We chose a panel of M structure inference SNPs for the detection and correction of population substructure in a GWAS with a total of N cases and controls. The genotype at a marker locus is coded as 0, 1 or 2, corresponding to the copy number of an arbitrary allele. Let gi,m be the genotype measured at SNP m for the ith subject, 1≤i≤N, 1≤m≤M. The PCA summarizes the information measured on M structure inference SNPs and represents study participants by their projected positions (called principal components, or PCs) along a few orthogonal axes with “large” genetic variations.
