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Background  Few high penetrance genes are known in Malignant Melanoma (MM), however, the involvement of low-penetrance genes such as  MC1R ,  OCA2, ASIP ,  SLC45A2  and  TYR  has been observed. Lately, genome-wide association studies (GWAS) have been the ideal strategy to identify new common, low-penetrance susceptibility loci. In this case–control study, we try to validate in our population nine melanoma associated markers selected from published GWAS in melanoma predisposition.    Methods  We genotyped the 9 markers corresponding to 8 genes ( PARP1, MX2, ATM, CCND1, NADSYN1, CASP8, IRF4  and  CYP2R1 ) in 566 cases and 347 controls from a Spanish population using KASPar probes. Genotypes were analyzed by logistic regression and adjusted by phenotypic characteristics.    Results  We confirm the protective role in MM of the rs3219090 located on the  PARP1  gene (p-value 0.027). Additionally, this SNP was also associated with eye color (p-value 0.002). A second polymorphism, rs12203592, located on the  IRF4  gene was associated with protection to develop MM for the dominant model (p-value 0.037). We have also observed an association of this SNP with both lentigines (p-value 0.014) and light eye color (p-value 3.76 × 10 -4 ). Furthermore, we detected a novel association with rs1485993, located on the  CCND1  gene, and dark eye color (p-value 4.96 × 10 -4 ). Finally, rs1801516, located on the  ATM  gene, showed a trend towards a protective role in MM similar to the one firstly described in a GWAS study.    Conclusions  To our knowledge, this is the first time that these SNPs have been associated with MM in a Spanish population. We confirmed the proposed role of rs3219090, located on the  PARP1  gene, and rs12203592, located on the  IRF4  gene, as protective to MM along the same lines as have previous genome-wide associated works. Finally, we have seen associations between  IRF4, PARP1 , and  CCND1  and phenotypic characteristics, confirming previous results for the  IRF4  gene and presenting novel data for the last two, suggesting that pigmentation characteristics correlated with eye color are potential mediators between  PARP1  and MM protection.

Genetic variants in PARP1 (rs3219090) and IRF4(rs12203592) genes associated with melanoma susceptibility in a Spanish population