Details of the genotyping procedures are provided in (Miller et al., in press). In short, genome-wide genotyping was done on the Illumina Human660W-Quad Array, which contains a total of 561,490 SNPs. Markers were excluded if: 1) they had been identified as a poorly genotyped marker by Illumina; 2) had more than one mismatch in duplicated QC samples; 3) had a call rate <99%; 4) had a MAF <1%; 5) had more than 2 Mendelian inconsistencies across families; 6) significantly deviated from Hardy-Weinberg equilibrium at p<1e-7; 7) was an autosomal marker but associated with sex at p<1e-7; 8) had a significant batch effect at p<1e-7; or 8) there were more than 2 heterozygous X chromosome calls for males or mitochondrial calls for anyone. A total of 32,153, or 5.7% of the markers attempted, failed one or more of these quality control filters, leaving 527,829 markers that passed all QC filters. Of these, 515,384 were autosomal and used in the present study. Genotyping was attempted on samples from 7,438 participants. Samples were eliminated if: 1) they had >5000 no-calls; 2) had a
