Sample and SNP QC were initially performed within each platform separately (Figure S1). Samples were removed for autosomal call rates <98%, discrepancy between phenotypic and genetic sex, and indeterminate genetic sex. In addition, all 151 cases from one site were removed due to increased rates of missing SNP data relative to other sites (Figure S2). Platform-specific SNP QC included removing monomorphic SNPs, CNV-targeted SNP probes, SNPs with genotyping rate <98%, and strand-ambiguous SNPs with significant allele frequency differences or aberrant LD correlations with adjacent SNPs based on the entire HapMap2 reference panel. Concordance was checked between 82 duplicates genotyped both on the 610-Quad (Broad) and 370K (Yale), as well as 41 duplicates genotyped on the 610Quad and 550v1. In addition, concordance was examined in HapMap duplicates from the Illumina database genotyped on 2 or more platforms used in this study. No SNPs were identified with significant association between the two 610-Quad genotyping batches.
