Ancestrally poorly-matched public controls and batch genotype effects that can occur when genotyping study samples and public controls from different populations at different times can have detrimental effects on power and type I error. We evaluated the impact of these factors for a study design that included 2,000 study cases, 2,000 study controls, and 5,000 public controls for a multiplicative disease model with susceptibility allele frequency fD = 0.3, K = 0.10 and GRR = 1.3 (Model 1).
