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Variants at the 9p21 locus and melanoma risk

Livia Maccioni1, Panduranga Sivaramakrishna Rachakonda1, Justo Lorenzo Bermejo2, Dolores Planelles3, Celia Requena4, Kari Hemminki15, Eduardo Nagore46 and Rajiv Kumar1*

Author Affiliations

1 Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany

2 Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany

3 Laboratory of Histocompatibility-Molecular Biology, Center for Blood Transfusion, Valencia, Spain

4 Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain

5 Center for Primary Health Care Research, Lund University, Malmö, Sweden

6 Universidad Católica de Valencia, Valencia, Spain

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BMC Cancer 2013, 13:325  doi:10.1186/1471-2407-13-325

Published: 2 July 2013



The influence of variants at the 9p21 locus on melanoma risk has been reported through investigation of CDKN2A variants through candidate gene approach as well as by genome wide association studies (GWAS).


In the present study we genotyped, 25 SNPs that tag 273 variants on chromosome 9p21 in 837 melanoma cases and 1154 controls from Spain. Ten SNPs were selected based on previous associations, reported in GWAS, with either melanocytic nevi or melanoma risk or both. The other 15 SNPs were selected to fine map the CDKN2A gene region.


All the 10 variants selected from the GWAS showed statistically significant association with melanoma risk. Statistically significant association with melanoma risk was also observed for the carriers of the variant T-allele of rs3088440 (540 C>T) at the 3’ UTR of CDKN2A gene with an OR 1.52 (95% CI 1.14-2.04). Interaction analysis between risk associated polymorphisms and previously genotyped MC1R variants, in the present study, did not show any statistically significant association. Statistical significant association was observed for the interaction between phototypes and the rs10811629 (located in intron 5 of MTAP). The strongest association was observed between the homozygous carrier of the A–allele and phototype II with an OR of 15.93 (95% CI 5.34-47.54).


Our data confirmed the association of different variants at chromosome 9p21 with melanoma risk and we also found an association of a variant with skin phototypes.