SNPs were genotyped for all members of all families in the Minnesota Center for Twin and Family Research (N = 7438) on an Illumina 660quad array using DNA derived from whole blood for approximately 90% of the sample and from saliva samples for the remainder. For quality control purposes, each 96-well plate included DNA from two members of a single CEPH family (rotated across plates) and one duplicate sample. Markers were excluded if (see ref (Miller, et al., submitted) for additional details): 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. In total, 32,153
