Genotyping was performed using the Illumina 1M and Illumina OmniExpress (Illumina, San Diego, CA), and Smokescreen (BioRelm, Walnut, CA) arrays. The reported pedigree structure was assessed using a pruned set of 1,519,440 SNPs. Family structures were altered, as needed, and SNP genotypes were tested for Mendelian inconsistencies (Pedcheck; O’Connell & Weeks, 1998) with the revised family structure. Genotype inconsistencies were set to missing. Genotypes were imputed to 1000 Genomes (EUR and AFR, Phase 3, b37, October 2014; build hg19) using SHAPEIT (Delaneau, Zagury, & Marchini, 2013) and then IMPUTE2 (Howie, Fuchsberger, Stephens, Marchini, & Abecasis, 2012). Imputed SNPs with information (INFO) scores < 0.30 or individual genotype probability scores < 0.90 were excluded, as were palindromic SNPs (A/T or C/G), monomorphic SNPs, SNPs with a genotyping rate of < 95%, SNPs that did not pass Hardy-Weinberg equilibrium (HWE; p < 1 × 10−6), and SNPs with a minor allele frequency (MAF) < 0.05%. In total, 6,881,872 SNPs were available for analysis after passing quality control and data cleaning thresholds.
