Modern commercial genotyping platforms have increasingly high accuracy in genotype calling, but small systematic biases in genotyping calling when genotyping cases and controls at different times or on different platforms can create artificial differences in genotype frequencies between them. Careful study design can alleviate these concerns when genotyping study cases and controls at the same time, but using public controls will always be a concern. We assessed the impact of batch genotype effects on power for the one- and two-stage designs. We assumed that batch genotype effects would result in systematic and over or under calling of the susceptibility allele on an allele-by-allele basis (i.e. the probability an allele in a genotype being miscalled was assumed to be independent of the calling for the other allele). We additionally assumed that all subjects genotyped at the same time were subject to the same batch effect, effecting any cases and controls genotyped together equally. Over or under calling of the susceptibility allele was allowed to occur with different probabilities for each genotyping platform (e.g. for our proposed two-stage design there were three
