Operational details of each of the 16 GWAS (including genotyping platforms, quality control filters for individuals and SNPs, and imputation and data analysis methods) can be found in Table S5. In summary, stage 1 genotypes were derived using different genotyping platforms; Affymetrix 500 k, Illumina HumanHap 550, Illumina HumanCNV-370DUO, Illumina HumanHap300 Duo Infinium, or Illumina HumanHap 300. To obtain a marker set that was common to all studies, and to increase overall coverage of the whole genome, we imputed all SNPs reported in the CEU sample in HapMap Phase II using imputation algorithms, yielding a maximum of 2,573,738 million SNPs available for analysis in one or more studies. Imputations were performed after excluding samples and SNPs that did not meet the study-specific quality control criteria. Genotypes were imputed for SNPs not present in the genome-wide arrays or for those where genotyping had failed to meet the QC criteria. We used either of two different software packages for the imputation: MACH [33] (http://www.sph.umich.edu/csg/abecasis/MACH/index.html) and IMPUTE [34] (http://www.stats.ox.ac.uk/~marchini/software).
