Summary files on a common set of SNPs were shared among the EVE investigators. The common set of SNPs consisted of all Phase 2, Release 21 consensus HapMap variants. Prior to genotype imputation, each center oriented their SNPs to the plus strand, and filtered for call rates (> 95%) and consistency with Hardy-Weinberg expectations (p > 10−5 for case/control studies, p > 10−6 for trio studies). Genotype imputation using HapMap reference panels were performed separately in each sample with the program MACH25, and associations were tested using the genotype dosages that are part of the imputation algorithms output, with adjustments for admixture in the African American and Latino case-control samples (see Supplementary Note online). The shared summary files contained the SNP identifiers (rs number, chromosome, position, alleles), SNP QC metrics (call rate, Hardy-Weinberg equilibrium p-value, imputation quality metrics), and information related to the test for association (allele frequencies in cases and controls or in the transmitted and untransmitted alleles in trios, association p-value, odds ratios with standard errors). Reference alleles were assigned as the allele coded 0 in the HapMap
