As previously described in more detail (Shi et al. 2009), DNA samples were genotyped using the Affymetrix 6.0 array at the Broad Institute. Samples (5.3%) were excluded for high missing data rates, outlier proportions of heterozygous genotypes, incorrect sex or genotypic relatedness to other subjects. SNPs (7% for AA, 25% for EA and 27% for combined analyses) were excluded for minor allele frequencies < 1%, high missing data rates, Hardy–Weinberg deviation (controls), excessive Mendelian errors (trios), discordant genotypes (duplicate samples) or large allele frequency differences among DNA plates. Principal component scores reflecting continental and within-Europe ancestries of each subject were computed and outliers were excluded. Genomic control λ values for autosomes after quality control procedures were 1.005 and 0.998 for the AA and EA samples, respectively.
