Population stratification was assessed through multidimensional scaling (MDS) analysis; individuals of non-European ancestry and extreme outliers on each of the MDS components were removed (Supplemental Methods and Figure S1). Case-control matching was verified across all MDS components. The final post-quality control GWAS2 sample contained 2,711 cases and 3,762 ancestry-matched controls and 550,550 SNPs; the final GWAS2 FAM sample contained 548 cases/family members, 597 ancestry-matched controls and 236,748 SNPs. The final TIC sample included 591 cases and 1206 ancestry-matched controls and 581,774 SNPs (Table S2).
