Clearly the greatest cause for concern when using public control genotype data is that observed allele frequency differences between public controls and study cases may be the consequence of systematic bias due to population stratification or batch genotype effects from differential allele calling between the two samples (Moskvina et al., 2006;Neale and Purcell, 2008). Greater differences in background ancestry will likely occur between public controls and study cases than between study cases and a carefully selected set of study controls from the same community. The impact of population stratification can be largely remedied by employing appropriate analytic methods (Price et al., 2006;Roeder and Luca, 2009;Yu et al., 2008), though these methods may not adequately alleviate biased results for a relatively small number of genetic markers under strong selective pressure such as those witnessed by the WTCCC study, that found highly significant differences in allele frequencies for a small number of loci between individuals of Caucasian descent from different communities in Great Britain (Wellcome Trust Case Control Consortium, 2007). Results from several GWA studies that have included public control genotype data
