Centralized repositories for genome-wide association study (GWAS) data, such as the database of Genotypes and Phenotypes (dbGaP) and the European Genome-phenome Archive (EGA), were established to encourage data sharing in an effort to advance medical science while maximizing use of publicly funded resources. One of the great promises of publicly sharing GWAS data through these repositories is the potential to create composite sets of public controls for new studies. Combining phenotypic and genotypic data from several studies into a single population control group and pairing these combined data with cases of the phenotype of interest allow for powerful opportunities to identify new genetic associations. Publicly available controls might also be used to augment study controls to increase sample size and boost statistical power (Ho and Lange 2010; Mukherjee et al. 2011; Zhuang et al. 2010). These study designs provide a cost-effective strategy to obtain the large number of control subjects needed for GWAS analyses, which may be particularly beneficial for ancestry groups with fewer available samples (e.g., African Americans) (Hartz et al. 2011). However, publicly available GWAS differ in many
