Genotyping for the eMERGE network was performed by the Center for Inherited Disease Research (CIDR) and the Broad Institute. All individuals that met the inclusion criteria (n = 501) were genotyped for >1.1 million SNPs using the Illumina 1M BeadChip at the Broad Institute. Data were cleaned by the eMERGE QC pipeline (Zuvich et al. 2011). Individuals with cryptic relatedness, ancestry inconsistent with observer- or self-reported ancestry, anomalous X-chromosome heterozygosity or poor genotyping efficiency were removed from further analysis (n = 46). All markers that were intensity only probes that had technical failure, minor allele frequency ≤ 0.05, genotyping efficiency <99%, discordant calls with duplicates, and Mendelian errors >0 were removed. Tests of association were performed with and without SNP that deviated from Hardy Weinberg Equilibrium (p-value <1.0 × 10 −4), and consistent findings were observed for both SNP sets (data not shown).
