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

MacGregor, Stuart; Montgomery, Grant W.; Liu, Jimmy Z.; Zhao, Zhen Zhen; Henders, Anjali K.; Stark, Mitchell; Schmid, Helen; Holland, Elizabeth A.; Duffy, David L. and Zhang, Mingfeng, et al. (2011) In Nature Genetics 43(11). p.104-1114
Abstract
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 MTAP-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 x 10(-11), OR in combined replication cohorts of... (More)
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 MTAP-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 x 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 x 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. (Less)
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Nature Genetics
volume
43
issue
11
pages
104 - 1114
publisher
Nature Publishing Group
external identifiers
  • wos:000296584000016
  • scopus:80055002815
ISSN
1546-1718
DOI
10.1038/ng.958
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English
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yes
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fe24832a-21d8-4a12-9d3c-24fb4f672090 (old id 2254280)
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@article{fe24832a-21d8-4a12-9d3c-24fb4f672090,
  abstract     = {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 MTAP-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 x 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 x 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.},
  author       = {MacGregor, Stuart and Montgomery, Grant W. and Liu, Jimmy Z. and Zhao, Zhen Zhen and Henders, Anjali K. and Stark, Mitchell and Schmid, Helen and Holland, Elizabeth A. and Duffy, David L. and Zhang, Mingfeng and Painter, Jodie N. and Nyholt, Dale R. and Maskiell, Judith A. and Jetann, Jodie and Ferguson, Megan and Cust, Anne E. and Jenkins, Mark A. and Whiteman, David C. and Olsson, Håkan and Puig, Susana and Bianchi-Scarra, Giovanna and Hansson, Johan and Demenais, Florence and Landi, Maria Teresa and Debniak, Tadeusz and Mackie, Rona and Azizi, Esther and Bressac-de Paillerets, Brigitte and Goldstein, Alisa M. and Kanetsky, Peter A. and Gruis, Nelleke A. and Elder, David E. and Newton-Bishop, Julia A. and Bishop, D. Timothy and Iles, Mark M. and Helsing, Per and Amos, Christopher I. and Wei, Qingyi and Wang, Li-E and Lee, Jeffrey E. and Qureshi, Abrar A. and Kefford, Richard F. and Giles, Graham G. and Armstrong, Bruce K. and Aitken, Joanne F. and Han, Jiali and Hopper, John L. and Trent, Jeffrey M. and Brown, Kevin M. and Martin, Nicholas G. and Mann, Graham J. and Hayward, Nicholas K.},
  issn         = {1546-1718},
  language     = {eng},
  number       = {11},
  pages        = {104--1114},
  publisher    = {Nature Publishing Group},
  series       = {Nature Genetics},
  title        = {Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3},
  url          = {http://dx.doi.org/10.1038/ng.958},
  volume       = {43},
  year         = {2011},
}