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Genome-wide association study identifies three new melanoma susceptibility loci

Barrett, Jennifer H.; Iles, Mark M.; Harland, Mark; Taylor, John C.; Aitken, Joanne F.; Andresen, Per Arne; Akslen, Lars A.; Armstrong, Bruce K.; Avril, Marie-Francoise and Azizi, Esther, et al. (2011) In Nature Genetics 43(11). p.98-1108
Abstract
We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with melanoma and 1,982 study-specific control individuals of European ancestry, as well as an additional 6,426 control subjects from French or British populations, all of whom were genotyped for 317,000 or 610,000 single-nucleotide polymorphisms (SNPs). Our analysis replicated previously known melanoma susceptibility loci. Seven new regions with at least one SNP with P < 10(-5) and further local imputed or genotyped support were selected for replication using two other genome-wide studies (from Australia and Texas, USA). Additional replication came from case-control series from the UK and... (More)
We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with melanoma and 1,982 study-specific control individuals of European ancestry, as well as an additional 6,426 control subjects from French or British populations, all of whom were genotyped for 317,000 or 610,000 single-nucleotide polymorphisms (SNPs). Our analysis replicated previously known melanoma susceptibility loci. Seven new regions with at least one SNP with P < 10(-5) and further local imputed or genotyped support were selected for replication using two other genome-wide studies (from Australia and Texas, USA). Additional replication came from case-control series from the UK and The Netherlands. Variants at three of the seven loci replicated at P < 10(-3): an SNP in ATM (rs1801516, overall P = 3.4 x 10(-9)), an SNP in MX2 (rs45430, P = 2.9 x 10-9) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 x 10(-10)). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 x 10(-7) under a fixed-effects model and P = 1.2 x 10(-3) under a random-effects model). These newly associated variants showed no association with nevus or pigmentation phenotypes in a large British case-control series. (Less)
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Nature Genetics
volume
43
issue
11
pages
98 - 1108
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Nature Publishing Group
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  • wos:000296584000015
  • scopus:80054996042
ISSN
1546-1718
DOI
10.1038/ng.959
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English
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@article{a377bfc7-3220-4e86-aa3b-acc8b4b00ab7,
  abstract     = {We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with melanoma and 1,982 study-specific control individuals of European ancestry, as well as an additional 6,426 control subjects from French or British populations, all of whom were genotyped for 317,000 or 610,000 single-nucleotide polymorphisms (SNPs). Our analysis replicated previously known melanoma susceptibility loci. Seven new regions with at least one SNP with P &lt; 10(-5) and further local imputed or genotyped support were selected for replication using two other genome-wide studies (from Australia and Texas, USA). Additional replication came from case-control series from the UK and The Netherlands. Variants at three of the seven loci replicated at P &lt; 10(-3): an SNP in ATM (rs1801516, overall P = 3.4 x 10(-9)), an SNP in MX2 (rs45430, P = 2.9 x 10-9) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 x 10(-10)). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 x 10(-7) under a fixed-effects model and P = 1.2 x 10(-3) under a random-effects model). These newly associated variants showed no association with nevus or pigmentation phenotypes in a large British case-control series.},
  author       = {Barrett, Jennifer H. and Iles, Mark M. and Harland, Mark and Taylor, John C. and Aitken, Joanne F. and Andresen, Per Arne and Akslen, Lars A. and Armstrong, Bruce K. and Avril, Marie-Francoise and Azizi, Esther and Bakker, Bert and Bergman, Wilma and Bianchi-Scarra, Giovanna and Bressac-de Paillerets, Brigitte and Calista, Donato and Cannon-Albright, Lisa A. and Corda, Eve and Cust, Anne E. and Debniak, Tadeusz and Duffy, David and Dunning, Alison M. and Easton, Douglas F. and Friedman, Eitan and Galan, Pilar and Ghiorzo, Paola and Giles, Graham G. and Hansson, Johan and Hocevar, Marko and Hoeiom, Veronica and Hopper, John L. and Ingvar, Christian and Janssen, Bart and Jenkins, Mark A. and Jönsson, Göran B and Kefford, Richard F. and Landi, Giorgio and Landi, Maria Teresa and Lang, Julie and Lubinski, Jan and Mackie, Rona and Malvehy, Josep and Martin, Nicholas G. and Molven, Anders and Montgomery, Grant W. and van Nieuwpoort, Frans A. and Novakovic, Srdjan and Olsson, Håkan and Pastorino, Lorenza and Puig, Susana and Puig-Butille, Joan Anton and Randerson-Moor, Juliette and Snowden, Helen and Tuominen, Rainer and VanBelle, Patricia and van der Stoep, Nienke and Whiteman, David C. and Zelenika, Diana and Han, Jiali and Fang, Shenying and Lee, Jeffrey E. and Wei, Qingyi and Lathrop, G. Mark and Gillanders, Elizabeth M. and Brown, Kevin M. and Goldstein, Alisa M. and Kanetsky, Peter A. and Mann, Graham J. and MacGregor, Stuart and Elder, David E. and Amos, Christopher I. and Hayward, Nicholas K. and Gruis, Nelleke A. and Demenais, Florence and Bishop, Julia A. Newton and Bishop, D. Timothy},
  issn         = {1546-1718},
  language     = {eng},
  number       = {11},
  pages        = {98--1108},
  publisher    = {Nature Publishing Group},
  series       = {Nature Genetics},
  title        = {Genome-wide association study identifies three new melanoma susceptibility loci},
  url          = {http://dx.doi.org/10.1038/ng.959},
  volume       = {43},
  year         = {2011},
}