Subjects within SAGE were genotyped using the ILLUMINA Human 1M platform. Quality control of the sample included: (1) removal of non-autosomal SNPs, (2) removal of markers with an allele frequency <1%, (3) exclusion of markers with a call rate less than 98%, and (4) removal of SNPs that show evidence of deviation from Hardy–Weinberg Equilibrium (HWE; p-value < 0.0001) to minimize any possible bias due to assortative mating (Agrawal et al., 2006, Grant et al., 2007). A total of 796,125 autosomal SNPs were carried forward in the analyses. These same SNPs were also used to conduct the aforementioned selection of distantly related EA individuals from the entire set of SAGE participants (N=4121) (i.e., using the software package: Genomewide Complex Trait Analysis [GCTA])(Yang et al., 2010, Lee et al., 2011, Yang et al., 2011).
