For replication, we chose Coronary Artery Disease (CAD), LDL cholesterol levels, Triglyceride levels, and schizophrenia, which had closely related phenotypes in the GERA study and had a sufficiently large number of Bonferroni significant associations in the discovery set. Analysis and replication of the type 2 diabetes phenotype can be found in ref. 38. Coronary artery disease hits were compared with “Any cardiac event,” LDL cholesterol and triglyceride level signals were compared with “Dyslipidemia,” and schizophrenia was compared to “Any psychiatric event” in GERA.
