There are several additional issues other than the type I error inflation arising from PS to consider when evaluating the appropriateness of convenience controls versus controls selected to reflect the study-base that produced the cases. There may be differential genotyping error between cases and controls due to variation in the processing of biological samples. Also, selection bias for non-genetic covariates that can not be corrected by PCA could lead to misleading estimates of interactions [35]. The selection of cases and controls from a common prospective cohort tends to minimize potential discrepancies.
