Analyses of the effects of the polygenic personality scores on mood disorders in the four separate studies indicated that for BD, results were consistent over studies, whereas for MDD, results were mainly driven by the GAIN-MDD study. There does not seem to be an obvious explanation for the absence of effect in the MDD2000+ sample. The overlap in SNPs used to calculate polygenic scores was far lower in the MDD2000+ sample than in the GAIN-MDD sample because of the use of different reference sets for the imputation, HapMap3 in MDD2000+ and HapMap2 in MDD-GAIN. HapMap3 includes less SNPs but is based on more subjects. However, the overlap in SNPs was also lower in the WTCCC sample, whereas their results were similar to the results in the STEP-BD sample, which had a high overlap in SNPs. Therefore, the low overlap in SNPs does not seem to explain the difference in results between the MDD2000+ and the MDD-GAIN sample. Given the repeatedly found genetic correlation between N and MDD, it seems most likely that the finding in MDD2000+ is a false negative finding.
