in the cases then power increased to 0.99. A similar pattern, but less dramatic differences, were observed for the single-stage study design with both public and study controls. Both single-stage studies that include public controls experienced some loss in power when accounting for the mean systematic inflation in the test statistics for all other SNPs across the genome due to batch genotype effects. Regardless of batch effects, the single-stage study that includes both public and study controls always had greater power than the single-stage study with only study controls.
