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. 2013 Apr;45(4):428-32, 432e1.
doi: 10.1038/ng.2571. Epub 2013 Mar 3.

A variant in FTO shows association with melanoma risk not due to BMI

Mark M Iles  1 , Matthew H Law, Simon N Stacey, Jiali Han, Shenying Fang, Ruth Pfeiffer, Mark Harland, Stuart Macgregor, John C Taylor, Katja K Aben, Lars A Akslen, Marie-Françoise Avril, Esther Azizi, Bert Bakker, Kristrun R Benediktsdottir, Wilma Bergman, Giovanna Bianchi Scarrà, Kevin M Brown, Donato Calista, Valérie Chaudru, Maria Concetta Fargnoli, Anne E Cust, Florence Demenais, Anne C de Waal, Tadeusz Dębniak, David E Elder, Eitan Friedman, Pilar Galan, Paola Ghiorzo, Elizabeth M Gillanders, Alisa M Goldstein, Nelleke A Gruis, Johan Hansson, Per Helsing, Marko Hočevar, Veronica Höiom, John L Hopper, Christian Ingvar, Marjolein Janssen, Mark A Jenkins, Peter A Kanetsky, Lambertus A Kiemeney, Julie Lang, G Mark Lathrop, Sancy Leachman, Jeffrey E Lee, Jan Lubiński, Rona M Mackie, Graham J Mann, Nicholas G Martin, Jose I Mayordomo, Anders Molven, Suzanne Mulder, Eduardo Nagore, Srdjan Novaković, Ichiro Okamoto, Jon H Olafsson, Håkan Olsson, Hubert Pehamberger, Ketty Peris, Maria Pilar Grasa, Dolores Planelles, Susana Puig, Joan Anton Puig-Butille, Juliette Randerson-Moor, Celia Requena, Licia Rivoltini, Monica Rodolfo, Mario Santinami, Bardur Sigurgeirsson, Helen Snowden, Fengju Song, Patrick Sulem, Kristin Thorisdottir, Rainer Tuominen, Patricia Van Belle, Nienke van der Stoep, Michelle M van Rossum, Qingyi Wei, Judith Wendt, Diana Zelenika, Mingfeng Zhang, Maria Teresa Landi, Gudmar Thorleifsson, D Timothy Bishop, Christopher I Amos, Nicholas K Hayward, Kari Stefansson, Julia A Newton Bishop, Jennifer H Barrett; GenoMEL Consortium; Q-MEGA and AMFS Investigators
Affiliations

A variant in FTO shows association with melanoma risk not due to BMI

Mark M Iles et al. Nat Genet. 2013 Apr.

Abstract

We report the results of an association study of melanoma that is based on the genome-wide imputation of the genotypes of 1,353 cases and 3,566 controls of European origin conducted by the GenoMEL consortium. This revealed an association between several SNPs in intron 8 of the FTO gene, including rs16953002, which replicated using 12,313 cases and 55,667 controls of European ancestry from Europe, the USA and Australia (combined P = 3.6 × 10(-12), per-allele odds ratio for allele A = 1.16). In addition to identifying a new melanoma-susceptibility locus, this is to our knowledge the first study to identify and replicate an association with SNPs in FTO not related to body mass index (BMI). These SNPs are not in intron 1 (the BMI-related region) and exhibit no association with BMI. This suggests FTO's function may be broader than the existing paradigm that FTO variants influence multiple traits only through their associations with BMI and obesity.

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Figures

Figure 1
Figure 1
Results of stratified trend tests of imputed data for association with melanoma in region around FTO in GenoMEL Phase 1 and 2 data combined. −log10p values for association between SNPs in the region of FTO and melanoma case-control status are shown adjusted for geographic region. Colour of points indicates degree of LD with rs16953002 (indicated by purple square). SNPs genotyped in all GenoMEL samples are plotted as circles, SNPs imputed in all samples as crosses and SNPs genotyped in some samples and imputed in others (as a result of chip differences) as squares. Positions of genes are given underneath the graph and estimated recombination rates also given by the blue line along the bottom, with scale on the right hand axis. Plot produced using LocusZoom.
Figure 2
Figure 2
Forest plot of estimated per-allele ORs and p-values for effect of rs16953002 on melanoma risk. Horizontal bars indicate 95% confidence intervals. Results shown for GenoMEL Phase 1 discovery data and subsequent replication data with meta-analysis for replication data only and all data.
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