After basic quality control, 77,986 autosomal SNPs directly genotyped on all four GWAS platforms were extracted and pruned to remove SNPs in LD (r2> 0.05) or with minor allele frequency < 0.05, leaving 39,239 SNPs suitable for robust relatedness testing and population structure analysis. Relatedness testing was done with PLINK90 and pairs of subjects with π(x00302) > 0.2 were identified and one member of each relative pair removed at random. Principal component estimation was done with the same collection of SNPs. We tested 20 principal components for phenotype association (using logistic regression with batch indicator variables included as covariates) and evaluated their impact on the genome-wide test statistics using λ 19 after genome-wide association of the specified principal component, and 11 principal components were included in all association analyses.
