje Nord, Janna Lilyquist, Curtis Olswold, Emily Hallberg, Simona Agata, Habibul Ahsan, Kristiina Aittomäki, Christine Ambrosone, Irene L. Andrulis, Hoda Anton-Culver, Volker Arndt, Banu K. Arun, Brita Arver, Monica Barile, Rosa B. Barkardottir, Daniel Barrowdale, Lars Beckmann, Matthias W. Beckmann, Javier Benitez, Stephanie V. Blank, Carl Blomqvist, Natalia V. Bogdanova, Stig E. Bojesen, Manjeet K. Bolla, Bernardo Bonanni, Hiltrud Brauch, Hermann Brenner, Barbara Burwinkel, Saundra S. Buys, Trinidad Caldes, Maria A. Caligo, Federico Canzian, Jane Carpenter, Jenny Chang-Claude, Stephen J. Chanock, Wendy K. Chung, Kathleen B. M. Claes, Angela Cox, Simon S. Cross, Julie M. Cunningham, Kamila Czene, Mary B. Daly, Francesca Damiola, Hatef Darabi, Miguel de la Hoya, Peter Devilee, Orland Diez, Yuan C. Ding, Riccardo Dolcetti, Susan M. Domchek, Cecilia M. Dorfling, Isabel dos-Santos-Silva, Martine Dumont, Alison M. Dunning, Diana M. Eccles, Hans Ehrencrona, Arif B. Ekici, Heather Eliassen, Steve Ellis, Peter A. Fasching, Jonine Figueroa, Dieter Flesch-Janys, Asta Försti, Florentia Fostira, William D. Foulkes, Tara Friebel, Eitan Friedman, Debra Frost, Marike Gabrielson, Marilie D. Gammon, Patricia A. Ganz, Susan M. Gapstur, Judy Garber, Mia M. Gaudet, Simon A. Gayther, Anne-Marie Gerdes, Maya Ghoussaini, Graham G. Giles, Gord Glendon, Andrew K. Godwin, Mark S. Goldberg, David E. Goldgar, Anna González-Neira, Mark H. Greene, Jacek Gronwald, Pascal Guénel, Marc Gunter, Lothar Haeberle, Christopher A. Haiman, Ute Hamann, Thomas V. O. Hansen, Steven Hart, Sue Healey, Tuomas Heikkinen, Brian E. Henderson, Josef Herzog, Frans B. L. Hogervorst, Antoinette Hollestelle, Maartje J. Hooning, Robert N. Hoover, John L. Hopper, Keith Humphreys, David J. Hunter, Tomasz Huzarski, Evgeny N. Imyanitov, Claudine Isaacs, Anna Jakubowska, Paul James, Ramunas Janavicius, Uffe Birk Jensen, Esther M. John, Michael Jones, Maria Kabisch, Siddhartha Kar, Beth Y. Karlan, Sofia Khan, Kay-Tee Khaw, Muhammad G. Kibriya, Julia A. Knight, Yon-Dschun Ko, Irene Konstantopoulou, Veli-Matti Kosma, Vessela Kristensen, Ava Kwong, Yael Laitman, Diether Lambrechts, Conxi Lazaro, Eunjung Lee, Loic Le Marchand, Jenny Lester, Annika Lindblom, Noralane Lindor, Sara Lindstrom, Jianjun Liu, Jirong Long, Jan Lubinski, Phuong L. Mai, Enes Makalic, Kathleen E. Malone, Arto Mannermaa, Siranoush Manoukian, Sara Margolin, Frederik Marme, John W. M. Martens, Lesley McGuffog, Alfons Meindl, Austin Miller, Roger L. Milne, Penelope Miron, Marco Montagna, Sylvie Mazoyer, Anna M. Mulligan, Taru A. Muranen, Katherine L. Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Børge G. Nordestgaard, Robert L. Nussbaum, Kenneth Offit, Edith Olah, Olufunmilayo I. Olopade, Janet E. Olson, Ana Osorio, Sue K. Park, Petra H. Peeters, Bernard Peissel, Paolo Peterlongo, Julian Peto, Catherine M. Phelan, Robert Pilarski, Bruce Poppe, Katri Pylkäs, Paolo Radice, Nazneen Rahman, Johanna Rantala, Christine Rappaport, Gad Rennert, Andrea Richardson, Mark Robson, Isabelle Romieu, Anja Rudolph, Emiel J. Rutgers, Maria-Jose Sanchez, Regina M. Santella, Elinor J. Sawyer, Daniel F. Schmidt, Marjanka K. Schmidt, Rita K. Schmutzler, Fredrick Schumacher, Rodney Scott, Leigha Senter, Priyanka Sharma, Jacques Simard, Christian F. Singer, Olga M. Sinilnikova, Penny Soucy, Melissa Southey, Doris Steinemann, Marie Stenmark-Askmalm, Dominique Stoppa-Lyonnet, Anthony Swerdlow, Csilla I. Szabo, Rulla Tamimi, William Tapper, Manuel R. Teixeira, Soo-Hwang Teo, Mary B. Terry, Mads Thomassen, Deborah Thompson, Laima Tihomirova, Amanda E. Toland, Robert A. E. M. Tollenaar, Ian Tomlinson, Thérèse Truong, Helen Tsimiklis, Alex Teulé, Rosario Tumino, Nadine Tung, Clare Turnbull, Giski Ursin, Carolien H. M. van Deurzen, Elizabeth J. van Rensburg, Raymonda Varon-Mateeva, Zhaoming Wang, Shan Wang-Gohrke, Elisabete Weiderpass, Jeffrey N. Weitzel, Alice Whittemore, Hans Wildiers, Robert Winqvist, Xiaohong R. Yang, Drakoulis Yannoukakos, Song Yao, M Pilar Zamora, Wei Zheng, Per Hall, Peter Kraft, Celine Vachon, Susan Slager, Georgia Chenevix-Trench, Paul D. P. Pharoah, Alvaro A. N. Monteiro, Montserrat García-Closas, Douglas F. Easton, and Antonis C. Antoniou
Subjects: Science
Abstract: Oestrogen negative breast cancer is associated with a poor prognosis. In this study, the authors perform a meta-analysis of 11 breast cancer genome-wide association studies and identify four new loci associated with oestrogen negative breast cancer risk. These findings may aid in stratifying patients in the clinic.
Published: 2016
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3. RAD51B in Familial Breast Cancer.

Author: Liisa M Pelttari, Sofia Khan, Mikko Vuorela, Johanna I Kiiski, Sara Vilske, Viivi Nevanlinna, Salla Ranta, Johanna Schleutker, Robert Winqvist, Anne Kallioniemi, Thilo Dörk, Natalia V Bogdanova, Jonine Figueroa, Paul D P Pharoah, Marjanka K Schmidt, Alison M Dunning, Montserrat García-Closas, Manjeet K Bolla, Joe Dennis, Kyriaki Michailidou, Qin Wang, John L Hopper, Melissa C Southey, Efraim H Rosenberg, Peter A Fasching, Matthias W Beckmann, Julian Peto, Isabel Dos-Santos-Silva, Elinor J Sawyer, Ian Tomlinson, Barbara Burwinkel, Harald Surowy, Pascal Guénel, Thérèse Truong, Stig E Bojesen, Børge G Nordestgaard, Javier Benitez, Anna González-Neira, Susan L Neuhausen, Hoda Anton-Culver, Hermann Brenner, Volker Arndt, Alfons Meindl, Rita K Schmutzler, Hiltrud Brauch, Thomas Brüning, Annika Lindblom, Sara Margolin, Arto Mannermaa, Jaana M Hartikainen, Georgia Chenevix-Trench, kConFab/AOCS Investigators, Laurien Van Dyck, Hilde Janssen, Jenny Chang-Claude, Anja Rudolph, Paolo Radice, Paolo Peterlongo, Emily Hallberg, Janet E Olson, Graham G Giles, Roger L Milne, Christopher A Haiman, Fredrick Schumacher, Jacques Simard, Martine Dumont, Vessela Kristensen, Anne-Lise Borresen-Dale, Wei Zheng, Alicia Beeghly-Fadiel, Mervi Grip, Irene L Andrulis, Gord Glendon, Peter Devilee, Caroline Seynaeve, Maartje J Hooning, Margriet Collée, Angela Cox, Simon S Cross, Mitul Shah, Robert N Luben, Ute Hamann, Diana Torres, Anna Jakubowska, Jan Lubinski, Fergus J Couch, Drakoulis Yannoukakos, Nick Orr, Anthony Swerdlow, Hatef Darabi, Jingmei Li, Kamila Czene, Per Hall, Douglas F Easton, Johanna Mattson, Carl Blomqvist, Kristiina Aittomäki, and Heli Nevanlinna
Subjects: Medicine, Science
Abstract: Common variation on 14q24.1, close to RAD51B, has been associated with breast cancer: rs999737 and rs2588809 with the risk of female breast cancer and rs1314913 with the risk of male breast cancer. The aim of this study was to investigate the role of RAD51B variants in breast cancer predisposition, particularly in the context of familial breast cancer in Finland. We sequenced the coding region of RAD51B in 168 Finnish breast cancer patients from the Helsinki region for identification of possible recurrent founder mutations. In addition, we studied the known rs999737, rs2588809, and rs1314913 SNPs and RAD51B haplotypes in 44,791 breast cancer cases and 43,583 controls from 40 studies participating in the Breast Cancer Association Consortium (BCAC) that were genotyped on a custom chip (iCOGS). We identified one putatively pathogenic missense mutation c.541C>T among the Finnish cancer patients and subsequently genotyped the mutation in additional breast cancer cases (n = 5259) and population controls (n = 3586) from Finland and Belarus. No significant association with breast cancer risk was seen in the meta-analysis of the Finnish datasets or in the large BCAC dataset. The association with previously identified risk variants rs999737, rs2588809, and rs1314913 was replicated among all breast cancer cases and also among familial cases in the BCAC dataset. The most significant association was observed for the haplotype carrying the risk-alleles of all the three SNPs both among all cases (odds ratio (OR): 1.15, 95% confidence interval (CI): 1.11-1.19, P = 8.88 x 10-16) and among familial cases (OR: 1.24, 95% CI: 1.16-1.32, P = 6.19 x 10-11), compared to the haplotype with the respective protective alleles. Our results suggest that loss-of-function mutations in RAD51B are rare, but common variation at the RAD51B region is significantly associated with familial breast cancer risk.
Published: 2016
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4. Genetic predisposition to in situ and invasive lobular carcinoma of the breast.

Author: Elinor Sawyer, Rebecca Roylance, Christos Petridis, Mark N Brook, Salpie Nowinski, Efterpi Papouli, Olivia Fletcher, Sarah Pinder, Andrew Hanby, Kelly Kohut, Patricia Gorman, Michele Caneppele, Julian Peto, Isabel Dos Santos Silva, Nichola Johnson, Ruth Swann, Miriam Dwek, Katherine-Anne Perkins, Cheryl Gillett, Richard Houlston, Gillian Ross, Paolo De Ieso, Melissa C Southey, John L Hopper, Elena Provenzano, Carmel Apicella, Jelle Wesseling, Sten Cornelissen, Renske Keeman, Peter A Fasching, Sebastian M Jud, Arif B Ekici, Matthias W Beckmann, Michael J Kerin, Federick Marme, Andreas Schneeweiss, Christof Sohn, Barbara Burwinkel, Pascal Guénel, Therese Truong, Pierre Laurent-Puig, Pierre Kerbrat, Stig E Bojesen, Børge G Nordestgaard, Sune F Nielsen, Henrik Flyger, Roger L Milne, Jose Ignacio Arias Perez, Primitiva Menéndez, Javier Benitez, Hermann Brenner, Aida Karina Dieffenbach, Volker Arndt, Christa Stegmaier, Alfons Meindl, Peter Lichtner, Rita K Schmutzler, Magdalena Lochmann, Hiltrud Brauch, Hans-Peter Fischer, Yon-Dschun Ko, GENICA Network, Heli Nevanlinna, Taru A Muranen, Kristiina Aittomäki, Carl Blomqvist, Natalia V Bogdanova, Thilo Dörk, Annika Lindblom, Sara Margolin, Arto Mannermaa, Vesa Kataja, Veli-Matti Kosma, Jaana M Hartikainen, Georgia Chenevix-Trench, KConFab Investigators, Diether Lambrechts, Caroline Weltens, Erik Van Limbergen, Sigrid Hatse, Jenny Chang-Claude, Anja Rudolph, Petra Seibold, Dieter Flesch-Janys, Paolo Radice, Paolo Peterlongo, Bernardo Bonanni, Sara Volorio, Graham G Giles, Gianluca Severi, Laura Baglietto, Catriona A McLean, Christopher A Haiman, Brian E Henderson, Fredrick Schumacher, Loic Le Marchand, Jacques Simard, Mark S Goldberg, France Labrèche, Martine Dumont, Vessela Kristensen, Robert Winqvist, Katri Pylkäs, Arja Jukkola-Vuorinen, Saila Kauppila, Irene L Andrulis, Julia A Knight, Gord Glendon, Anna Marie Mulligan, Peter Devillee, Rob A E M Tollenaar, Caroline M Seynaeve, Mieke Kriege, Jonine Figueroa, Stephen J Chanock, Mark E Sherman, Maartje J Hooning, Antoinette Hollestelle, Ans M W van den Ouweland, Carolien H M van Deurzen, Jingmei Li, Kamila Czene, Keith Humphreys, Angela Cox, Simon S Cross, Malcolm W R Reed, Mitul Shah, Anna Jakubowska, Jan Lubinski, Katarzyna Jaworska-Bieniek, Katarzyna Durda, Anthony Swerdlow, Alan Ashworth, Nicholas Orr, Minouk Schoemaker, Fergus J Couch, Emily Hallberg, Anna González-Neira, Guillermo Pita, M Rosario Alonso, Daniel C Tessier, Daniel Vincent, Francois Bacot, Manjeet K Bolla, Qin Wang, Joe Dennis, Kyriaki Michailidou, Alison M Dunning, Per Hall, Doug Easton, Paul Pharoah, Marjanka K Schmidt, Ian Tomlinson, and Montserrat Garcia-Closas
Subjects: Genetics, QH426-470
Abstract: Invasive lobular breast cancer (ILC) accounts for 10-15% of all invasive breast carcinomas. It is generally ER positive (ER+) and often associated with lobular carcinoma in situ (LCIS). Genome-wide association studies have identified more than 70 common polymorphisms that predispose to breast cancer, but these studies included predominantly ductal (IDC) carcinomas. To identify novel common polymorphisms that predispose to ILC and LCIS, we pooled data from 6,023 cases (5,622 ILC, 401 pure LCIS) and 34,271 controls from 36 studies genotyped using the iCOGS chip. Six novel SNPs most strongly associated with ILC/LCIS in the pooled analysis were genotyped in a further 516 lobular cases (482 ILC, 36 LCIS) and 1,467 controls. These analyses identified a lobular-specific SNP at 7q34 (rs11977670, OR (95%CI) for ILC = 1.13 (1.09-1.18), P = 6.0 × 10(-10); P-het for ILC vs IDC ER+ tumors = 1.8 × 10(-4)). Of the 75 known breast cancer polymorphisms that were genotyped, 56 were associated with ILC and 15 with LCIS at P
Published: 2014
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5. Supplementary Tables and References from BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

Author: Fergus J. Couch, Maaike P.G. Vreeswijk, Aura Carreira, David E. Goldgar, Alvaro N.A. Monteiro, Harry Vrieling, Peter Devilee, Amanda Spurdle, Douglas F. Easton, Setareh Moghadasi, Liliana Varesco, Kathleen B.M. Claes, Florentia Fostira, Lenka Foretova, Logan Walker, Jennifer Leary, Ying Zheng, Wei Zheng, Jyh-Cherng Yu, Anna H. Wu, Robert Winqvist, Qin Wang, Lizet E. van der Kolk, Christi J. van Asperen, Thérèse Truong, Diana Torres, Ian Tomlinson, Soo H. Teo, Anthony Swerdlow, Daniel O. Stram, Melissa C. Southey, Susan Slager, Xiao-Ou Shu, Martha Shrubsole, Chen-Yang Shen, Mitul Shah, Caroline Seynaeve, Minouk J. Schoemaker, Marjanka K. Schmidt, Elinor J. Sawyer, Suleeporn Sangrajrang, Anja Rudolph, Valerie Rhenius, Muhammad Usman Rashid, Paolo Radice, Katri Pylkäs, Paul D.P. Pharoah, Julian Peto, Paolo Peterlongo, Ana Osorio, Jan J.C. Oosterwijk, Curtis Olswold, Janet E. Olson, Heli Nevanlinna, Susan L. Neuhausen, Kenneth Muir, Roger L. Milne, Kyriaki Michailidou, Hui Miao, Keitaro Matsuo, Frederik Marme, Sara Margolin, Arto Mannermaa, Eva Machackova, Jan Lubinski, Artitaya Lophatananon, Annika Lindblom, Jingmei Li, Loic Le Marchand, Diether Lambrechts, Kah-Nyin Lai, Vessela Kristensen, Veli-Matti Kosma, Daehee Kang, Anna Jakubowska, Hidemi Ito, John L. Hopper, Antoinette Hollestelle, Frans B. Hogervorst, Mikael Hartman, Ute Hamann, Per Hall, Christopher A. Haiman, Pascal Guénel, Gord Glendon, Graham G. Giles, Montserrat García-Closas, Henrik Flyger, Jonine Figueroa, Peter A. Fasching, Alison M. Dunning, Isabel dos-Santos-Silva, Thilo Dörk, Joe Dennis, Hatef Darabi, Kamila Czene, Simon S. Cross, Angela Cox, J. Margriet Collée, Ji-Yeob Choi, Ching-Yu Cheng, Georgia Chenevix-Trench, Jenny Chang-Claude, Barbara Burwinkel, Thomas Brüning, Barbara Brouwers, Annegien Broeks, Hermann Brenner, Paul Brennan, Hiltrud Brauch, Anne-Lise Borresen-Dale, Manjeet K. Bolla, Stig E. Bojesen, Natalia V. Bogdanova, Javier Benitez, Matthias W. Beckmann, Volker Arndt, Hoda Anton-Culver, Irene Andrulis, Kristiina Aittomäki, Cora M. Aalfs, Chunling Hu, Jenna Lilyquist, Jamie Hinton, Emily Hallberg, Huong Meeks, Fabienne M.G.R. Calléja, Charlotte Martin, Lucia Guidugli, Asa Ehlen, Catharina Von Nicolai, Romy L.S. Mesman, and Hermela Shimelis
Abstract: Table S1: Description of the BCAC studies contributing to COGS. Table S2: Predicted effects of BRCA1 and BRCA2 variants included in the iCOGS array on protein function. Table S3: Frequency of BRCA1 and BRCA2 variants from iCOGS in breast cancer cases and controls. Table S4: Family studies of Y3035S showing scores for each family by constant relative risk and 75% penetrance. Supplementary References.
Published: 2023
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6. Data from BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

Author: Fergus J. Couch, Maaike P.G. Vreeswijk, Aura Carreira, David E. Goldgar, Alvaro N.A. Monteiro, Harry Vrieling, Peter Devilee, Amanda Spurdle, Douglas F. Easton, Setareh Moghadasi, Liliana Varesco, Kathleen B.M. Claes, Florentia Fostira, Lenka Foretova, Logan Walker, Jennifer Leary, Ying Zheng, Wei Zheng, Jyh-Cherng Yu, Anna H. Wu, Robert Winqvist, Qin Wang, Lizet E. van der Kolk, Christi J. van Asperen, Thérèse Truong, Diana Torres, Ian Tomlinson, Soo H. Teo, Anthony Swerdlow, Daniel O. Stram, Melissa C. Southey, Susan Slager, Xiao-Ou Shu, Martha Shrubsole, Chen-Yang Shen, Mitul Shah, Caroline Seynaeve, Minouk J. Schoemaker, Marjanka K. Schmidt, Elinor J. Sawyer, Suleeporn Sangrajrang, Anja Rudolph, Valerie Rhenius, Muhammad Usman Rashid, Paolo Radice, Katri Pylkäs, Paul D.P. Pharoah, Julian Peto, Paolo Peterlongo, Ana Osorio, Jan J.C. Oosterwijk, Curtis Olswold, Janet E. Olson, Heli Nevanlinna, Susan L. Neuhausen, Kenneth Muir, Roger L. Milne, Kyriaki Michailidou, Hui Miao, Keitaro Matsuo, Frederik Marme, Sara Margolin, Arto Mannermaa, Eva Machackova, Jan Lubinski, Artitaya Lophatananon, Annika Lindblom, Jingmei Li, Loic Le Marchand, Diether Lambrechts, Kah-Nyin Lai, Vessela Kristensen, Veli-Matti Kosma, Daehee Kang, Anna Jakubowska, Hidemi Ito, John L. Hopper, Antoinette Hollestelle, Frans B. Hogervorst, Mikael Hartman, Ute Hamann, Per Hall, Christopher A. Haiman, Pascal Guénel, Gord Glendon, Graham G. Giles, Montserrat García-Closas, Henrik Flyger, Jonine Figueroa, Peter A. Fasching, Alison M. Dunning, Isabel dos-Santos-Silva, Thilo Dörk, Joe Dennis, Hatef Darabi, Kamila Czene, Simon S. Cross, Angela Cox, J. Margriet Collée, Ji-Yeob Choi, Ching-Yu Cheng, Georgia Chenevix-Trench, Jenny Chang-Claude, Barbara Burwinkel, Thomas Brüning, Barbara Brouwers, Annegien Broeks, Hermann Brenner, Paul Brennan, Hiltrud Brauch, Anne-Lise Borresen-Dale, Manjeet K. Bolla, Stig E. Bojesen, Natalia V. Bogdanova, Javier Benitez, Matthias W. Beckmann, Volker Arndt, Hoda Anton-Culver, Irene Andrulis, Kristiina Aittomäki, Cora M. Aalfs, Chunling Hu, Jenna Lilyquist, Jamie Hinton, Emily Hallberg, Huong Meeks, Fabienne M.G.R. Calléja, Charlotte Martin, Lucia Guidugli, Asa Ehlen, Catharina Von Nicolai, Romy L.S. Mesman, and Hermela Shimelis
Abstract: Breast cancer risks conferred by many germline missense variants in the BRCA1 and BRCA2 genes, often referred to as variants of uncertain significance (VUS), have not been established. In this study, associations between 19 BRCA1 and 33 BRCA2 missense substitution variants and breast cancer risk were investigated through a breast cancer case–control study using genotyping data from 38 studies of predominantly European ancestry (41,890 cases and 41,607 controls) and nine studies of Asian ancestry (6,269 cases and 6,624 controls). The BRCA2 c.9104A>C, p.Tyr3035Ser (OR = 2.52; P = 0.04), and BRCA1 c.5096G>A, p.Arg1699Gln (OR = 4.29; P = 0.009) variant were associated with moderately increased risks of breast cancer among Europeans, whereas BRCA2 c.7522G>A, p.Gly2508Ser (OR = 2.68; P = 0.004), and c.8187G>T, p.Lys2729Asn (OR = 1.4; P = 0.004) were associated with moderate and low risks of breast cancer among Asians. Functional characterization of the BRCA2 variants using four quantitative assays showed reduced BRCA2 activity for p.Tyr3035Ser compared with wild-type. Overall, our results show how BRCA2 missense variants that influence protein function can confer clinically relevant, moderately increased risks of breast cancer, with potential implications for risk management guidelines in women with these specific variants. Cancer Res; 77(11); 2789–99. ©2017 AACR.
Published: 2023
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7. Supplementary Figures from BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

Author: Fergus J. Couch, Maaike P.G. Vreeswijk, Aura Carreira, David E. Goldgar, Alvaro N.A. Monteiro, Harry Vrieling, Peter Devilee, Amanda Spurdle, Douglas F. Easton, Setareh Moghadasi, Liliana Varesco, Kathleen B.M. Claes, Florentia Fostira, Lenka Foretova, Logan Walker, Jennifer Leary, Ying Zheng, Wei Zheng, Jyh-Cherng Yu, Anna H. Wu, Robert Winqvist, Qin Wang, Lizet E. van der Kolk, Christi J. van Asperen, Thérèse Truong, Diana Torres, Ian Tomlinson, Soo H. Teo, Anthony Swerdlow, Daniel O. Stram, Melissa C. Southey, Susan Slager, Xiao-Ou Shu, Martha Shrubsole, Chen-Yang Shen, Mitul Shah, Caroline Seynaeve, Minouk J. Schoemaker, Marjanka K. Schmidt, Elinor J. Sawyer, Suleeporn Sangrajrang, Anja Rudolph, Valerie Rhenius, Muhammad Usman Rashid, Paolo Radice, Katri Pylkäs, Paul D.P. Pharoah, Julian Peto, Paolo Peterlongo, Ana Osorio, Jan J.C. Oosterwijk, Curtis Olswold, Janet E. Olson, Heli Nevanlinna, Susan L. Neuhausen, Kenneth Muir, Roger L. Milne, Kyriaki Michailidou, Hui Miao, Keitaro Matsuo, Frederik Marme, Sara Margolin, Arto Mannermaa, Eva Machackova, Jan Lubinski, Artitaya Lophatananon, Annika Lindblom, Jingmei Li, Loic Le Marchand, Diether Lambrechts, Kah-Nyin Lai, Vessela Kristensen, Veli-Matti Kosma, Daehee Kang, Anna Jakubowska, Hidemi Ito, John L. Hopper, Antoinette Hollestelle, Frans B. Hogervorst, Mikael Hartman, Ute Hamann, Per Hall, Christopher A. Haiman, Pascal Guénel, Gord Glendon, Graham G. Giles, Montserrat García-Closas, Henrik Flyger, Jonine Figueroa, Peter A. Fasching, Alison M. Dunning, Isabel dos-Santos-Silva, Thilo Dörk, Joe Dennis, Hatef Darabi, Kamila Czene, Simon S. Cross, Angela Cox, J. Margriet Collée, Ji-Yeob Choi, Ching-Yu Cheng, Georgia Chenevix-Trench, Jenny Chang-Claude, Barbara Burwinkel, Thomas Brüning, Barbara Brouwers, Annegien Broeks, Hermann Brenner, Paul Brennan, Hiltrud Brauch, Anne-Lise Borresen-Dale, Manjeet K. Bolla, Stig E. Bojesen, Natalia V. Bogdanova, Javier Benitez, Matthias W. Beckmann, Volker Arndt, Hoda Anton-Culver, Irene Andrulis, Kristiina Aittomäki, Cora M. Aalfs, Chunling Hu, Jenna Lilyquist, Jamie Hinton, Emily Hallberg, Huong Meeks, Fabienne M.G.R. Calléja, Charlotte Martin, Lucia Guidugli, Asa Ehlen, Catharina Von Nicolai, Romy L.S. Mesman, and Hermela Shimelis
Abstract: Figure S1: BCRA2 p.Y3035S Pedigrees. Figure S2: Western blot of ectopically expressed full-length wildtype and mutant hBRCA2 protein in VC8 DR-GFP cells subjected to HDR assay. Figure S3: Purification of wildtype and mutant BRCA2 from human cells. Figure S4: Position of BRCA2 DNA binding domain (DBD) variants on a ribbon diagram of the murine DBD crystal structure.
Published: 2023
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8. BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

Author: Ian Tomlinson, Thérèse Truong, Henrik Flyger, Martha J. Shrubsole, Manjeet K. Bolla, Paolo Radice, Janet E. Olson, Xiao-Ou Shu, Ching-Yu Cheng, Kyriaki Michailidou, John L. Hopper, Annika Lindblom, Lizet E. van der Kolk, Paolo Peterlongo, Cora M. Aalfs, Susan L. Neuhausen, Hermela Shimelis, Jonine D. Figueroa, Florentia Fostira, Ji Yeob Choi, Fabienne Calléja, Setareh Moghadasi, Barbara Brouwers, Hui Miao, Pascal Guénel, Graham G. Giles, Roger L. Milne, Gord Glendon, Hidemi Ito, Per Hall, Jingmei Li, Elinor J. Sawyer, Javier Benitez, Isabel dos-Santos-Silva, Melissa C. Southey, Jyh-Cherng Yu, Curtis Olswold, Julian Peto, Valerie Rhenius, Katri Pylkäs, Anne Lise Børresen-Dale, Robert Winqvist, J. Margriet Collée, Mitul Shah, Minouk J. Schoemaker, Barbara Burwinkel, Pharoah Pd, Hermann Brenner, Keitaro Matsuo, Eva Machackova, Caroline M. Seynaeve, David E. Goldgar, Anna Jakubowska, Paul Brennan, Kathleen Claes, Montserrat Garcia-Closas, Vessela N. Kristensen, Douglas F. Easton, Hoda Anton-Culver, Åsa Ehlén, Stig E. Bojesen, Maaike P.G. Vreeswijk, Irene L. Andrulis, Annegien Broeks, Joe Dennis, Daniel O. Stram, Simon S. Cross, Christopher A. Haiman, Hatef Darabi, Veli-Matti Kosma, Daehee Kang, Frans B. L. Hogervorst, Alison M. Dunning, Aura Carreira, Antoinette Hollestelle, Kenneth Muir, Susan L. Slager, Thilo Dörk, Jennifer A. Leary, Sara Margolin, Jenna Lilyquist, Jenny Chang-Claude, Liliana Varesco, Amanda B. Spurdle, Georgia Chenevix-Trench, Diana Torres, Emily Hallberg, Marjanka K. Schmidt, Kristiina Aittomäki, Harry Vrieling, Loic Le Marchand, Catharina von Nicolai, Angela Cox, Matthias W. Beckmann, Natalia Bogdanova, Volker Arndt, Anja Rudolph, Arto Mannermaa, Heli Nevanlinna, Jamie Hinton, Lenka Foretova, Logan C. Walker, Muhammad Usman Rashid, Wei Zheng, Ying Zheng, Peter Devilee, Lucia Guidugli, Frederik Marme, Jan C. Oosterwijk, Alvaro N.A. Monteiro, Anna H. Wu, Anthony J. Swerdlow, Mikael Hartman, Soo H. Teo, Hiltrud Brauch, Thomas Brüning, Artitaya Lophatananon, Peter A. Fasching, Diether Lambrechts, Christi J. van Asperen, Chen-Yang Shen, Suleeporn Sangrajrang, Huong Meeks, Jan Lubinski, Kah-Nyin Lai, Ana Osorio, Chunling Hu, Qin Wang, Kamila Czene, Romy L. S. Mesman, Fergus J. Couch, Ute Hamann, Charlotte Martin, Dennis, Joe [0000-0003-4591-1214], Dunning, Alison [0000-0001-6651-7166], Pharoah, Paul [0000-0001-8494-732X], Rhenius, Valerie [0000-0003-4215-3235], Easton, Douglas [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Damage and Repair in Cancer Development and Cancer Treatment (DARE), Targeted Gynaecologic Oncology (TARGON), Clinical Genetics, Medical Oncology, Human Genetics, Human genetics, and CCA - Cancer biology and immunology
Subjects: 0301 basic medicine, Risk, Cancer Research, GENES, endocrine system diseases, Genotype, DNA-BINDING, Mutation, Missense, Breast Neoplasms, Biology, Bioinformatics, OVARIAN-CANCER, CLASSIFICATION, Article, 03 medical and health sciences, Mice, Breast cancer, Germline mutation, SDG 3 - Good Health and Well-being, medicine, UNCLASSIFIED VARIANTS, SEQUENCE VARIANTS, Missense mutation, Animals, Humans, skin and connective tissue diseases, Germ-Line Mutation, Aged, BRCA2 Protein, UNKNOWN CLINICAL-SIGNIFICANCE, Case-control study, Cancer, FUNCTIONAL-EVALUATION, medicine.disease, 3. Good health, 030104 developmental biology, Oncology, CELL-BASED ASSAY, Amino Acid Substitution, UNCERTAIN SIGNIFICANCE, Case-Control Studies, Female, Ovarian cancer
Abstract: Breast cancer risks conferred by many germline missense variants in the BRCA1 and BRCA2 genes, often referred to as variants of uncertain significance (VUS), have not been established. In this study, associations between 19 BRCA1 and 33 BRCA2 missense substitution variants and breast cancer risk were investigated through a breast cancer case–control study using genotyping data from 38 studies of predominantly European ancestry (41,890 cases and 41,607 controls) and nine studies of Asian ancestry (6,269 cases and 6,624 controls). The BRCA2 c.9104A>C, p.Tyr3035Ser (OR = 2.52; P = 0.04), and BRCA1 c.5096G>A, p.Arg1699Gln (OR = 4.29; P = 0.009) variant were associated with moderately increased risks of breast cancer among Europeans, whereas BRCA2 c.7522G>A, p.Gly2508Ser (OR = 2.68; P = 0.004), and c.8187G>T, p.Lys2729Asn (OR = 1.4; P = 0.004) were associated with moderate and low risks of breast cancer among Asians. Functional characterization of the BRCA2 variants using four quantitative assays showed reduced BRCA2 activity for p.Tyr3035Ser compared with wild-type. Overall, our results show how BRCA2 missense variants that influence protein function can confer clinically relevant, moderately increased risks of breast cancer, with potential implications for risk management guidelines in women with these specific variants. Cancer Res; 77(11); 2789–99. ©2017 AACR.
Published: 2017
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9. A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer

Author: Harald Surowy, Rulla M. Tamimi, Javier Benitez, Wing-Yee Lo, Celine M. Vachon, Nadege Presneau, John J. Spinelli, Ann Smeets, Hoda Anton-Culver, Veli-Matti Kosma, Christopher A. Haiman, Martha J. Shrubsole, Ross L. Prentice, Diana Eccles, Ursula Eilber, Loic Le Marchand, Katri Pylkäs, Jirong Long, Michael P. Lux, Sara Margolin, Hedy S. Rennert, Tom Maishman, Mary B. Daly, Rita K. Schmutzler, Julian Peto, Sune F. Nielsen, Eric Hahnen, Niclas Håkansson, Børge G. Nordestgaard, Mitul Shah, Matthias W. Beckmann, Anthony J. Swerdlow, Barbara Burwinkel, Rudolf Kaaks, Usha Menon, William J. Tapper, Argyrios Ziogas, Peter Hillemanns, Fares Al-Ejeh, Roger L. Milne, Wolfgang Janni, Pascal Guénel, Mikael Eriksson, Clarice R. Weinberg, Kyriaki Michailidou, Jonathan Beesley, Marike Gabrielson, J. Esteban Castelao, Margriet Collée, Janet E. Olson, Gad Rennert, Per Broberg, Rob A. E. M. Tollenaar, David Cox, Paolo Peterlongo, Helian Feng, Brian D. Carter, Nichola Johnson, Emmanouil Saloustros, Dijana Plaseska-Karanfilska, Kimberly F. Doheny, Paul L. Auer, Hans Wildiers, Jacques Simard, Michael Untch, Per Hall, Martine Dumont, Julie M. Cunningham, Thilo Dörk, Mary Beth Terry, Jenny Chang-Claude, Lang Wu, Irene L. Andrulis, Xiaohong R. Yang, Caroline Baynes, Isabel dos-Santos-Silva, Douglas F. Easton, Wei Shi, Emily Hallberg, Camilla Wendt, Hiltrud Brauch, Diana Torres, Olufunmilayo I. Olopade, David Van Den Berg, Georgia Chenevix-Trench, Alfons Meindl, Stig E. Bojesen, Jonine D. Figueroa, Dale P. Sandler, Vessela N. Kristensen, Christine L. Clarke, Wei Zheng, Manuela Gago-Dominguez, E Rozali, Henrik Flyger, Sheila Seal, Guanmengqian Huang, Marjanka K. Schmidt, Håkan Olsson, Christopher G. Scott, Kamila Czene, Laura Fachal, Rodney J. Scott, Jennifer Stone, Sara Y. Brucker, Qin Wang, David J. Hunter, Maya Ghoussaini, Christoph Engel, Keith Humphreys, Susan M. Gapstur, Daniel C. Tessier, Paolo Radice, John L. Hopper, Audrey Y. Jung, Lucy Xia, Atocha Romero, Chenjie Zeng, Peter A. Fasching, Jan Lubinski, Anna González-Neira, Nazneen Rahman, Robert N. Hoover, Thérèse Truong, Fergus J. Couch, Anna Marie Mulligan, Robert J. MacInnis, Ute Hamann, Hanne Meijers-Heijboer, Brigitte Rack, Simon S. Cross, Federico Canzian, J.-P. Meyer, Sara Lindström, Natalia Bogdanova, Trinidad Caldés, Olivia Fletcher, Peter Kraft, Elinor J. Sawyer, Alexander Gusev, Louise A. Brinton, Diether Lambrechts, Bingshan Li, Kristan J. Aronson, Jane Romm, Anja Rudolph, Peter Devilee, Qiuyin Cai, Arto Mannermaa, Elad Ziv, Alice S. Whittemore, Abigail Thomas, Hermann Brenner, Montserrat Garcia-Closas, Patrick Neven, Kristine Jones, Miriam Dwek, Sibylle Loibl, Heli Nevanlinna, Jolanta Lissowska, Susan L. Neuhausen, Elza Khusnutdinova, Marina Bermisheva, Alicja Wolk, Lin Fritschi, Xingyi Guo, Angela Cox, Michael Jones, Xiaoqing Chen, Esther M. John, Richard Barfield, Volker Arndt, Patricia Harrington, Quinten Waisfisz, Daniel Vincent, Antoinette Hollestelle, Dimitrios Mavroudis, JoAnn E. Manson, Joe Dennis, Walter C. Willett, Stacey L. Edwards, Melissa C. Southey, Andreas Schneeweiss, Jack A. Taylor, Robert Winqvist, Mia M. Gaudet, David E. Goldgar, Anna Jakubowska, Paul D.P. Pharoah, Kathrin Thöne, Dieter Flesch-Janys, Mark S. Goldberg, Craig Luccarini, Sten Cornelissen, Jingmei Li, Michael J. Kerin, Myrto Barrdahl, Xiao-Ou Shu, Alison M. Dunning, Manjeet K. Bolla, Carl Blomqvist, Graham G. Giles, Hans Christiansen, A. Heather Eliassen, Valerie Rhenius, Alexander Hein, Belynda Hicks, Ivana Maleva Kostovska, Tongguang Cheng, Yingchang Lu, CCA - Cancer biology and immunology, Amsterdam Neuroscience - Complex Trait Genetics, Human genetics, Amsterdam Reproduction & Development (AR&D), Clinical Genetics, Medical Oncology, Guo, Xingyi [0000-0001-5269-1294], Al-Ejeh, Fares [0000-0002-1553-0077], Li, Bingshan [0000-0003-2129-168X], Gusev, Alexander [0000-0002-7980-4620], Andrulis, Irene L [0000-0002-4226-6435], Arndt, Volker [0000-0001-9320-8684], Brauch, Hiltrud [0000-0001-7531-2736], Collée, Margriet [0000-0002-9272-9346], Cox, Angela [0000-0002-5138-1099], Cunningham, Julie M [0000-0002-8159-3025], Fachal, Laura [0000-0002-7256-9752], Fletcher, Olivia [0000-0001-9387-7116], Hein, Alexander [0000-0003-2601-3398], Hicks, Belynda [0000-0001-8014-4888], Hollestelle, Antoinette [0000-0003-1166-1966], Jakubowska, Anna [0000-0002-5650-0501], Khusnutdinova, Elza [0000-0003-2987-3334], Li, Jingmei [0000-0001-8587-7511], Menon, Usha [0000-0003-3708-1732], Nevanlinna, Heli [0000-0002-0916-2976], Nordestgaard, Børge G [0000-0002-1954-7220], Pylkäs, Katri [0000-0002-2449-0521], Rennert, Gad [0000-0002-8512-068X], Romero, Atocha [0000-0002-1634-7397], Saloustros, Emmanouil [0000-0002-0485-0120], Scott, Christopher G [0000-0003-1340-0647], Shrubsole, Martha J [0000-0002-5591-7575], Wolk, Alicja [0000-0001-7387-6845], Ziogas, Argyrios [0000-0003-4529-3727], Pharoah, Paul DP [0000-0001-8494-732X], Milne, Roger L [0000-0001-5764-7268], Easton, Douglas F [0000-0003-2444-3247], Zheng, Wei [0000-0003-1226-070X], Apollo - University of Cambridge Repository, Human Genetics, and ARD - Amsterdam Reproduction and Development
Subjects: 0301 basic medicine, Risk, medicine.medical_specialty, Gene Expression, Genome-wide association study, Breast Neoplasms, Biology, Genome-wide association studies, Polymorphism, Single Nucleotide, Article, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, SDG 3 - Good Health and Well-being, Genetic model, Genetics, medicine, Humans, Genetic Predisposition to Disease, Genetic association, medicine.disease, 3. Good health, 030104 developmental biology, 030220 oncology & carcinogenesis, Case-Control Studies, Expression quantitative trait loci, Medical genetics, Female, Gene expression, Breast Cancer Genetics, Genome-Wide Association Study
Abstract: The breast cancer risk variants identified in genome-wide association studies explain only a small fraction of the familial relative risk, and the genes responsible for these associations remain largely unknown. To identify novel risk loci and likely causal genes, we performed a transcriptome-wide association study evaluating associations of genetically predicted gene expression with breast cancer risk in 122,977 cases and 105,974 controls of European ancestry. We used data from the Genotype-Tissue Expression Project to establish genetic models to predict gene expression in breast tissue and evaluated model performance using data from The Cancer Genome Atlas. Of the 8,597 genes evaluated, significant associations were identified for 48 at a Bonferroni-corrected threshold of P −6, including 14 genes at loci not yet reported for breast cancer. We silenced 13 genes and showed an effect for 11 on cell proliferation and/or colony-forming efficiency. Our study provides new insights into breast cancer genetics and biology.
Published: 2019
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10. Heterogeneity of luminal breast cancer characterised by immunohistochemical expression of basal markers

Author: Jenny Chang-Claude, Curtis Olswold, Veli-Matti Kosma, Penny Coulson, Jonine D. Figueroa, Qin Wang, Melissa C. Southey, Paul D.P. Pharoah, Manjeet K. Bolla, Carl Blomqvist, Vesa Kataja, Janet E. Olson, Graham G. Giles, H. Raza Ali, Rulla M. Tamimi, A. Heather Eliassen, Hyuna Sung, Angela Cox, Douglas F. Easton, Heli Nevanlinna, Päivi Heikkilä, Fergus J. Couch, William J. Howat, Marjanka K. Schmidt, Xiaohong R. Yang, Reijo Sironen, Rainer Fagerholm, Emily Hallberg, Roger L. Milne, Fiona M. Blows, Simon S. Cross, Montserrat Garcia-Closas, Mark E. Sherman, Catriona McLean, Peter Kraft, and Arto Mannermaa
Subjects: 0301 basic medicine, Cancer Research, Pathology, Receptor, ErbB-2, CK5/6, Body Mass Index, Basal (phylogenetics), 0302 clinical medicine, Risk Factors, Epidermal growth factor receptor, biology, Carcinoma, Ductal, Breast, Age Factors, Middle Aged, Prognosis, Immunohistochemistry, 3. Good health, Tumor Burden, luminal A tumour, ErbB Receptors, Parity, Oncology, Receptors, Estrogen, 030220 oncology & carcinogenesis, Female, Menopause, Receptors, Progesterone, Adult, medicine.medical_specialty, EGFR, Breast Neoplasms, 03 medical and health sciences, Cytokeratin, Breast cancer, breast cancer, medicine, Carcinoma, Biomarkers, Tumor, Humans, Molecular Diagnostics, Aged, Neoplasm Staging, Menarche, tumour characteristics, Keratin-6, Cancer, medicine.disease, Keratin 5, Carcinoma, Lobular, 030104 developmental biology, biology.protein, Keratin-5, Neoplasm Grading
Abstract: Background: Luminal A breast cancer defined as hormone receptor positive and human epidermal growth factor receptor 2 (HER2) negative is known to be heterogeneous. Previous study showed that luminal A tumours with the expression of basal markers ((cytokeratin (CK) 5 or CK5/6) or epidermal growth factor receptor (EGFR)) were associated with poorer prognosis compared with those that stained negative for basal markers. Prompted by this study, we assessed whether tumour characteristics and risk factors differed by basal marker status within luminal A tumours.\ud \ud Methods: We pooled 5040 luminal A cases defined by immunohistochemistry (4490 basal-negative ((CK5 (or CK5/6))− and EGFR−) and 550 basal-positive ((CK5 (or CK5/6+)) or EGFR+)) from eight studies participating in the Breast Cancer Association Consortium. Case–case comparison was performed using unconditional logistic regression.\ud \ud Results: Tumour characteristics and risk factors did not vary significantly by the expression of basal markers, although results suggested that basal-positive luminal tumours tended to be smaller and node negative, and were more common in women with a positive family history and lower body mass index.\ud \ud Conclusions: Most established breast cancer risk factors were similar in basal-positive and basal-negative luminal A tumours. The non-significant but suggestive differences in tumour features and family history warrant further investigations.
Published: 2015

11. Publisher Correction: Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation

Author: Maya Ghoussaini, Stacey L. Edwards, Kyriaki Michailidou, Silje Nord, Richard Cowper-Sal·lari, Kinjal Desai, Siddhartha Kar, Kristine M. Hillman, Susanne Kaufmann, Dylan M. Glubb, Jonathan Beesley, Joe Dennis, Manjeet K. Bolla, Qin Wang, Ed Dicks, Qi Guo, Marjanka K. Schmidt, Mitul Shah, Robert Luben, Judith Brown, Kamila Czene, Hatef Darabi, Mikael Eriksson, Daniel Klevebring, Stig E. Bojesen, Børge G. Nordestgaard, Sune F. Nielsen, Henrik Flyger, Diether Lambrechts, Bernard Thienpont, Patrick Neven, Hans Wildiers, Annegien Broeks, Laura J. Van’t Veer, Emiel J. Th Rutgers, Fergus J. Couch, Janet E. Olson, Emily Hallberg, Celine Vachon, Jenny Chang-Claude, Anja Rudolph, Petra Seibold, Dieter Flesch-Janys, Julian Peto, Isabel dos-Santos-Silva, Lorna Gibson, Heli Nevanlinna, Taru A. Muranen, Kristiina Aittomäki, Carl Blomqvist, Per Hall, Jingmei Li, Jianjun Liu, Keith Humphreys, Daehee Kang, Ji-Yeob Choi, Sue K. Park, Dong-Young Noh, Keitaro Matsuo, Hidemi Ito, Hiroji Iwata, Yasushi Yatabe, Pascal Guénel, Thérèse Truong, Florence Menegaux, Marie Sanchez, Barbara Burwinkel, Frederik Marme, Andreas Schneeweiss, Christof Sohn, Anna H. Wu, Chiu-chen Tseng, David Van Den Berg, Daniel O. Stram, Javier Benitez, M Pilar Zamora, Jose Ignacio Arias Perez, Primitiva Menéndez, Xiao-Ou Shu, Wei Lu, Yu-Tang Gao, Qiuyin Cai, Angela Cox, Simon S. Cross, Malcolm W. R. Reed, Irene L. Andrulis, Julia A. Knight, Gord Glendon, Sandrine Tchatchou, Elinor J. Sawyer, Ian Tomlinson, Michael J. Kerin, Nicola Miller, Christopher A. Haiman, Brian E. Henderson, Fredrick Schumacher, Loic Le Marchand, Annika Lindblom, Sara Margolin, Soo Hwang Teo, Cheng Har Yip, Daphne S. C. Lee, Tien Y. Wong, Maartje J. Hooning, John W. M. Martens, J. Margriet Collée, Carolien H. M. van Deurzen, John L. Hopper, Melissa C. Southey, Helen Tsimiklis, Miroslav K. Kapuscinski, Chen-Yang Shen, Pei-Ei Wu, Jyh-Cherng Yu, Shou-Tung Chen, Grethe Grenaker Alnæs, Anne-Lise Borresen-Dale, Graham G. Giles, Roger L. Milne, Catriona McLean, Kenneth Muir, Artitaya Lophatananon, Sarah Stewart-Brown, Pornthep Siriwanarangsan, Mikael Hartman, Hui Miao, Shaik Ahmad Bin Syed Buhari, Yik Ying Teo, Peter A. Fasching, Lothar Haeberle, Arif B. Ekici, Matthias W. Beckmann, Hermann Brenner, Aida Karina Dieffenbach, Volker Arndt, Christa Stegmaier, Anthony Swerdlow, Alan Ashworth, Nick Orr, Minouk J. Schoemaker, Montserrat García-Closas, Jonine Figueroa, Stephen J. Chanock, Jolanta Lissowska, Jacques Simard, Mark S. Goldberg, France Labrèche, Martine Dumont, Robert Winqvist, Katri Pylkäs, Arja Jukkola-Vuorinen, Hiltrud Brauch, Thomas Brüning, Yon-Dschun Koto, Paolo Radice, Paolo Peterlongo, Bernardo Bonanni, Sara Volorio, Thilo Dörk, Natalia V. Bogdanova, Sonja Helbig, Arto Mannermaa, Vesa Kataja, Veli-Matti Kosma, Jaana M. Hartikainen, Peter Devilee, Robert A. E. M. Tollenaar, Caroline Seynaeve, Christi J. Van Asperen, Anna Jakubowska, Jan Lubinski, Katarzyna Jaworska-Bieniek, Katarzyna Durda, Susan Slager, Amanda E. Toland, Christine B. Ambrosone, Drakoulis Yannoukakos, Suleeporn Sangrajrang, Valerie Gaborieau, Paul Brennan, James McKay, Ute Hamann, Diana Torres, Wei Zheng, Jirong Long, Hoda Anton-Culver, Susan L. Neuhausen, Craig Luccarini, Caroline Baynes, Shahana Ahmed, Mel Maranian, Catherine S. Healey, Anna González-Neira, Guillermo Pita, M Rosario Alonso, Nuria Álvarez, Daniel Herrero, Daniel C. Tessier, Daniel Vincent, Francois Bacot, Ines de Santiago, Jason Carroll, Carlos Caldas, Melissa A. Brown, Mathieu Lupien, Vessela N. Kristensen, Paul D. P. Pharoah, Georgia Chenevix-Trench, Juliet D. French, Douglas F. Easton, and Alison M. Dunning
Subjects: Oncology, medicine.medical_specialty, Multidisciplinary, business.industry, Published Erratum, MEDLINE, General Physics and Astronomy, Locus (genetics), General Chemistry, medicine.disease, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, 030220 oncology & carcinogenesis, Internal medicine, medicine, 030212 general & internal medicine, business
Abstract: GWAS have identified a breast cancer susceptibility locus on 2q35. Here we report the fine mapping of this locus using data from 101,943 subjects from 50 case-control studies. We genotype 276 SNPs using the ‘iCOGS’ genotyping array and impute genotypes for a further 1,284 using 1000 Genomes Project data. All but two, strongly correlated SNPs (rs4442975 G/T and rs6721996 G/A) are excluded as candidate causal variants at odds against >100:1. The best functional candidate, rs4442975, is associated with oestrogen receptor positive (ER+) disease with an odds ratio (OR) in Europeans of 0.85 (95% confidence interval=0.84−0.87; P=1.7 × 10−43) per t-allele. This SNP flanks a transcriptional enhancer that physically interacts with the promoter of IGFBP5 (encoding insulin-like growth factor-binding protein 5) and displays allele-specific gene expression, FOXA1 binding and chromatin looping. Evidence suggests that the g-allele confers increased breast cancer susceptibility through relative downregulation of IGFBP5, a gene with known roles in breast cell biology., Previous studies identified an association between the 2q35 locus and breast cancer. Here, the authors show that a SNP at 2q35, rs4442975, is associated with oestrogen receptor positive disease and suggest that this effect is mediated through the downregulation of a known breast cancer gene, IGFBP5.
Published: 2018

12. Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer

Author: Javier Benitez, Marie Stenmark-Askmalm, Susan L. Neuhausen, Pascal Guénel, Jane Carpenter, Christine B. Ambrosone, Dominique Stoppa-Lyonnet, Nadine Tung, Gad Rennert, Stephen J. Chanock, Andrew K. Godwin, Regina M. Santella, Brita Arver, Karoline Kuchenbaecker, Kamila Czene, Vessela N. Kristensen, Natalia Bogdanova, Nazneen Rahman, Jianjun Liu, Federico Canzian, Hoda Anton-Culver, Maya Ghoussaini, Mark E. Robson, Sue K. Park, Manjeet K. Bolla, Roger L. Milne, Veli-Matti Kosma, Siranoush Manoukian, Angela Cox, Daniel F. Schmidt, Kay-Tee Khaw, Rosario Tumino, Melissa C. Southey, Ramunas Janavicius, Irene Konstantopoulou, Carl Blomqvist, John L. Hopper, Sue Healey, Christine Rappaport, Marco Montagna, SA Gayther, Heather Eliassen, Carolien H.M. van Deurzen, Jacques Simard, Emiel J. Rutgers, Jonine Figueroa, Maria A. Caligo, Volker Arndt, Sylvie Mazoyer, Diana Eccles, M.J. Hooning, Antoinette Hollestelle, Mary B. Daly, Robert Winqvist, Antonis C. Antoniou, Patricia A. Ganz, Orland Diez, Priyanka Sharma, Ana Osorio, Daniel Barrowdale, Loic Le Marchand, Drakoulis Yannoukakos, Elinor J. Sawyer, Conxi Lázaro, Soo-Hwang Teo, Penny Soucy, Paolo Radice, John W. M. Martens, Steve Ellis, David E. Goldgar, Anna Jakubowska, Maria Kabisch, Raymonda Varon-Mateeva, Diether Lambrechts, Paul D.P. Pharoah, Leigha Senter, Anna González-Neira, Cecilia M. Dorfling, Brian E. Henderson, Rulla M. Tamimi, Sara Margolin, Susan M. Gapstur, Ian Tomlinson, Thérèse Truong, Robert A.E.M. Tollenaar, Amanda E. Toland, Anna Marie Mulligan, Irene L. Andrulis, Isabelle Romieu, Monica Barile, Florentia Fostira, Johanna Rantala, Enes Makalic, Eitan Friedman, Zhaoming Wang, Mark H. Greene, Noralane M. Lindor, Julie M. Cunningham, Riccardo Dolcetti, Steven N. Hart, Mary Beth Terry, Jenny Chang-Claude, Austin Miller, Georgia Chenevix-Trench, Asta Försti, Kathleen E. Malone, Paolo Peterlongo, Lothar Haeberle, Celine M. Vachon, Elizabeth J. van Rensburg, Michael Jones, Laima Tihomirova, Penelope Miron, Eunjung Lee, María José Sánchez, Hatef Darabi, Frans B. L. Hogervorst, Matthias W. Beckmann, Edith Olah, Annika Lindblom, Phuong L. Mai, Emily Hallberg, Alison M. Dunning, Kathleen Claes, Esther M. John, Sofia Khan, David J. Hunter, Kristiina Aittomäki, Katherine L. Nathanson, Lars Beckmann, Stephanie V. Blank, Wei Zheng, Olufunmilayo I. Olopade, Heli Nevanlinna, Miguel de la Hoya, Olga M. Sinilnikova, Bruce Poppe, Catherine M. Phelan, S. Lindstrom, Stig E. Bojesen, Curtis Olswold, Fredrick R. Schumacher, Janet E. Olson, Tuomas Heikkinen, Judy Garber, Fergus J. Couch, Tara M. Friebel, Isabel dos-Santos-Silva, Douglas F. Easton, Song Yao, Dieter Flesch-Janys, Hans Ehrencrona, Simon S. Cross, Rodney J. Scott, Kenneth Offit, Petra H.M. Peeters, Clare Turnbull, Taru A. Muranen, William J. Tapper, Trinidad Caldés, Jenny Lester, Robert L. Nussbaum, Paul A. James, Marike Gabrielson, Susan M. Domchek, Mads Thomassen, Marilie D. Gammon, Susan L. Slager, Graham G. Giles, Silje Nord, Hans Wildiers, Hiltrud Brauch, Gustavo Mendoza-Fandiño, Christopher A. Haiman, Martine Dumont, Mark S. Goldberg, Bernardo Bonanni, Jirong Long, Kyriaki Michailidou, Ute Hamann, Wendy K. Chung, Marc J. Gunter, Mia M. Gaudet, Keith Humphreys, Per Hall, Yuan C. Ding, Simona Agata, Julia A. Knight, Robert Pilarski, Claudine Isaacs, Alvaro A.N. Monteiro, Montserrat Garcia-Closas, Rosa B. Barkardottir, Beth Y. Karlan, Uffe Birk Jensen, Arif B. Ekici, Evgeny N. Imyanitov, Alex Teulé, Anne-Marie Gerdes, Frederik Marme, Debra Frost, Anthony J. Swerdlow, Yon Ko, Xiaohong R. Yang, Jan Lubinski, Peter A. Fasching, Lesley McGuffog, Jacek Gronwald, Katri Pylkäs, Banu Arun, Josef Herzog, Gord Glendon, Doris Steinemann, Tomasz Huzarski, Peter Kraft, Anja Rudolph, Arto Mannermaa, Habibul Ahsan, Christian F. Singer, Rita K. Schmutzler, Julian Peto, Giski Ursin, Shan Wang-Gohrke, Andrea L. Richardson, Jeffrey N. Weitzel, Børge G. Nordestgaard, Marjanka K. Schmidt, Alice S. Whittemore, Hermann Brenner, Barbara Burwinkel, D Thompson, Csilla I. Szabo, M. Pilar Zamora, Janna Lilyquist, Muhammad G. Kibriya, Yael Laitman, Helen Tsimiklis, W. D. Foulkes, Thomas Hansen, Francesca Damiola, Robert N. Hoover, Ava Kwong, Alfons Meindl, Siddhartha Kar, Manuel R. Teixeira, Elisabete Weiderpass, Bernard Peissel, Saundra S. Buys, Peter Devilee, Unión Europea. Comisión Europea. 7 Programa Marco, Cancer Research UK (Reino Unido), National Institutes of Health (Estados Unidos), Canadian Institutes of Health Research, Florida Breast Cancer Foundation (Estados Unidos), Dunning, Alison [0000-0001-6651-7166], Ghoussaini, Maya [0000-0002-2415-2143], Khaw, Kay-Tee [0000-0002-8802-2903], Thompson, Deborah [0000-0003-1465-5799], Pharoah, Paul [0000-0001-8494-732X], Easton, Douglas [0000-0003-2444-3247], Antoniou, Antonis [0000-0001-9223-3116], Apollo - University of Cambridge Repository, Medical Oncology, Obstetrics & Gynecology, Pathology, Cell biology, Medicum, Kristiina Aittomäki / Principal Investigator, Department of Medical and Clinical Genetics, Clinicum, Department of Oncology, Department of Obstetrics and Gynecology, HUS Gynecology and Obstetrics, and [ 1 ] Mayo Clin, Dept Lab Med & Pathol, Rochester, MN 55905 USA [ 2 ] Mayo Clin, Dept Hlth Sci Res, Rochester, MN 55905 USA [ 3 ] Univ Cambridge, Dept Publ Hlth & Primary Care, Ctr Canc Genet 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Subjects: 0301 basic medicine, Oncology, General Physics and Astronomy, Genome-wide association study, Cyclophilins, Breast cancer, 3123 Gynaecology and paediatrics, Risk Factors, Brjóstakrabbamein, Genotype, BRCA2 MUTATION CARRIERS, Medicine and Health Sciences, CONFER SUSCEPTIBILITY, skin and connective tissue diseases, Cancer, GENE-EXPRESSION, Genetics, RISK, tRNA Methyltransferases, Multidisciplinary, Genome, VDP::Medisinske Fag: 700::Helsefag: 800::Samfunnsmedisin, sosialmedisin: 801, Loci, BRCA1 Protein, Chromosome Mapping, COMMON VARIANTS, IDENTIFY, PANCREATIC-CANCER, 3. Good health, Multidisciplinary Sciences, Biological sciences, Receptors, Estrogen, Chromosomes, Human, Pair 2, Science & Technology - Other Topics, Female, NAF12, medicine.medical_specialty, Heterozygote, Science, 3122 Cancers, Locus (genetics), Breast Neoplasms, Biology, Breast Neoplasms/genetics, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, Càncer de mama, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Internal medicine, Pancreatic cancer, MD Multidisciplinary, medicine, Genetic predisposition, Journal Article, Humans, Genetic Predisposition to Disease, GENOME-WIDE ASSOCIATION, METAANALYSIS, Cancer och onkologi, Science & Technology, VDP::Medical disciplines: 700::Clinical medical disciplines: 750::Oncology: 762, General Chemistry, Arfgengi, medicine.disease, TRNA Methyltransferases, VDP::Medisinske Fag: 700::Klinisk medisinske fag: 750::Onkologi: 762, 030104 developmental biology, Cancer and Oncology, Expression quantitative trait loci, Mutation, TELOMERE LENGTH, 3111 Biomedicine, Gene expression, VDP::Medical disciplines: 700::Health sciences: 800::Community medicine, Social medicine: 801, Genome-Wide Association Study
Abstract: Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations (P, B.C.A.C. was funded through a European Community Seventh Framework Programme under grant agreement no 223175 (HEALTH-F2-2009-223175; COGS); Cancer Research UK (C1287/A10118, C1287/A10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692); the National Institutes of Health Specialized Program of Research Excellence (SPORE) in Breast Cancer (CA116201), R01 grants (CA128978, CA176785, CA192393), and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 CA148065 and 1U19 CA148112 - the GAME-ON initiative); the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, the Breast Cancer Res. Foundation, and the Ovarian Cancer Research Fund. CIMBA genotyping was supported by National Institutes of Health grant (CA128978); the Department of Defence (W81XWH-10-1-0341); and the Breast Cancer Res. Foundation. CIMBA data management and data analysis were supported by Cancer Research UK grants C12292/A11174 and C1287/A10118. This study made use of data generated by the Wellcome Trust Case Control consortium. Functional studies were supported by the Florida Breast Cancer Foundation. A full description of funding and acknowledgments is provided in Supplementary Note 1.
Published: 2018
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13. Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

Author: Vesa Kataja, Aida Karina Dieffenbach, Chia-Ni Hsiung, Catherine S. Healey, Gie Hooi Tan, Soo Hwang Teo, Domenico Palli, Frederik Marme, Katri Pylkäs, Roger L. Milne, Jaana M. Hartikainen, Gord Glendon, Susan L. Slager, Chen-Yang Shen, Fredrick R. Schumacher, Daniel F. Schmidt, Suleeporn Sangrajrang, Kee Seng Chia, Lorna Gibson, Pascal Guénel, Alice S. Whittemore, Jenny Chang-Claude, Yu Tang Gao, Hidemi Ito, Simon S. Cross, Sofia Khan, Marie Sanchez, Daniel Vincent, Daniel Herrero, Nicola Miller, Antoinette Hollestelle, Caroline M. Seynaeve, Christopher A. Haiman, Hermann Brenner, Kay-Tee Khaw, Loris Bernard, Habibul Ahsan, Melissa C. Southey, David Van Den Berg, Martha J. Shrubsole, Daniel O. Stram, William Blot, Mel Maranian, Robert Winqvist, Keitaro Matsuo, John W. M. Martens, Heli Nevanlinna, Mia M. Gaudet, Anna Jakubowska, Christine D. Berg, Paul D.P. Pharoah, Jacques Simard, Manjeet K. Bolla, Dieter Flesch-Janys, Mark S. Goldberg, Paul Brennan, Ching Wan Chan, Sune F. Nielsen, Sara Lindström, Mitul Shah, Matthias W. Beckmann, Craig Luccarini, Jonathan Beesley, Kyriaki Michailidou, Paolo Peterlongo, Marc J. Gunter, Anna González-Neira, Ji Yeob Choi, Per Hall, Sarah Stewart-Brown, Keith Humphreys, Hui Cai, Kathleen E. Malone, Elinor J. Sawyer, Louise A. Brinton, Marjanka K. Schmidt, Xiao-Ou Shu, Barbara Perkins, Lotte Maxild Mortensen, Chiu-Chen Tseng, Hanne Meijers-Heijboer, Minouk J. Schoemaker, Keun-Young Yoo, Julia A. Knight, Alan Ashworth, Stig E. Bojesen, Kamila Czene, Artitaya Lophatananon, Graham G. Giles, S. Ahmed, Kazuo Tajima, Douglas F. Easton, Maria Kabisch, Arja Jukkola-Vuorinen, Wei Lu, Peter A. Fasching, Irene L. Andrulis, Clare Turnbull, Caroline Baynes, Christine B. Ambrosone, Jan Lubinski, Muriel A. Adank, A. Meindl, Taru A. Muranen, Siranoush Manoukian, Susan M. Gapstur, Natalia Bogdanova, Alexander Hein, Annika Lindblom, Nazneen Rahman, Annegien Broeks, Lothar Haeberle, Federico Canzian, G Pita, Ming-Feng Hou, Hiroji Iwata, Drakoulis Yannoukakos, Diana Torres, Vessela N. Kristensen, Peter Devilee, Qiuyin Cai, Christi J Asperen, John L. Hopper, Diether Lambrechts, Michael Lush, Hans Wildiers, Joe Dennis, Sandra L. Halverson, Carl Blomqvist, Erik Van Limbergen, Malin Sund, Daehee Kang, Grethe I. Grenaker Alnæs, Marilie D. Gammon, Ursula Eilber, Ian Tomlinson, Thérèse Truong, Amanda E. Toland, Anna Marie Mulligan, Kirsimari Aaltonen, Olivia Fletcher, Jonine D. Figueroa, Angela Cox, Pei Ei Wu, Maartje J. Hooning, Catriona McLean, Georgia Chenevix-Trench, Pornthep Siriwanarangsan, Malcolm W.R. Reed, Emily Hallberg, Sara Margolin, Volker Arndt, Montserrat Garcia-Closas, Francois Bacot, Rita K. Schmutzler, Julian Peto, David J. Hunter, Thomas Brüning, Katarzyna Jaworska, Christof Sohn, Børge G. Nordestgaard, Enes Makalic, Hatef Darabi, Barbara Burwinkel, Petra P.H. Peeters, J. Margriet Collée, Rongxi Yang, Robert N. Hoover, Eiliv Lund, Fergus J. Couch, Ute Hamann, Jirong Long, Wei Zheng, Sabine Behrens, Giske Ursin, Muhammad G. Kibriya, Claire Mulot, Laure Dossus, Helen Tsimiklis, Tomasz Huzarski, Peter Kraft, Anja Rudolph, Arto Mannermaa, Alison M. Dunning, Lisa B. Signorello, Valerie Gaborieau, Kenneth Muir, Anthony J. Swerdlow, Javier Benitez, Judith S. Brand, Sander Canisius, Hoda Anton-Culver, Veli-Matti Kosma, Thilo Dörk, Sten Cornelissen, Christa Stegmaier, Cheng Har Yip, Brian E. Henderson, Harald Surowy, Jingmei Li, Nur Aishah Taib, W. Ryan Diver, Carmel Apicella, Janet E. Olson, Kristiina Aittomäki, Celine M. Vachon, Regina M. Santella, Dimitrios Trichopoulos, Jianjun Liu, Nick Orr, Martine Dumont, Christian Sutter, Sue K. Park, Mikael Hartman, Susan L. Neuhausen, Hui Miao, M. Pilar Zamora, Anna H. Wu, Rob B. van der Luijt, Isabel dos-Santos-Silva, Graham Casey, Henrik Flyger, M. Rosario Alonso, Nuria Álvarez, Michael J. Kerin, Loic Le Marchand, Jose Ignacio Arias Perez, Mikael Eriksson, Esther M. John, Quinten Waisfisz, Qin Wang, Daniel C. Tessier, Paolo Radice, Robert A.E.M. Tollenaar, James McKay, Silje Nord, Hiltrud Brauch, José María Huerta, Stephen J. Chanock, Mervi Grip, Patrick Neven, Senno Verhoef, Clinical Genetics, Obstetrics & Gynecology, Medical Oncology, Cardiothoracic Surgery, Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Khaw, Kay-Tee [0000-0002-8802-2903], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Human genetics, and CCA - Oncogenesis
Subjects: Breast Neoplasms, Single-nucleotide polymorphism, Genome-wide association study, Biology, Research Support, Polymorphism, Single Nucleotide, N.I.H, Cohort Studies, brca1, Breast cancer, Research Support, N.I.H., Extramural, Meta-Analysis as Topic, SDG 3 - Good Health and Well-being, common variants, Journal Article, estrogen, chek2-asterisk-1100delc, Genetics, medicine, Humans, Genetic Predisposition to Disease, 1000 Genomes Project, Non-U.S. Gov't, genotype imputation, risk, Genetic association, Research Support, Non-U.S. Gov't, Chromatin binding, Extramural, Cancer, Microarray Analysis, confer susceptibility, medicine.disease, 3. Good health, ovarian-cancer, Genetic Loci, Case-Control Studies, alleles, Female, Imputation (genetics), Genome-Wide Association Study, metaanalysis
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 15,748 breast cancer cases and 18,084 controls together with 46,785 cases and 42,892 controls from 41 studies genotyped on a 211,155-marker custom array (iCOGS). Analyses were restricted to women of European ancestry. We generated genotypes for more than 11 million SNPs by imputation using the 1000 Genomes Project reference panel, and we identified 15 new loci associated with breast cancer at P < 5 × 10(-8). Combining association analysis with ChIP-seq chromatin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we identified likely target genes in two regions: SETBP1 at 18q12.3 and RNF115 and PDZK1 at 1q21.1. One association appears to be driven by an amino acid substitution encoded in EXO1. ispartof: Nature Genetics vol:47 issue:4 pages:373-80 ispartof: location:United States status: published
Published: 2015
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14. Inherited Mutations in 17 Breast Cancer Susceptibility Genes Among a Large Triple-Negative Breast Cancer Cohort Unselected for Family History of Breast Cancer

Author: Angela Cox, Heli Nevanlinna, Judy Garber, Liisa M. Pelttari, Florentia Fostira, Arif B. Ekici, Xianshu Wang, Susan L. Slager, Lorraine Durcan, Penelope Miron, Drakoulis Yannoukakos, Seth W. Slettedahl, William J. Tapper, Curtis Olswold, Brigitte Rack, Wolfgang Janni, Celine M. Vachon, Jaime I. Davila, Irene Konstantopoulou, Charles L. Shapiro, Robert Pilarski, Fergus J. Couch, Lucia Guidugli, Hiltrud Brauch, Peter A. Fasching, V. Shane Pankratz, Athanassios Vratimos, Priyanka Sharma, Diana Eccles, Matthias W. Beckmann, George Fountzilas, Simon S. Cross, Christine B. Ambrosone, Emily Hallberg, Song Yao, Janet E. Olson, Jennifer R. Klemp, Andrew K. Godwin, Dennis J. Slamon, Steven N. Hart, and Amanda E. Toland
Subjects: Adult, Oncology, Cancer Research, medicine.medical_specialty, PALB2, DNA Mutational Analysis, Triple Negative Breast Neoplasms, Cohort Studies, Young Adult, Germline mutation, Breast cancer, Internal medicine, medicine, Humans, Genetic Predisposition to Disease, Genetic Testing, Family history, Germ-Line Mutation, Triple-negative breast cancer, Aged, Genetic testing, Aged, 80 and over, BRCA2 Protein, Family Health, Ovarian Neoplasms, Genetics, medicine.diagnostic_test, BRCA1 Protein, business.industry, Cancer, Middle Aged, medicine.disease, 3. Good health, Female, business
Abstract: Purpose Recent advances in DNA sequencing have led to the development of breast cancer susceptibility gene panels for germline genetic testing of patients. We assessed the frequency of mutations in 17 predisposition genes, including BRCA1 and BRCA2, in a large cohort of patients with triple-negative breast cancer (TNBC) unselected for family history of breast or ovarian cancer to determine the utility of germline genetic testing for those with TNBC. Patients and Methods Patients with TNBC (N = 1,824) unselected for family history of breast or ovarian cancer were recruited through 12 studies, and germline DNA was sequenced to identify mutations. Results Deleterious mutations were identified in 14.6% of all patients. Of these, 11.2% had mutations in the BRCA1 (8.5%) and BRCA2 (2.7%) genes. Deleterious mutations in 15 other predisposition genes were detected in 3.7% of patients, with the majority observed in genes involved in homologous recombination, including PALB2 (1.2%) and BARD1, RAD51D, RAD51C, and BRIP1 (0.3% to 0.5%). Patients with TNBC with mutations were diagnosed at an earlier age (P < .001) and had higher-grade tumors (P = .01) than those without mutations. Conclusion Deleterious mutations in predisposition genes are present at high frequency in patients with TNBC unselected for family history of cancer. Mutation prevalence estimates suggest that patients with TNBC, regardless of age at diagnosis or family history of cancer, should be considered for germline genetic testing of BRCA1 and BRCA2. Although mutations in other predisposition genes are observed among patients with TNBC, better cancer risk estimates are needed before these mutations are used for clinical risk assessment in relatives.
Published: 2015
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15. PHIP - a novel candidate breast cancer susceptibility locus on 6q14.1

Author: Qin Wang, kConFab, Paolo Radice, Tao Liu, Isabel dos-Santos-Silva, Douglas F. Easton, Joe Dennis, Qi Guo, Michael Lush, Jessada Thutkawkorapin, Diether Lambrechts, Barbara Kremeyer, Fergus J. Couch, Pascal Guénel, Melanie Gündert, Rita K. Schmutzler, William J. Blot, Julian Peto, Christine B. Ambrosone, Wei Zheng, Mikael Eriksson, Ute Hamann, Johanna Rantala, Barbara Burwinkel, Michael J. Kerin, Johanna Lundin, Graham G. Giles, Hiltrud Brauch, Hoda Anton-Culver, Veli-Matti Kosma, Marjanka K. Schmidt, Aocs Investigators, Paula Maguire, Marike Gabrielson, Judith S. Brand, Simone Picelli, Rajeshwari Marikkannu, Quan Du, Irene L. Andrulis, Valerie Rhenius, Kyriaki Michailidou, Susan L. Neuhausen, Vinaykumar Kontham, Alison M. Dunning, Hermann Brenner, Thilo Dörk, Elinor J. Sawyer, Christopher A. Haiman, Anna González-Neira, Thérèse Truong, Peter Devilee, Qiuyin Cai, Susanna von Holst, Peter A. Fasching, Anna Marie Mulligan, Bernardo Bonanni, Javier Benítez, Kamila Czene, Loic Le Marchand, Katri Pylkäs, Henrik Flyger, Jacques Simard, Manjeet K. Bolla, Alfons Meindl, Per Hall, Simon S. Cross, Annika Lindblom, Emily Hallberg, Christos Aravidis, Sara Margolin, Vessela N. Kristensen, Carl Blomqvist, Annegien Broeks, John W.M. Martens, Jonine D. Figueroa, Xiang Jiao, Montserrat Garcia-Closas, Mitul Shah, Matthias W. Beckmann, Thomas Brüning, Guanmengqian Huang, John L. Hopper, Jan Lubinski, Michael Jones, Anthony J. Swerdlow, Roger L. Milne, Patricia Harrington, Caroline Seynaeve, Arto Mannermaa, Liping Luo, Natalia Antonenkova, Tatjana Adamovic, Angela Cox, Maartje J. Hooning, Volker Arndt, Dieter Flesch-Janys, Camilla Wendt, Stig E. Bojesen, Melissa C. Southey, Robert Winqvist, Anna Jakubowska, Paul D.P. Pharoah, Bram Boeckx, Sandra Deming-Halverson, Heli Nevanlinna, Jenny Chang-Claude, School of Medicine / Clinical Medicine, Cardiology, Medical Oncology, Department of Oncology, Clinicum, University of Helsinki, HUS Gynecology and Obstetrics, Department of Obstetrics and Gynecology, and HUS Comprehensive Cancer Center
Subjects: EXPRESSION, 0301 basic medicine, Cellbiologi, 3122 Cancers, DNA-SEQUENCING DATA, Locus (genetics), Single-nucleotide polymorphism, Biology, Genome, FAMILIES, risk haplotype, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, SDG 3 - Good Health and Well-being, 3123 Gynaecology and paediatrics, Genetic linkage, Journal Article, medicine, linkage analysis, Allele, Gene, WIDE LINKAGE SCAN, Genetics, Cancer och onkologi, MUTATIONS, familial breast cancer, Haplotype, LOCALIZATION, ASSOCIATION, sequencing, Cell Biology, medicine.disease, GENE, 3. Good health, GENOME, 030104 developmental biology, Oncology, DISCOVERY, Cancer and Oncology, 030220 oncology & carcinogenesis, Priority Research Paper
Abstract: Most non-BRCA1/2 breast cancer families have no identified genetic cause. We used linkage and haplotype analyses in familial and sporadic breast cancer cases to identify a susceptibility locus on chromosome 6q. Two independent genome-wide linkage analysis studies suggested a 3 Mb locus on chromosome 6q and two unrelated Swedish families with a LOD >2 together seemed to share a haplotype in 6q14.1. We hypothesized that this region harbored a rare high-risk founder allele contributing to breast cancer in these two families. Sequencing of DNA and RNA from the two families did not detect any pathogenic mutations. Finally, 29 SNPs in the region were analyzed in 44,214 cases and 43,532 controls from BCAC, and the original haplotypes in the two families were suggested as low-risk alleles for European and Swedish women specifically. There was also some support for one additional independent moderate-risk allele in Swedish familial samples. The results were consistent with our previous findings in familial breast cancer and supported a breast cancer susceptibility locus at 6q14.1 around the PHIP gene., published version, peerReviewed
Published: 2017
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16. Evaluation of polygenic risk scores for breast and ovarian cancer risk prediction in BRCA1 and BRCA2 mutation carriers

Author: Kuchenbaecker, Karoline B., Lesley, Mcguffog, Daniel, Barrowdale, Andrew, Lee, Penny, Soucy, Sue, Healey, Joe, Dennis, Michael, Lush, Mark, Robson, Spurdle, Amanda B., Ramus, Susan J., Nasim, Mavaddat, Mary Beth Terry, Neuhausen, Susan L., Ute, Hamann, Melissa, Southey, John, Esther M., Chung, Wendy K., Daly, Mary B., Buys, Saundra S., Goldgar, David E., Dorfling, Cecilia M., van Rensburg, Elizabeth J., Yuan Chun Ding, Bent, Ejlertsen, Anne-Marie, Gerdes, Hansen, Thomas V. O., Susan, Slager, Emily, Hallberg, Javier, Benitez, Ana, Osorio, Nancy, Cohen, William, Lawler, Weitzel, Jeffrey N., Paolo, Peterlongo, Valeria, Pensotti, Riccardo, Dolcetti, Monica, Barile, Bernardo, Bonanni, Jacopo, Azzollini, Siranoush, Manoukian, Bernard, Peissel, Paolo, Radice, Antonella, Savarese, Papi, Laura, Giannini, Giuseppe, Florentia, Fostira, Irene, Konstantopoulou, Julian, Adlard, Carole, Brewer, Jackie, Cook, Rosemarie, Davidson, Diana, Eccles, Ros, Eeles, Steve, Ellis, Embrace, Debra, Frost, Shirley, Hodgson, Louise, Izatt, Fiona, Lalloo, Kai-ren, Ong, Godwin, Andrew K., Norbert, Arnold, Bernd, Dworniczak, Christoph, Engel, Andrea, Gehrig, Eric, Hahnen, Jan, Hauke, Karin, Kast, Alfons, Meindl, Dieter, Niederacher, Rita Katharina Schmutzler, Raymonda, Varon-Mateeva, Shan, Wang-Gohrke, Barbara, Wappenschmidt, Laure, Barjhoux, Marie-Agne`s, Collonge-Rame, Camille, Elan, GEMO Study Collaborators, Lisa, Golmard, Emmanuelle, Barouk-Simonet, Fabienne, Lesueur, Sylvie, Mazoyer, Joanna, Sokolowska, Dominique Stoppa- Lyonnet, Claudine, Isaacs, Claes, Kathleen B. M., Bruce, Poppe, Miguel de la Hoya, Vanesa, Garcia-Barberan, Kristiina, Aittom€aki, Heli, Nevanlinna, Ausems, Margreet G. E. M., de Lange, J. L., Gomez Garcia, Encarna B., Hebon, Hogervorst, Frans B. L., Kets, Carolien M., Meijers-Heijboer, Hanne E. J., Oosterwijk, Jan C., Rookus, Matti A., van Asperen, Christi J., van den Ouweland, Ans M. W., van Doorn, Helena C., van Os, Theo A. M., Ava, Kwong, Edith, Olah, Orland, Diez, Joan, Brunet, Conxi, Lazaro, Alex, Teule´, Jacek, Gronwald, Anna, Jakubowska, Katarzyna, Kaczmarek, Jan, Lubinski, Grzegorz, Sukiennicki, Barkardottir, Rosa B., Jocelyne, Chiquette, Simona, Agata, Marco, Montagna, Teixeira, Manuel R., Kconfab, Investigators, Sue Kyung Park, Curtis, Olswold, Marc, Tischkowitz, Lenka, Foretova, Pragna, Gaddam, Joseph, Vijai, Georg, Pfeiler, Christine, Rappaport-Fuerhauser, Singer, Christian F., Tea, Muy-Kheng M., Greene, Mark H., Loud, Jennifer T., Gad, Rennert, Imyanitov, Evgeny N., Hulick, Peter J., Hays, John L., Marion, Piedmonte, Rodriguez, Gustavo C., Julie, Martyn, Gord, Glendon, Anna Marie Mulligan, Andrulis, Irene L., Amanda Ewart Toland, Uffe Birk Jensen, Kruse, Torben A., Inge Sokilde Pedersen, Mads, Thomassen, Caligo, Maria A., Soo-Hwang, Teo, Raanan, Berger, Eitan, Friedman, Yael, Laitman, Brita, Arver, Ake, Borg, Hans, Ehrencrona, Johanna, Rantala, Olopade, Olufunmilayo I., Ganz, Patricia A., Nussbaum, Robert L., Bradbury, Angela R., Domchek, Susan M., Nathanson, Katherine L., Arun, Banu K., Paul, James, Karlan, Beth Y., Jenny, Lester, Jacques, Simard, Pharoah, Paul D. P., Kenneth, Offit, Couch, Fergus J., Georgia, Chenevix-Trench, Easton, Douglas F., and Antoniou, Antonis C.
Subjects: Adult, Cancer Research, Heterozygote, Multifactorial Inheritance, Adolescent, Breast Neoplasms, Female, Genetic Predisposition to Disease, Humans, Middle Aged, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Prognosis, Proportional Hazards Models, Receptors, Estrogen, Risk Assessment, Risk Factors, Young Adult, Genes, BRCA1, Genes, BRCA2, Mutation, Oncology, endocrine system diseases, SUSCEPTIBILITY ALLELES, MODIFIERS, Article, Receptors, Medicine and Health Sciences, LOCUS, COHORT, Polymorphism, FUNCTIONAL VARIANTS, skin and connective tissue diseases, EARLY BILATERAL OOPHORECTOMY, IDENTIFICATION, MORTALITY, Biology and Life Sciences, WOMEN, Single Nucleotide, BRCA1, Estrogen, BRCA2, WIDE ASSOCIATION ANALYSIS, Genes
Abstract: Background: Genome-wide association studies (GWAS) have identified 94 common single-nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk and 18 associated with ovarian cancer (OC) risk. Several of these are also associated with risk of BC or OC for women who carry a pathogenic mutation in the high-risk BC and OC genes BRCA1 or BRCA2. The combined effects of these variants on BC or OC risk for BRCA1 and BRCA2 mutation carriers have not yet been assessed while their clinical management could benefit from improved personalized risk estimates. Methods: We constructed polygenic risk scores (PRS) using BC and OC susceptibility SNPs identified through population-based GWAS: for BC (overall, estrogen receptor [ER]-positive, and ER-negative) and for OC. Using data from 15 252 female BRCA1 and 8211 BRCA2 carriers, the association of each PRS with BC or OC risk was evaluated using a weighted cohort approach, with time to diagnosis as the outcome and estimation of the hazard ratios (HRs) per standard deviation increase in the PRS. Results: The PRS for ER-negative BC displayed the strongest association with BC risk in BRCA1 carriers (HR = 1.27, 95% confidence interval [CI] = 1.23 to 1.31, P = 8.2 x 10(53)). In BRCA2 carriers, the strongest association with BC risk was seen for the overall BC PRS (HR = 1.22, 95% CI = 1.17 to 1.28, P = 7.2 x 10(-20)). The OC PRS was strongly associated with OC risk for both BRCA1 and BRCA2 carriers. These translate to differences in absolute risks (more than 10% in each case) between the top and bottom deciles of the PRS distribution; for example, the OC risk was 6% by age 80 years for BRCA2 carriers at the 10th percentile of the OC PRS compared with 19% risk for those at the 90th percentile of PRS. Conclusions: BC and OC PRS are predictive of cancer risk in BRCA1 and BRCA2 carriers. Incorporation of the PRS into risk prediction models has promise to better inform decisions on cancer risk management.
Published: 2017

17. Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

Author: Emmi Tikkanen, Pascal Guénel, Rico Rueedi, Hamdi Mbarek, Gerardo Heiss, Hilary K. Finucane, Jing Hua Zhao, Peter K. Joshi, Mark I. McCarthy, Frank B. Hu, Stephen J. Chanock, Manjeet K. Bolla, Sandosh Padmanabhan, Vilmundur Gudnason, Chunyan He, Aarno Palotie, Reedik Mägi, Joe Dennis, Nicholas G. Martin, Behrooz Z. Alizadeh, Elisabeth Widen, Caroline Hayward, Penelope A. Lind, Magdalena Zoledziewska, Ayellet V. Segrè, Fergus J. Couch, Massimo Mangino, Melissa C. Southey, Immaculata De Vivo, Yongmei Liu, Ute Hamann, Angela Cox, Maartje J. Hooning, Iffat Rahman, Mitul Shah, Eric Boerwinkle, Matthias W. Beckmann, Catharina A. Hartman, Tanguy Corre, Kathryn L. Lunetta, Thérèse Truong, Anna Marie Mulligan, Caterina Barbieri, Robert Winqvist, Lili Milani, Cristina Menni, Frits R. Rosendaal, Pau Navarro, Christian Gieger, Ken K. Ong, Stig E. Bojesen, Susan M. Ring, Marjanka K. Schmidt, George McMahon, Deborah J. Thompson, Robert Karlsson, Nicholas J. Timpson, M. Arfan Ikram, Alexander Teumer, Jingmei Li, Christa Meisinger, Diana L. Cousminer, Doris Stöckl, Heli Nevanlinna, Teresa Nutile, Tim D. Spector, Eva Albrecht, Murielle Bochud, Linda Broer, Felix R. Day, Sven Bergmann, Renée de Mutsert, Nicholas J. Wareham, Marjo-Riitta Järvelin, Marzyeh Amini, Elisabeth Altmaier, Isabel dos-Santos-Silva, Peter Vollenweider, Douglas F. Easton, Tamara B. Harris, Ellen A. Nohr, Paul D.P. Pharoah, David J. Porteous, Jenny A. Visser, Ilja M. Nolte, Genevieve Lachance, Thomas Meitinger, Archie Campbell, Thomas Brüning, Graham G. Giles, Johan G. Eriksson, Nancy L. Pedersen, George Davey Smith, Gonneke Willemsen, Joanne M. Murabito, Francesco Cucca, Daniel I. Chasman, Eleonora Porcu, Nora Franceschini, Thibaud Boutin, Ulla Sovio, Roger L. Milne, Annette Peters, Lisette Stolk, Paul M. Ridker, Claudia Langenberg, Patrick Sulem, Toshiko Tanaka, Marike Gabrielson, Judith S. Brand, Unnur Thorsteindottir, Alison M. Dunning, Marina Ciullo, Julie E. Buring, Harold Snieder, Lude Franke, Meir J. Stampfer, Po-Ru Loh, Julian Peto, Ellen W. Demerath, Sheila Ulivi, Ivana Kolcic, Maristella Steri, Jouke J. Hottenga, Amanda B. Spurdle, Tõnu Esko, Katherine S. Pollard, Eulalia Catamo, Anneli Pouta, Kyriaki Michailidou, Dieter Flesch-Janys, James F. Wilson, Kamila Czene, Sean Whalen, Diether Lambrechts, Abhishek Sarkar, Laura Crisponi, Jonathan Tyrer, Antonietta Robino, Sara Lindström, Harald Grallert, Stefania Lenarduzzi, Peter Kraft, Patrik K. E. Magnusson, Lavinia Paternoster, Digna R. Velez Edwards, Mike A. Nalls, Per Hall, Joyce Y. Tung, Cinzia Sala, Lindsay Fernández-Rhodes, Ayush Giri, Hiltrud Brauch, André G. Uitterlinden, Alkes L. Price, Tracy A. O'Mara, Lynda M. Rose, John L. Hopper, David A. Hinds, Katherine S. Ruth, Arto Mannermaa, Uwe Völker, Rossella Sorice, Zoltán Kutalik, Debbie A Lawlor, Georgia Chenevix-Trench, Anna Murray, Albertine J. Oldehinkel, Bruce H. R. Wolffenbuttel, Hae Kyung Im, Dale R. Nyholt, Lenore J. Launer, Andres Metspalu, Irene L. Andrulis, Konstantin Strauch, Albert V. Smith, Daniela Toniolo, Eco J. C. de Geus, Jenny Chang-Claude, Marek Zygmunt, Dorret I. Boomsma, Harry Campbell, Peter Devilee, Henry Völzke, Daniela Ruggiero, Dennis O. Mook-Kanamori, John R. B. Perry, Javier Benitez, Grant W. Montgomery, David J. Hunter, David Karasik, Luigi Ferrucci, Emily Hallberg, Stefania Bandinelli, Hermann Brenner, Raymond Noordam, Sarah E. Medland, Peter A. Fasching, Qin Wang, Ilaria Gandin, Manolis Kellis, Hannes Helgason, Igor Rudan, Paolo Radice, Michela Traglia, Jian'an Luan, Robert A. Scott, Brumat Marco, Veronique Vitart, Kari Stefansson, Katharina E. Schraut, Ko Willems van Dijk, Ozren Polasek, Daniel F. Gudbjartsson, Natalia Perjakova, Joop S.E. Laven, Life Course Epidemiology (LCE), Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Interdisciplinary Centre Psychopathology and Emotion regulation (ICPE), Lifestyle Medicine (LM), Center for Liver, Digestive and Metabolic Diseases (CLDM), Stem Cell Aging Leukemia and Lymphoma (SALL), Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET), Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Mental Health, APH - Methodology, Art and Culture, History, Antiquity, Day, Felix R., Thompson, Deborah J., Helgason, Hanne, Chasman, Daniel I., Finucane, Hilary, Sulem, Patrick, Ruth, Katherine S., Whalen, Sean, Sarkar, Abhishek K., Albrecht, Eva, Altmaier, Elisabeth, Amini, Marzyeh, Barbieri, CATERINA MARIA, Boutin, Thibaud, Campbell, Archie, Demerath, Ellen, Giri, Ayush, He, Chunyan, Hottenga, Jouke J., Karlsson, Robert, Kolcic, Ivana, Loh, Po Ru, Lunetta, Kathryn L., Mangino, Massimo, Brumat, Marco, Mcmahon, George, Medland, Sarah E., Nolte, Ilja M., Noordam, Raymond, Nutile, Teresa, Paternoster, Lavinia, Perjakova, Natalia, Porcu, Eleonora, Rose, Lynda M., Schraut, Katharina E., Segrã¨, Ayellet V., Smith, Albert V., Stolk, Lisette, Teumer, Alexander, Andrulis, Irene L., Bandinelli, Stefania, Beckmann, Matthias W., Benitez, Javier, Bergmann, Sven, Bochud, Murielle, Boerwinkle, Eric, Bojesen, Stig E., Bolla, Manjeet K., Brand, Judith S., Brauch, Hiltrud, Brenner, Hermann, Broer, Linda, Brã¼ning, Thoma, Buring, Julie E., Campbell, Harry, Catamo, Eulalia, Chanock, Stephen, Chenevix Trench, Georgia, Corre, Tanguy, Couch, Fergus J., Cousminer, Diana L., Cox, Angela, Crisponi, Laura, Czene, Kamila, Davey Smith, George, De Geus, Eco J. C. N., De Mutsert, Renã©e, De Vivo, Immaculata, Dennis, Joe, Devilee, Peter, Dos Santos Silva, Isabel, Dunning, Alison M., Eriksson, Johan G., Fasching, Peter A., FernÃ¡ndez Rhodes, Lindsay, Ferrucci, Luigi, Flesch Janys, Dieter, Franke, Lude, Gabrielson, Marike, Gandin, Ilaria, Giles, Graham G., Grallert, Harald, Gudbjartsson, Daniel F., Guã©nel, Pascal, Hall, Per, Hallberg, Emily, Hamann, Ute, Harris, Tamara B., Hartman, Catharina A., Heiss, Gerardo, Hooning, Maartje J., Hopper, John L., Hu, Frank, Hunter, David J., Ikram, M. Arfan, Im, Hae Kyung, Jã¤rvelin, Marjo Riitta, Joshi, Peter K., Karasik, David, Kellis, Manoli, Kutalik, Zoltan, Lachance, Genevieve, Lambrechts, Diether, Langenberg, Claudia, Launer, Lenore J., Laven, Joop S. E., Lenarduzzi, Stefania, Li, Jingmei, Lind, Penelope A., Lindstrom, Sara, Liu, Yongmei, Luan, Jian'An, Mã¤gi, Reedik, Mannermaa, Arto, Mbarek, Hamdi, Mccarthy, Mark I., Meisinger, Christa, Meitinger, Thoma, Menni, Cristina, Metspalu, Andre, Michailidou, Kyriaki, Milani, Lili, Milne, Roger L., Montgomery, Grant W., Mulligan, Anna M., Nalls, Mike A., Navarro, Pau, Nevanlinna, Heli, Nyholt, Dale R., Oldehinkel, Albertine J., O'Mara, Tracy A., Padmanabhan, Sandosh, Palotie, Aarno, Pedersen, Nancy, Peters, Annette, Peto, Julian, Pharoah, Paul D. P., Pouta, Anneli, Radice, Paolo, Rahman, Iffat, Ring, Susan M., Robino, Antonietta, Rosendaal, Frits R., Rudan, Igor, Rueedi, Rico, Ruggiero, Daniela, Sala, Cinzia F., Schmidt, Marjanka K., Scott, Robert A., Shah, Mitul, Sorice, Rossella, Southey, Melissa C., Sovio, Ulla, Stampfer, Meir, Steri, Maristella, Strauch, Konstantin, Tanaka, Toshiko, Tikkanen, Emmi, Timpson, Nicholas J., Traglia, Michela, Truong, Thã©rã¨se, Tyrer, Jonathan P., Uitterlinden, AndrÃ© G., Edwards, Digna R. Velez, Vitart, Veronique, Vã¶lker, Uwe, Vollenweider, Peter, Wang, Qin, Widen, Elisabeth, Van Dijk, Ko Willem, Willemsen, Gonneke, Winqvist, Robert, Wolffenbuttel, Bruce H. R., Zhao, Jing Hua, Zoledziewska, Magdalena, Zygmunt, Marek, Alizadeh, Behrooz Z., Boomsma, Dorret I., Ciullo, Marina, Cucca, Francesco, Esko, Tãµnu, Franceschini, Nora, Gieger, Christian, Gudnason, Vilmundur, Hayward, Caroline, Kraft, Peter, Lawlor, Debbie A., Magnusson, Patrik K. E., Martin, Nicholas G., Mook Kanamori, Dennis O., Nohr, Ellen A., Polasek, Ozren, Porteous, David, Price, Alkes L., Ridker, Paul M., Snieder, Harold, Spector, Tim D., Stã¶ckl, Dori, Toniolo, Daniela, Ulivi, Sheila, Visser, Jenny A., Vã¶lzke, Henry, Wareham, Nicholas J., Wilson, James F., LifeLines Cohort, Study, Interact, Consortium, Kconfab/aocs, Investigator, Endometrial Cancer Association, Consortium, Ovarian Cancer Association, Consortium, Practical, Consortium, Spurdle, Amanda B., Thorsteindottir, Unnur, Pollard, Katherine S., Easton, Douglas F., Tung, Joyce Y., Chang Claude, Jenny, Hinds, David, Murray, Anna, Murabito, Joanne M., Stefansson, Kari, Ong, Ken K., Perry, John R. B., Internal Medicine, Erasmus MC other, Medical Oncology, Epidemiology, Obstetrics & Gynecology, Day, Felix [0000-0003-3789-7651], Thompson, Deborah [0000-0003-1465-5799], Dennis, Joe [0000-0003-4591-1214], Dunning, Alison [0000-0001-6651-7166], Langenberg, Claudia [0000-0002-5017-7344], Luan, Jian'an [0000-0003-3137-6337], Pharoah, Paul [0000-0001-8494-732X], Sovio, Ulla [0000-0002-0799-1105], Tyrer, Jonathan [0000-0003-3724-4757], Zhao, Jing Hua [0000-0003-4930-3582], Wareham, Nicholas [0000-0003-1422-2993], Easton, Douglas [0000-0003-2444-3247], Ong, Kenneth [0000-0003-4689-7530], Perry, John [0000-0001-6483-3771], Apollo - University of Cambridge Repository, Massachusetts Institute of Technology. Department of Mathematics, and Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Subjects: 0301 basic medicine, Male, Netherlands Twin Register (NTR), Ovarian Cancer Association Consortium, LOCI, Genome-wide association study, cancer risk, Menarche/genetics, Bioinformatics, GWAS, menarche, puberty, Body Mass Index, Risk Factors, Neoplasms, Databases, Genetic, WIDE ASSOCIATION, Endometrial Cancer Association Consortium, Ribonucleoproteins/genetics, 2. Zero hunger, Genetics, Age Factors, Genetics GWAS menarche, reproductive disorders, Neoplasms/genetics, 3. Good health, Ribonucleoproteins, Menarche, MENDELIAN RANDOMIZATION, Intercellular Signaling Peptides and Proteins, GROWTH, Female, TRAITS, Population variance, Intercellular Signaling Peptides and Proteins/genetics, Adolescent, Ubiquitin-Protein Ligases, kConFab/AOCS Investigators, Quantitative Trait Loci, Quantitative trait locus, Biology, METABOLISM, INHERITANCE, Polymorphism, Single Nucleotide, PRACTICAL consortium, 03 medical and health sciences, Genomic Imprinting, SDG 3 - Good Health and Well-being, Mendelian randomization, REGRESSION, medicine, Journal Article, Humans, cancer, Genetic Predisposition to Disease, 1000 Genomes Project, Membrane Proteins/genetics, METAANALYSIS, Puberty, Calcium-Binding Proteins, Membrane Proteins, Cancer, InterAct Consortium, Heritability, medicine.disease, BODY-MASS INDEX, 030104 developmental biology, genome-wide association studies, Puberty/genetics, LifeLines Cohort Study, Genome-Wide Association Study
Abstract: The timing of puberty is a highly polygenic childhood trait that is epidemiologically associated with various adult diseases. Using 1000 Genomes Project-imputed genotype data in up to similar to 370,000 women, we identify 389 independent signals (P
Published: 2017
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18. Investigation of gene-environment interactions between 47 newly identified breast cancer susceptibility loci and environmental risk factors

Author: Manuela Gago-Dominguez, Catriona McLean, Georgia Chenevix-Trench, Malcolm W.R. Reed, Doug Easton, Ellen G. Engelhardt, Keith Humphreys, Judith S. Brand, Laura Baglietto, Sune F. Nielsen, Stephen J. Chanock, Børge G. Nordestgaard, Qin Wang, Simon S. Cross, Arif B. Ekici, Yon-Dschun Ko, Jolanta Lissowska, A.K. Dieffenbach, Javier Benitez, Montserrat Garcia-Closas, Thomas Brüning, Henrik Flyger, Betül T. Yesilyurt, Vesa Kataja, Lothar Häberle, Fergus J. Couch, Jenny Chang-Claude, Dieter Flesch-Janys, Veli-Matti Kosma, Manjeet K. Bolla, Celine M. Vachon, Florence Menegaux, Giuseppe Floris, John L. Hopper, Christa Stegmaier, J. Esteban Castelao, Stig E. Bojesen, Peter A. Fasching, Hannah Munday, Mitul Shah, Matthias W. Beckmann, Jose Ignacio Arias Perez, Elena Provenzano, Mikael Eriksson, Diether Lambrechts, Alison M. Dunning, Marjanka K. Schmidt, Sabine Behrens, Jaana M. Hartikainen, Melissa C. Southey, Gord Glendon, Anthony J. Swerdlow, Emilie Cordina-Duverger, Ursula Eilber, Emiel J. Th. Rutgers, Paul D.P. Pharoah, Angela Cox, Volker Arndt, Karin Leunen, Pascal Guénel, Minouk J. Schoemaker, Jingmei Li, Carmel Apicella, Annegien Broeks, María Dolores Torres, Mark E. Sherman, Irene L. Andrulis, Emily Hallberg, Janet E. Olson, Roger L. Milne, Joe Dennis, Nick Orr, Ute Hamann, Hatef Darabi, Amanda B. Spurdle, Kamila Czene, Anja Rudolph, Arto Mannermaa, Anna González-Neira, Thérèse Truong, Anna Marie Mulligan, Per Hall, Hermann Brenner, Julia A. Knight, Petra Seibold, Alan Ashworth, Graham G. Giles, and Angel Carracedo
Subjects: Oncology, Genetics, Cancer Research, medicine.medical_specialty, Single-nucleotide polymorphism, Genome-wide association study, Biology, medicine.disease, Breast cancer, Polymorphism (computer science), Internal medicine, medicine, Genetic predisposition, SNP, Risk factor, Gene–environment interaction
Abstract: A large genotyping project within the Breast Cancer Association Consortium (BCAC) recently identified 41 associations between single nucleotide polymorphisms (SNPs) and overall breast cancer (BC) risk. We investigated whether the effects of these 41 SNPs, as well as six SNPs associated with estrogen receptor (ER) negative BC risk are modified by 13 environmental risk factors for BC. Data from 22 studies participating in BCAC were pooled, comprising up to 26,633 cases and 30,119 controls. Interactions between SNPs and environmental factors were evaluated using an empirical Bayes-type shrinkage estimator. Six SNPs showed interactions with associated p-values (pint )
Published: 2014
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19. Incidence of chronic lymphocytic leukemia and high-count monoclonal B-cell lymphocytosis using the 2008 guidelines

Author: Celine M. Vachon, Susan L. Slager, Kari G. Rabe, Sara J. Achenbach, Tait D. Shanafelt, Timothy G. Call, Aaron D. Norman, Neil E. Kay, Emily Hallberg, Curtis A. Hanson, James R. Cerhan, Wei Ding, and Clive S. Zent
Subjects: Cancer Research, medicine.medical_specialty, Lymphocytosis, business.industry, Incidence (epidemiology), Chronic lymphocytic leukemia, Cancer, medicine.disease, Rochester Epidemiology Project, Immunophenotyping, Oncology, hemic and lymphatic diseases, Internal medicine, Epidemiology, Immunology, medicine, Monoclonal B-cell lymphocytosis, medicine.symptom, business
Abstract: BACKGROUND The 1996 National Cancer Institute Working Group (NCI-WG 96) guidelines classified disease in individuals who had a B-cell clone with chronic lymphocytic leukemia (CLL) immunophenotype as CLL if their absolute lymphocyte count was ≥5 × 109/L. The 2008 International Workshop on CLL guidelines (IWCLL 2008) classified disease as CLL if the absolute B-cell count was ≥5 × 109/L or as monoclonal B-cell lymphocytosis (MBL) if the absolute B-cell count was
Published: 2014
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20. Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21

Author: Melissa C. Southey, Qin Wang, Paolo Radice, Robert Winqvist, Vesa Kataja, Anna Jakubowska, Audrey Lemaçon, Elinor J. Sawyer, Hermann Brenner, Pascal Guénel, Heli Nevanlinna, Judith S. Brand, Patrick Neven, Mark S. Goldberg, Jan Lubinski, P. D. P Pharoah, Sara Margolin, Vessela N. Kristensen, Bernardo Bonanni, Anna González-Neira, Ian Tomlinson, Thérèse Truong, Anne Lise Børresen-Dale, Natalia Bogdanova, Marjanka K. Schmidt, Thilo Dörk, Grethe I. GrenakerAlnæs, Wei Zheng, Celine M. Vachon, Diether Lambrechts, Isabel dos-Santos-Silva, Alison M. Dunning, Annegien Broeks, Douglas F. Easton, Javier Benitez, Michael Jones, Hoda Anton-Culver, Véronique Adoue, Sander Canisius, Roger L. Milne, Ans M.W. van den Ouweland, Yosr Hamdi, Mel Maranian, Angela Cox, Aocs Investigators, Maartje J. Hooning, Dijana Plaseska-Karanfilska, Frederik Marmé, Volker Arndt, Simon S. Cross, Silje Nord, Stig E. Bojesen, Kyriaki Michailidou, Penny Soucy, Joe Dennis, Hiltrud Brauch, Anja Rudolph, Rob A. E. M. Tollenaar, Arto Mannermaa, Maria Kabisch, Christopher A. Haiman, Susan L. Neuhausen, Loic Le Marchand, Katri Pylkäs, Irene L. Andrulis, Xiao-Ou Shu, Caroline Baynes, kConFab, Peter Devilee, Georgia Chenevix-Trench, Annika Lindblom, Emily Hallberg, Diana Torres, Anthony J. Swerdlow, Graham G. Giles, Jenny Chang-Claude, Lothar Haeberle, Tomi Pastinen, Curtis Olswold, Peter A. Fasching, Montserrat Garcia-Closas, Manjeet K. Bolla, Carl Blomqvist, Mikael Eriksson, Henrik Flyger, Kamila Czene, John L. Hopper, Fergus J. Couch, Ute Hamann, Jacques Simard, Arnaud Droit, Per Hall, Jonine D. Figueroa, Hatef Darabi, Julian Peto, Barbara Burwinkel, Canadian Institutes of Health Research, Norwegian Regional Health authorities, Cancer Research UK (Reino Unido), Unión Europea, United States of Department of Health & Human Services, Post-Cancer GWAS initiative, KWF Kankerbestrijding, Instituto de Salud Carlos III, California Breast Cancer Research Program, California Department of Public Health, Federal Ministry of Education & Research (Alemania), Finlands Akademi (Finlandia), United States Army Medical Research and Development Command, Stichting tegen Kanker, Deutsche Krebshilfe, Fondazione IRCCS Istituto Nazionale Tumori, National Health and Medical Research Council (Australia), Ministère du Développement économique, de Innovation et de Exportation (Canadá), The Research Council of Norway, Southern and Eastern Norway Regional Health Authority, Norwegian Cancer Society, Biobanking and BioMolecular resources Research Infrastructure (Países Bajos), Yorkshire Cancer Research, BRL (Basic Research Laboratory) program through the National Research Foundation of Korea - Ministry of Education, Science and Technology, Agency for Science, Technology and Research (Singapur), NIH - National Cancer Institute (NCI). Specialized Programs of Research Excellence (SPOREs) (Estados Unidos), Medical Oncology, Clinical Genetics, Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Dunning, Alison [0000-0001-6651-7166], Pharoah, Paul [0000-0001-8494-732X], Easton, Douglas [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Canadian Institutes of Health Research (CIHR), Cancer Research UK, European Union (EU), United States Department of Health & Human Services National Institutes of Health (NIH) - USA, Instituto de Salud Carlos III - ISCIII, California Breast Cancer Research Fund, Federal Ministry of Education & Research (BMBF), Academy of Finland, U.S. Army Medical Research & Materiel Command (USAMRMC), National Health and Medical Research Council of Australia, Ministry of Economic Development, Innovation and Export Trade, Research Council of Norway, South Eastern Norway Health Authority, Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-NL), Agency for Science Technology & Research (ASTAR), and Specialized Program of Research Excellence (SPORE) in Breast Cancer
Subjects: 0301 basic medicine, Genome-wide association study, chromatin features, ANALYSES REVEAL, Linkage Disequilibrium, 0302 clinical medicine, Gene Frequency, Risk Factors, Odds Ratio, Medicine, CONFER SUSCEPTIBILITY, health care economics and organizations, Genetics, COMMON VARIANTS, 3. Good health, Multicenter Study, Europe, Phenotype, Oncology, association studies, 030220 oncology & carcinogenesis, Female, Chromosomes, Human, Pair 4, Canada, Quantitative Trait Loci, Single-nucleotide polymorphism, DNA-DAMAGE RESPONSE, MISSENSE SUBSTITUTIONS, Breast Neoplasms, cis-regulatory variants, Quantitative trait locus, News, Polymorphism, Single Nucleotide, Risk Assessment, OVARIAN-CANCER, Mitochondrial Proteins, 03 medical and health sciences, Breast cancer, breast cancer, SDG 3 - Good Health and Well-being, Biomarkers, Tumor, Journal Article, Humans, Genetic Predisposition to Disease, GENOME-WIDE ASSOCIATION, Allele, FUNCTIONAL VARIANTS, Gene, Genetic Association Studies, Genetic association, genome-wide association study, business.industry, HUMAN-CELLS, DNA Helicases, Cancer, medicine.disease, susceptibility loci, 030104 developmental biology, Case-Control Studies, differential allelic expression, enhancer, business, Carrier Proteins, BRCA1 MUTATION CARRIERS, Priority Research Paper, genetic susceptibility
Abstract: There are significant inter-individual differences in the levels of gene expression. Through modulation of gene expression, cis-acting variants represent an important source of phenotypic variation. Consequently, cis-regulatory SNPs associated with differential allelic expression are functional candidates for further investigation as disease-causing variants. To investigate whether common variants associated with differential allelic expression were involved in breast cancer susceptibility, a list of genes was established on the basis of their involvement in cancer related pathways and/or mechanisms. Thereafter, using data from a genome-wide map of allelic expression associated SNPs, 313 genetic variants were selected and their association with breast cancer risk was then evaluated in 46,451 breast cancer cases and 42,599 controls of European ancestry ascertained from 41 studies participating in the Breast Cancer Association Consortium. The associations were evaluated with overall breast cancer risk and with estrogen receptor negative and positive disease. One novel breast cancer susceptibility locus on 4q21 (rs11099601) was identified (OR = 1.05, P = 5.6x10-6). rs11099601 lies in a 135 kb linkage disequilibrium block containing several genes, including, HELQ, encoding the protein HEL308 a DNA dependant ATPase and DNA Helicase involved in DNA repair, MRPS18C encoding the Mitochondrial Ribosomal Protein S18C and FAM175A (ABRAXAS), encoding a BRCA1 BRCT domain-interacting protein involved in DNA damage response and double-strand break (DSB) repair. Expression QTL analysis in breast cancer tissue showed rs11099601 to be associated with HELQ (P = 8.28x10-14), MRPS18C (P = 1.94x10-27) and FAM175A (P = 3.83x10-3), explaining about 20%, 14% and 1%, respectively of the variance inexpression of these genes in breast carcinomas. This work was supported by the Canadian Institutes of Health Research for the "CIHR Team in Familial Risks of Breast Cancer" program - grant # CRN-87521, the Ministry of Economy Innovation and Exportations-grant # PSR-SIIRI-701 and by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research, and the Ministere de l'Economie, de la Science et de l'Innovation du Quebec through Genome Quebec and The Quebec Breast Cancer Foundation for the PERSPECTIVE project. Jacques Simard is Chairholder of the Canada Research Chair in Oncogenetics. Silje Nord is financed by a carrier grant from the Norwegian Regional Health authorities (Grant number 2014061). BCAC is funded by Cancer Research UK [C1287/A10118, C1287/A12014] and by the European Community's Seventh Framework Programme under grant agreement number 223175 (grant number HEALTH-F2-2009-223175) (COGS). Funding for the iCOGS infrastructure came from: the European Community's Seventh Framework Programme under grant agreement no 223175 (HEALTH-F2-2009-223175) (COGS), Cancer Research UK (C1287/A10118, C1287/A 10710, C12292/A11174, C1281/A12014, C5047/A8384, C5047/A15007, C5047/A10692, C8197/A16565), the National Institutes of Health (CA128978) and Post-Cancer GWAS initiative (1U19 CA148537, 1U19 CA148065 and 1U19 CA148112 - the GAME-ON initiative), the Department of Defence (W81XWH-10-1-0341), the Canadian Institutes of Health Research (CIHR) for the CIHR Team in Familial Risks of Breast Cancer, Komen Foundation for the Cure, the Breast Cancer Research Foundation, and the Ovarian Cancer Research Fund. The Australian Breast Cancer Family Study (ABCFS) was supported by grant UM1 CA164920 from the National Cancer Institute (USA). The content of this manuscript does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the Breast Cancer Family Registry (BCFR), nor does mention of trade names, commercial products, or organizations imply endorsement by the USA Government or the BCFR. The ABCFS was also supported by the National Health and Medical Research Council of Australia, the New South Wales Cancer Council, the Victorian Health Promotion Foundation (Australia) and the Victorian Breast Cancer Research Consortium. J.L.H. is a National Health and Medical Research Council (NHMRC) Senior Principal Research Fellow. M.C.S. is a NHMRC Senior Research Fellow. The ABCS study was supported by the Dutch Cancer Society [grants NKI 2007-3839; 2009 4363]; BBMRI-NL, which is a Research Infrastructure financed by the Dutch government (NWO 184.021.007); and the Dutch National Genomics Initiative. The work of the BBCC was partly funded by ELAN-Fond of the University Hospital of Erlangen. The BBCS is funded by Cancer Research UK and Breast Cancer Now and acknowledges NHS funding to the NIHR Biomedical Research Centre, and the National Cancer Research Network (NCRN). ES is supported by NIHR Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust in partnership with King's College London, United Kingdom. IT is supported by the Oxford Biomedical Research Center. The BSUCH study was supported by the Dietmar-Hopp Foundation, the Helmholtz Society and the German Cancer Research Center (DKFZ). The CECILE study was funded by Fondation de France, Institut National du Cancer (INCa), Ligue Nationale contre le Cancer, Ligue contre le Cancer Grand Ouest, Agence Nationale de Securite Sanitaire (ANSES), Agence Nationale de la Recherche (ANR). The CGPS was supported by the Chief Physician Johan Boserup and Lise Boserup Fund, the Danish Medical Research Council and Herlev Hospital. The CNIO-BCS was supported by the Instituto de Salud Carlos III, the Red Tematica de Investigacion Cooperativa en Cancer and grants from the Asociacion Espanola Contra el Cancer and the Fondo de Investigacion Sanitario (PI11/00923 and PI12/00070). The CTS was initially supported by the California Breast Cancer Act of 1993 and the California Breast Cancer Research Fund (contract 97-10500) and is currently funded through the National Institutes of Health (R01 CA77398). Collection of cancer incidence data was supported by the California Department of Public Health as part of the statewide cancer reporting program mandated by California Health and Safety Code Section 103885. HAC receives support from the Lon V Smith Foundation (LVS39420). The ESTHER study was supportd by a grant from the Baden Wurttemberg Ministry of Science, Research and Arts. Additional cases were recruited in the context of the VERDI study, which was supported by a grant from the German Cancer Aid (Deutsche Krebshilfe). The GENICA was funded by the Federal Ministry of Education and Research (BMBF) Germany grants 01KW9975/5, 01KW9976/8, 01KW9977/0 and 01KW0114, the Robert Bosch Foundation, Stuttgart, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, the Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, as well as the Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany. The HEBCS was financilly supported by the Helsinki University Central Hospital Research Fund, Academy of Finland (266528), the Finnish Cancer Society, The Nordic Cancer Union and the Sigrid Juselius Foundation. The HMBCS was supported by a grant from the Friends of Hannover Medical School and by the Rudolf Bartling Foundation. Financial support for KARBAC was provided through the regional agreement on medical training and clinical research (ALF) between Stockholm County Council and Karolinska Institutet, the Swedish Cancer Society, The Gustav V Jubilee foundation and and Bert von Kantzows foundation. The KBCP was financially supported by the special Government Funding (EVO) of Kuopio University Hospital grants, Cancer Fund of North Savo, the Finnish Cancer Organizations, and by the strategic funding of the University of Eastern Finland. kConFab is supported by a grant from the National Breast Cancer Foundation, and previously by the National Health and Medical Research Council (NHMRC), the Queensland Cancer Fund, the Cancer Councils of New South Wales, Victoria, Tasmania and South Australia, and the Cancer Foundation of Western Australia. Financial support for the AOCS was provided by the United States Army Medical Research and Materiel Command [DAMD17-01-1-0729], Cancer Council Victoria, Queensland Cancer Fund, Cancer Council New South Wales, Cancer Council South Australia, The Cancer Foundation of Western Australia, Cancer Council Tasmania and the National Health and Medical Research Council of Australia (NHMRC; 400413, 400281, 199600). G.C.T. and P.W. are supported by the NHMRC. RB was a Cancer Institute NSW Clinical Research Fellow. LMBC is supported by the 'Stichting tegen Kanker' (232-2008 and 196-2010). Diether Lambrechts is supported by the FWO and the KULPFV/10/016-SymBioSysII. The MARIE study was supported by the Deutsche Krebshilfe e.V. [70-2892-BR I, 106332, 108253, 108419], the Hamburg Cancer Society, the German Cancer Research Center (DKFZ) and the Federal Ministry of Education and Research (BMBF) Germany [01KH0402]. MBCSG (Milan Breast Cancer Study Group) is supported by grants from the Italian Association for Cancer Research (AIRC) and by funds from the Italian citizens who allocated the 5/1000 share of their tax payment in support of the Fondazione IRCCS Istituto Nazionale Tumori, according to Italian laws (INT-Institutional strategic projects "5x1000"). The MCBCS was supported by the NIH grants CA192393, CA116167, CA176785 an NIH Specialized Program of Research Excellence (SPORE) in Breast Cancer [CA116201], and the Breast Cancer Research Foundation and a generous gift from the David F. and Margaret T. Grohne Family Foundation. MCCS cohort recruitment was funded by VicHealth and Cancer Council Victoria. The MCCS was further supported by Australian NHMRC grants 209057, 251553 and 504711 and by infrastructure provided by Cancer Council Victoria. Cases and their vital status were ascertained through the Victorian Cancer Registry (VCR) and the Australian Institute of Health and Welfare (AIHW), including the National Death Index and the Australian Cancer Database. The MEC was support by NIH grants CA63464, CA54281, CA098758 and CA132839. The work of MTLGEBCS was supported by the Quebec Breast Cancer Foundation, the Canadian Institutes of Health Research for the "CIHR Team in Familial Risks of Breast Cancer" program - grant # CRN-87521 and the Ministry of Economic Development, Innovation and Export Trade - grant # PSR-SIIRI-701. The NBCS has been supported by the Research Council of Norway grant 193387/V50 (to A-L Borresen-Dale and V.N. Kristensen) and grant 193387/H10 (to A-L Borresen-Dale and V.N. Kristensen), South Eastern Norway Health Authority (grant 39346 to A-L Borresen-Dale and 27208 to V.N. Kristensen) and the Norwegian Cancer Society (to A-L Borresen-Dale and 419616 - 71248 - PR-2006-0282 to V.N. Kristensen). It has received funding from the K.G. Jebsen Centre for Breast Cancer Research (2012-2015). The OBCS was supported by research grants from the Finnish Cancer Foundation, the Academy of Finland (grant number 250083, 122715 and Center of Excellence grant number 251314), the Finnish Cancer Foundation, the Sigrid Juselius Foundation, the University of Oulu, the University of Oulu Support Foundation and the special Governmental EVO funds for Oulu University Hospital-based research activities. The Ontario Familial Breast Cancer Registry (OFBCR) was supported by grant UM1 CA164920 from the National Cancer Institute (USA). The content of this manuscript does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the Breast Cancer Family Registry (BCFR), nor does mention of trade names, commercial products, or organizations imply endorsement by the USA Government or the BCFR. The ORIGO study was supported by the Dutch Cancer Society (RUL 1997-1505) and the Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-NL CP16). The PBCS was funded by Intramural Research Funds of the National Cancer Institute, Department of Health and Human Services, USA. The pKARMA study was supported by Marit and Hans Rausings Initiative against Breast Cancer. The RBCS was funded by the Dutch Cancer Society (DDHK 2004-3124, DDHK 2009-4318). The SASBAC study was supported by funding from the Agency for Science, Technology and Research of Singapore (A*STAR), the US National Institute of Health (NIH) and the Susan G. Komen Breast Cancer Foundation. The SBCS was supported by Yorkshire Cancer Research S295, S299, S305PA and Sheffield Experimental Cancer Medicine Centre. SEARCH is funded by a programme grant from Cancer Research UK [C490/A10124] and supported by the UK National Institute for Health Research Biomedical Research Centre at the University of Cambridge. SEBCS was supported by the BRL (Basic Research Laboratory) program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology (2012-0000347). SGBCC is funded by the NUS start-up Grant, National University Cancer Institute Singapore (NCIS) Centre Grant and the NMRC Clinician Scientist Award. Additional controls were recruited by the Singapore Consortium of Cohort Studies-Multi-ethnic cohort (SCCS-MEC), which was funded by the Biomedical Research Council, grant number: 05/1/21/19/425. SKKDKFZS is supported by the DKFZ. The SZBCS was supported by Grant PBZ_KBN_122/P05/2004. The TNBCC was supported by: a Specialized Program of Research Excellence (SPORE) in Breast Cancer (CA116201), a grant from the Breast Cancer Research Foundation, a generous gift from the David F. and Margaret T. Grohne Family Foundation. The UKBGS is funded by Breast Cancer Now and the Institute of Cancer Research (ICR), London. ICR acknowledges NHS funding to the NIHR Biomedical Research Centre. Sí
Published: 2016
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21. Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility

Author: Nora Franceschini, Rico Rueedi, Gerardo Heiss, Behrooz Z. Alizadeh, Marike Gabrielson, Henry Völzke, Daniela Ruggiero, Judith S. Brand, Stig E. Bojesen, Iffat Rahman, Fergus J. Couch, Patrick Sulem, Harold Snieder, Jenny Chang-Claude, Caterina Barbieri, Ute Hamann, Hinds D, Pascal Guénel, Amanda B. Spurdle, Paul M. Ridker, Ulla Sovio, Roger L. Milne, Hamdi Mbarek, H Brenner, Hilary K. Finucane, Maristella Steri, Lude Franke, Emmi Tikkanen, Ivana Kolcic, Vitart, Ken K. Ong, Alison M. Dunning, Aarno Palotie, Caroline Hayward, Jouke J. Hottenga, Abhishek Sarkar, Stefania Lenarduzzi, Nicholas G. Martin, Katharina E. Schraut, Eva Albrecht, Hiltrud Brauch, Lisette Stolk, Joop S.E. Laven, Penelope A. Lind, Ilaria Gandin, Patrik K. E. Magnusson, Ellen A. Nohr, Tanguy Corre, Jing Hua Zhao, N J Timpson, Jenny A. Visser, Harald Grallert, P. A. Fasching, Susan M. Ring, Stöckl D, Grant W. Montgomery, Marzyeh Amini, Velez Edwards Dr, Thomas Meitinger, Qinghua Wang, David Karasik, Daniel I. Chasman, Nicholas J. Wareham, Alexander Teumer, Mellissa C. Southey, Kathryn L. Lunetta, S. E. Medland, Dieter Flesch-Janys, Maartje J. Hooning, Lili Milani, D Lambrechts, Ozren Polasek, Po-Ru Loh, James F. Wilson, Campbell A, Julian Peto, Ellen W. Demerath, Christian Gieger, de Geus Ej, Cox A, Javier Benítez, Mitul Shah, Eric Boerwinkle, Matthias W. Beckmann, Thorsteindottir U, Julie E. Buring, De Vivo I, Hannes Helgason, Paolo Radice, Tracy A. O'Mara, L. J. Launer, D. F. Gudbjartsson, Frits R. Rosendaal, C.A. Hartman, Stefania Bandinelli, Felix R. Day, Lynda M. Rose, van Dijk Kw, Natalia Perjakova, Anneli Pouta, Igor Rudan, Sven Bergmann, Kamila Czene, Georgia Chenevix-Trench, Pau Navarro, Sean Whalen, Heli Nevanlinna, Teresa Nutile, Diana L. Cousminer, Albert V. Smith, Massimo Mangino, Uwe Völker, Michela Traglia, Lindsay Fernández-Rhodes, Ayush Giri, Linda Broer, Albertine J. Oldehinkel, Isabel dos-Santos-Silva, Peter Vollenweider, Jian'an Luan, Nancy L. Pedersen, Irene L. Andrulis, Reedik Mägi, Robert Winqvist, Gonneke Willemsen, John L. Hopper, Gudnason, Marjanka K. Schmidt, David G. Hunter, Robert A. Scott, T.B. Harris, Joanne M. Murabito, David J. Porteous, Harry Campbell, Eleonora Porcu, D.I. Boomsma, Thibaud Boutin, M. A. Ikram, Doug Easton, Magdalena Zoledziewska, Meir J. Stampfer, Katherine S. Pollard, Eulalia Catamo, Tõnu Esko, M-R Jarvelin, Laura Crisponi, Claudia Langenberg, Marek Zygmunt, Antonietta Robino, Emily Hallberg, Manjeet K. Bolla, Ruth Ks, Bruce H W Wolffenbuttel, Lavinia Paternoster, Tyrer Jp, P. Kraft, George Davey-Smith, Robert Karlsson, Graham G. Giles, Jingmei Li, Pharoah Pd, Segrè Av, Marina Ciullo, Perry, Brumat Marco, Peter K. Joshi, Chunyan He, Sara Lindström, Joe Dennis, Thérèse Truong, Yongmei Liu, Anna Marie Mulligan, Mike A. Nalls, Cinzia Sala, K. Stefansson, Murray A, Debbie A Lawlor, Tung Jy, Deborah J. Thompson, Dennis O. Mook-Kanamori, Daniela Toniolo, Luigi Ferrucci, Peter Devilee, S. Chanock, Cristina Menni, George McMahon, Murielle Bochud, A. Metspalu, Tomohiro Tanaka, E. Widen, Hae Kyung Im, Dale R. Nyholt, Ilja M. Nolte, Thomas Brüning, Christina Meisinger, Annette Peters, Kyriaki Michailidou, Per Hall, Rossella Sorice, Genevieve Lachance, Johan G. Eriksson, Francesco Cucca, A.G. Uitterlinden, Z. Kutalik, Mark I. McCarthy, Frank B. Hu, Konstantin Strauch, Tim D. Spector, Elisabeth Altmaier, S. Ulivi, Alkes L. Price, Arto Mannermaa, Raymond Noordam, and de Mutsert R
Subjects: Genetics, 0303 health sciences, 03 medical and health sciences, 0302 clinical medicine, 030220 oncology & carcinogenesis, Genotype, Menarche, Trait, Cancer susceptibility, Genomics, Biology, 030304 developmental biology
Abstract: The timing of puberty is a highly polygenic childhood trait that is epidemiologically associated with various adult diseases. Here, we analyse 1000-Genome reference panel imputed genotype data on up to ~370,000 women and identify 389 independent signals (all P−8) for age at menarche, a notable milestone in female pubertal development. In Icelandic data from deCODE, these signals explain ~7.4% of the population variance in age at menarche, corresponding to one quarter of the estimated heritability. We implicate over 250 genes via coding variation or associated gene expression, and demonstrate enrichment across genes active in neural tissues. We identify multiple rare variants near the imprinted genes MKRN3 and DLK1 that exhibit large effects on menarche only when paternally inherited. Disproportionate effects of variants on early or late puberty timing are observed: single variant and heritability estimates are larger for early than late puberty timing in females. The opposite pattern is seen in males, with larger estimates for late than early puberty timing. Mendelian randomization analyses indicate causal inverse associations, independent of BMI, between puberty timing and risks for breast and endometrial cancers in women, and prostate cancer in men. In aggregate, our findings reveal new complexity in the genetic regulation of puberty timing and support new causal links with adult cancer risks.
Published: 2016
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22. Impact that Timing of Genetic Mutation Diagnosis has on Surgical Decision Making and Outcome for BRCA1/BRCA2 Mutation Carriers with Breast Cancer

Author: Fergus J. Couch, Courtney N. Heins, Akiko Chiba, Emily Hallberg, Tanya L. Hoskin, Jodie A. Cogswell, and Judy C. Boughey
Subjects: Adult, Heterozygote, animal structures, Time Factors, endocrine system diseases, medicine.medical_treatment, Decision Making, Genes, BRCA2, Genes, BRCA1, Kaplan-Meier Estimate, Bioinformatics, Mastectomy, Segmental, Article, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Breast cancer, Mutation Carrier, Surgical oncology, medicine, Unilateral Breast Neoplasms, Humans, 030212 general & internal medicine, Genetic Testing, skin and connective tissue diseases, Genetic testing, Aged, Neoplasm Staging, medicine.diagnostic_test, business.industry, BRCA mutation, Prophylactic Mastectomy, Middle Aged, medicine.disease, female genital diseases and pregnancy complications, Oncology, 030220 oncology & carcinogenesis, Mutation, Surgery, Female, business, Mastectomy
Abstract: Deleterious BRCA mutation carriers with breast cancer are at increased risk for additional breast cancer events. This study evaluated the impact that timing of identification of BRCA+ status has on surgical decision and outcome.The authors reviewed all BRCA carriers at their institution whose breast cancer was diagnosed between January 1996 and June 2015. Patient surveys, medical records, and institutional databases were used to collect data. Differences in surgical choice were analyzed using the chi-square test, and rates of subsequent breast cancer events were estimated using the Kaplan-Meier method.The study investigated 173 BRCA carriers with breast cancer (100 BRCA1, 73 BRCA2). Of the women with known BRCA mutation before surgery and unilateral stages 0 to 3 breast cancer (n = 63), 12.7 % underwent lumpectomy, 4.8 % underwent unilateral mastectomy (UM), and 82.5 % underwent bilateral mastectomy (BM). These surgical choices differed significantly (p 0.0001) from those of patients unaware of their mutation at the time of surgery (n = 93) (51.6 % had lumpectomy, 19.4 % had UM, 29 % had BM). Of the patients with BRCA mutation identified after surgery who underwent lumpectomy or UM, 36 (59 %) of 66 underwent delayed BM. The patients with BRCA+ known before diagnosis presented with significantly lower-stage disease (p = 0.02) at diagnosis (69 % stage 0 or 1) than those whose BRCA mutation was identified after cancer diagnosis (40 % stage 0 or 1).The study findings showed that BRCA mutation status influences surgical decision. The rates of BM were higher for the patients with BRCA mutation known before surgery. Identification of BRCA mutation after surgery frequently leads to subsequent breast surgery. Genetic testing before surgery is important for patients at elevated risk for BRCA mutation.
Published: 2016

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

Author: Kenneth Offit, Hoda Anton-Culver, Ans M.W. van den Ouweland, Siranoush Manoukian, Christine L. Clarke, Kyriaki Michailidou, Antonis C. Antoniou, Maria Kabisch, Isabel dos-Santos-Silva, Douglas F. Easton, Curtis Olswold, Graham G. Giles, Tien Yin Wong, Ursula Eilber, Mads Thomassen, Christopher A. Haiman, Alice J. Sigurdson, Lothar Haeberle, Florence Menegaux, Ana Osorio, Marco Montagna, Katarzyna Jaworska-Bieniek, Eitan Friedman, Simon S. Cross, Daniel Barrowdale, Elinor J. Sawyer, Adam N. Freeman, Caroline Seynaeve, Min Hyuk Lee, Arnaud Droit, Per Hall, Minouk J. Schoemaker, Trinidad Caldés, Peter Hillemanns, Frederik Marmé, Jenny Lester, Michele M. Doody, Bernard Peissel, Peter Kraft, Elza Khusnutdinova, Anna H. Wu, Stéphanie Peeters, Georg Pfeiler, Pascal Guénel, Hidemi Ito, Xingyi Guo, Antoinette Hollestelle, Heli Nevanlinna, Kathleen Claes, Ylva Paulsson-Karlsson, Cecilia M. Dorfling, Roger L. Milne, Daehee Kang, Judith S. Brand, Diether Lambrechts, Olufunmilayo I. Olopade, Simona Agata, Saundra S. Buys, Muhammad Usman Rashid, Fabienne Lesueur, Alicia Beeghly-Fadiel, Peter Devilee, Manjeet K. Bolla, Natalia Antonenkova, Irene Konstantopoulou, Claudine Isaacs, Anja Rudolph, Carl Blomqvist, Tjoung Won Park-Simon, Judy Garber, Csilla Szabo, Francois Bacot, Arto Mannermaa, Yu-Tang Gao, Stig E. Bojesen, Susan L. Neuhausen, Marina Bermisheva, Qiuyin Cai, Zakaria Einbeigi, Christian F. Singer, Qin Wang, Kerstin Rhiem, Sofia Khan, Fiona Lalloo, Robert L. Nussbaum, Thilo Dörk, William J. Blot, Sylvie Mazoyer, Julia A. Knight, Katherine L. Nathanson, Clare Turnbull, Nazneen Rahman, Anne Lise Børresen-Dale, Chuen Neng Lee, Annegien Broeks, Martha J. Shrubsole, Ava Kwong, Jirong Long, Ian G. Campbell, Sara Margolin, Fergus J. Couch, Laima Tihomirova, Mary Beth Terry, Jenny Chang-Claude, Alice S. Whittemore, Joseph Vijai, Alfons Meindl, Xiao-Ou Shu, Shan Wang-Gohrke, Wei Zheng, Beth Y. Karlan, Jacques Simard, Angela Cox, Shahana Ahmed, Polly A. Newcomb, Ritu Salani, Chen-Yang Shen, Adalgeir Arason, Sandrine Tchatchou, Ute Hamann, Elizabeth J. van Rensburg, Michael Jones, Mark H. Greene, Anthony J. Swerdlow, Senno Verhoef, Jonine Figueroa, Hermann Brenner, Volker Arndt, Charles Joly Beauparlant, Esther M. John, Nadege Presneau, Jingmei Li, Laura Papi, Marjanka K. Schmidt, Montserrat Garcia-Closas, Uffe Birk Jensen, Georgia Chenevix-Trench, Paolo Peterlongo, Penny Soucy, Thomas Brüning, Jaana M. Hartikainen, Siddhartha Kar, Ji Yeob Choi, Manuel R. Teixeira, Phuong L. Mai, Alex Teulé, Jyh Cherng Yu, Paul Brennan, Maya Ghoussaini, Edith Olah, Henrik Flyger, Michael Friedlander, Soo Hwang Teo, Frans B. L. Hogervorst, Kathleen M. Egan, David J. Hunter, Kristiina Aittomäki, Joe Dennis, Anna González-Neira, Mikael Hartman, Alison M. Dunning, Doris Steinemann, Debra Frost, Melissa C. Southey, Ramunas Janavicius, Evgeny N. Imyanitov, Catherine M. Phelan, Amanda E. Toland, Anna Marie Mulligan, David ven den Berg, Rita K. Schmutzler, Julian Peto, Irene L. Andrulis, Chenjie Zeng, Kenneth Muir, Peter Schürmann, Saila Kauppila, Banu Arun, Jane Carpenter, Jeffrey N. Weitzel, Yael Laitman, Susan M. Domchek, Robert Winqvist, Caroline Baynes, Brita Arver, Marc Tischkowitz, Kamila Czene, Keitaro Matsuo, Barbara Burwinkel, Miriam Dwek, Kim De Leeneer, David E. Goldgar, Anna Jakubowska, Paul D.P. Pharoah, Peter A. Fasching, Bernd Dworniczak, Susan J. Ramus, Lesley McGuffog, Andrea Gehrig, Michael J. Kerin, Thomas Hansen, Francesca Damiola, John L. Hopper, Loic Le Marchand, Peter J. Hulick, Annika Lindblom, Emily Hallberg, Miguel de la Hoya, Gaetana Gambino, Martine Dumont, Susan L. Slager, Bernardo Bonanni, Bent Ejlertsen, Norhashimah Hassan, Sue Healey, Orland Diez, Mary B. Daly, Carolyn B. Hendricks, Artitaya Lophatananon, Annelie Liljegren, Steven N. Hart, Jan Lubinski, Natalia Bogdanova, Drakoulis Yannoukakos, Steve Ellis, Silje Nord, Hiltrud Brauch, Gad Rennert, Conxi Lázaro, Daniel C. Tessier, Paolo Radice, Dominique Stoppa-Lyonnet, Nadine Tung, Andrew K. Godwin, Suleeporn Sangrajrang, Karoline Kuchenbaecker, Javier Benitez, Critical care, Anesthesiology, Peri-operative and Emergency medicine (CAPE), Damage and Repair in Cancer Development and Cancer Treatment (DARE), Targeted Gynaecologic Oncology (TARGON), Medicum, Kristiina Aittomäki / Principal Investigator, Department of Medical and Clinical Genetics, Clinicum, Department of Oncology, Department of Obstetrics and Gynecology, School of Medicine / Clinical Medicine, Wang, Jean [0000-0002-9139-0627], Dennis, Joe [0000-0003-4591-1214], Tischkowitz, Marc [0000-0002-7880-0628], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Antoniou, Antonis [0000-0001-9223-3116], Easton, Douglas [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Clinical Genetics, Medical Oncology, and Obstetrics & Gynecology
Subjects: 0301 basic medicine, Fine-scale mapping, Genome-wide association study, HORMONE-RELATED PROTEIN, Epigenesis, Genetic, Breast cancer, Medizinische Fakultät, Databases, Genetic, Genotype, BRCA2 MUTATION CARRIERS, Odds Ratio, Medicine and Health Sciences, Pair 12, Medicine, Genetic risk factor, Promoter Regions, Genetic, Medicine(all), Genetics, BRCA1 Protein, PTHLH-CCDC91, Chromosome Mapping, LOCALIZATION, Single Nucleotide, PTHLH, 3. Good health, Enhancer Elements, Genetic, Population Surveillance, Female, Medical Genetics, BRAC1 mutation carriers, CCDC91, Alleles, Breast Neoplasms, Case-Control Studies, Computational Biology, European Continental Ancestry Group, Haplotypes, Heterozygote, Humans, Mutation, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Risk, Chromosomes, Human, Pair 12, Genetic Predisposition to Disease, Genome-Wide Association Study, Human, Research Article, EXPRESSION, Enhancer Elements, SUSCEPTIBILITY LOCI, 3122 Cancers, Single-nucleotide polymorphism, Chromosomes, White People, OVARIAN-CANCER, Càncer de mama, Promoter Regions, Databases, 03 medical and health sciences, Research Support, N.I.H., Extramural, SDG 3 - Good Health and Well-being, Genetic, Journal Article, ddc:610, Polymorphism, GENOME-WIDE ASSOCIATION, Medicinsk genetik, Genetic association, Cancer och onkologi, business.industry, Haplotype, Case-control study, Biology and Life Sciences, Odds ratio, medicine.disease, ENHANCERS, 030104 developmental biology, Cancer and Oncology, METASTASIS, 3111 Biomedicine, GENETIC MODIFIERS, business, Genètica, Epigenesis
Abstract: Article, 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, published version, peerReviewed
Published: 2016
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24. Combined genetic and splicing analysis of BRCA1 c.[594-2A > C; 641A > G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms

Author: Barbara Wappenschmidt, Fergus J. Couch, Norbert Arnold, Claude Houdayer, Manjeet K. Bolla, Omar Soukarieh, Sean V. Tavtigian, Irene L. Andrulis, Alexandra Becker, Alexandra Martins, Qin Wang, Sara Margolin, Paolo Radice, Janet E. Olson, Mitul Shah, Juul T. Wijnen, Amanda B. Spurdle, Nichola Johnson, Carole Brewer, Harald Surowy, Graham G. Giles, Ana Blanco, Kamila Czene, Thomas Hansen, Wendy S. Rubinstein, Anja Rudolph, Christian F. Singer, Antonis C. Antoniou, Douglas F. Easton, Fiona M. Blows, Michael T. Parsons, kConFab Investigators, Annika Lindblom, Nicola K. Poplawski, Melissa C. Southey, Emily Hallberg, Vanessa Lattimore, Yvette van Ierland, Logan C. Walker, Joe Dennis, Gord Glendon, Ana Vega, Diether Niederacher, Laurent Castera, David E. Goldgar, Ulrike Faust, Roger L. Milne, Marta Santamariña, Lesley McGuffog, Jan Hauke, Christi J. van Asperen, Michela Raponi, Irene López-Perolio, Diana Baralle, Tina Pesaran, Huong Meeks, Peter J. Hulick, Miguel de la Hoya, Philip Whiley, Raquel Behar, Jenny Chang-Claude, Elizabeth C. Chao, Henrik Flyger, Doris Steinemann, Pham Phuong Mai, Stig E. Bojesen, Maaike P.G. Vreeswijk, Sandrine M. Caputo, Jan Sullivan, Julian Peto, Barbara Burwinkel, Laura Galastri, Per Hall, Kyriaki Michailidou, Bernd Dworniczak, Molecular Oncology Laboratory, Hospital Clínico San Carlos, Génétique du cancer et des maladies neuropsychiatriques (GMFC), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques (GPMCND), Instituto de Investigación Sanitaria del Hospital Clínico San Carlos [Madrid, Spain] (IdISSC), Fundación Pública Galega Medicina Xenómica-SERGAS & Grupo de Medicina Xenómica--USC, CIBER de Enfermedades Raras (CIBERER), Division of Genetics and Population Health, Queensland Institute of Medical Research, Genetics, University of Southampton, University of Otago [Dunedin, Nouvelle-Zélande], Department of Clinical Genetics and GROM, School for Oncology and Developmental Biology, Human Genetics Division [Southampton], Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, Institut Laue-Langevin (ILL), University of Melbourne, Division of Oncology, Department of Gynaecology and Obstetrics, University Hospital Schleswig–Holstein, Institute of Cell and Molecular Pathology, Medizinische Hochschule Hannover (MHH), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), DIEP/DSV (DIEP/DSV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre Régional de Lutte contre le Cancer François Baclesse [Caen] (UNICANCER/CRLC), Normandie Université (NU)-UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN), Ambry Genetics [Aliso Viejo, CA, USA], Department of Clinical Genetics, Royal Devon & Exeter Hospital, Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia, Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Division of Special Gynecology, Medizinische Universität Wien = Medical University of Vienna-Department of OB/GYN, Metabolic Unit, Dept Clinical Chemistry, Division of Cancer Epidemiology and Genetics, National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH)-National Institutes of Health [Bethesda] (NIH), Non-Communicable Disease Epidemiology Unit, London School of Hygiene and Tropical Medicine (LSHTM), Molecular Epidemiology Research Group, German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Department of Breast Surgery, Herlev and Gentofte Hospital, Karolinska University Hospital [Stockholm], Division of Cancer Epidemiology, Unit of Genetic Susceptibility to Cancer, Department of Experimental Oncology and Molecular Medici, Cancer Epidemiology Centre, Cancer Council Victoria, Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto-Cancer Care Ontario, Ontario Cancer Genetics Network, Cancer Care Ontario, Department of Medical Epidemiology and Biostatistics (MEB), Karolinska Institutet [Stockholm], University of Science and Technology Beijing [Beijing] (USTB), Strangeways Research Laboratory, University of Cambridge [UK] (CAM)-Department of Public Health and Primary Care-Centre for Cancer Genetic Epidemiology, Cancer Research U.K. Genetic Epidemiology Unit, Department of Laboratory Medicine and Pathology, Mayo Clinic, Department of Oncological Sciences, University of Utah-Huntsman Cancer Institute, Center for Human and Clinical Genetics, Université de Pau et des Pays de l'Adour (UPPA), International Agency for Cancer Research (IACR), ILL, Service de Biochimie et de Biologie Moléculaire [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), UNICANCER-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU), Wang, Jean [0000-0002-9139-0627], Dennis, Joe [0000-0003-4591-1214], Antoniou, Antonis [0000-0001-9223-3116], Easton, Douglas [0000-0003-2444-3247], Apollo - University of Cambridge Repository, and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)
Subjects: 0301 basic medicine, Adult, RNA Splicing, [SDV]Life Sciences [q-bio], DNA Mutational Analysis, Breast Neoplasms, Biology, 03 medical and health sciences, Exon, Genetics, Humans, Allele, Molecular Biology, Gene, Genetics (clinical), ComputingMilieux_MISCELLANEOUS, Aged, Ovarian Neoplasms, Messenger RNA, BRCA1 Protein, Tumor Suppressor Proteins, Alternative splicing, RNA, General Medicine, Articles, Exons, Middle Aged, Splicing regulatory element, 3. Good health, Gene Expression Regulation, Neoplastic, Alternative Splicing, 030104 developmental biology, RNA splicing, Mutation, Female, RNA Splice Sites
Abstract: A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A>C (IVS9-2A>C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A>C. The combined odds for causality considering case-control, segregation, and breast tumor pathology information was 3.23x10-8. Our data indicate that c.594-2A>C is always in cis with c.641A>G.The spliceogenic effect of c.[594-2A>C;641A>G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A>C; 641A>G] caused exon 10 skipping, albeit not due to c.594-2A>C impairing the acceptor site but rather by c.641A>G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile comprised of ?70-80% truncating transcripts, and ?20-30% of in-frame ?9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.We confirm that BRCA1c.[594-2A>C;641A>G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.
Published: 2016
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25. RAD51B in Familial Breast Cancer

Author: kConFab, Jonine Figueroa, Elinor J. Sawyer, Manjeet K. Bolla, Carl Blomqvist, Jaana M. Hartikainen, Sara Margolin, Mitul Shah, Matthias W. Beckmann, Fredrick Schumacher, Vessela N. Kristensen, Graham G. Giles, Isabel dos-Santos-Silva, Kamila Czene, Douglas F. Easton, Qin Wang, Javier Benitez, Janet E. Olson, Georgia Chenevix-Trench, John L. Hopper, Alicia Beeghly-Fadiel, Hoda Anton-Culver, Paolo Radice, Aocs Investigators, Nick Orr, Jacques Simard, Mervi Grip, Salla Ranta, Fergus J. Couch, Marjanka K. Schmidt, Kristiina Aittomäki, Caroline Seynaeve, Ute Hamann, Johanna Schleutker, Hilde Janssen, Robert Luben, Anna González-Neira, Peter A. Fasching, Pascal Guénel, Anja Rudolph, Arto Mannermaa, Melissa C. Southey, Ian Tomlinson, Thérèse Truong, Alison M. Dunning, Margriet Collée, Robert Winqvist, Johanna Mattson, Mikko Vuorela, Sara Vilske, Anne Lise Børresen-Dale, Johanna I. Kiiski, Paolo Peterlongo, Anna Jakubowska, Paul D.P. Pharoah, Alfons Meindl, Anthony J. Swerdlow, Roger L. Milne, Hermann Brenner, Joe Dennis, Montserrat Garcia-Closas, Thomas Brüning, Christopher A. Haiman, Martine Dumont, Wei Zheng, Per Hall, Gord Glendon, Jingmei Li, Laurien Van Dyck, Susan L. Neuhausen, Simon S. Cross, Irene L. Andrulis, Peter Devilee, Annika Lindblom, Emily Hallberg, Diana Torres, Sofia Khan, Kyriaki Michailidou, Rita K. Schmutzler, Julian Peto, Harald Surowy, Børge G. Nordestgaard, Barbara Burwinkel, Natalia Bogdanova, Drakoulis Yannoukakos, Heli Nevanlinna, Jan Lubinski, Liisa M. Pelttari, Efraim H. Rosenberg, Hiltrud Brauch, Thilo Dörk, Angela Cox, Viivi Nevanlinna, Maartje J. Hooning, Volker Arndt, Anne Kallioniemi, Stig E. Bojesen, Jenny Chang-Claude, Hatef Darabi, Obstetrics & Gynecology, Clinical Genetics, Gastroenterology & Hepatology, Medical Oncology, Brusgaard, Klaus, Department of Obstetrics and Gynecology, Clinicum, Department of Oncology, Medicum, Kristiina Aittomäki / Principal Investigator, Department of Medical and Clinical Genetics, HUS Gynecology and Obstetrics, Pelttari, LM, Khan, S, Vuorela, M, Kiiski, JI, Thierry, B, Zeps, N, Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Luben, Robert [0000-0002-5088-6343], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Oncology, Male, Heredity, XRCC2, Genotyping Techniques, lcsh:Medicine, Genome-wide association study, 14Q24.1 RAD51L1, VARIANTS, Geographical Locations, 3123 Gynaecology and paediatrics, Cancer screening, Breast Tumors, Medicine and Health Sciences, CONFER SUSCEPTIBILITY, Ethnicities, lcsh:Science, Finland, Genetics, RISK, education.field_of_study, Multidisciplinary, GERMLINE MUTATIONS, Genomics, Middle Aged, 3. Good health, Ovarian Cancer, Europe, DNA-Binding Proteins, Genetic Mapping, Male breast cancer, Female, Cancer Screening, Research Article, medicine.medical_specialty, Heterozygote, General Science & Technology, Population, 3122 Cancers, Mutation, Missense, Single-nucleotide polymorphism, Variant Genotypes, Breast Neoplasms, Genome Complexity, Polymorphism, Single Nucleotide, OVARIAN-CANCER, 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Internal medicine, Breast Cancer, medicine, Cancer Detection and Diagnosis, Journal Article, Humans, Genetic Predisposition to Disease, GENOME-WIDE ASSOCIATION, education, Evolutionary Biology, Population Biology, business.industry, lcsh:R, Cancers and Neoplasms, Biology and Life Sciences, Computational Biology, Odds ratio, medicine.disease, ta3122, GENE, Introns, 030104 developmental biology, Haplotypes, FANCONI-ANEMIA, People and Places, lcsh:Q, Population Groupings, business, Ovarian cancer, Gynecological Tumors, Population Genetics, Finns
Abstract: Common variation on 14q24.1, close to RAD51B, has been associated with breast cancer: rs999737 and rs2588809 with the risk of female breast cancer and rs1314913 with the risk of male breast cancer. The aim of this study was to investigate the role of RAD51B variants in breast cancer predisposition, particularly in the context of familial breast cancer in Finland. We sequenced the coding region of RAD51B in 168 Finnish breast cancer patients from the Helsinki region for identification of possible recurrent founder mutations. In addition, we studied the known rs999737, rs2588809, and rs1314913 SNPs and RAD51B haplotypes in 44,791 breast cancer cases and 43,583 controls from 40 studies participating in the Breast Cancer Association Consortium (BCAC) that were genotyped on a custom chip (iCOGS). We identified one putatively pathogenic missense mutation c.541C>T among the Finnish cancer patients and subsequently genotyped the mutation in additional breast cancer cases (n = 5259) and population controls (n = 3586) from Finland and Belarus. No significant association with breast cancer risk was seen in the meta-analysis of the Finnish datasets or in the large BCAC dataset. The association with previously identified risk variants rs999737, rs2588809, and rs1314913 was replicated among all breast cancer cases and also among familial cases in the BCAC dataset. The most significant association was observed for the haplotype carrying the risk-alleles of all the three SNPs both among all cases (odds ratio (OR): 1.15, 95% confidence interval (CI): 1.11-1.19, P = 8.88 x 10-16) and among familial cases (OR: 1.24, 95% CI: 1.16-1.32, P = 6.19 x 10-11), compared to the haplotype with the respective protective alleles. Our results suggest that loss-of-function mutations in RAD51B are rare, but common variation at the RAD51B region is significantly associated with familial breast cancer risk. ispartof: PLoS One vol:11 issue:5 ispartof: location:United States status: published
Published: 2016
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26. Fine scale mapping of the 17q22 breast cancer locus using dense SNPs, genotyped within the Collaborative Oncological Gene-Environment Study (COGs)

Author: Stacey L. Edwards, Daniel Vincent, Antoinette Hollestelle, Melissa C. Southey, Thilo Dörk, Jonine Figueroa, Robert Winqvist, Wei Zheng, Keitaro Matsuo, Fergus J. Couch, Don M. Conroy, Anna Jakubowska, Paul D.P. Pharoah, Sara Margolin, Simon S. Cross, Joe Dennis, Rebecca Mayes, Annegien Broeks, Mitul Shah, Matthias W. Beckmann, Mahdi Moradi Marjaneh, Pei-Ei Wu, Javier Benitez, Hanna Fues Wahl, Ute Hamann, Rita K. Schmutzler, Guillermo Pita, Nichola Johnson, Suleeporn Sangrajrang, James McKay, Barbara Burwinkel, Hoda Anton-Culver, Pascal Guénel, Douglas F. Easton, Veli-Matti Kosma, Hidemi Ito, Angela Cox, Georgia Chenevix-Trench, M. Rosario Alonso, Mark S. Goldberg, Hatef Darabi, Volker Arndt, Qin Wang, Manjeet K. Bolla, Nick Orr, Soo Hwang Teo, Soo-Chin Lee, Penny Soucy, Jonathan Beesley, Paolo Peterlongo, Ji Yeob Choi, Anthony J. Swerdlow, Jacques Simard, Kamila Czene, Anna González-Neira, Jenny Chang-Claude, Heli Nevanlinna, Ian Tomlinson, Thérèse Truong, Chen-Yang Shen, Harald Surowy, Henrik Flyger, Marjanka K. Schmidt, Graham G. Giles, John L. Hopper, Celine M. Vachon, Olivia Fletcher, Stig E. Bojesen, Mikael Hartman, Arnaud Droit, Per Hall, Cheng Har Yip, Maya Ghoussaini, Artitaya Lophatananon, Mieke Kriege, Anna H. Wu, Siranoush Manoukian, Kyriaki Michailidou, Christopher A. Haiman, Roger L. Milne, Xiao-Ou Shu, Daniel O. Stram, Katri Pylkäs, Sofia Khan, Irene L. Andrulis, Annika Lindblom, Emily Hallberg, Diana Torres, Anja Rudolph, Arto Mannermaa, Hermann Brenner, Vessela N. Kristensen, Daehee Kang, Caroline Seynaeve, Elinor J. Sawyer, Silje Nord, Hiltrud Brauch, Jan Lubinski, Natalia Bogdanova, Juliet D. French, Susan L. Neuhausen, Montserrat Garcia-Closas, Thomas Brüning, Loic Le Marchand, Peter A. Fasching, Diether Lambrechts, Daniel C. Tessier, Peter Devilee, Eva Galle, Alfons Meindl, Alison M. Dunning, Siddhartha Kar, Kenneth Muir, Curtis Olswold, Wang, Jean [0000-0002-9139-0627], Dennis, Joe [0000-0003-4591-1214], Easton, Douglas [0000-0003-2444-3247], Pharoah, Paul [0000-0001-8494-732X], Dunning, Alison [0000-0001-6651-7166], Apollo - University of Cambridge Repository, Department of Obstetrics and Gynecology, Clinicum, School of Medicine / Clinical Medicine, Cancer Research UK (Reino Unido), European Research Council, NIH - National Cancer Institute (NCI) (Estados Unidos), Post-cancer GWAS Initiative, Dutch Cancer Society (Holanda), Biobanking and BioMolecular resources Research Infrastructure (Países Bajos), Instituto de Salud Carlos III, Finlands Akademi (Finlandia), Ministry of Education, Culture, Sports, Science, and Technology (Japón), Japan Agency for Medical Research and Development, United States Army Medical Research and Development Command, California Breast Cancer Research Program, Stichting tegen Kanker, Deutsche Krebshilfe, National Health and Medical Research Council (Australia), Ministry of Economic Development, Innovation and Export Trade, Ministry of Higher Education (Malasia), Agency for Science, Technology and Research (Singapur), National Medical Research Council (Singapur), The Research Council of Norway, Southern and Eastern Norway Regional Health Authority, Finnish Cancer (Center of Excellence grant), Genetic Associations and Mechanisms in Oncology (GAME-ON) Initiative, Yorkshire Cancer Research, BRL (Basic Research Laboratory) program through the National Research Foundation of Korea - Ministry of Education, Science and Technology, NIH - National Cancer Institute (NCI). Specialized Programs of Research Excellence (SPOREs) (Estados Unidos), Hellenic Cooperative Oncology Group research grant, Institute of Cancer Research (Reino Unido), United States of Department of Health & Human Services, Medical Oncology, and Obstetrics & Gynecology
Subjects: 0301 basic medicine, Vesicular Transport Proteins, Genome-wide association study, 0302 clinical medicine, Breast cancer, Genetics research, Medicine and Health Sciences, HUMAN GENOME, Genetics, Multidisciplinary, Chromosome Mapping, ASSOCIATION, Tag SNP, 3. Good health, 030220 oncology & carcinogenesis, Female, EXPRESSION, SUSCEPTIBILITY LOCI, Genotype, European Continental Ancestry Group, 3122 Cancers, Quantitative Trait Loci, Locus (genetics), Single-nucleotide polymorphism, Breast Neoplasms, Biology, Polymorphism, Single Nucleotide, Article, White People, REGION, RC0254, 03 medical and health sciences, SDG 3 - Good Health and Well-being, REVEALS, medicine, SNP, Humans, Genetic Predisposition to Disease, FUNCTIONAL VARIANTS, Genetic association, RISK LOCUS, CONSORTIUM, medicine.disease, ENHANCERS, 030104 developmental biology, Risk factors, Imputation (genetics), Chromosomes, Human, Pair 17, Genome-Wide Association Study
Abstract: Genome-wide association studies have found SNPs at 17q22 to be associated with breast cancer risk. To identify potential causal variants related to breast cancer risk, we performed a high resolution fine-mapping analysis that involved genotyping 517 SNPs using a custom Illumina iSelect array (iCOGS) followed by imputation of genotypes for 3,134 SNPs in more than 89,000 participants of European ancestry from the Breast Cancer Association Consortium (BCAC). We identified 28 highly correlated common variants, in a 53 Kb region spanning two introns of the STXBP4 gene, that are strong candidates for driving breast cancer risk (lead SNP rs2787486 (OR = 0.92; CI 0.90–0.94; P = 8.96 × 10−15)) and are correlated with two previously reported risk-associated variants at this locus, SNPs rs6504950 (OR = 0.94, P = 2.04 × 10−09, r2 = 0.73 with lead SNP) and rs1156287 (OR = 0.93, P = 3.41 × 10−11, r2 = 0.83 with lead SNP). Analyses indicate only one causal SNP in the region and several enhancer elements targeting STXBP4 are located within the 53 kb association signal. Expression studies in breast tumor tissues found SNP rs2787486 to be associated with increased STXBP4 expression, suggesting this may be a target gene of this locus., published version, peerReviewed
Published: 2016
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27. Inheritance of deleterious mutations at both BRCA1 and BRCA2 in an international sample of 32,295 women

Author: Kenneth Offit, D. Gareth Evans, Dominique Stoppa-Lyonnet, Edith Olah, Nadine Tung, Andrew K. Godwin, Irene L. Andrulis, Jeffrey N. Weitzel, Eitan Friedman, Gord Glendon, Mary B. Daly, Kathleen Claes, Laima Tihomirova, Bella Kaufman, kConFab Investigators, Aleksandra Tołoczko-Grabarek, Katarzyna Jaworska-Bieniek, Fergus J. Couch, Jonathan Carter, Ute Hamann, Embrace, Emily Hallberg, Olufunmilayo I. Olopade, Niklas Loman, Claudine Isaacs, Raanan Berger, Caroline Seynaeve, Patricia A. Ganz, Trinidad Caldés, Jenny Lester, Steve Ellis, Fei Wan, Stephanie Chen, Cezary Cybulski, Saundra S. Buys, Åke Borg, Jamal Zidan, Matti A. Rookus, Javier Benitez, Csilla Szabo, Gillian Mitchell, Douglas F. Easton, Jocelyne Chiquette, Katherine L. Nathanson, Mary Beth Terry, Kristin K. Zorn, Danylo Villano, Mads Thomassen, Nandita Mitra, Mariella Tancredi, Conxi Lázaro, Hebon, Jacek Gronwald, Paolo Radice, Katarzyna Durda, Pascaline Berthet, Shan Wang-Gohrke, Orland Diez, Siranoush Manoukian, Amanda E. Toland, Ava Kwong, Barbara Wappenschmidt, Tara M. Friebel, Lenka Foretova, Beth Y. Karlan, Marco Montagna, Yael Laitman, Georgia Chenevix-Trench, Antonis C. Antoniou, Paraskevi Apostolou, Susan J. Ramus, Jacques Simard, Daniel Barrowdale, Timothy R. Rebbeck, Thomas Hansen, Jan Lubinski, Manuel R. Teixeira, Eric Hahnen, Grzegorz Sukiennicki, Christine Lasset, Sue K. Park, Christian F. Singer, Debra Frost, Elizabeth J. van Rensburg, Esther M. John, Susan L. Neuhausen, Lesley McGuffog, Dieter Niederacher, Penny Soucy, Heli Nevanlinna, Judy Garber, Norbert Arnold, Robert L. Nussbaum, Susan M. Domchek, Melissa C. Southey, Ramunas Janavicius, Mark H. Greene, Anna Jakubowska, Marc Tischkowitz, Christine Rappaport-Fuerhauser, Marion Piedmonte, Miguel de la Hoya, Soo Hwang Teo, Evgeny N. Imyanitov, Banu Arun, Hematology, Medical Oncology, Tischkowitz, Marc [0000-0002-7880-0628], Easton, Douglas [0000-0003-2444-3247], Antoniou, Antonis [0000-0001-9223-3116], Apollo - University of Cambridge Repository, Critical care, Anesthesiology, Peri-operative and Emergency medicine (CAPE), Damage and Repair in Cancer Development and Cancer Treatment (DARE), Targeted Gynaecologic Oncology (TARGON), Department of Obstetrics and Gynecology, and Clinicum
Subjects: DOUBLE HETEROZYGOSITY, 0301 basic medicine, endocrine system diseases, Genes, BRCA2, Genes, BRCA1, CANCER SUSCEPTIBILITY GENE, Loss of Heterozygosity, Estrogen receptor, medicine.disease_cause, Loss of heterozygosity, 0302 clinical medicine, Breast cancer, 3123 Gynaecology and paediatrics, Medicine and Health Sciences, Medicine, Promoter Regions, Genetic, skin and connective tissue diseases, SPORADIC BREAST-CANCER, Medicine(all), Mutation, UNKNOWN CLINICAL-SIGNIFICANCE, Exons, GERMLINE MUTATIONS, female genital diseases and pregnancy complications, transheterozygosity, 3. Good health, Phenotype, Population Surveillance, WILD-TYPE CHROMOSOME, 030220 oncology & carcinogenesis, Female, Transheterozygosity, Research Article, Heterozygote, medicine.medical_specialty, 3122 Cancers, Hereditary breast and ovarian cancer, Breast Neoplasms, DNA-SEQUENCE VARIANTS, hereditary breast and ovarian cancer, OVARIAN-CANCER, Càncer de mama, SPORADIC, 03 medical and health sciences, Germline mutation, GERMLINE, Progesterone receptor, Humans, BREAST-CANCER, Allele, neoplasms, Alleles, Germ-Line Mutation, Gynecology, MUTATIONS, business.industry, Biology and Life Sciences, medicine.disease, BRCA1, BRCA2, HETEROGENIC LOSS, 030104 developmental biology, FANCONI-ANEMIA, business, Ovarian cancer
Abstract: BACKGROUND: Most BRCA1 or BRCA2 mutation carriers have inherited a single (heterozygous) mutation. Transheterozygotes (TH) who have inherited deleterious mutations in both BRCA1 and BRCA2 are rare, and the consequences of transheterozygosity are poorly understood. METHODS: From 32,295 female BRCA1/2 mutation carriers, we identified 93 TH (0.3 %). 'Cases' were defined as TH, and 'controls' were single mutations at BRCA1 (SH1) or BRCA2 (SH2). Matched SH1 'controls' carried a BRCA1 mutation found in the TH 'case'. Matched SH2 'controls' carried a BRCA2 mutation found in the TH 'case'. After matching the TH carriers with SH1 or SH2, 91 TH were matched to 9316 SH1, and 89 TH were matched to 3370 SH2. RESULTS: The majority of TH (45.2 %) involved the three common Jewish mutations. TH were more likely than SH1 and SH2 women to have been ever diagnosed with breast cancer (BC; p = 0.002). TH were more likely to be diagnosed with ovarian cancer (OC) than SH2 (p = 0.017), but not SH1. Age at BC diagnosis was the same in TH vs. SH1 (p = 0.231), but was on average 4.5 years younger in TH than in SH2 (p, published_or_final_version
Published: 2016
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28. A comprehensive evaluation of interaction between genetic variants and use of menopausal hormone therapy on mammographic density

Author: Isabel dos-Santos-Silva, Christopher A. Haiman, Douglas F. Easton, Loic Le Marchand, Miroslav Kapuscinski, Janet E. Olson, Celine M. Vachon, Melissa C. Southey, Adam F Lee, Fergus J. Couch, Fredrick R. Schumacher, Gertraud Maskarinec, Judith S. Brand, Peter A. Fasching, Paul D.P. Pharoah, Sabine Behrens, Roger L. Milne, Robert Luben, Deborah J. Thompson, Qin Wang, Per Hall, Matthias W. Beckmann, Kamila Czene, Jingmei Li, Carmel Apicella, V. Shane Pankratz, Julia A. Knight, John L. Hopper, Anja Rudolph, Kathleen R. Brandt, Irene L. Andrulis, Christopher G. Scott, Lothar Haeberle, Emily Hallberg, Graham G. Giles, Arif B. Ekici, Manjeet K. Bolla, Kay-Tee Khaw, Jenny Chang-Claude, Ursula Eilber, Wang, Jean [0000-0002-9139-0627], Thompson, Deborah [0000-0003-1465-5799], Khaw, Kay-Tee [0000-0002-8802-2903], Luben, Robert [0000-0002-5088-6343], Pharoah, Paul [0000-0001-8494-732X], Easton, Douglas [0000-0003-2444-3247], and Apollo - University of Cambridge Repository
Subjects: Oncology, medicine.medical_specialty, Hormone Replacement Therapy, medicine.medical_treatment, Single-nucleotide polymorphism, Genome-wide association study, Breast Neoplasms, Polymorphism, Single Nucleotide, 03 medical and health sciences, 0302 clinical medicine, Breast cancer, Breast Cancer Risk Factor, Risk Factors, Medizinische Fakultät, Internal medicine, medicine, Mammography, Humans, Breast, ddc:610, Mammary Glands, Human, 030304 developmental biology, Aged, Breast Density, Gynecology, Aged, 80 and over, Medicine(all), 0303 health sciences, medicine.diagnostic_test, business.industry, Case-control study, Hormone replacement therapy (menopause), Middle Aged, medicine.disease, 3. Good health, Postmenopause, 030220 oncology & carcinogenesis, Case-Control Studies, Female, business, Tamoxifen, Research Article, medicine.drug, Genome-Wide Association Study
Abstract: Introduction Mammographic density is an established breast cancer risk factor with a strong genetic component and can be increased in women using menopausal hormone therapy (MHT). Here, we aimed to identify genetic variants that may modify the association between MHT use and mammographic density. Methods The study comprised 6,298 postmenopausal women from the Mayo Mammography Health Study and nine studies included in the Breast Cancer Association Consortium. We selected for evaluation 1327 single nucleotide polymorphisms (SNPs) showing the lowest P-values for interaction (Pint) in a meta-analysis of genome-wide gene-environment interaction studies with MHT use on risk of breast cancer, 2541 SNPs in candidate genes (AKR1C4, CYP1A1-CYP1A2, CYP1B1, ESR2, PPARG, PRL, SULT1A1-SULT1A2 and TNF) and ten SNPs (AREG-rs10034692, PRDM6-rs186749, ESR1-rs12665607, ZNF365-rs10995190, 8p11.23-rs7816345, LSP1-rs3817198, IGF1-rs703556, 12q24-rs1265507, TMEM184B-rs7289126, and SGSM3-rs17001868) associated with mammographic density in genome-wide studies. We used multiple linear regression models adjusted for potential confounders to evaluate interactions between SNPs and current use of MHT on mammographic density. Results No significant interactions were identified after adjustment for multiple testing. The strongest SNP-MHT interaction (unadjusted Pint
Published: 2015

29. Height and Breast Cancer Risk: Evidence From Prospective Studies and Mendelian Randomization

Author: S. Lindstrom, Javier Benitez, Natalia Bogdanova, Christine B. Ambrosone, Judith S. Brand, Joe Dennis, Hoda Anton-Culver, Carl Blomqvist, Katarzyna Durda, Loic Le Marchand, Hiltrud Brauch, Aida Karina Dieffenbach, Veli-Matti Kosma, Heli Nevanlinna, Caroline Seynaeve, Drakoulis Yannoukakos, Gord Glendon, Stephen Burgess, Kyriaki Michailidou, Jolanta Lissowska, Thilo Dörk, Paolo Peterlongo, Helen Tsimiklis, J Lubinski, Melissa C. Southey, Robert Winqvist, Kamila Czene, Sune F. Nielsen, Anja Rudolph, Vessela N. Kristensen, Alison M. Dunning, Catherine S. Healey, Diether Lambrechts, Christi J. van Asperen, M. Rosario Alonso, C. Stegmaier, Giuseppe Floris, Per Hall, Jaana M. Hartikainen, Chun Li, Malcolm W.R. Reed, Nuria Álvarez, Anna Jakubowska, Paul D.P. Pharoah, Sara Margolin, John L. Hopper, Barbara Perkins, Francois Bacot, Michael Jones, Jacques Simard, Katarzyna Jaworska-Bieniek, Fredrick R. Schumacher, Angela Cox, Jonine D. Figueroa, Julia A. Knight, Petra Seibold, Alan Ashworth, Arja Jukkola-Vuorinen, Arif B. Ekici, Mervi Grip, Rongxi Yang, Esther M. John, Kathleen E. Malone, Vesa Kataja, Qin Wang, Fergus J. Couch, Keith Humphreys, Katja van den Hurk, Michael J. Kerin, Anna González-Neira, Jenny Chang-Claude, Daniel Vincent, Wei Zheng, Ian Tomlinson, Madeleine M. A. Tilanus-Linthorst, Ute Hamann, Amanda E. Toland, Xiao-Ou Shu, Dieter Flesch-Janys, Volker Arndt, Graham G. Giles, Rita K. Schmutzler, Julian Peto, Craig Luccarini, Børge G. Nordestgaard, Grethe I. Grenaker Alnæs, Alice S. Whittemore, Olivia Fletcher, Guillermo Pita, Matti A. Rookus, Barbara Burwinkel, Lothar Haeberle, Hermann Brenner, John W. M. Martens, Mitul Shah, Marilie D. Gammon, Patrick Neven, Emilie Cordina-Duverger, Jose Ignacio Arias Perez, Ben Zhang, Martine Dumont, Mel Maranian, Annika Lindblom, Habibul Ahsan, Susan L. Neuhausen, Mikael Eriksson, Jingmei Li, Carmel Apicella, Frederik Marmé, Peter Kraft, Hatef Darabi, Ulrike Peters, Hans Wildiers, Arto Mannermaa, J. Margriet Collée, Pascal Guénel, Peter Devilee, M.J. Hooning, Daniel C. Tessier, Shahana Ahmed, Paolo Radice, Montserrat Garcia-Closas, Elinor J. Sawyer, Louise A. Brinton, Susan L. Slager, Bernardo Bonanni, Peter A. Fasching, Simon S. Cross, Thérèse Truong, Matthias W. Beckmann, Catriona McLean, Douglas F. Easton, Georgia Chenevix-Trench, David J. Hunter, Kristiina Aittomäki, Janet E. Olson, Henrik Flyger, Chenjie Zeng, Nick Orr, Siranoush Manoukian, Antonenkova Nn, Stig E. Bojesen, Wan-Qing Wen, Jirong Long, Nicola Miller, Brandon L. Pierce, Ryan J. Delahanty, Anthony J. Swerdlow, Brian E. Henderson, Harald Surowy, Yon-Dschun Ko, Celine M. Vachon, Daniel Herrero, Christopher A. Haiman, Sandrine Tchatchou, Florence Menegaux, Katri Pylkäs, Taru A. Muranen, Roger L. Milne, Thomas Brüning, Marjanka K. Schmidt, Manjeet K. Bolla, M. Pilar Zamora, Irene L. Andrulis, Caroline Baynes, Emily Hallberg, D. Seminara, Isabel dos-Santos-Silva, Diana Torres, Wim L. A. M. de Kort, Nichola Johnson, Public and occupational health, Clinical Genetics, Virology, Medical Oncology, Surgery, and Landsteiner Laboratory
Subjects: Oncology, Cancer Research, medicine.medical_specialty, Pathology, coronary-artery-disease, prospective cohort, Genome-wide association study, Breast Neoplasms, Article, different anatomic sites, Breast cancer, SDG 3 - Good Health and Well-being, Risk Factors, Internal medicine, common variants, Mendelian randomization, Odds Ratio, Medicine, Humans, Prospective Studies, Risk factor, Prospective cohort study, Evidence-Based Medicine, business.industry, body-fat distribution, Mendelian Randomization Analysis, multiple genetic-variants, Odds ratio, medicine.disease, susceptibility loci, Body Height, interleukin-6 receptor, adult human height, Relative risk, genome-wide association, Female, business
Abstract: Background: Epidemiological studies have linked adult height with breast cancer risk in women. However, the magnitude of the association, particularly by subtypes of breast cancer, has not been established. Furthermore, the mechanisms of the association remain unclear. Methods: We performed a meta-analysis to investigate associations between height and breast cancer risk using data from 159 prospective cohorts totaling 5 216 302 women, including 113 178 events. In a consortium with individual-level data from 46 325 case patients and 42 482 control subjects, we conducted a Mendelian randomization analysis using a genetic score that comprised 168 height-associated variants as an instrument. This association was further evaluated in a second consortium using summary statistics data from 16 003 case patients and 41 335 control subjects. Results: The pooled relative risk of breast cancer was 1.17 (95% confidence interval [CI] = 1.15 to 1.19) per 10 cm increase in height in the meta-analysis of prospective studies. In Mendelian randomization analysis, the odds ratio of breast cancer per 10 cm increase in genetically predicted height was 1.22 (95% CI = 1.13 to 1.32) in the first consortium and 1.21 (95% CI = 1.05 to 1.39) in the second consortium. The association was found in both premenopausal and postmenopausal women but restricted to hormone receptor-positive breast cancer. Analyses of height-associated variants identified eight new loci associated with breast cancer risk after adjusting for multiple comparisons, including three loci at 1q21.2, DNAJC27, and CCDC91 at genome-wide significance level P < 5 × 10-8. Conclusions: Our study provides strong evidence that adult height is a risk factor for breast cancer in women and certain genetic factors and biological pathways affecting adult height have an important role in the etiology of breast cancer.
Published: 2015
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30. Associations Between Cancer Predisposition Testing Panel Genes and Breast Cancer

Author: Abigail Thomas, Bing Jian Feng, Emily Hallberg, Chunling Hu, Tina Pesaran, Robert Huether, Fergus J. Couch, Rachel McFarland, Holly LaDuca, Raymond Moore, Jill S. Dolinsky, David E. Goldgar, Hermela Shimelis, Steven N. Hart, Jie Na, Eric C. Polley, Jenna Lilyquist, and Elizabeth C. Chao
Subjects: 0301 basic medicine, Oncology, Cancer Research, Cell Cycle Proteins, Ataxia Telangiectasia Mutated Proteins, 0302 clinical medicine, Risk Factors, Breast, skin and connective tissue diseases, Mismatch Repair Endonuclease PMS2, Ovarian Neoplasms, MRE11 Homologue Protein, Neurofibromin 1, medicine.diagnostic_test, Nuclear Proteins, Middle Aged, Fanconi Anemia Complementation Group Proteins, Acid Anhydride Hydrolases, DNA-Binding Proteins, MutS Homolog 2 Protein, Phenotype, 030220 oncology & carcinogenesis, Population study, Female, Fanconi Anemia Complementation Group N Protein, MutL Protein Homolog 1, RNA Helicases, Adult, medicine.medical_specialty, Ubiquitin-Protein Ligases, PALB2, Breast Neoplasms, MLH1, White People, Article, 03 medical and health sciences, Breast cancer, Internal medicine, medicine, Cyclin-Dependent Kinase Inhibitor p18, Humans, Genetic Predisposition to Disease, Genetic Testing, CHEK2, Cyclin-Dependent Kinase Inhibitor p16, Germ-Line Mutation, Genetic testing, business.industry, Tumor Suppressor Proteins, Cancer, medicine.disease, Checkpoint Kinase 2, DNA Repair Enzymes, 030104 developmental biology, Case-Control Studies, business, Ovarian cancer
Abstract: Importance Germline pathogenic variants in BRCA1 and BRCA2 predispose to an increased lifetime risk of breast cancer. However, the relevance of germline variants in other genes from multigene hereditary cancer testing panels is not well defined. Objective To determine the risks of breast cancer associated with germline variants in cancer predisposition genes. Design, Setting, and Participants A study population of 65 057 patients with breast cancer receiving germline genetic testing of cancer predisposition genes with hereditary cancer multigene panels. Associations between pathogenic variants in non- BRCA1 and non- BRCA2 predisposition genes and breast cancer risk were estimated in a case-control analysis of patients with breast cancer and Exome Aggregation Consortium reference controls. The women underwent testing between March 15, 2012, and June 30, 2016. Main Outcomes and Measures Breast cancer risk conferred by pathogenic variants in non- BRCA1 and non- BRCA2 predisposition genes. Results The mean (SD) age at diagnosis for the 65 057 women included in the analysis was 48.5 (11.1) years. The frequency of pathogenic variants in 21 panel genes identified in 41 611 consecutively tested white women with breast cancer was estimated at 10.2%. After exclusion of BRCA1 , BRCA2 , and syndromic breast cancer genes ( CDH1 , PTEN , and TP53 ), observed pathogenic variants in 5 of 16 genes were associated with high or moderately increased risks of breast cancer: ATM (OR, 2.78; 95% CI, 2.22-3.62), BARD1 (OR, 2.16; 95% CI, 1.31-3.63), CHEK2 (OR, 1.48; 95% CI, 1.31-1.67), PALB2 (OR, 7.46; 95% CI, 5.12-11.19), and RAD51D (OR, 3.07; 95% CI, 1.21-7.88). Conversely, variants in the BRIP1 and RAD51C ovarian cancer risk genes; the MRE11A , RAD50 , and NBN MRN complex genes; the MLH1 and PMS2 mismatch repair genes; and NF1 were not associated with increased risks of breast cancer. Conclusions and Relevance This study establishes several panel genes as high- and moderate-risk breast cancer genes and provides estimates of breast cancer risk associated with pathogenic variants in these genes among individuals qualifying for clinical genetic testing.
Published: 2017
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31. Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation

Author: Suleeporn Sangrajrang, James McKay, Jirong Long, Gord Glendon, Qi Guo, Malcolm W.R. Reed, Yon Dschun Koto, Sara Margolin, Francois Bacot, Julian Peto, Shaik Ahmad Buhari, Fredrick R. Schumacher, Jose Ignacio Arias Perez, Børge G. Nordestgaard, Kamila Czene, Barbara Burwinkel, Mikael Eriksson, Lorna Gibson, Mitul Shah, Matthias W. Beckmann, Shahana Ahmed, Anthony J. Swerdlow, Frederik Marmé, Pascal Guénel, Hidemi Ito, Mark S. Goldberg, Laura J. van't Veer, John W.M. Martens, Wei Zheng, John L. Hopper, Susanne Kaufmann, Carlos Caldas, Jonathan Beesley, Paolo Peterlongo, Ji Yeob Choi, Daniel O. Stram, Sarah Stewart-Brown, Elinor J. Sawyer, Craig Luccarini, Anja Rudolph, Qin Wang, Javier Benitez, Marie Sanchez, Daniel Herrero, Catherine S. Healey, Arto Mannermaa, Daniel C. Tessier, Paolo Radice, David Van Den Berg, Jacques Simard, Hoda Anton-Culver, Stephen J. Chanock, Christopher A. Haiman, Ines de Santiago, Minouk J. Schoemaker, Irene L. Andrulis, Veli-Matti Kosma, Isabel dos-Santos-Silva, Caroline Baynes, Douglas F. Easton, Stacey L. Edwards, Florence Menegaux, Hatef Darabi, Kyriaki Michailidou, Anna H. Wu, Carolien H.M. van Deurzen, Annegien Broeks, Paul Brennan, Sonja Helbig, Melissa C. Southey, Daniel Klevebring, Loic Le Marchand, Katri Pylkäs, J. Margriet Collée, Ed Dicks, Robert A.E.M. Tollenaar, Henrik Flyger, Jenny Chang-Claude, Annika Lindblom, Christine B. Ambrosone, Lothar Haeberle, Janet E. Olson, Sune F. Nielsen, Robert Winqvist, M. Pilar Zamora, Emily Hallberg, Vessela N. Kristensen, Hermann Brenner, Diana Torres, Valerie Gaborieau, Keitaro Matsuo, Yu-Tang Gao, Yik Ying Teo, Anna Jakubowska, Paul D.P. Pharoah, Patrick Neven, Vesa Kataja, Fergus J. Couch, Robert Luben, Ute Hamann, Katarzyna Jaworska-Bieniek, Dylan M. Glubb, Nick Orr, Christi J. van Asperen, Sara Volorio, Tien Yin Wong, Keith Humphreys, Jianjun Liu, Helen Tsimiklis, Thilo Dörk, Jaana M. Hartikainen, Guillermo Pita, Daniel Vincent, Roger L. Milne, M. Rosario Alonso, Nuria Álvarez, Chiu-Chen Tseng, Daehee Kang, Martine Dumont, Richard Cowper-Sal-lari, Mathieu Lupien, Anna González-Neira, Ian Tomlinson, Thérèse Truong, Amanda E. Toland, Xiao-Ou Shu, Brian E. Henderson, Miroslav Kapuscinski, Hui Miao, Angela Cox, Caroline Seynaeve, Stig E. Bojesen, Jason S. Carroll, Nicola Miller, Marjanka K. Schmidt, Taru A. Muranen, Celine M. Vachon, Manjeet K. Bolla, Hans Wildiers, Carl Blomqvist, Maartje J. Hooning, Sandrine Tchatchou, Maya Ghoussaini, Cheng Har Yip, Artitaya Lophatananon, Graham G. Giles, Penny Webb, Yasushi Yatabe, Aida Karina Dieffenbach, Mikael Hartman, Volker Arndt, Simon S. Cross, Per Hall, Soo Hwang Teo, Arif B. Ekici, Joe Dennis, Heli Nevanlinna, Arja Jukkola-Vuorinen, Wei Lu, Peter A. Fasching, Jonine D. Figueroa, Julia A. Knight, Petra Seibold, Jolanta Lissowska, Kinjal Desai, Alan Ashworth, Jan Lubinski, Primitiva Menéndez, Pei Ei Wu, Natalia Bogdanova, Kristine M. Hillman, Juliet D. French, Andreas Schneeweiss, Drakoulis Yannoukakos, Montserrat Garcia-Closas, Catriona McLean, Georgia Chenevix-Trench, Pornthep Siriwanarangsan, Thomas Brüning, Kristiina Aittomäki, Silje Nord, Jyh Cherng Yu, Hiltrud Brauch, Peter Devilee, Anne Lise Børresen-Dale, Susan L. Slager, Melissa A. Brown, Qiuyin Cai, Hiroji Iwata, Diether Lambrechts, Bernardo Bonanni, Katarzyna Durda, Emiel J. Th. Rutgers, Grethe I. Grenaker Alnæs, Anna de Fazio, Siddhartha Kar, Mel Maranian, Susan L. Neuhausen, Judith E. Brown, Christof Sohn, Sue K. Park, Christa Stegmaier, Shou Tung Chen, Dong-Young Noh, Bernard Thienpont, Alison M. Dunning, Kenneth Muir, Daphne S.C. Lee, Michael J. Kerin, Dieter Flesch-Janys, Jingmei Li, Chen-Yang Shen, Clinical Genetics, Obstetrics & Gynecology, Medical Oncology, Pathology, Cardiothoracic Surgery, International Institute of Social Studies, Ghoussaini, Maya [0000-0002-2415-2143], Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Dicks, Ed [0000-0002-0617-0401], Luben, Robert [0000-0002-5088-6343], Carroll, Jason [0000-0003-3643-0080], Caldas, Carlos [0000-0003-3547-1489], Pharoah, Paul [0000-0001-8494-732X], Easton, Douglas [0000-0003-2444-3247], Dunning, Alison [0000-0001-6651-7166], and Apollo - University of Cambridge Repository
Subjects: General Physics and Astronomy, Genome-wide association study, in-vivo, Genotype, phase, cyclin d1 expression, Promoter Regions, Genetic, CYCLIN D1 EXPRESSION, IN-VIVO, Genetics, Multidisciplinary, FACTOR-BINDING PROTEIN-5, foxa1, ASSOCIATION, Chromatin, 3. Good health, Multidisciplinary Sciences, Chromosomes, Human, Pair 2, functional variants, MCF-7 Cells, Science & Technology - Other Topics, GROWTH, Female, Hepatocyte Nuclear Factor 3-alpha, growth, PHASE, Breast Neoplasms, Locus (genetics), Single-nucleotide polymorphism, Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Breast cancer, SDG 3 - Good Health and Well-being, Cell Line, Tumor, medicine, Humans, SNP, Genetic Predisposition to Disease, RNA, Messenger, FUNCTIONAL VARIANTS, Gene, Science & Technology, association, Correction, General Chemistry, medicine.disease, CELLS, factor-binding protein-5, cells, FOXA1, Insulin-Like Growth Factor Binding Protein 5
Abstract: GWAS have identified a breast cancer susceptibility locus on 2q35. Here we report the fine mapping of this locus using data from 101,943 subjects from 50 case-control studies. We genotype 276 SNPs using the 'iCOGS' genotyping array and impute genotypes for a further 1,284 using 1000 Genomes Project data. All but two, strongly correlated SNPs (rs4442975 G/T and rs6721996 G/A) are excluded as candidate causal variants at odds against >100:1. The best functional candidate, rs4442975, is associated with oestrogen receptor positive (ER+) disease with an odds ratio (OR) in Europeans of 0.85 (95% confidence interval=0.84-0.87; P=1.7 × 10(-43)) per t-allele. This SNP flanks a transcriptional enhancer that physically interacts with the promoter of IGFBP5 (encoding insulin-like growth factor-binding protein 5) and displays allele-specific gene expression, FOXA1 binding and chromatin looping. Evidence suggests that the g-allele confers increased breast cancer susceptibility through relative downregulation of IGFBP5, a gene with known roles in breast cell biology. ispartof: Nature communications vol:5 pages:4999- ispartof: location:England status: published
Published: 2014

32. Abstract 810: The CARRIERS consortium: Establishing refined breast cancer risk estimates in known predisposition genes

Author: Raymond Moore, Susan M. Domchek, Emily Hallberg, Peter Kraft, Katherine L. Nathanson, Chunling Hu, David E. Goldgar, Jenna Lilyquist, Jeffrey N. Weitzel, Rohan Gnanaolivu, Steven N. Hart, and Fergus J. Couch
Subjects: Genetics, Oncology, Cancer Research, medicine.medical_specialty, education.field_of_study, business.industry, Population, Cancer, medicine.disease, Penetrance, Breast cancer, Internal medicine, Mutation screening, Medicine, Clinical significance, Family history, business, education, Gene
Abstract: Breast cancer is the most common type of cancer, and has a strong heritable component, with approximately 15 percent of new cases having family history of breast cancer. Genetic panel testing for patients with a family history of breast cancer has become a popular clinical resource. However, the risk of breast cancer associated with inactivating mutations in the predisposition genes is largely undefined, creating critical limitations in the interpretations of the results from panel testing and subsequent medical management. The Cancer Risk Estimates Related to Susceptibility Genes (CARRIERS) consortium was established to determine the risk of cancers associated with truncating mutations in the known predisposition genes and to extend these studies to the clinical classification of variants of uncertain significance (VUS) in the relevant genes. CARRIERS involves screening of approximately 30,000 population-based breast cancer cases and 30,000 study matched controls for mutations in 28 established or proposed breast cancer predisposition genes. Population-based risks for breast cancer associated with mutations in each gene will be estimated. In parallel, 10,000 breast cancer cases from moderate and high-risk breast cancer families will be similarly screened for mutations and the penetrance of the mutations in high-risk families will be estimated. Furthermore, VUS identified by mutation screening will be characterized by functional and family-based studies and models for classification of the clinical relevance of VUS in each gene will be developed. These data are expected to lead to improvements in cancer risk assessment and improved management of patients found to carry mutations or VUS in breast cancer predisposition. Citation Format: Jenna Lilyquist, Peter Kraft, Steven N. Hart, Emily J. Hallberg, Chunling Hu, Raymond Moore, Rohan Gnanaolivu, Susan M. Domchek, Jeffrey N. Weitzel, Katherine L. Nathanson, David E. Goldgar, Fergus J. Couch. The CARRIERS consortium: Establishing refined breast cancer risk estimates in known predisposition genes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 810.
Published: 2016
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33. Abstract 2597: Breast and ovarian cancer risks associated with cancer predisposition gene mutations identified by multigene panel testing

Author: David E. Goldgar, Emily Hallberg, Fergus J. Couch, Huong Meeks, Raymond Moore, Elizabeth C. Chao, Steven N. Hart, Holly LaDuca, Jill S. Dolinsky, and Robert Huether
Subjects: Cancer Research, business.industry, PALB2, Cancer, medicine.disease, MLH1, MSH6, Breast cancer, Oncology, MSH2, medicine, Cancer research, Ovarian cancer, business, CHEK2
Abstract: Multigene panel testing (MGPT) for hereditary cancer is increasing in popularity in the USA. Many panels include genes identified as hereditary breast and/or ovarian cancer (HBOC) genes despite limited data regarding the precise cancer risks associated with mutations in these genes. Here we report on results from BreastNext and OvaNext panel testing of 20 genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, TP53) in a cohort of 15,083 individuals. The majority of individuals were from high-risk breast and/or ovarian (Br/Ov) cancer families, with 92.4% of all probands meeting National Comprehensive Cancer Network HBOC testing criteria. Pathogenic mutations were identified in 9.4% of the overall cohort. To estimate gene-specific breast and ovarian cancer risks, case-control analyses were performed comparing the frequencies of pathogenic mutations from Caucasian breast or ovarian cancer cases from BreastNext and OvaNext with frequencies from Caucasian, non-Finnish, non-TCGA controls from the Exome Aggregation Consortium (ExAC) database. Mutations in the well studied ATM and CHEK2 genes were associated with moderate risks (OR>2) of breast cancer and mutations in PALB2 were associated with high-risks (OR>5) of breast cancer, consistent with previous reports. In addition, the study suggested that pathogenic mutations in MSH6, RAD51D, CDH1, and NF1 are associated with moderate to high risks of breast cancer. In contrast, RAD51C, RAD51D, and BRIP1 mutations were associated with high risks of ovarian cancer, PALB2 mutations were associated with moderate risks, but ATM and CHEK2 mutations were not associated with increased ovarian cancer risk. In addition, modeling of missense mutations in the predisposition genes using in silico prediction algorithms suggested that missense mutations in CDH1, CHEK2, MSH2, and MSH6 are associated with moderate risks of breast cancer and missense mutations in RAD51C increase risks of ovarian cancer. This large breast and ovarian cancer case-control analysis provides useful data for many predisposition genes previously lacking risk estimates, and should prove useful for clinical risk management of patients after clinical panel testing. Citation Format: Fergus J. Couch, David E. Goldgar, Steven N. Hart, Emily Hallberg, Raymond Moore, Huong Meeks, Robert Huether, Holly LaDuca, Elizabeth Chao, Jill Dolinsky. Breast and ovarian cancer risks associated with cancer predisposition gene mutations identified by multigene panel testing. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2597.
Published: 2016
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34. Risks of triple negative breast cancer associated with cancer predisposition gene mutations

Author: Raymond Moore, Jill S. Dolinsky, Holly LaDuca, Fergus J. Couch, Margaret Akinhanmi, Huong Meeks, David E. Goldgar, Elizabeth C. Chao, Robert Huether, Hermela Shimelis, Steven N. Hart, Chunling Hu, and Emily Hallberg
Subjects: Oncology, Cancer Research, medicine.medical_specialty, Cancer predisposition, business.industry, Cancer, Gene mutation, medicine.disease, Breast cancer, Internal medicine, Cohort, medicine, skin and connective tissue diseases, Ovarian cancer, business, Gene, Triple-negative breast cancer
Abstract: 1513Background: Multigene panel testing for hereditary cancer includes genes identified as hereditary breast and/or ovarian cancer (HBOC) genes despite limited data regarding the precise cancer risks associated with mutations in these genes. Here we report on risks of breast cancer and separately risks of triple negative breast cancer associated with mutations in 20 predisposition genes. Methods: A cohort of 10,091 individuals with breast cancer, including 2,400 with triple negative breast cancer, were tested for mutations with the BreastNext and OvaNext clinical genetic testing panels. A further 2,100 individuals with triple negative breast cancer were tested for the same genes by custom capture-based sequencing. Case-control analyses were performed comparing the frequencies of pathogenic mutations from Caucasian breast cancer cases with frequencies from Caucasian study matched controls, and Caucasian, non-Finnish, non-TCGA controls from the ExAC database. Results: Pathogenic mutations were identified in...
Published: 2016
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35. Novel H1N1 influenza hospitalizations: Minneapolis-St. Paul metropolitan area, 2008-2009

Author: Laura, Fleege, Emily, Hallberg, Craig, Morin, Richard, Danila, and Ruth, Lynfield
Subjects: Adult, Male, Adolescent, Urban Population, Incidence, Minnesota, Infant, Middle Aged, Hospitalization, Young Adult, Cross-Sectional Studies, Influenza A Virus, H1N1 Subtype, Pregnancy, Child, Preschool, Population Surveillance, Influenza, Human, Humans, Female, Child, Aged
Abstract: The influenza season of 2008-2009 will be remembered for the initial wave of novel influenza A (nH1N1) that was noted in the spring. This strain of influenza rapidly spread throughout the United States and Minnesota. Notable features in Minnesota include a higher incidence rate among children, a higher proportion of patients who also had asthma, and a higher incidence rate of pneumonia at discharge among hospitalized nH1N1 cases compared with seasonal influenza A cases.
Published: 2010

36. Abstract 4685: Characterization of variants of uncertain significance (VUS) in breast and ovarian cancer predisposition genes

Author: Hermela Shimelis, Emily Hallberg, Edwin S. Iversen, Chunling Hu, Gary Bruce Lipton, Fergus J. Couch, Noralane M. Lindor, and Andreas S. Schroeder
Subjects: Genetics, Oncology, Cancer Research, medicine.medical_specialty, Mutation, medicine.diagnostic_test, PALB2, In silico, Cancer, Biology, medicine.disease, medicine.disease_cause, Homology directed repair, Internal medicine, medicine, Missense mutation, RAD51C, Genetic testing
Abstract: Panel-based germline genetic testing of established breast and ovarian cancer predisposition genes is widely used in high-risk clinics to inform on risks of breast and ovarian cancer. While most protein truncating mutations identified in predisposition genes are associated with moderate to high risks of these cancers, variants of uncertain significance (VUS), in the form of missense and intronic variants, have an undefined relevance to cancer. Many hundreds of VUS in BRCA1 and BRCA2 identified by clinical genetic testing over the last 20 years still have uncertain clinical relevance. In addition, VUS in other known predisposition genes are being identified by current panel-testing in up to 10% of individuals without BRCA1 or BRCA2 mutations. These VUS cause problems in cancer risk estimation and clinical management of patients undergoing clinical genetic testing. In an effort to evaluate the clinical significance of VUS in cancer predisposition genes we have developed functional assays that characterize the impact of the variants on the functions of the proteins encoded by the predisposition genes. In particular, a homology directed repair reporter assay providing a quantitative measure of homologous recombination repair of DNA double strand breaks has been developed for characterization of VUS in homologous recombination associated genes. When applied to 13 known pathogenic and 30 known neutral variants from the DNA binding domain of BRCA2, this assay exhibits 100% specificity and 100% sensitivity. Based on these results a model estimating the probability of pathogenicity of each BRCA2 VUS was developed. The HDR assay and probability model has now been applied to 230 BRCA2 VUS identified through genetic testing. Here we identify 80 BRCA2 variants that are deficient in HDR activity. We further combined these results with prior probabilities of pathogenicity derived from the sequence based Align GVGD in silico prediction model to estimate the posterior probability of pathogenicity for each VUS. Our results suggest that in the absence of family based segregation information, results from the HDR functional assay and in silico prediction models can be used to predict the pathogenicity of BRCA2 VUS. The assay has also been used to characterize VUS in the PALB2 and RAD51C predisposition genes, leading to identification of a subset of missense variants that are deficient in HDR repair activity and may be associated with increased risk of breast and ovarian cancer. These results will prove useful for improved risk assessment of carriers of these BRCA2, PALB2 and RAD51C variants and their family members and for validation of other approaches to mutation classification. Citation Format: Fergus J. Couch, Hermela Shimelis, Andreas Schroeder, Chunling Hu, Emily Hallberg, Gary Lipton, Edwin Iversen, Noralane M. Lindor. Characterization of variants of uncertain significance (VUS) in breast and ovarian cancer predisposition genes. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4685. doi:10.1158/1538-7445.AM2015-4685
Published: 2015
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37. Real-world self-reported adherence to endocrine therapy in a large longitudinal cohort of breast cancer patients

Author: Emily Hallberg, Curtis Olswold, Fergus J. Couch, Sithara Vivek, Patricia J. Marshman, Janet E. Olson, Matthew P. Goetz, Susan L. Slager, Raina M. Ferzoco, Kathryn J. Ruddy, Jamie Hinton, and Jodie A. Cogswell
Subjects: Oncology, Cancer Research, medicine.medical_specialty, business.industry, Endocrine therapy, Estrogen receptor, medicine.disease, Poor adherence, Breast cancer, Internal medicine, medicine, Endocrine system, Longitudinal cohort, business
Abstract: e20630 Background: Endocrine therapy plays an important role in the treatment of estrogen receptor (ER) -positive breast cancer. Multiple prior studies have shown poor adherence to oral endocrine t...
Published: 2015
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38. Abstract 274: Occupational exposure to agricultural pesticides and CLL risk

Author: Kari G. Rabe, Susan L. Slager, Tait D. Shanafelt, Mark Liebow, Cristine Allmer, Emily Hallberg, Timothy G. Call, Sara J. Achenbach, Neil E. Kay, and James R. Cerhan
Subjects: Cancer Research, business.industry, Chronic lymphocytic leukemia, Cancer, Odds ratio, Pesticide, Agricultural pesticides, medicine.disease, Logistic regression, Confidence interval, Toxicology, Oncology, hemic and lymphatic diseases, Environmental health, medicine, Risk factor, business
Abstract: Background Previous literature regarding the association between occupational exposure to agricultural pesticides and non-Hodgkin lymphoma (NHL) risk has been inconsistent, particularly when looking at specific lymphoma subtypes. Most recently, a large European case-control study showed an elevated risk of chronic lymphocytic leukemia (CLL) among those ever exposed to inorganic and organic pesticides with the strongest association among those exposed to organophosphates. However, when restricting the analysis to subjects with high confidence of exposure, these associations were attenuated (Cocco P., 2013). We used case-control data from the Mayo Clinic to evaluate whether there is an increased risk of CLL among individuals with known occupational exposure to agricultural pesticides. Methods We evaluated pesticide exposure and CLL risk in a clinic-based study of newly diagnosed CLL cases and frequency-matched controls enrolled at the Mayo Clinic from 2002-2012. 200 CLL cases and 474 controls returned a detailed farming and pesticide exposure questionnaire that was modeled after the Agricultural Health Study, where exposure was based on pesticide-specific application. Unconditional logistic regression, adjusted for age and sex, was used to estimate odds ratios (ORs) and 95% confidence intervals (CI). We evaluated the effect of each pesticide individually, by chemical class of pesticides, and by an aggregate of multiple pesticide exposure on CLL risk. Results Among those participants with detailed farming data, the mean age of CLL diagnosis was 66 years and 76% were male; for controls, the mean age at enrollment was 65 years and 66% were male. Risk of CLL was mildly elevated, but not significant, amongst those with application of any pesticide (OR 1.39; 95% C.I. 0.92-2.10). When broken down by chemical class, risk of CLL was also mildly elevated, but not significant, for application of organophosphates and carbamates (OR 1.21; 95% CI 0.84-1.73; OR 1.21; 95% 0.85-1.73, respectively). Organochlorines, phenoxy compounds, pyrethriods and triazines showed no evidence of an elevated risk, nor did we see evidence of a trend that CLL risk increases with number of pesticides applied. Discussion Our preliminary results provide inconclusive support for the role of pesticide exposure as a possible risk factor for CLL. However our sample size was small. Additional data will be incorporated, including confidence of exposure measures, as well as other modifying factors, to further evaluate these results. Citation Format: Emily J. Hallberg, Sara J. Achenbach, Kari G. Rabe, Timothy G. Call, Cristine Allmer, Tait D. Shanafelt, Mark Liebow, Neil E. Kay, James R. Cerhan, Susan L. Slager. Occupational exposure to agricultural pesticides and CLL risk. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 274. doi:10.1158/1538-7445.AM2014-274
Published: 2014
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39. Abstract 2287: Incidence of chronic lymphocytic leukemia and monoclonal B-cell lymphocytosis in Olmsted county, 2000-2010: impact of the 2008 International Workshop on CLL Guidelines

Author: Clive S. Zent, James R. Cerhan, Neil E. Kay, Wei Ding, Celine M. Vachon, Sara J. Achenbach, Susan L. Slager, Tait D. Shanafelt, Timothy G. Call, Emily Hallberg, Kari G. Rabe, Aaron D. Norman, and Curtis A. Hanson
Subjects: Oncology, Cancer Research, medicine.medical_specialty, Lymphocytosis, Proportional hazards model, business.industry, Chronic lymphocytic leukemia, Incidence (epidemiology), medicine.disease, Leukemia, Immunophenotyping, Rochester Epidemiology Project, hemic and lymphatic diseases, Internal medicine, Immunology, medicine, Monoclonal B-cell lymphocytosis, medicine.symptom, business
Abstract: Background: Chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL) is the most common adult leukemia in the United States. Prior studies in Olmsted County, Minnesota, showed a CLL age and sex adjusted incidence rate of 6.6 per 100,000 during 1985-89. Subsequently, the definition of CLL is now based on the 2008 International Workshop on CLL (IWCLL) Guidelines. Individuals having a CLL immunophenotype by flow cytometry are classified as CLL if the absolute B-cell count (ABC) is >5 x 109/L or classified as monoclonal B-cell lymphocytosis (MBL) if ABC is Methods Using diagnostic indexes available through the Rochester Epidemiology Project and the Mayo CLL database, we identified all CLL and clinically identified MBL cases from 2000-2010. Incidence rates and demographics were compared between the older National Cancer Institute-Working Groups 1996 guidelines (NCI-WG 96) defined as absolute lymphocyte count (ALC)> 5 x 109/L and the IWCLL 2008 guidelines defined as ABC > 5 x 109/L. Incidence rates were age and sex adjusted using the 2010 US white population. Time to treatment (TTT) survival analyses was from time of diagnosis to date of first treatment or last follow-up and Cox regression analysis was used. Results Using the NCI-WG 96 classification, there were 8 MBL cases and 115 CLLs in whom 61% were Rai stage 0, 34% were Rai stage 1-2, and 5% were Rai stage 3-4. Using the IWCLL 2008 classification, there were 44 MBL cases and 79 CLLs in whom 43% Rai stage 0, 49% were Rai stage 1-2 and 8% Rai stage 3-4. Median ALC at diagnosis was 8.1 x 109/L for CLL and 5.9 x 109/L for MBL. Median ABC count at diagnosis was 7.1 x 109/L for CLL and 2.8 x 109/L for MBL. The age and sex adjusted incidence rate (per 100,000) for CLL for 2000-2010 was 10.0 using NCI-WG 96 and 6.8 using IWCLL 2008. Rates for MBL were 0.66 using NCI-WG 96 and 3.5 using IWCLL 2008. The median TTT for CLL was 9.2 years using NCI-WG 96 and 6.5 years by IWCLL 2008. Discussion This study demonstrates that reclassification of CLL using the IWCLL 2008 guidelines decreases CLL incidence relative to the NCI-WG 96 criteria. For the first time, this population based study also establishes an incidence rate for clinically identified MBL. Approximately 50% of previously labeled Rai 0 CLL are now reclassified as MBL. Re-classification increases the percent of Rai stage 1-2 and decreases the percent of Rai 0 cases at diagnosis. Reclassification also substantially shortens the median TTT for newly diagnosed CLL cases classified by the 2008 criteria relative to the NCI-WG 96 criteria. In summary, the IWCLL 2008 reclassification has significant implications for incidence studies, staging, and prognosis of CLL and MBL. Citation Format: Aaron D. Norman, Timothy G. Call, Curtis A. Hanson, Neil E. Kay, Clive S. Zent, Wei Ding, James R. Cerhan, Sara J. Achenbach, Kari G. Rabe, Celine M. Vachon, Emily J. Hallberg, Tait D. Shanafelt, Susan L. Slager. Incidence of chronic lymphocytic leukemia and monoclonal B-cell lymphocytosis in Olmsted county, 2000-2010: impact of the 2008 International Workshop on CLL Guidelines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2287. doi:10.1158/1538-7445.AM2013-2287
Published: 2013
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40. TP53-based interaction analysis identifies cis-eQTL variants for TP53BP2, FBXO28, and FAM53A that associate with survival and treatment outcome in breast cancer

Author: Manjeet K. Bolla, Carl Blomqvist, Qin Wang, Qi Guo, Melissa C. Southey, Giuseppe Floris, Kristiina Aittomäki, Joe Dennis, Douglas F. Easton, Peter A. Fasching, Sofia Khan, Jenny Chang-Claude, Paul D.P. Pharoah, Jonathan Beesley, Rainer Fagerholm, Diether Lambrechts, Alison M. Dunning, Jianjun Liu, Fiona M. Blows, Päivi Heikkilä, Jonine D. Figueroa, Sabine Behrens, kConFab, Montserrat Garcia-Closas, Irene L. Andrulis, Bernd Holleczek, Aocs Investigators, Maral Jamshidi, Elena Provenzano, Fergus J. Couch, Jani Saarela, Ute Hamann, Michael Lush, Agnes Jager, Renske Keeman, Gord Glendon, Veli-Matti Kosma, Emily Hallberg, Annika Lindblom, Kamila Czene, Matthias W. Beckmann, John L. Hopper, H. Raza Ali, Heli Nevanlinna, Chenevix-Trench G, Maria Kabisch, Arto Mannermaa, Hermann Brenner, Maartje J. Hooning, Marjanka K. Schmidt, Per Hall, Mitul Shah, Sara Margolin, Kyriaki Michailidou, Medical Oncology, School of Medicine / Clinical Medicine, Ali, Raza [0000-0001-7587-0906], Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], Pharoah, Paul [0000-0001-8494-732X], and Apollo - University of Cambridge Repository
Subjects: Adult, 0301 basic medicine, Oncology, medicine.medical_specialty, Genotype, Anthracycline, Quantitative Trait Loci, SNP, Estrogen receptor, Breast Neoplasms, Single-nucleotide polymorphism, Gene mutation, anthracycline, Bioinformatics, Polymorphism, Single Nucleotide, survival, Young Adult, 03 medical and health sciences, breast cancer, 0302 clinical medicine, Breast cancer, SDG 3 - Good Health and Well-being, Internal medicine, medicine, Journal Article, Humans, Anthracyclines, TP53, Survival analysis, Aged, Aged, 80 and over, SKP Cullin F-Box Protein Ligases, Predictive marker, business.industry, Middle Aged, medicine.disease, Survival Analysis, 3. Good health, Treatment Outcome, 030104 developmental biology, 030220 oncology & carcinogenesis, Female, Tumor Suppressor Protein p53, Apoptosis Regulatory Proteins, business, Research Paper
Abstract: TP53 overexpression is indicative of somatic TP53 mutations and associates with aggressive tumors and poor prognosis in breast cancer. We utilized a two-stage SNP association study to detect variants associated with breast cancer survival in a TP53-dependent manner. Initially, a genome-wide study (n = 575 cases) was conducted to discover candidate SNPs for genotyping and validation in the Breast Cancer Association Consortium (BCAC). The SNPs were then tested for interaction with tumor TP53 status (n = 4,610) and anthracycline treatment (n = 17,828). For SNPs interacting with anthracycline treatment, siRNA knockdown experiments were carried out to validate candidate genes. In the test for interaction between SNP genotype and TP53 status, we identified one locus, represented by rs10916264 (p(interaction) = 3.44 × 10-5; FDR-adjusted p = 0.0011) in estrogen receptor (ER) positive cases. The rs10916264 AA genotype associated with worse survival among cases with ER-positive, TP53-positive tumors (hazard ratio [HR] 2.36, 95% confidence interval [C.I] 1.45 - 3.82). This is a cis-eQTL locus for FBXO28 and TP53BP2; expression levels of these genes were associated with patient survival specifically in ER-positive, TP53-mutated tumors. Additionally, the SNP rs798755 was associated with survival in interaction with anthracycline treatment (p(interaction) = 9.57 × 10-5, FDR-adjusted p = 0.0130). RNAi-based depletion of a predicted regulatory target gene, FAM53A, indicated that this gene can modulate doxorubicin sensitivity in breast cancer cell lines. If confirmed in independent data sets, these results may be of clinical relevance in the development of prognostic and predictive marker panels for breast cancer., published version, peerReviewed
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41. Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with prognosis of estrogen receptor-negative breast cancer after chemotherapy

Author: Chen-Yang Shen, Keun-Young Yoo, Kazuo Tajima, Georgia Chenevix-Trench, Qin Wang, William J. Tapper, Kristiina Aittomäki, Douglas F. Easton, Anne Lise Børresen-Dale, Ann Smeets, Hidemi Ito, Heli Nevanlinna, Kamila Czene, Sabine C. Linn, Soo Hwang Teo, Tom Maishman, Ursula Eilber, Robert Luben, Jolanta Lissowska, Cheng Har Yip, Keitaro Matsuo, Sue K. Park, Sandrine Tchatchou, Lothar Haeberle, Anja Rudolph, Sajjad Rafiq, Ellen L. Goode, Nur Aishah Taib, Arto Mannermaa, Keith Humphreys, Sabine Behrens, Silje Nord, Javier Benitez, Alison M. Dunning, Irene L. Andrulis, Jaana M. Hartikainen, Sandra Alexandra J van den Broek, Joe Dennis, Gord Glendon, Taru A. Muranen, Arif B. Ekici, Veli-Matti Kosma, Madeleine M.A. Tilanus-Linthorst, Annika Lindblom, Emily Hallberg, Vessela N. Kristensen, Diana Eccles, Maartje J. Hooning, Sten Cornelissen, Stephen J. Chanock, Paul P.D. Pharoah, Diana Torres, Carolien H.M. van Deurzen, Jingmei Li, Celine M. Vachon, Pei-Ei Wu, Jenny Chang-Claude, Fergus J. Couch, Hans-Ulrich Ulmer, Jieping Lei, Sigrid Hatse, Vesa Kataja, Ute Hamann, Sara Margolin, Daehee Kang, Marjanka K. Schmidt, Hans Wildiers, Lara Sucheston, Janet E. Olson, Mitul Shah, Matthias W. Beckmann, Manjeet K. Bolla, Ji Yeob Choi, Per Hall, Carl Blomqvist, Thomas Rüdiger, Gwo Fuang Ho, Jonine D. Figueroa, Julia A. Knight, Petra Seibold, Chia-Ni Hsiung, Ming-Feng Hou, Hiroji Iwata, Diether Lambrechts, Kelly-Anne Phillips, Grethe I. Grenaker Alnæs, Peter A. Fasching, Montserrat Garcia-Closas, Kirsten B. Moysich, Agnes Jager, Pharoah, Paul [0000-0001-8494-732X], Dennis, Joe [0000-0003-4591-1214], Wang, Jean [0000-0002-9139-0627], Luben, Robert [0000-0002-5088-6343], Dunning, Alison [0000-0001-6651-7166], Easton, Douglas [0000-0003-2444-3247], Apollo - University of Cambridge Repository, Medical Oncology, Clinical Genetics, Pathology, and Surgery
Subjects: Oncology, medicine.medical_treatment, Estrogen receptor, 32 Biomedical and Clinical Sciences, Genome-wide association study, Kaplan-Meier Estimate, 0302 clinical medicine, Medizinische Fakultät, Surgical oncology, Antineoplastic Combined Chemotherapy Protocols, 2.1 Biological and endogenous factors, Prospective cohort study, health care economics and organizations, Cancer, 2 Aetiology, Medicine(all), 0303 health sciences, Interleukin-12 Subunit p40, Hazard ratio, Genomics, Middle Aged, Prognosis, Tumor Burden, 3. Good health, 3204 Immunology, Treatment Outcome, Receptors, Estrogen, 030220 oncology & carcinogenesis, Female, 4.2 Evaluation of markers and technologies, Signal Transduction, Research Article, Adult, medicine.medical_specialty, Breast Neoplasms, Single-nucleotide polymorphism, Protein Serine-Threonine Kinases, Polymorphism, Single Nucleotide, Immunomodulation, 03 medical and health sciences, Breast cancer, SDG 3 - Good Health and Well-being, Internal medicine, Breast Cancer, Genetics, Biomarkers, Tumor, medicine, Humans, ddc:610, Neoplasm Staging, 030304 developmental biology, Chemotherapy, business.industry, Receptor, Transforming Growth Factor-beta Type II, 3211 Oncology and Carcinogenesis, medicine.disease, Cancer research, Neoplasm Grading, 4 Detection, screening and diagnosis, business, Receptors, Transforming Growth Factor beta
Abstract: Introduction Tumor lymphocyte infiltration is associated with clinical response to chemotherapy in estrogen receptor (ER) negative breast cancer. To identify variants in immunosuppressive pathway genes associated with prognosis after adjuvant chemotherapy for ER-negative patients, we studied stage I-III invasive breast cancer patients of European ancestry, including 9,334 ER-positive (3,151 treated with chemotherapy) and 2,334 ER-negative patients (1,499 treated with chemotherapy). Methods We pooled data from sixteen studies from the Breast Cancer Association Consortium (BCAC), and employed two independent studies for replications. Overall 3,610 single nucleotide polymorphisms (SNPs) in 133 genes were genotyped as part of the Collaborative Oncological Gene-environment Study, in which phenotype and clinical data were collected and harmonized. Multivariable Cox proportional hazard regression was used to assess genetic associations with overall survival (OS) and breast cancer-specific survival (BCSS). Heterogeneity according to chemotherapy or ER status was evaluated with the log-likelihood ratio test. Results Three independent SNPs in TGFBR2 and IL12B were associated with OS (P C) (per allele hazard ratio (HR) 1.54 (95% confidence interval (CI) 1.22 to 1.95), P = 3.08 × 10−4) was not found in ER-negative patients without chemotherapy or ER-positive patients with chemotherapy (P for interaction A) with poorer OS (HR 1.50 (95% CI 1.21 to 1.86), P = 1.81 × 10−4), and rs2853694 (A > C) with improved OS (HR 0.73 (95% CI 0.61 to 0.87), P = 3.67 × 10−4). Similar associations were observed with BCSS. Association with TGFBR2 rs1367610 but not IL12B variants replicated using BCAC Asian samples and the independent Prospective Study of Outcomes in Sporadic versus Hereditary Breast Cancer Study and yielded a combined HR of 1.57 ((95% CI 1.28 to 1.94), P = 2.05 × 10−5) without study heterogeneity. Conclusions TGFBR2 variants may have prognostic and predictive value in ER-negative breast cancer patients treated with adjuvant chemotherapy. Our findings provide further insights into the development of immunotherapeutic targets for ER-negative breast cancer.
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42. Inherited mutations in 17 breast cancer susceptibility genes among a large triple-negative breast cancer cohort unselected for family history of breast cancer.

Author: Couch FJ, Hart SN, Sharma P, Toland AE, Wang X, Miron P, Olson JE, Godwin AK, Pankratz VS, Olswold C, Slettedahl S, Hallberg E, Guidugli L, Davila JI, Beckmann MW, Janni W, Rack B, Ekici AB, Slamon DJ, Konstantopoulou I, Fostira F, Vratimos A, Fountzilas G, Pelttari LM, Tapper WJ, Durcan L, Cross SS, Pilarski R, Shapiro CL, Klemp J, Yao S, Garber J, Cox A, Brauch H, Ambrosone C, Nevanlinna H, Yannoukakos D, Slager SL, Vachon CM, Eccles DM, and Fasching PA
Subjects: Adult, Aged, Aged, 80 and over, BRCA1 Protein genetics, BRCA2 Protein genetics, Cohort Studies, DNA Mutational Analysis, Family Health, Female, Humans, Middle Aged, Ovarian Neoplasms diagnosis, Ovarian Neoplasms genetics, Triple Negative Breast Neoplasms diagnosis, Young Adult, Genetic Predisposition to Disease genetics, Genetic Testing methods, Germ-Line Mutation, Triple Negative Breast Neoplasms genetics
Abstract: Purpose: Recent advances in DNA sequencing have led to the development of breast cancer susceptibility gene panels for germline genetic testing of patients. We assessed the frequency of mutations in 17 predisposition genes, including BRCA1 and BRCA2, in a large cohort of patients with triple-negative breast cancer (TNBC) unselected for family history of breast or ovarian cancer to determine the utility of germline genetic testing for those with TNBC., Patients and Methods: Patients with TNBC (N = 1,824) unselected for family history of breast or ovarian cancer were recruited through 12 studies, and germline DNA was sequenced to identify mutations., Results: Deleterious mutations were identified in 14.6% of all patients. Of these, 11.2% had mutations in the BRCA1 (8.5%) and BRCA2 (2.7%) genes. Deleterious mutations in 15 other predisposition genes were detected in 3.7% of patients, with the majority observed in genes involved in homologous recombination, including PALB2 (1.2%) and BARD1, RAD51D, RAD51C, and BRIP1 (0.3% to 0.5%). Patients with TNBC with mutations were diagnosed at an earlier age (P < .001) and had higher-grade tumors (P = .01) than those without mutations., Conclusion: Deleterious mutations in predisposition genes are present at high frequency in patients with TNBC unselected for family history of cancer. Mutation prevalence estimates suggest that patients with TNBC, regardless of age at diagnosis or family history of cancer, should be considered for germline genetic testing of BRCA1 and BRCA2. Although mutations in other predisposition genes are observed among patients with TNBC, better cancer risk estimates are needed before these mutations are used for clinical risk assessment in relatives., (© 2014 by American Society of Clinical Oncology.)
Published: 2015
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