The CHARGE consortium was developed after each cohort study had contracted for their genotyping platforms and decided on the selection of the individuals to be included in the GWAS. Indeed, the five cohorts used four different platforms (Table 3), which have fewer than about 60,000 SNPs in common. To maximize the availability of comparable genetic data and coverage of the genome, each cohort used recently developed methods (18,19) to impute for Europeans and European Americans their genotypes at each of the 2.5 million autosomal CEPH HapMap SNPs. Prior to imputation, individuals were excluded for low call rates or sex mismatches (Table 3). Next, criteria such as high levels of missingness, highly significant departures from Hardy-Weinberg equilibrium, or low minor allele frequencies (MAF) were used to determine which SNPs to include in the imputation step. All the remaining individuals and SNPs entered the imputation process, which provided estimates for all the HapMap SNPs, including any that may have failed the data-cleaning criteria.
