Additionally, eQTL were generated separately in SCZ cases and controls, and the combination of those samples (excluding AFF cases). However, permutation of disease status indicated that the overlaps between case-derived eQTL and control-derived eQTL were similar to the amount expected for two homogeneous sets of these sample sizes, and there was limited evidence for condition-specific eQTL. Nevertheless, to potentially identify eQTL that differ by disease state, a disease-genotype interaction term was also explicitly tested, but only a handful of such associations were found to be significant after controlling for FDR.
