Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3

Stuart MacGregor*, Grant W. Montgomery, Jimmy Z. Liu, Zhen Zhen Zhao, Anjali K. Henders, Mitchell Stark, Helen Schmid, Elizabeth A. Holland, David L. Duffy, Mingfeng Zhang, Jodie N. Painter, Dale R. Nyholt, Judith A. Maskiell, Jodie Jetann, Megan Ferguson, Anne E. Cust, Mark A. Jenkins, David C. Whiteman, Håkan Olsson, Susana PuigGiovanna Bianchi-Scarrà, Johan Hansson, Florence Demenais, Maria Teresa Landi, Tadeusz Dȩbniak, Rona MacKie, Esther Azizi, Brigitte Bressac-De Paillerets, Alisa M. Goldstein, Peter A. Kanetsky, Nelleke A. Gruis, David E. Elder, Julia A. Newton-Bishop, D. Timothy Bishop, Mark M. Iles, Per Helsing, Christopher I. Amos, Qingyi Wei, Li E. Wang, Jeffrey E. Lee, Abrar A. Qureshi, Richard F. Kefford, Graham G. Giles, Bruce K. Armstrong, Joanne F. Aitken, Jiali Han, John L. Hopper, Jeffrey M. Trent, Kevin M. Brown, Nicholas G. Martin, Graham J. Mann, Nicholas K. Hayward

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

121 Scopus citations


We performed a genome-wide association study of melanoma in a discovery cohort of 2,168 Australian individuals with melanoma and 4,387 control individuals. In this discovery phase, we confirm several previously characterized melanoma-associated loci at MC1R, ASIP and MTAPĝ€" CDKN2A. We selected variants at nine loci for replication in three independent case-control studies (Europe: 2,804 subjects with melanoma, 7,618 control subjects; United States 1: 1,804 subjects with melanoma, 1,026 control subjects; United States 2: 585 subjects with melanoma, 6,500 control subjects). The combined meta-analysis of all case-control studies identified a new susceptibility locus at 1q21.3 (rs7412746, P = 9.0 × 10 -11, OR in combined replication cohorts of 0.89 (95% CI 0.85-0.95)). We also show evidence suggesting that melanoma associates with 1q42.12 (rs3219090, P = 9.3 × 10 -8). The associated variants at the 1q21.3 locus span a region with ten genes, and plausible candidate genes for melanoma susceptibility include ARNT and SETDB1. Variants at the 1q21.3 locus do not seem to be associated with human pigmentation or measures of nevus density.

Original languageEnglish
Pages (from-to)1114-1118
Number of pages5
JournalNature Genetics
Issue number11
StatePublished - Nov 2011
Externally publishedYes


FundersFunder number
6th Framework ProgrammeLSHC-CT-2006-018702
Australian National Health and Medical Research Council613705, CA109544, 496674
Cancer Councils New South Wales, Victoria and Queensland
Cerylid Biosciences
Fondo de Investigaciones Sanitarias09/1393
University of Sydney Medical Foundation
National Institutes of HealthCA100264, CA122838, CA87969, CA49449, CA83115, CA88363, CA055075
National Cancer InstituteP30CA016672, R01CA133996
Melanoma Research Alliance
Bushfire Cooperative Research Centre
Wellcome TrustWT084766/Z/08/Z
National Computational Infrastructure
Division of Cancer Epidemiology and Genetics, National Cancer Institute
Cancer Research UKHHSN268200782096C, HG004446, C588/A4994, 2P50CA093459
European Commission
National Health and Medical Research Council107359, 339462, 389892, 389891, 402761, 241944, 552485, 442981, 443036, 552498, 496739, 200071, 389875, 380385, 442915, 496675, 496610, 389927, 389938
Australian Cancer Research Foundation
Cancer Institute NSW10/ECF/2-06


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