Title |
Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions
|
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Published in |
International Journal of Cancer, August 2014
|
DOI | 10.1002/ijc.29099 |
Pubmed ID | |
Authors |
Jennifer H. Barrett, John C. Taylor, Chloe Bright, Mark Harland, Alison M. Dunning, Lars A. Akslen, Per A. Andresen, Marie‐Françoise Avril, Esther Azizi, Giovanna Bianchi Scarrà, Myriam Brossard, Kevin M. Brown, Tadeusz Dębniak, David E. Elder, Eitan Friedman, Paola Ghiorzo, Elizabeth M. Gillanders, Nelleke A. Gruis, Johan Hansson, Per Helsing, Marko Hočevar, Veronica Höiom, Christian Ingvar, Maria Teresa Landi, Julie Lang, G. Mark Lathrop, Jan Lubiński, Rona M. Mackie, Anders Molven, Srdjan Novaković, Håkan Olsson, Susana Puig, Joan Anton Puig‐Butille, Nienke van der Stoep, Remco van Doorn, Wilbert van Workum, Alisa M. Goldstein, Peter A. Kanetsky, Paul D. P. Pharoah, Florence Demenais, Nicholas K. Hayward, Julia A. Newton Bishop, D. Timothy Bishop, Mark M. Iles, on behalf of the GenoMEL Consortium |
Abstract |
At least 17 genomic regions are established as harboring melanoma susceptibility variants, in most instances with genome-wide levels of significance and replication in independent samples. Based on genome-wide single nucleotide polymorphism (SNP) data augmented by imputation to the 1,000 Genomes reference panel, we have fine mapped these regions in over 5,000 individuals with melanoma (mainly from the GenoMEL consortium) and over 7,000 ethnically matched controls. A penalized regression approach was used to discover those SNP markers that most parsimoniously explain the observed association in each genomic region. For the majority of the regions, the signal is best explained by a single SNP, which sometimes, as in the tyrosinase region, is a known functional variant. However in five regions the explanation is more complex. At the CDKN2A locus, for example, there is strong evidence that not only multiple SNPs but also multiple genes are involved. Our results illustrate the variability in the biology underlying genome-wide susceptibility loci and make steps toward accounting for some of the "missing heritability." |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 1 | 2% |
Belgium | 1 | 2% |
Unknown | 54 | 96% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 14 | 25% |
Researcher | 12 | 21% |
Professor > Associate Professor | 5 | 9% |
Student > Bachelor | 4 | 7% |
Professor | 3 | 5% |
Other | 7 | 13% |
Unknown | 11 | 20% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 15 | 27% |
Agricultural and Biological Sciences | 13 | 23% |
Medicine and Dentistry | 13 | 23% |
Mathematics | 1 | 2% |
Veterinary Science and Veterinary Medicine | 1 | 2% |
Other | 2 | 4% |
Unknown | 11 | 20% |