We used the Versatile Gene-based Association Study (VEGAS) program to conduct gene-based tests of association (Liu et al., 2010). VEGAS assigns individual SNPs to each of the 17,787 autosomal genes (by physical position on the UCSC hg18 Genome Browser assembly). P-values from the GWAS are converted to upper-tailed chi-square statistics and then used to examine whether the chi-square distribution for each gene deviates from the null distribution. Due to differing linkage disequilibrium patterns across ethnicities, gene-based association was conducted on results when EA (using CEU) and AA (using YRI) subjects were analyzed separately.
