Quality control (QC) was first performed on genotype data generated from the OmniExpress. Genotypes for individuals with a genotype rate <98% were excluded from analysis, and SNPs with a genotyping rate <98% were excluded from analysis. Further details can be found in Kang et al (Kang et al., 2012). Genotypes of the 51 overlapping individuals were then compared. There were 571 of 544,276 SNPs genotyped on both arrays with two or more non-missing and different genotypes, which were excluded from all further analyses. There were 442 genotyped founders used to remove SNPs which violated Hardy-Weinberg equilibrium (HWE; p<10−6). SNPs with minor allele frequency less than 5% were also removed from further analysis. After combining the data generated from the two arrays in the members of these 118 families, pedigree structure was reviewed and modified, as described in Kang et al (Kang et al., 2012).
