We split the controls by data source (iControl vs. SAGE controls) and performed the following QC steps using PLINK. We implemented stringent thresholds and removed additional SNPs showing low levels of differential missingness between cases and controls (p<0.05), modest deviation from Hardy-Weinberg expectation (p<0.05), and significant platform effect after adjustment for all ten principal components (p<0.001). In addition, individuals with genotype call rate <99.9%, or with a high degree of relatedness (pi-hat>0.05) were removed (Table S1). To assess any residual cross-platform artifacts that might artificially elevate the heritability estimate, we conducted a dummy case-control GWAS by assigning case status to the iControl data (N = 1,104) and control status to the SAGE Controls (N = 2,190). We detected no significant association with platform “phenotype” by logistic regression (Figure S1) or “heritability” between cross-platform controls (h2 = 10−6, se = 0.11) (Table S2). Additionally, we analyzed ten permutations of the dummy case phenotype and detected no significant heritability in any permuted analysis. In addition to these QC steps, we examined the data for any possible residual population stratification or cryptic relatedness, which is described in depth in the Supplementary Methods (Figures S1, S2, S3, S4). The quality control and matching steps
