Association analysis identifies 65 new breast cancer risk loci (original) (raw)

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• 08 March 2018

The link to Supplementary Table 20 was corrected.

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Acknowledgements

We thank all the individuals who took part in these studies and all the researchers, clinicians, technicians and administrative staff who have enabled this work to be carried out. Genotyping of the OncoArray was principally funded from three sources: the PERSPECTIVE project, funded by the Government of Canada through Genome Canada and the Canadian Institutes of Health Research, the ‘Ministère de l’Économie, de la Science et de l’Innovation du Québec’ through Genome Québec, and the Quebec Breast Cancer Foundation; the NCI Genetic Associations and Mechanisms in Oncology (GAME-ON) initiative and Discovery, Biology and Risk of Inherited Variants in Breast Cancer (DRIVE) project (NIH Grants U19 CA148065 and X01HG007492); and Cancer Research UK (C1287/A10118 and C1287/A16563). BCAC is funded by Cancer Research UK (C1287/A16563), by the European Community’s Seventh Framework Programme under grant agreement 223175 (HEALTH-F2-2009-223175) (COGS) and by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreements 633784 (B-CAST) and 634935 (BRIDGES). Genotyping of the iCOGS array was funded by the European Union (HEALTH-F2-2009-223175), Cancer Research UK (C1287/A10710), the Canadian Institutes of Health Research for the ‘CIHR Team in Familial Risks of Breast Cancer’ program, and the Ministry of Economic Development, Innovation and Export Trade of Quebec, grant PSR-SIIRI-701. Combining of the GWAS data was supported in part by The National Institute of Health (NIH) Cancer Post-Cancer GWAS initiative grant U19 CA 148065 (DRIVE, part of the GAME-ON initiative). For a full description of funding and acknowledgments, see Supplementary Note.

Author information

Author notes

1. Lists of participants and their affiliations appear in the Supplementary Information.
2. Kyriaki Michailidou, Sara Lindström, Joe Dennis, Jonathan Beesley, Shirley Hui and Siddhartha Kar: These authors contributed equally to this work.
3. Jacques Simard, Peter Kraft and Douglas F. Easton: These authors jointly supervised this work.

Authors and Affiliations

1. Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
   Kyriaki Michailidou, Joe Dennis, Manjeet K. Bolla, Qin Wang, Andrew Lee, Jamie Allen, Antonis C. Antoniou, Paul D. P. Pharoah & Douglas F. Easton
2. Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
   Kyriaki Michailidou
3. Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA
   Sara Lindström
4. Program in Genetic Epidemiology and Statistical Genetics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
   Sara Lindström, Xia Jiang, Hilary Finucane, Rulla Tamimi, David J. Hunter & Peter Kraft
5. Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
   Jonathan Beesley, Dylan Glubb, Juliet D. French, Xiao Qing Chen, Karen McCue, Stacey L. Edwards & Georgia Chenevix-Trench
6. The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
   Shirley Hui, Asha Rostamianfar & Gary D. Bader
7. Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
   Siddhartha Kar, Jonathan Tyrer, Ed Dicks, Laura Fachal, Maya Ghoussaini, Caroline Baynes, Don M. Conroy, Patricia Harrington, Craig Luccarini, Valerie Rhenius, Mitul Shah, Paul D. P. Pharoah, Alison M. Dunning & Douglas F. Easton
8. Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Canada, Quebec
   Audrey Lemaçon, Penny Soucy, Martine Dumont, Arnaud Droit & Jacques Simard
9. Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
   Zhaoming Wang
10. Division of Cancer Epidemiology and Genetics, Cancer Genomics Research Laboratory (CGR), National Cancer Institute, Rockville, Maryland, USA
    Zhaoming Wang, Belynda Hicks, Kristine Jones & Bin Zhu
11. Division of Molecular Pathology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
    Renske Keeman, Annegien Broeks, Sten Cornelissen & Marjanka K. Schmidt
12. Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
    Ursula Eilber, Myrto Barrdahl, Sabine Behrens, Rudolf Kaaks, Anja Rudolph & Jenny Chang-Claude
13. UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
    Amy E. McCart Reed & Sunil R. Lakhani
14. Cancer Research UK Cambridge Research Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
    Jason S. Carroll
15. Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Hilary Finucane
16. Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Marcia Adams, Kimberly F. Doheny, Elizabeth Pugh & Jane Romm
17. Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
    Muriel A. Adank, Hanne Meijers-Heijboer & Quinten Waisfisz
18. Center for Cancer Epidemiology and Prevention, The University of Chicago, Chicago, Illinois, USA
    Habibul Ahsan & Ling Tong
19. Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
    Kristiina Aittomäki
20. Department of Epidemiology, University of California Irvine, Irvine, California, USA
    Hoda Anton-Culver & Argyrios Ziogas
21. N. N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
    Natalia N. Antonenkova & Natalia V. Bogdanova
22. Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
    Volker Arndt, Hermann Brenner & Katja Butterbach
23. Department of Public Health Sciences, and Cancer Research Institute, Queen’s University, Kingston, Ontario, Canada
    Kristan J. Aronson
24. Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
    Banu Arun
25. Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    Paul L. Auer & Ross Prentice
26. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
    Paul L. Auer
27. McGill University and Génome Québec Innovation Centre, Montréal, Quebec, Canada
    François Bacot, Nathalie Hamel, Daniel C. Tessier & Daniel Vincent
28. Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
    Matthias W. Beckmann, Peter A. Fasching, Lothar Haeberle, Alexander Hein, Michael P. Lux & Matthias Ruebner
29. Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
    Javier Benitez & Anna González-Neira
30. Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
    Javier Benitez
31. Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
    Marina Bermisheva & Elza Khusnutdinova
32. Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California, USA
    Leslie Bernstein & Susan L. Neuhausen
33. Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
    Carl Blomqvist
34. Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
    Natalia V. Bogdanova & Hans Christiansen
35. Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
    Natalia V. Bogdanova, Thilo Dörk, Peter Hillemanns, Tjoung-Won Park-Simon & Peter Schürmann
36. Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
    Stig E. Bojesen, Sune F. Nielsen & Børge G. Nordestgaard
37. Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
    Stig E. Bojesen, Sune F. Nielsen & Børge G. Nordestgaard
38. Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
    Stig E. Bojesen & Børge G. Nordestgaard
39. Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
    Bernardo Bonanni
40. Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
    Anne-Lise Børresen-Dale, Grethe I. Grenaker Alnæs & Vessela N. Kristensen
41. Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
    Judith S. Brand, Kamila Czene, Mikael Eriksson, Marike Gabrielson, Keith Humphreys, Jingmei Li & Per Hall
42. Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
    Hiltrud Brauch & Wing-Yee Lo
43. University of Tübingen, Tübingen, Germany
    Hiltrud Brauch & Wing-Yee Lo
44. German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
    Hiltrud Brauch & Hermann Brenner
45. International Agency for Research on Cancer, Lyon, France
    Paul Brennan, Valerie Gaborieau & James McKay
46. Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
    Hermann Brenner
47. Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
    Louise Brinton, Jonine Figueroa, Robert N. Hoover, Xiaohong R. Yang, Montserrat García-Closas & Stephen J. Chanock
48. Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
    Per Broberg, Carolina Ellberg, Ute Krüger & Håkan Olsson
49. Department of Oncology and Metabolism, Sheffield Institute for Nucleic Acids (SInFoNiA), University of Sheffield, Sheffield, UK
    Ian W. Brock & Angela Cox
50. Genome Sciences Centre, BC Cancer Agency, Vancouver, British, Columbia, Canada
    Angela Brooks-Wilson
51. Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British, Columbia, Canada
    Angela Brooks-Wilson
52. Department of Gynecology and Obstetrics, University of Tübingen, Tübingen, Germany
    Sara Y. Brucker
53. Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum, Bochum, Germany
    Thomas Brüning
54. Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
    Barbara Burwinkel, Andreas Schneeweiss & Harald Surowy
55. Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), Heidelberg, Germany
    Barbara Burwinkel & Harald Surowy
56. Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
    Qiuyin Cai, Hui Cai, Jirong Long, Martha J. Shrubsole, Xiao-Ou Shu & Wei Zheng
57. Medical Oncology Department, Hospital Clínico San Carlos, IdISSC (Centro Investigacion Biomedica en Red), CIBERONC (Instituto de Investigación Sanitaria San Carlos), Madrid, Spain
    Trinidad Caldés, José A. García-Sáenz & Atocha Romero
58. Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
    Federico Canzian
59. Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago De, Compostela, Spain
    Angel Carracedo & Manuela Gago-Dominguez
60. Centro de Investigación en Red de Enfermedades Raras (CIBERER) y Centro Nacional de Genotipado (CEGEN-PRB2), Universidad de Santiago de Compostela, Santiago De, Compostela, Spain
    Angel Carracedo
61. Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
    Brian D. Carter, Susan M. Gapstur & Mia M. Gaudet
62. Oncology and Genetics Unit, Instituto de Investigacion Biomedica (IBI) Orense-Pontevedra-Vigo, Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
    Jose E. Castelao
63. Hong Kong Hereditary Breast Cancer Family Registry, Happy Valley, Hong Kong
    Tsun L. Chan, Ava Kwong & Edmond S. K. Ma
64. Department of Pathology, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong
    Tsun L. Chan, Dona N. Ho & Edmond S. K. Ma
65. Division of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
    Ting-Yuan David Cheng
66. Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
    Kee Seng Chia, Mikael Hartman & Hui Miao
67. Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
    Ji-Yeob Choi, Daehee Kang & Sue K. Park
68. Cancer Research Institute, Seoul National University, Seoul, South Korea
    Ji-Yeob Choi, Daehee Kang & Sue K. Park
69. Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
    Christine L. Clarke
70. Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
    Margriet Collée & Ans M. W. van den Ouweland
71. Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
    Emilie Cordina-Duverger, Pascal Guénel & Thérèse Truong
72. Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
    David G. Cox
73. INSERM U1052, Cancer Research Center of Lyon, Lyon, France
    David G. Cox
74. Department of Neuroscience, Academic Unit of Pathology, University of Sheffield, Sheffield, UK
    Simon S. Cross
75. Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
    Julie M. Cunningham, Jeffery Meyer, Jason Vollenweider & Fergus J. Couch
76. Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    Mary B. Daly
77. Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
    Peter Devilee
78. Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Peter Devilee
79. Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
    Isabel dos-Santos-Silva & Julian Peto
80. Southampton Clinical Trials Unit, Faculty of Medicine, University of Southampton, Southampton, UK
    Lorraine Durcan & Tom Maishman
81. Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
    Lorraine Durcan, Diana M. Eccles & Tom Maishman
82. Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
    Miriam Dwek & Nadege Presneau
83. Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
    Arif B. Ekici
84. Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
    A. Heather Eliassen & Rulla Tamimi
85. Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
    A. Heather Eliassen, JoAnn E. Manson, Rulla Tamimi, Walter Willett, David J. Hunter & Peter Kraft
86. Department of Clinical Sciences, Oncology and Pathology, Lund University, Lund, Sweden
    Carolina Ellberg
87. Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
    Mingajeva Elvira, Elza Khusnutdinova & Darya Prokofyeva
88. Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
    Christoph Engel
89. LIFE—Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
    Christoph Engel
90. Department of Medicine Division of Hematology and Oncology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
    Peter A. Fasching
91. Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
    Jonine Figueroa
92. Institute for Medical Biometrics and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
    Dieter Flesch-Janys
93. Department of Cancer Epidemiology, Clinical Cancer Registry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
    Dieter Flesch-Janys & Kathrin Thöne
94. Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
    Olivia Fletcher, Nichola Johnson & Nick Orr
95. Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
    Henrik Flyger
96. School of Public Health, Curtin University, Perth, Australia
    Lin Fritschi
97. Moores Cancer Center, University of California San Diego, La Jolla, California, USA
    Manuela Gago-Dominguez & Maria Elena Martinez
98. Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
    Yu-Tang Gao
99. Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
    Vassilios Georgoulias & Dimitrios Mavroudis
100. Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
     Graham G. Giles, Robert J. MacInnis & Roger L. Milne
101. Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
     Graham G. Giles, John L. Hopper, Robert J. MacInnis, Enes Makalic, Kelly-Anne Phillips, Daniel F. Schmidt & Roger L. Milne
102. Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
     Gord Glendon & Irene L. Andrulis
103. Department of Medicine, McGill University, Montréal, Quebec, Canada
     Mark S. Goldberg
104. Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montréal, Quebec, Canada
     Mark S. Goldberg
105. Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
     David E. Goldgar
106. Department of Surgery, Oulu University Hospital, University of Oulu, Oulu, Finland
     Mervi Grip
107. Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
     Jacek Gronwald, Anna Jakubowska, Katarzyna Kaczmarek & Jan Lubinski
108. Centre de Recherche du Centre Hospitalier de Université de Montréal (CHUM), Université de Montréal, Montréal, Quebec, Canada
     Anne Grundy
109. Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
     Eric Hahnen & Rita K. Schmutzler
110. Center for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
     Eric Hahnen & Rita K. Schmutzler
111. Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
     Eric Hahnen & Rita K. Schmutzler
112. Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
     Christopher A. Haiman, Eunjung Lee, Grace Sheng, Daniel O. Stram, Chiu-Chen Tseng, David Van Den Berg, Anna H. Wu & Lucy Xia
113. Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
     Niclas Håkansson & Alicja Wolk
114. Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
     Ute Hamann, Guanmengqian Huang, Maria Kabisch & Diana Torres
115. Department of Biostatistics & Epidemiology, University of Massachusetts, Amherst, Amherst, Massachusetts, USA
     Susan Hankinson
116. Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
     Steven N. Hart, Jenna Lilyquist, Aaron Norman, Janet E. Olson, Curtis Olswold, Christopher Scott & Celine Vachon
117. Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
     Jaana M. Hartikainen, Veli-Matti Kosma, Arto Mannermaa & Maria Tengström
118. Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
     Jaana M. Hartikainen, Veli-Matti Kosma & Arto Mannermaa
119. Department of Clinical Pathology, Imaging Center, Kuopio University Hospital, Kuopio, Finland
     Jaana M. Hartikainen, Veli-Matti Kosma & Arto Mannermaa
120. Department of Surgery, National University Health System, Singapore, Singapore
     Mikael Hartman & Chuen Neng Lee
121. School of Population Health, University of Western Australia, Perth, Australia
     Jane Heyworth
122. Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
     Antoinette Hollestelle, Maartje J. Hooning & Caroline Seynaeve
123. Division of Breast Surgery, Department of Surgery, Kaohsiung Medical University, Kaohsiung, Taiwan
     Ming-Feng Hou
124. Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
     Chia-Ni Hsiung
125. Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
     Junko Ishiguro & Hidemi Ito
126. Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
     Junko Ishiguro, Hidemi Ito & Keitaro Matsuo
127. Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
     Motoki Iwasaki & Taiki Yamaji
128. Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
     Hiroji Iwata
129. Department of Gynecology and Obstetrics, University Hospital Ulm, Ulm, Germany
     Wolfgang Janni
130. Department of Epidemiology, Cancer Prevention Institute of California, Fremont, California, USA
     Esther M. John
131. Department of Health Research and Policy–Epidemiology, Stanford University School of Medicine, Stanford, California, USA
     Esther M. John & Alice S. Whittemore
132. Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
     Esther M. John & Alice S. Whittemore
133. Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
     Michael Jones, Minouk J. Schoemaker & Anthony Swerdlow
134. Department of Oncology, Oulu University Hospital, University of Oulu, Oulu, Finland
     Arja Jukkola-Vuorinen
135. Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
     Daehee Kang & Sue K. Park
136. Department of Surgery, Nagano Matsushiro General Hospital, Nagano, Japan
     Yoshio Kasuga
137. School of Medicine, National University of Ireland, Galway, Ireland
     Michael J. Kerin & Nicola Miller
138. Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
     Sofia Khan, Johanna I. Kiiski & Heli Nevanlinna
139. Department of Surgery, Daerim Saint Mary’s Hospital, Seoul, South Korea
     Sung-Won Kim
140. Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
     Julia A. Knight
141. Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
     Julia A. Knight
142. Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
     Vessela N. Kristensen
143. Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
     Vessela N. Kristensen
144. Department of Surgery, The University of Hong Kong, Pok Fu Lam, Hong Kong
     Ava Kwong
145. Department of Surgery, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong
     Ava Kwong
146. Vesalius Research Center, VIB, Leuven, Belgium
     Diether Lambrechts
147. Department of Oncology, Laboratory for Translational Genetics, University of Leuven, Leuven, Belgium
     Diether Lambrechts
148. University of Hawaii Cancer Center, Honolulu, Hawaii, USA
     Loic Le Marchand
149. Department of Surgery, Soonchunhyang University College of Medicine and Soonchunhyang University Hospital, Seoul, South Korea
     Min Hyuk Lee
150. Department of Surgery, University of Ulsan College of Medicine and Asan Medical Center, Seoul, South Korea
     Jong Won Lee
151. Department of Cardiac, Thoracic and Vascular Surgery, National University Health System, Singapore, Singapore
     Chuen Neng Lee
152. Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
     Flavio Lejbkowicz, Mila Pinchev, Gadi Rennert & Hedy S. Rennert
153. Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
     Annika Lindblom
154. Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Warsaw, Poland
     Jolanta Lissowska
155. German Breast Group GmbH, Neu Isenburg, Germany
     Sibylle Loibl
156. Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
     Artitaya Lophatananon, Kenneth Muir & Sarah Stewart-Brown
157. Institute of Population Health, University of Manchester, Manchester, UK
     Artitaya Lophatananon & Kenneth Muir
158. Division of Public Health Sciences, Epidemiology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
     Kathleen E. Malone
159. Research Centre for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
     Ivana Maleva Kostovska & Dijana Plaseska-Karanfilska
160. Department of Preventive and Predictive Medicine, Unit of Medical Genetics, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Milan, Italy
     Siranoush Manoukian
161. Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
     JoAnn E. Manson
162. Department of Oncology–Pathology, Karolinska Institutet, Stockholm, Sweden
     Sara Margolin & Camilla Wendt
163. Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
     Shivaani Mariapun & Soo H. Teo
164. Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California, USA
     Maria Elena Martinez
165. Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
     Keitaro Matsuo
166. Anatomical Pathology, The Alfred Hospital, Melbourne, Australia
     Catriona McLean
167. Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
     Alfons Meindl
168. Servicio de Anatomía Patológica, Hospital Monte Naranco, Oviedo, Spain
     Primitiva Menéndez
169. Department of Women’s Cancer, Gynaecological Cancer Research Centre, Institute for Women’s Health, University College London, London, UK
     Usha Menon
170. Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
     Nur Aishah Mohd Taib & Soo H. Teo
171. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
     Anna Marie Mulligan
172. Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
     Anna Marie Mulligan
173. Université Paris Sorbonne Cité, INSERM UMR-S1147, Paris, France
     Claire Mulot
174. Department of Oncology, Leuven Multidisciplinary Breast Center, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
     Patrick Neven, Ann Smeets & Hans Wildiers
175. Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
     Dong-Young Noh
176. Center for Clinical Cancer Genetics and Global Health, The University of Chicago, Chicago, Illinois, USA
     Olufunmilayo I. Olopade
177. University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico, USA
     V. Shane Pankratz
178. The Curtin UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, Australia
     Rachel Lloyd & Jennifer Stone
179. Servicio de Cirugía General y Especialidades, Hospital Monte Naranco, Oviedo, Spain
     Jose I. A. Perez
180. IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
     Paolo Peterlongo
181. Peter MacCallum Cancer Center, Melbourne, Australia
     Kelly-Anne Phillips
182. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
     Kelly-Anne Phillips
183. Department of Medicine, St Vincent’s Hospital, The University of Melbourne, Fitzroy, Australia
     Kelly-Anne Phillips
184. Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
     Katri Pylkäs & Robert Winqvist
185. Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
     Katri Pylkäs & Robert Winqvist
186. Department of Gynecology and Obstetrics, Ludwig-Maximilians University of Munich, Munich, Germany
     Brigitte Rack
187. Department of Preventive and Predictive Medicine, Unit of Molecular Bases of Genetic Risk and Genetic Testing, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Milan, Italy
     Paolo Radice
188. Section of Cancer Genetics, The Institute of Cancer Research, London, UK
     Nazneen Rahman & Sheila Seal
189. Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
     Atocha Romero
190. Department of Oncology, Mayo Clinic, Rochester, Minnesota, USA
     Kathryn J. Ruddy
191. Institute of Pathology, Staedtisches Klinikum Karlsruhe, Karlsruhe, Germany
     Thomas Rüdiger
192. Department of Surgery, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
     Emiel J. T. Rutgers
193. Hereditary Cancer Clinic, University Hospital of Heraklion, Heraklion, Greece
     Emmanouil Saloustros
194. Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
     Dale P. Sandler & Jack A. Taylor
195. National Cancer Institute, Bangkok, Thailand
     Suleeporn Sangrajrang
196. Research Oncology, Guy’s Hospital, King’s College London, London, UK
     Elinor J. Sawyer
197. National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
     Andreas Schneeweiss & Christof Sohn
198. Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
     Fredrick Schumacher
199. Division of Molecular Medicine, Pathology North, John Hunter Hospital, Newcastle, Australia
     Rodney J. Scott
200. Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Callaghan, Australia
     Rodney J. Scott
201. Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
     Priyanka Sharma
202. School of Public Health, China Medical University, Taichung, Taiwan
     Chen-Yang Shen
203. Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
     Chen-Yang Shen
204. Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland, USA
     Mark E. Sherman
205. Department of Pathology, Genetic Epidemiology Laboratory, The University of Melbourne, Melbourne, Australia
     Melissa C. Southey
206. Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
     John J. Spinelli
207. School of Population and Public Health, University of British Columbia, Vancouver, British, Columbia, Canada
     John J. Spinelli
208. Saarland Cancer Registry, Saarbrücken, Germany
     Christa Stegmaier
209. Department of Obstetrics and Gynaecology, University of Melbourne and the Royal Women’s Hospital, Melbourne, Australia
     Jennifer Stone
210. Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
     Anthony Swerdlow
211. Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North, Carolina, USA
     Jack A. Taylor
212. Cancer Center, Kuopio University Hospital, Kuopio, Finland
     Maria Tengström
213. Institute of Clinical Medicine, Oncology, University of Eastern Finland, Kuopio, Finland
     Maria Tengström
214. Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
     Mary Beth Terry
215. National Cancer Institute, Ministry of Public Health, Nonthaburi, Thailand
     Somchai Thanasitthichai
216. Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
     Rob A. E. M. Tollenaar
217. Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
     Ian Tomlinson
218. Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
     Diana Torres
219. Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
     Shoichiro Tsugane
220. Frauenklinik der Stadtklinik Baden-Baden, Baden-Baden, Germany
     Hans-Ulrich Ulmer
221. Cancer Registry of Norway, Oslo, Norway
     Giske Ursin
222. Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
     Giske Ursin
223. Department of Gynecology and Obstetrics, Helios Clinics Berlin-Buch, Berlin, Germany
     Michael Untch
224. Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
     Christi J. van Asperen
225. Family Cancer Clinic, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
     Lizet van der Kolk
226. Division of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
     Rob B. van der Luijt
227. Department of Gynaecology and Obstetrics, University of Ulm, Ulm, Germany
     Shan Wang-Gohrke
228. Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, USA
     Clarice R. Weinberg
229. Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
     Walter Willett
230. Subang Jaya Medical Centre, Subang Jaya, Selangor, Malaysia
     Cheng Har Yip
231. Seoul National University College of Medicine, Seoul, South Korea
     Keun-Young Yoo
232. Armed Forces Capital Hospital, Seongnam, South Korea
     Keun-Young Yoo
233. Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
     Jyh-Cherng Yu
234. Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
     Ying Zheng
235. Department of Medicine, Institute for Human Genetics, UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
     Elad Ziv
236. Pathology Queensland, The Royal Brisbane and Women’s Hospital, Brisbane, 4029, Australia
     Sunil R. Lakhani
237. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
     Irene L. Andrulis
238. Department of Biomedical Data Science, Center for Genomic Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
     Christopher I. Amos
239. University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
     Jenny Chang-Claude
240. Department of Oncology, Södersjukhuset, Stockholm, Sweden
     Per Hall
241. Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
     Marjanka K. Schmidt

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ConFab/AOCS Investigators

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Writing group: K.Mi., S.Li., J.Bee., S.Hu., S.Ka., P.So., S.L.E., G.D.B., G.C.-T., J.Si., P.K. and D.F.E. Conceived the OncoArray and obtained financial support: C.I.A., J.Si., P.K. and D.F.E. Designed the OncoArray: J.D., E.D., A. Lee, Z.W., A.C.A., C.I.A., S.J.C., P.K. and D.F.E. Led the COGS project: P.Hal. Led the DRIVE project: D.J.H. Led the PERSPECTIVE project: J.Si. Led the working groups of BCAC: A.C.A., I.L.A., P.D.P.P., J.C.-C., R.L.M., M.G.-C., M.K.S. and A.M.D. Data management: J.D., M.K.B., Q.Wan., R.Ke., U.E., S.B., J.C.-C. and M.K.S. Bioinformatics analysis: J.D., J.Bee., A.Lem., P.So., J.A., M.Gh., J.C., A.D., A.E.M.R., S.R.L. Statistical analysis: K.Mi., S.Li., S.Hu., S.Ka., A.Ros., J.T., X.Q.C., L.Fa., X.J., H.Fi., G.D.B., P.K. and D.F.E. Functional analysis: D.G., X.Q.C., J.Bee., J.D.F., K.Mc., S.L.E. and G.C.-T. OncoArray genotyping: M.A., F.B., C.Ba., D.M.C., J.M.C., K.F.D., N.Ha., B.H., K.J., C.L., J.Me., E.P., J.R., G.S., D.C.T., D.V.D.B., D.V., J.V., L.X., B.Z. and A.M.D. Provided DNA samples and/or phenotypic data: M.A.A., H.A., K.A., H.A.-C., N.N.A., V.A., K.J.A., B.A., P.L.A., M.Ba., M.W.B., J.Ben., M.Be., L.Be., C.Bl., N.V.B., S.E.B., B.Bo., A.-L.B.-D., J.S.B., H.Bra., P.Bre., H.Bre., L.Br., P.Bro., I.W.B., A.B., A.B.-W., S.Y.B., T.B., B.Bu., K.B., H.Ca., Q.C., T.C., F.C., A.Ca., B.D.C., J.E.C., T.L.C., T.-Y.D.C., K.S.C., J.-Y.C., H.Ch., C.L.C., M.C., E.C.-D., S.C., A.Co., D.G.C., S.S.C., K.C., M.B.D., P.D., T.D., I.d.-S.-S., M.Du., L.D., M.Dw., D.M.E., A.B.E., A.H.E., C.El., M.El., C.En., M.Er., P.A.F., J.F., D.F.-J., O.F., H.Fl., L.Fr., V.Ga., M.Ga., M.G.-D., Y.-T.G., S.M.G., J.A.G.-S., M.M.G., V.Ge., G.G.G., G.G., M.S.G., D.E.G., A.G.-N., G.I.G.A., M.Gr., J.G., A.G., P.G., L.H., E.H., C.A.H., N.Hå., U.H., S.Ha., P.Har., S.N.H., J.M.H., M.H., A.He., J.H., P.Hi., D.N.H., A.Ho., M.J.H., R.N.H., J.L.H., M.-F.H., C.-N.H., G.H., K.H., J.I., H.It., M.I., H.Iw., A.J., W.J., E.M.J., N.J., M.J., A.J.-V., R.Ka., M.K., K.K., D.K., Y.K., M.J.K., S.Kh., E.K., J.I.K., S.-W.K., J.A.K., V.-M.K., I.M.K., V.N.K., U.K., A.K., D.L., L.L.M., C.N.L., E.L., J.W.L., M.H.L., F.L., J. Li, J.Lil., A.Li., J.Lis., R.L., W.-Y.L., S.Lo., J.Lo., A.Lo., J.Lu., M.P.L., E.S.K.M., R.J.M., T.M., E.M., K.E.M., A.Ma., S.Man., J.E.M., S.Marg., S.Mari., M.E.M., K.Ma., D.M., J.Mc., C.Mc., H.M.-H., A.Me., P.M., U.M., H.M., N.M., K.Mu., A.M.M., C.Mu., S.L.N., H.N., P.N., S.F.N., D.-Y.N., B.G.N., A.N., O.I.O., J.E.O., H.O., C.O., N.O., V.S.P., S.K.P., T.-W.P.-S., J.I.A.P., P.P., J.P., K.-A.P., M.P., D.P.-K., R.P., N.P., D.P., K.P., B.R., P.R., N.R., G.R., H.S.R., V.R., A.Rom., K.J.R., T.R., A.Ru., M.R., E.J.T.R., E.S., D.P.S., S.Sa., E.J.S., D.F.S., R.K.S., A.Sc., M.J.Sc., F.S., P.Sc., C.Sc., R.J.S., S.Se., C.Se., M.S., P.Sh., C.-Y.S., M.E.S., M.J.Sh., X.-O.S., A.Sm., C.So., M.C.S., J.J.S., C.St., S.S.-B., J.St., D.O.S., H.S., A.Sw., N.A.M.T., R.T., J.A.T., M.T., S.H.T., M.B.T., S.Th., K.T., R.A.E.M.T., I.T., L.T., D.T., T.T., C.-C.T., S.Ts., H.-U.U., M.U., G.U., C.V., C.J.v.A., A.M.W.v.d.O., L.v.d.K., R.B.v.d.L., Q.Wai., S.W.-G., C.R.W., C.W., A.S.W., H.W., W.W., R.W., A.W., A.H.W., T.Y., X.R.Y., C.H.Y., K.-Y.Y., J.-C.Y., W.Z., Y.Z., A.Z., E.Z., ABCTB Investigators, kConFab/AOCS Investigators, NBCS Collaborators, A.C.A., I.L.A., F.J.C., P.D.P.P., J.C.-C., P.Hal., D.J.H., R.L.M., M.G.-C., M.K.S., G.D.B., J.Si., P.K. and D.F.E. All authors read and approved the final version of the manuscript.

Corresponding author

Correspondence toDouglas F. Easton.

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The authors declare no competing financial interests.

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Lists of participants and their affiliations appear in the Supplementary Information.

Lists of participants and their affiliations appear in the Supplementary Information.

Lists of participants and their affiliations appear in the Supplementary Information.

Extended data figures and tables

Extended Data Figure 1 Global mapping of biofeatures across novel loci associated with overall breast cancer risk.

The overlaps between potential genomic predictors in relevant breast cell lines and credible risk variants (CRVs) within each locus. On the x axis, each column represents a CRV (see Methods). The most significant SNPs are identified in each region. On the y axis, biofeatures are grouped into five functional categories: genomic structure (red), enhancer markers (dark green), histone markers (blue), open chromatin markers (dark blue) and transcription factor binding sites (dark violet). Coloured elements indicate SNPs for which the feature is present. For data sources, see Methods (In silico analysis of CRVs).

Extended Data Figure 2 Pathway enrichment map for susceptibility loci based on summary association statistics.

Each coloured circle (node) represents a pathway (gene set), coloured by enrichment score where redder nodes indicate lower FDRs. Larger nodes indicate pathways with more genes. Green lines connect pathways with overlapping genes (minimum overlap 0.55). Pathways are grouped by similarity and organized into major themes (large labelled circles).

Extended Data Figure 3 Heat map showing patterns of cell-type-specific enrichments for breast tissue across three histone marks (H3K4me1, H3K4me3 and H3K9ac) for all breast cancer types, ER-positive breast cancer and ER-negative breast cancer as well as 16 other traits.

BC_ERneg, ER-negative breast cancer; BC_ERpos, ER-positive breast cancer; BC_overall, all breast cancer types; BMI, body mass index; CAD, cardiovascular disease; CD, Crohn’s disease; HDL, high-density lipoprotein; LDL, low-density lipoprotein; RA, rheumatoid arthritis; T2D, type 2 diabetes; TG, triglycerides; UC, ulcerative colitis; vHMEC, variant human mammary epithelial cells.

Extended Data Figure 4 Heat map showing patterns of cell-type-specific enrichments for histone mark H3K27ac in all breast cancer types, ER-positive and ER-negative breast cancer as well as 16 other traits.

Extended Data Figure 5 Heat map showing patterns of cell-type-specific enrichments for histone mark H3K4me1 in all breast cancer types, ER-positive and ER-negative breast cancer as well as 16 other traits.

Extended Data Figure 6 Heat map showing patterns of cell-type-specific enrichments for histone mark H3K4me3 in breast cancer overall, ER+ and ER- breast cancer as well as 16 other traits.

Extended Data Figure 7 Heat map showing patterns of cell-type-specific enrichments for histone marker H3K9ac in all breast cancer types, ER-positive and ER-negative breast cancer as well as 16 other traits.

Extended Data Figure 8 Functional assessment of regulatory variants at 1p36, 11p15 and 1p34 risk loci.

a, b, The KLHDC7A (a) or PIDD1 (b) promoter regions, containing the reference (prom-Ref) or risk alleles (prom-Hap), were cloned upstream of the pGL3 luciferase reporter gene. MCF7 or Bre-80 cells were transfected with constructs and assayed for luciferase activity after 24 h. The means and 95% confidence intervals are shown. (n = 3). P values were determined by two-way ANOVA followed by Dunnett’s multiple comparisons test (*P < 0.05, **P < 0.01, ***P < 0.001). c, 3C assays. Top, a physical map of the region analysed by 3C. Grey boxes depict the PREs, blue vertical lines indicate the risk-associated SNPs and the black dotted line represents chromatin looping. Bottom, graphs representing three independent 3C interaction profiles. 3C libraries were generated with EcoRI, grey vertical boxes indicate the interacting restriction fragment (containing PRE1 and PRE2). Means and standard deviations are shown. d, PRE1 or PRE2 containing the reference (PRE-ref) or risk (PRE-Hap) haplotypes were cloned downstream of a CITED4 promoter-driven luciferase construct (CITED4 prom). MCF7 or Bre-80 cells were transfected with constructs and assayed for luciferase activity after 24 h. Error bars denote 95% CI (n = 3). P values were determined by two-way ANOVA followed by Dunnett’s multiple comparisons test (**P < 0.01, ***P < 0.001).

Extended Data Figure 9 Functional assessment of regulatory variants at the 7q22 risk locus.

a–e, 3C assays. Top, a physical map of the region interrogated by 3C. Grey horizontal boxes depict the putative regulatory elements (PREs), blue vertical lines indicate the risk-associated SNPs and the black dotted line represents chromatin looping. Bottom, graphs represent three independent 3C interaction profiles between the CUX1 (a), PRKRIP1 (b, d) or RASA4 (c, e) promoter regions and PREs. 3C libraries were generated with EcoRI, grey vertical boxes indicate the interacting restriction fragment (containing PRE1 and/or PRE2). Means and standard deviations are shown. f, g, Allele-specific 3C. 3C followed by Sanger sequencing for the _PRKRIP1_-PRE2 (f) or _RASA4_-PRE1 or -PRE2 (g) in heterozygous MDA-MB-231 breast cancer cells.

Extended Data Table 1 INQUISIT, DEPICT and the nearest gene as predictors of driver status

Full size table

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1, 2 and 24, a Supplementary Note, Funding Information, Study Acknowledgments, Members of Consortia listed as Authors, Supplementary References and a Supplementary Table Guide. (PDF 659 kb)

Reporting Summary (PDF 68 kb)

Supplementary Data

This file contains Supplementary Tables 3–5, 7, 9–12, 14–17, 21–23 and 25–33 – see the Supplementary Table Guide in the Supplementary Information document for full descriptions. (XLSX 1115 kb)

Supplementary Table 6

This table contains sixty-five newly identified susceptibility loci for overall breast cancer. (XLSX 17 kb)

Supplementary Table 8

This table contains summary statistics for all variants for which the association with overall breast cancer in the combined dataset was significant at P<0.00001. (XLSX 17279 kb)

Supplementary Table 13

This table contains a list of 2,221 credible variants at 65 novel loci, with annotations, UCSC Genome Browser links, and sources for genomic annotation data. (XLSX 684 kb)

Supplementary Table 18

This table displays eQTL associations significant at P<0.05 in the TCGA and METABRIC datasets, for credible risk variants from the analyses for overall breast cancer (see Methods), together with the corresponding results for the most significant eQTL association in the region for the same gene. (XLSX 3630 kb)

Supplementary Table 19

This table contains summary INQUISIT gene prediction scores. (XLSX 52 kb)

Supplementary Table 20

This table contains detailed INQUISIT gene prediction scores. (XLSX 102 kb)

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Michailidou, K., Lindström, S., Dennis, J. et al. Association analysis identifies 65 new breast cancer risk loci.Nature 551, 92–94 (2017). https://doi.org/10.1038/nature24284

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• Received: 21 June 2016
• Accepted: 17 September 2017
• Published: 23 October 2017
• Issue Date: 02 November 2017
• DOI: https://doi.org/10.1038/nature24284