To confirm pedigree structure, a set of 47,000 variants genotyped on all four arrays were used. These variants met the following criteria: 1. not in linkage disequilibrium (LD, defined as r2 <0.5); 2) minor allele frequency (MAF) >10%; 3) Hardy-Weinberg Equilibrium (HWE) p-value >0.001; and 4) missing rate <2%. Pairwise identity by descent was computed using PLINK (Purcell et al., 2007) to confirm family relationships. When necessary, family structures were altered accordingly. The same set of 47,000 variants was also used to estimate principal components (PCs) of population stratification using Eigenstrat (Price et al., 2006). Based on the first two PCs, each individual was assigned an ancestry (i.e. African-American, European-American, or Other). Family ancestry was assigned based on the individual ancestry of the greatest proportion of family members.
