SNP QC is detailed in the Supplementary Note. Briefly, QC included removal of SNPs for non-unique probe mapping to NCBI Build 37/UCSC hg19, low minor allele frequency (< 0.005, determined empirically), substantial deviation from HapMap3 CEU founder allele frequencies, deviation from Hardy-Weinberg equilibrium (pHWE < 1×10−8), or high missingness (> 0.05). Subjects were eliminated from analysis for high missingness (> 0.05), outlying genome-wide homozygosity or ancestry, discrepant genetic and phenotypic sex, or twin relatedness inconsistent with monozygosity or dizygosity. The resulting genotypes were of high quality, with relatively low SNP and subject missingness (97.5th percentiles of 0.035 and 0.020. Among 714 monozygotic twin pairs, the intrapair agreement for 686,895 autosomal SNPs was 0.9985. Prior genome-wide genotyping using a Perlegen four-chip platform was available for 2,219 subjects and 110,588 SNPs, 75 and had 0.9996 agreement with Affymetrix 6.0 genotyping.
