were very disimilar in terms of e.g. socioeconomic background, smoking patterns etc, resulting in phenotypic differences between cases and controls unrelated to the disease in question, but related to the environmental exposure patterns. These effects could possibly show up in a GWA analysis, although the effects would have to be large and the differential sampling would have to be very pronounced. Considering the current difficulty of finding small genuine effects for complex traits in optimally designed case and control studies, such generating of false positives due to confounding may not be a particular problem in practice, but, with ever increasing sample sizes in future, it may become so.
