To control for Type I error due to residual population stratification, case and control samples were separated into subpopulations of European (EU), South African Afrikaner (SA) and Ashkenazi Jewish (AJ) ancestry, using Multi-Dimensional Scaling (MDS) analysis (Supplementary Figures S2-4). Population stratification outliers and those lacking genomically-matched controls or cases were excluded, as were samples with excessive low-level relatedness to many others within each subpopulation. Separate association analyses were conducted for each of the case-control subsamples (EU, SA and AJ) and for the trio samples. For the former, logistic regression was employed using an additive test model (1 df), with diagnostic status as the dependent variable and each single SNP as the predictor, including specific ancestry-informative MDS axes as covariates (EU= 4 factors, SA= 2 factors, and AJ=1 factor). For the latter, the Transmission Disequilibrium Test (TDT) was used.
