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 on Caucasian samples have not revealed strong systematic differences in allele frequencies between previously genotyped public controls and study samples (Hom et al., 2008;Luca et al., 2008;Silverberg et al., 2009;Wrensch et al., 2009;Yu et al., 2008). However, results from a recent study that used public controls have raised concerns about the impact of batch genotype effects when cases and controls are genotyped on different platforms (Sebastiani et al., 2010). In our examples, modest systematic differences in ancestry between public and study samples had little impact on power (Table 3) or type I error (data not shown) when the estimated proportion of ancestry for each subject was included as a covariate in the model. These results are consistent with a recent report advocating the use of public controls (Zhuang et al., 2010). Batch genotype effects, before and after accounting for systematic batch effects across all SNPs, had either a negative or positive impact on power (Tables 4 and 5) and resulted
