The sample was genotyped on the Illumina HumanExome BeadChip array and the Illumina 660W Quad. Extensive description of the 660W-Quad genome-wide array in this sample was published previously(26) and is extremely similar to the description of the exome array, so we omit it for space. The Illumina HumanExome chip included 247,737 SNPs. All samples were clustered together in GenomeStudio, and markers showing evidence of poor quality, such as lower call rates, poor cluster separation, deviation from Hardy-Weinberg equilibrium, or rare (0≤MAF<0.0001) and incomplete call rate (<1.0), were manually reviewed and reclustered or discarded (n~5,000). After removing SNPs identified by Illumina as having technical defects we had 247,186 SNPs for further QC testing. A total of 1,250 markers were dropped in our QC screen: 503 SNPs had a no-call rate exceeding 1%, 52 had a Hardy-Weinberg test p-value less than the Bonferroni cutoff of 2e−7, 28 autosomal markers were associated with participant sex (p<2e−7) and 793 SNPs had two or more errors of any of these kinds: incorrect call in a CEPH sample, discordant calls in a pair of duplicated samples
