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

Research output: Contribution to journalArticlepeer-review

116 Citations (Scopus)


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
Publication statusPublished - Nov 2011
Externally publishedYes


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