Genome-wide association study of nevus count on the outer arm 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 nevus count the outer arms.

Sample: GWAS analysis only includes samples of European ancestry. total nevus count were counted by trained research nurse. outer arms were defined by what was visible to the nurse when the participants were standing face on to the nurse with arms rotated so the back of the hands were facing forwards.

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