Genome-wide association study of full body nevus count in the Brisbane Twin Nevus Study (BTNS)

The project uses the Brisbane Twin Nevus Study (BTNS) (N=3863)) to compare nevus counts on different anatomical sites to assess which anatomical site serves as best proxy for counting nevi on the whole body.In the project, a GWAS of nevus count on the whole body and GWAS of nevus count on the outer arm are performed.Here is the GWAS of total nevus count. Sample: GWAS analysis only includes samples of European ancestry. total nevus count were counted by trained research nurse. Genotype: All genotypes were imputed to a human haplotype map (HapMap) reference panel. Genome-wide association analyses were performed using Genome-wide Efficient Mixed model Association (GEMMA), which can account for genetically related individuals such as twins and siblings. Sex, age, age2, sex*age, sex*age2, sunburn, BSA, sun exposed hours weighted by UV index and 5 PCs, additionally two batch effect variables; were included as covariates. SNP imputation quality filter retained SNP with an INFO > 0.3. minor allele frequency frequency filter was applied to retain SNP MAF > 0.1 Columns include: CHR: Chromosome BP: Base pair SNP: rsID A1: Effect allele A2: Non-effect allele A1FQ: Effect allele frequency HWE: Hardy-Weinberg Equilibrium BETA: Effect estimate (of effect allele_ SEB: Standard error of beta PRB: P value N: Per SNP sample size