Here, we consider the use of imputation to pool subjects genotyped with different platforms within studies. For example, when the data of control groups such as the Wellcome Trust Case Control Consortium3 are reused, the cases are typically not matched regarding genotyping platforms or arrays.4 Another example concerns combining expression quantitative trait loci studies with data being generated at very different time points from different platforms, thereby requiring genotype imputation.5 Although reusing such existing data seems to be an efficient approach, it may increase chances of observing spurious associations due to chip differences. In this paper, we discuss whether more stringent quality controls (QCs) should be applied.
