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Abstract 1645: Genome-wide association studies identify several new loci for human pigmentation traits

Genome-wide association studies (GWASs) have been widely conducted and numerous new loci have been associated with various outcomes. Multiple GWASs have been completed in the Nurses’ Health Study and the Health Professionals Follow-up Study, and we have accrued more than 15,000 individuals with genome-wide genotype data. More recently, with the data released from the 1000 Genomes Project, we have imputed about 10 million SNPs based on the genotyped SNPs and haplotypes from the 1000 Genomes Project. Based on the knowledge that light human pigmentation is a host risk factor for skin cancer development, we conducted the GWASs on pigmentary traits in multiple GWAS datasets in the two cohorts using the newly imputed data. We systematically evaluated the traits of natural hair color (ordinal coding from blonde, light brown, dark brown to black, excluding red hair color), eye colors (blue, green and brown eye colors as co-dominant outcomes), tanning ability (ordinal coding from practically no tan, moderate tan to deep tan) and the number of sunburns (continuous variable). We adjusted for the four largest principal components of genetic variation in the regression model for each component dataset, and performed a meta-analysis to combine the results of all these datasets. No systematic deviation from the expected distribution was detected for any of these pigmentation GWASs. Using a multistage study design, we identified a new region on chromosome 13q22 associated with natural hair color that reached the GWAS significance level. The most significant SNP in this region reached a p-value of 2.4 ×10 −14 (p = 5.4×10 −9 in the discovery stage and p = 1.2×10 −6 in the replication stage). We also newly identified and replicated the association of a SNP on 1q32.3 with brown eye color (p = 7.0×10 −8 in the combined set), a SNP on 5p15 with green eye color (p = 9.1×10 −7 in the combined set), and a SNP on 11q25 with the number of sunburns (p = 5.6×10 −6 in the combined set). Of note, the SNP associated with the number of sunburns was also associated with the expression of a local gene based on the transcript expression profiling data of 87 HapMap CEU cell lines (NCBI GEO database, accession GSE7792). These novel pigmentation SNPs identified by our GWASs are strong candidates to evaluate skin cancer risk. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1645. doi:1538-7445.AM2012-1645