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Common sequence variants on 20q11.22 confer melanoma susceptibility

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Abstract

We conducted a genome-wide association pooling study for cutaneous melanoma and performed validation in samples totaling 2,019 cases and 2,105 controls. Using pooling, we identified a new melanoma risk locus on chromosome 20 (rs910873 and rs1885120), with replication in two further samples (combined P < 1 × 10−15). The per allele odds ratio was 1.75 (1.53, 2.01), with evidence for stronger association in early-onset cases.

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Figure 1: Association analysis of SNPs across a region of chromosome 20q11.22.
Figure 2: Association analysis of SNPs across a region of chromosome 20q11.22 for the combined sample.

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Acknowledgements

This work was supported by the National Cancer Institute (NCI) of the US National Institutes of Health (NIH) (CA88363, CA83115), the National Health and Medical Research Council of Australia (NHMRC) (380385, 389892, 496675, 402761), the Cancer Councils New South Wales, Victoria and Queensland, the Cancer Institute New South Wales, the Melanoma Research Foundation (MRF) and a charitable contribution from F. Najafi. N.K.H. and G.W.M. are supported by the NHMRC Fellowships scheme and J.L.H. is an Australia Fellow of the NHMRC. S.M. and K.M.B. are recipients of Career Development Awards from the NHMRC (496674) and MRF, respectively. K.M.B. and J.M.T. are supported by the NCI/NIH (respectively, CA109544 and CA083115; and CA109544). D.A.S. is supported by the US National Heart, Lung, and Blood Institute of the NIH (HL086528). B.K.A. is supported by the University of Sydney Medical Foundation. A.E.C. is supported by an NHMRC postdoctoral fellowship. The authors are grateful to M. Huentelman and S. Szelinger for technical assistance. The AMFS and Q-MEGA gratefully acknowledge all of their participants, the hard work of all its research interviewers and examiners, and C. Agha-Hamilton for managing the AMFS biospecimens. Q-MEGA thanks A. Baxter, M. de Nooyer, I. Gardner, D. Statham, B. Haddon, J. Palmer, B. Castellano, L. Bardsley, D. Smyth and H. Beeby for their input into project management, sample processing and database development.

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Author notes

  1. Kevin M Brown and Stuart MacGregor: These authors contributed equally to this work.

Authors and Affiliations

  1. Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, 85028, Arizona, USA

    Kevin M Brown & Kelly Iyadurai

  2. The Population Studies and Genetics Division, Queensland Institute of Medical Research, Brisbane, 4029, Queensland, Australia

    Stuart MacGregor, Grant W Montgomery, Zhen Zhen Zhao, Anjali K Henders, Megan J Campbell, Mitchell Stark, Shane Thomas, David L Duffy, David Whiteman, Adele Green, Nicholas G Martin & Nicholas K Hayward

  3. Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, 85028, Arizona, USA

    David W Craig & Dietrich A Stephan

  4. University of California Los Angeles, Los Angeles, 90095, California, USA

    Nils Homer

  5. Westmead Institute of Cancer Research and Sydney Melanoma Unit, University of Sydney at Westmead Millennium Institute, Westmead, 2145, New South Wales, Australia

    Helen Schmid, Elizabeth A Holland, Richard F Kefford & Graham J Mann

  6. Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, 21224, Maryland, USA

    Elizabeth M Gillanders

  7. Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, University of Melbourne, Melbourne, 3052, Victoria, Australia

    Judith A Maskiell, Anne E Cust & John L Hopper

  8. Viertel Centre for Research in Cancer Control, The Cancer Council Queensland, Brisbane, 4004, Queensland, Australia

    Jodie Jetann, Megan Ferguson & Joanne F Aitken

  9. Lund Cancer Center Department of Oncology, University Hospital, Lund, SE-22185, Sweden

    Håkan Olsson

  10. Dermatology Department, Melanoma Unit, Hospital Clínic, Institut de Investigació Biomèdica August Pi Suñe, Universitat de Barcelona, Barcelona, 08036, Spain

    Susana Puig

  11. Department of Oncology, Biology, and Genetics, University of Genova, Genova, 16132, Italy

    Paola Ghiorzo

  12. Department of Oncology-Pathology, Karolinska Institute and Karolinska University Hospital, Solna, S-171 76, Stockholm, Sweden

    Johan Hansson

  13. INSERM, U794, Fondation Jean-Dausset–CEPH, Paris, 75010, France

    Florence Demenais

  14. Division of Cancer Epidemiology and Genetics, Genetic Epidemiology Branch, National Cancer Institute, Bethesda, 20892, Maryland, USA

    Alisa M Goldstein

  15. Department of Dermatology, Leiden University Medical Center, Leiden, 2333 AL, The Netherlands

    Nelleke A Gruis

  16. Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, 19104, Pennsylvania, USA

    David E Elder

  17. Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK

    Julia Newton Bishop

  18. Cancer Epidemiology Centre, The Cancer Council Victoria, Carlton, 3053, Victoria, Australia

    Graham G Giles

  19. School of Public Health, University of Sydney, Sydney, 2006, New South Wales, Australia

    Bruce K Armstrong

  20. Genetic Basis of Human Disease Division, The Translational Genomics Research Institute, Phoenix, 85028, Arizona, USA

    Jeffrey M Trent

  21. On behalf of the Lund Melanoma Group.,

    Håkan Olsson

  22. On behalf of the International Melanoma Genetics Consortium (GenoMEL).,

    Håkan Olsson, Susana Puig, Paola Ghiorzo, Johan Hansson, Florence Demenais, Nelleke A Gruis, David E Elder & Julia Newton Bishop

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  1. Kevin M Brown
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  2. Stuart MacGregor
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  3. Grant W Montgomery
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  13. Elizabeth A Holland
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  18. Megan Ferguson
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  19. Dietrich A Stephan
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  20. Anne E Cust
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  21. David Whiteman
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  22. Adele Green
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  27. Florence Demenais
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  28. Alisa M Goldstein
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  29. Nelleke A Gruis
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  30. David E Elder
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  31. Julia Newton Bishop
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  32. Richard F Kefford
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  33. Graham G Giles
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  34. Bruce K Armstrong
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  36. John L Hopper
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  37. Nicholas G Martin
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  38. Jeffrey M Trent
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  39. Graham J Mann
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  40. Nicholas K Hayward
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Corresponding author

Correspondence to Stuart MacGregor.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Methods, Supplementary Tables 1–6 and Supplementary Figure 1 (PDF 172 kb)

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Brown, K., MacGregor, S., Montgomery, G. et al. Common sequence variants on 20q11.22 confer melanoma susceptibility. Nat Genet 40, 838–840 (2008). https://doi.org/10.1038/ng.163

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  • DOI: https://doi.org/10.1038/ng.163

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