Letter | Published:

Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2

Nature Genetics volume 41, pages 585590 (2009) | Download Citation

Abstract

Genome-wide association studies (GWAS) have identified seven breast cancer susceptibility loci, but these explain only a small fraction of the familial risk of the disease. Five of these loci were identified through a two-stage GWAS involving 390 familial cases and 364 controls in the first stage, and 3,990 cases and 3,916 controls in the second stage1. To identify additional loci, we tested over 800 promising associations from this GWAS in a further two stages involving 37,012 cases and 40,069 controls from 33 studies in the CGEMS collaboration and Breast Cancer Association Consortium. We found strong evidence for additional susceptibility loci on 3p (rs4973768: per-allele OR = 1.11, 95% CI = 1.08–1.13, P = 4.1 × 10−23) and 17q (rs6504950: per-allele OR = 0.95, 95% CI = 0.92–0.97, P = 1.4 × 10−8). Potential causative genes include SLC4A7 and NEK10 on 3p and COX11 on 17q.

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Acknowledgements

The initial GWAS, SEARCH, the replication genotyping through BCAC and the main analysis of this study were supported by Cancer Research UK grants C1287/A7497, C490/A11021, C1287/A10118 and C1287/A5260. D.F.E. and P.D.P.P. are supported by Cancer Research UK. Meetings of BCAC have been supported in part by ESF COST action BM0606.

The Nurses' Health Studies are supported by US National Institutes of Health grants CA65725, CA87969, CA49449, CA67262, CA50385 and 5UO1CA098233. The WHI program is supported by contracts from the National Heart, Lung, and Blood Institute, NIH. We thank the WHI investigators and staff for their dedication and the study participants for making the program possible. A full listing of WHI investigators can be found at http://www.whiscience.org/publications/WHI_investigators_shortlist.pdf. The ACS study is supported by UO1 CA098710. We thank C. Lichtman for data management and the participants on the CPS-II. The PLCO study is supported by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics and contracts from the Division of Cancer Prevention, National Cancer Institute, NIH and DHHS. We thank P. Prorok, Division of Cancer Prevention, National Cancer Institute, the Screening Center investigators and staff of the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) and T. Sheehy and staff at SAIC-Frederick. We acknowledge the study participants for their contributions to making this study possible. The ABCFS was supported by the National Health and Medical Research Council (NHMRC) of Australia (#145604), the US NIH (RO1 CA102740-01A2) and by the National Cancer Institute, NIH under RFA #CA-95-011 through cooperative agreements with members of the Breast Cancer Family Registry (Breast CFR) and principal investigators from Cancer Care Ontario (UO1 CA69467), Columbia University (U01 CA69398), Fox Chase Cancer Center (U01 CA69631), Huntsman Cancer Institute (U01 CA69446), Northern California Cancer Center (U01 CA69417) and University of Melbourne (U01 CA69638). The content of this manuscript does not necessarily reflect the views or policies of the National Cancer Institute or any of collaborating centers in the Breast CFR, nor does mention of trade names, commercial products or organizations imply endorsement by the US government or the Breast CFR. The ABCFS was initially supported by the NHMRC, the New South Wales Cancer Council and the Victorian Health Promotion Foundation. J.L.H. and M.C.S. are supported by NHMRC. We thank M. Angelakos, J. Maskiell and G. Dite. We thank X. Chen for genotyping the ABCFS, kConFab and AOCS samples, and H. Thorne, E. Niedermayr, all the kConFab research nurses and staff, the heads and staff of the Family Cancer Clinics and the Clinical Follow Up Study (funded by NHMRC grants 145684, 288704 and 454508) for their contributions to this resource, and the many families who contribute to kConFab. kConFab is supported by grants from the National Breast Cancer Foundation, the National Health and Medical Research Council (NHMRC) and by the Queensland Cancer Fund, the Cancer Councils of New South Wales, Victoria, Tasmania and South Australia, and the Cancer Foundation of Western Australia. The AOCS Management Group (D. Bowtell, G.C.-T., A. deFazio, D. Gertig, A. Green and P. Webb) gratefully acknowledges the contribution of all the clinical and scientific collaborators (see http://www.aocstudy.org/). The ACS Management Group (A. Green, P. Parsons, N. Hayward, P. Webb, D. Whiteman) thank all of the project staff, collaborating institutions and study participants. Financial support was provided by US Army Medical Research and Materiel Command under DAMD17-01-1-0729, the Cancer Council Tasmania and Cancer Foundation of Western Australia (AOCS study) and The National Health and Medical Research Council of Australia (199600) (ACS study). G.C.-T. is supported by NHMRC. Funding of the ABCS study was provided by the Dutch Cancer Society (grants NKI 2001-2423; 2007-3839) and the Dutch National Genomics Initiative. ABCS acknowledges L. Braaf, L. Van't Veer, F. Van Leeuwen, R. Tollenaar and other contributors to the 'BOSOM' study and the support of H.B. Bueno-de-Mesquita for organizing the release of control DNA. The British Breast Cancer Study is funded by Cancer Research UK and Breakthrough Breast Cancer. We acknowledge NHS funding to the NIHR Biomedical Research Centre, and the National Cancer Research Network (NCRN). The CGPS was supported by the Danish Medical Research Council and Copenhagen County. The CNIO-BCS was supported by the Genome Spain Foundation and grants from the Asociación Española Contra Cáncer and the Fondo de Investigación Sanitario (PI081120 and PI081583). We thank J.I. Arias from the Hospital Monte Naranco, P. Zamora from the Hospital La Paz and C. Alonso and T. Moreno from the CNIO. The GENICA study was supported by the German Human Genome Project and funded by the Federal Ministry of Education and Research (BMBF) Germany grants 01KW9975/5, 01KW9976/8, 01KW9977/0 and 01KW0114. Genotyping analysis was supported by the Robert Bosch Foundation of Medical Research. B. Pesch, V. Harth and T. Brüning were involved in the recruitment of study subjects and responsible for the collection of epidemiological data. The Genetic Epidemiology Study of Breast Cancer by Age 50 (GESBC) was supported by the Deutsche Krebshilfe e.V. (project number 70492) and the genotyping in part by the state of Baden-Württemberg through Medical Faculty of the University of Ulm (P.685). We thank U. Eilber and T. Koehler for their technical support. We cordially thank M. Bremer, A. Scharf and C. Sohn for their support of the breast cancer studies in Hannover. HABCS and HMBCS received funding through a Hannelore-Munke stipend to N.V.B. HUBCS was supported by a grant from the German Federal Ministry of Education and Research (RUS 08/017). HEBCS wishes to thank H. Jäntti and K. Aaltonen for help with the subject data. The Finnish Cancer registry is gratefully acknowledged for the cancer data. The HEBCS study has been financially supported by the Helsinki University Central Hospital Research Fund, Academy of Finland (110663), Finnish Cancer Society and the Sigrid Juselius Foundation. KARBAC was supported by The Swedish Cancer Foundation, The Gustav V Jubilee Foundation and the Bert von Kantzow Foundation. KBCP is grateful to E. Myöhänen for her assistance. KBCP was supported by special Government Funding (EVO) of Kuopio University Hospital, The Finnish Cancer Society, University of Kuopio and by the Northern Savo Cancer Society. MCBCS was supported by grants from the NIH (P50 CA116201 and R01 CA122340). We thank all the participants in the MCCS and the team of investigators, project and data managers and project assistants. The MCCS is supported by the Australian National Health and Medical Research Council (grants 209057, 251533, 396414 and 504711). Cohort recruitment and follow up is funded by The Cancer Council Victoria. The OFBCR was supported by the National Cancer Institute, NIH under RFA #CA-06-503 and through cooperative agreements with members of the Breast Cancer Family Registry and Cancer Care Ontario (U01 CA69467). We thank N. Weerasooriya, M. Gill, L. Collins and N. Gokgoz for their assistance. The ORIGO study was supported by the Dutch Cancer Society; we thank P.E.A. Huijts, E. Krol-Warmerdam and J. Blom for recruiting subjects, administering questionnaires and managing clinical information. RBCS was supported by the Dutch Cancer Society. SASBAC study was supported by funding from the Agency for Science, Technology and Research of Singapore (A*STAR), the US NIH and the Susan G. Komen Breast Cancer Foundation. The SBCS was supported by Yorkshire Cancer Research and the Breast Cancer Campaign. We thank S. Higham, H. Cramp, D. Connley and S. Balasubramanian for their contribution to the SBCS. The PBCS was funded by Intramural Research Funds of the US National Cancer Institute, DHHS. The PBCS thanks N. Szeszenia-Dabrowska, B. Peplonska, W. Zatonski, M. Sherman and P. Chao for their valuable contributions to the study. SEBCS was supported by a grant of the Korea Health 21 R&D Project, Ministry of Health & Welfare (R.O.K.) (AO30001) and by a grant from the National R&D program for Cancer Control, Ministry of Health & Welfare, Republic of Korea (0620410-1). The UCIBCS component of this research was supported by the US NIH, National Cancer Institute grants CA-58860 and CA-92044 and the Lon V. Smith Foundation grant LVS-39420.

Author information

Author notes

    • Shahana Ahmed
    • , Gilles Thomas
    • , Maya Ghoussaini
    • , Catherine S Healey
    •  & Manjeet K Humphreys

    These authors contributed equally to this work.

Affiliations

  1. Department of Oncology, University of Cambridge, Cambridge, UK.

    • Shahana Ahmed
    • , Maya Ghoussaini
    • , Catherine S Healey
    • , Radka Platte
    • , Melanie Maranian
    • , Bruce A J Ponder
    • , Paul D P Pharoah
    •  & Alison M Dunning
  2. Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA.

    • Gilles Thomas
    • , Kevin Jacobs
    • , Regina G Ziegler
    • , Montserrat Garcia-Closas
    • , Alice Sigurdson
    • , Michele Doody
    • , Parveen Bhatti
    •  & Robert N Hoover
  3. CR-UK Genetic Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.

    • Manjeet K Humphreys
    • , Jonathan Morrison
    • , Karen A Pooley
    • , Paul D P Pharoah
    •  & Douglas F Easton
  4. EPIC, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.

    • Robert Luben
  5. Wessex Clinical Genetics Service, Princess Ann Hospital, Southampton, UK.

    • Diana Eccles
  6. Regional Genetic Service, St. Mary's Hospital, Manchester, UK.

    • D Gareth Evans
  7. Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK.

    • Olivia Fletcher
    •  & Nichola Johnson
  8. London School of Hygiene and Tropical Medicine and Institute of Cancer Research, London, UK.

    • Olivia Fletcher
    • , Isabel dos Santos Silva
    •  & Julian Peto
  9. Institute of Cancer Research, Sutton, Surrey, UK.

    • Julian Peto
  10. Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

    • Michael R Stratton
  11. Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, UK.

    • Nazneen Rahman
  12. Bioinformed Consulting Services, Gaithersburg, Maryland, USA.

    • Kevin Jacobs
  13. Core Genotyping Facility, Advanced Technology Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, Maryland, USA.

    • Kevin Jacobs
  14. Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

    • Ross Prentice
    •  & Garnet L Anderson
  15. Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA.

    • Aleksandar Rajkovic
  16. Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii/Pacific Health Research Institute, Honolulu, Hawaii, USA.

    • J David Curb
  17. Division of Cancer Prevention, NCI, NIH, DHHS, Bethesda, Maryland, USA.

    • Christine D Berg
  18. Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.

    • Saundra S Buys
  19. The Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA.

    • Catherine A McCarty
  20. Department of Epidemiology and Surveillance Research, American Cancer Society, Atlanta, Georgia, USA.

    • Heather Spencer Feigelson
    • , Eugenia E Calle
    • , Michael J Thun
    •  & W Ryan Diver
  21. Department of Clinical Biochemistry, Copenhagen University Hospital, Herlev, Denmark

    • Stig Bojesen
    •  & Børge G Nordestgaard
  22. Copenhagen General Population Study, Copenhagen University Hospital, Herlev, Denmark

    • Stig Bojesen
    •  & Børge G Nordestgaard
  23. Department of Breast Surgery, Copenhagen University Hospital, Herlev, Denmark.

    • Henrik Flyger
  24. Departments of Obstetrics and Gynaecology, and

    • Thilo Dörk
    • , Peter Schürmann
    • , Peter Hillemanns
    • , Natalia V Bogdanova
    •  & Marina Bermisheva
  25. Radiation Oncology, Hannover Medical School, Hannover, Germany.

    • Johann H Karstens
    •  & Natalia V Bogdanova
  26. N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus.

    • Natalia V Bogdanova
    • , Natalia N Antonenkova
    •  & Iosif V Zalutsky
  27. Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia.

    • Marina Bermisheva
    •  & Elza Khusnutdinova
  28. Department of Medical Genetics, Yakut Research Center of Russian Academy of Medical Sciences, Yakutsk, Russia.

    • Sardana Fedorova
  29. Seoul National University College of Medicine, Seoul, Korea.

    • Daehee Kang
    • , Keun-Young Yoo
    • , Dong Young Noh
    •  & Sei-Hyun Ahn
  30. Departments of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

    • Peter Devilee
  31. Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands

    • Peter Devilee
  32. Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands

    • Christi J van Asperen
  33. Surgical Oncology, Leiden University Medical Center, Leiden, The Netherlands.

    • R A E M Tollenaar
  34. Department of Medical Oncology, Rotterdam Family Cancer Clinic, Erasmus MC-Daniel den Hoed Cancer Center, Rotterdam, The Netherlands.

    • Caroline Seynaeve
  35. Department of Epidemiology and Cancer Prevention, The M. Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland.

    • Jolanta Lissowska
  36. Hormonal and Reproductive Epidemiology Branch, National Cancer Institute, Rockville, Maryland, USA.

    • Louise Brinton
  37. Department of Occupational & Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland.

    • Beata Peplonska
  38. Departments of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland.

    • Heli Nevanlinna
    •  & Tuomas Heikkinen
  39. Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland.

    • Kristiina Aittomäki
  40. Departments of Oncology, Helsinki University Central Hospital, Helsinki, Finland.

    • Carl Blomqvist
  41. Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, Australia.

    • John L Hopper
    • , Graham G Giles
    • , Gianluca Severi
    • , Laura Baglietto
    •  & Dallas R English
  42. Department of Pathology, University of Melbourne, Melbourne, Australia.

    • Melissa C Southey
  43. Queensland Institute for Medical Research, Brisbane, Australia.

    • Letitia Smith
    • , Amanda B Spurdle
    • , Jonathan Beesley
    •  & Georgia Chenevix-Trench
  44. Netherlands Cancer Institute, Amsterdam, The Netherlands.

    • Marjanka K Schmidt
    • , Annegien Broeks
    • , Richard R van Hien
    •  & Sten Cornelissen
  45. Genetic and Molecular Epidemiology Group.

    • Roger L Milne
  46. Human Genetics Group.

    • Gloria Ribas
    •  & Javier Benitez
  47. National Genotyping Centre (CEGEN), Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

    • Anna González-Neira
    •  & Javier Benitez
  48. Department of Gynaecology and Obstetrics, Clinical Center University of Cologne, Köln, Germany.

    • Rita K Schmutzler
  49. Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.

    • Barbara Burwinkel
  50. Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany.

    • Barbara Burwinkel
  51. Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.

    • Claus R Bartram
  52. Department of Gynaecology and Obstetrics, Technical University of Munich, Munich, Germany.

    • Alfons Meindl
  53. Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.

    • Hiltrud Brauch
    •  & Christina Justenhoven
  54. University of Tuebingen, Tuebingen, Germany.

    • Hiltrud Brauch
    •  & Christina Justenhoven
  55. Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.

    • Ute Hamann
  56. Division of Cancer Epidemiology, German Cancer Research Center (DFKZ), Heidelberg, Germany.

    • Jenny Chang-Claude
    •  & Rebecca Hein
  57. Women's Hospital of University of Ulm, Ulm, Germany.

    • Shan Wang-Gohrke
  58. Department of Molecular Medicine and Surgery, Karolinska Institutet, S17176 Stockholm, Sweden.

    • Annika Lindblom
  59. Department of Oncology and Pathology, Karolinska Institutet, S17176 Stockholm, Sweden.

    • Sara Margolin
  60. Institute of Clinical Medicine, Pathology and Forensic Medicine and Biocenter Kuopio, University of Kuopio, Kuopio, Finland.

    • Arto Mannermaa
    •  & Veli-Matti Kosma
  61. Departments of Pathology, Kuopio University Hospital, Kuopio, Finland.

    • Arto Mannermaa
    •  & Veli-Matti Kosma
  62. Department of Oncology, Kuopio University Hospital, Kuopio, Finland.

    • Vesa Kataja
  63. Department of Oncology, Vaasa Central Hospital, Vaasa, Finland.

    • Vesa Kataja
  64. Mayo Clinic College of Medicine, Rochester, Minnesota, USA.

    • Janet E Olson
    • , Xianshu Wang
    • , Zachary Fredericksen
    • , Ellen L Goode
    •  & Fergus Couch
  65. Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.

    • Graham G Giles
    • , Gianluca Severi
    • , Laura Baglietto
    •  & Dallas R English
  66. Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Susan E Hankinson
    • , David G Cox
    •  & David J Hunter
  67. Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.

    • Peter Kraft
    •  & David J Hunter
  68. Department of Public Health, Norwegian University of Science and Technology, Trondheim, Norway.

    • Lars J Vatten
    •  & Kristian Hveem
  69. Institute of Community Medicine, University of Tromso, Tromso, Norway.

    • Merethe Kumle
  70. Division of Environmental Health Science, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA.

    • Bruce H Alexander
  71. Department of Medical Oncology, Rotterdam Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands.

    • Maartje J Hooning
    •  & Mieke Schutte
  72. Department of Clinical Genetics, Rotterdam Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands.

    • Ans M W van den Ouweland
    •  & Rogier A Oldenburg
  73. Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden.

    • Per Hall
    •  & Kamila Czene
  74. Population Genetics, Genome Institute of Singapore, Singapore.

    • Jianjun Liu
    •  & Yuqing Li
  75. Institute for Cancer Studies, University of Sheffield School of Medicine and Biomedical Sciences, Sheffield, UK.

    • Angela Cox
    • , Graeme Elliott
    •  & Ian Brock
  76. Academic Unit of Surgical Oncology, University of Sheffield School of Medicine and Biomedical Sciences, Sheffield, UK.

    • Malcolm W R Reed
  77. Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.

    • Chen-Yang Shen
  78. Graduate Institute of Environmental Science, China Medical University, Taichong, Taiwan.

    • Chen-Yang Shen
  79. Tri-Service General Hospital, Taipei, Taiwan.

    • Jyh-Cherng Yu
    •  & Giu-Cheng Hsu
  80. Changhua Christian Hospital, Changhua, Taiwan.

    • Shou-Tung Chen
  81. Department of Epidemiology, University of California Irvine, Irvine, California, USA.

    • Hoda Anton-Culver
    •  & Argyrios Ziogas
  82. Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.

    • Irene L Andrulis
    •  & Julia A Knight
  83. Ontario Familial Breast Cancer Registry, Cancer Care Ontario, Toronto, Ontario, Canada.

    • Irene L Andrulis
  84. Peter MacCallum Cancer Center, Melbourne, Australia.

  85. Cancer Research UK Cambridge Cancer Research Institute, Cambridge, UK.

    • Bruce A J Ponder
  86. Advanced Technology Center, National Cancer Institute, Gaithersburg, Maryland, USA.

    • Stephen J Chanock

Consortia

  1. SEARCH

    1. Department of Oncology, University of Cambridge
    2. CR-UK Genetic Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge
  2. The GENICA Consortium

    1. Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology
    2. University of Tuebingen
  3. kConFab

    1. Peter MacCallum Cancer Center
  4. Australian Ovarian Cancer Study Group

    1. Queensland Institute for Medical Research
    2. Peter MacCallum Cancer Center

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Contributions

D.F.E., A.M.D., P.D.P.P. and B.A.J.P. designed the study and obtained financial support. D.F.E. and P.D.P.P. conducted the statistical analysis. G.T., R.N.H., D.J.H. and S.J.C. directed the CGEMS study and designed and conducted the stage 3 experiment with D.F.E., S.A., M.G., C.S.H. and M.M. conducting the fine-scale mapping. M.K.H., J.M. and R.L. provided bioinformatics support. D.E., D.G.E., O.F., N.J., I.d.S.S., J.P., M.R.S. and N.R. co-ordinated the studies used in stage 1. The remaining authors coordinated the studies in stage 4 and/or undertook genotyping in those studies. D.F.E. drafted the manuscript, with substantial input from other authors. All authors contributed to the final paper.

Corresponding author

Correspondence to Douglas F Easton.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Tables 1–7

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/ng.354

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