In many consortia or collaborations, different studies' samples may be genotyped on different platforms or may be genotyped using different versions of the same technology. This is particularly true when large studies are conducted over time because the technology is continuously evolving. Imputation tries to address these differences [Li et al., 2009], but this, too, can create more uncertainties in data comparability when investigators use different software packages to impute data. In GENEVA, genotyping is being performed on both Affymetrix and Illumina platforms with varying degrees of single nucleotide polymorphism (SNP) coverage. In addition, the two platforms detect different sets of SNPs. Plans to conduct imputation vary widely across studies, and there has been considerable discussion regarding the comparability of imputation results performed at different sites using different HapMap reference panels [http://hapmap.ncbi.nlm.nih.gov] and software packages (MACH [http://www.sph.umich.edu/csg/abecasis/MACH/index.html; Li et al., 2009; Li et al., 2006], Impute [https://mathgen.stats.ox.ac.uk/impute/impute.html; Marchini et al., 2007; Howie et al., 2009] and BEAGLE [https:faculty.washington.edu/browning/beagle/beagle.html; Browning and Browning, 2009] being the most common). Most WGs are utilizing individual investigators' imputation results and reviewing preliminary analyses of individual
