Details of MGS subject recruitment and sample characteristics are provided in the online Full Methods (section A1). 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 African American, 25% for European-ancestry and 27% for combined analyses) were excluded for minor allele frequencies less than 1%, high missing data rates, Hardy-Weinberg deviation (controls), or 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 excluded. Genomic control λ values for autosomes after QC were 1.042 for African American and 1.087 for the larger European-ancestry and combined analyses.
