A genome-wide association study identifies novel gene associations with facial skin wrinkling and mole count in Latin Americans

Background Genome-wide association studies (GWASs) have identified genes influencing skin ageing and mole count in Europeans, but little is known about the relevance of these (or other genes) in non-Europeans. Objectives To conduct a GWAS for facial skin ageing and mole count in adults < 40 years old, of mixed European, Native American and African ancestry, recruited in Latin America. Methods Skin ageing and mole count scores were obtained from facial photographs of over 6000 individuals. After quality control checks, three wrinkling traits and mole count were retained for genetic analyses. DNA samples were genotyped with Illumina's HumanOmniExpress chip. Association testing was performed on around 8 703 729 single-nucleotide polymorphisms (SNPs) across the autosomal genome. Results Genome-wide significant association was observed at four genome regions: two were associated with wrinkling (in 1p13 center dot 3 and 21q21 center dot 2), one with mole count (in 1q32 center dot 3) and one with both wrinkling and mole count (in 5p13 center dot 2). Associated SNPs in 5p13 center dot 2 and in 1p13 center dot 3 are intronic within SLC45A2 and VAV3, respectively, while SNPs in 1q32 center dot 3 are near the SLC30A1 gene, and those in 21q21 center dot 2 occur in a gene desert. Analyses of SNPs in IRF4 and MC1R are consistent with a role of these genes in skin ageing. Conclusions We replicate the association of wrinkling with variants in SLC45A2, IRF4 and MC1R reported in Europeans. We identify VAV3 and SLC30A1 as two novel candidate genes impacting on wrinkling and mole count, respectively. We provide the first evidence that SLC45A2 influences mole count, in addition to variants in this gene affecting melanoma risk in Europeans.