Until recently the assumption that, for a given GWAS signal, the causal variant in that interval had been genotyped was unrealistic. However, the application of imputation techniques [17]–[19] can provide genotype information about the majority of common genetic variants. Therefore, in situations where a common variant drives the GWAS signal, it is now plausible that, in imputed datasets, genotype information about this variant is available. Nevertheless, limited imputation quality can invalidate this hypothesis. This prompted us to investigate the implication of not including the causal variant in the genotype panel.
