There are a total of 561,490 SNP markers (including sex chromosome and mitochondrial markers) on the Illumina Human660W-Quad array, but a set of 1,508 SNPs could not be called in any batch. The remaining 559,982 markers were subjected to nine separate QC filters. These QC filters along with both the number and percentage of markers failing each are listed here: (1) Identified by Illumina as a bad marker on the array (N=23, < 0.1%); (2) more than one mismatch in duplicated samples (N=70, < 0.1%); (3) call rate < 99% (N=3,924, 0.7%); (4) minor allele frequency less than 1% (N=19,999, 3.6%); (5) more than two Mendelian inconsistencies across families (N=9,117, 1.6%); (6) significant deviation from Hardy-Weinberg genotype frequencies in the white sample at p < 10−7 (N=1,200, 0.2%); (7) autosomal or X marker associated with participant sex at p < 10−7 (N=16, < 0.1%); (8) significantly associated with batch at p < 10−7 (N=17, < 0.1%); and (9) markers with more than 2 heterozygous calls if they were on the X chromosome in male samples or from mitochrondrial DNA in
