For the TDT associations with P < 10−4, we additionally utilized the cases that were excluded from the TDT due to missing parental data. We matched 90 independent and unrelated cases with 1,476 NIMH control samples genotyped on the Affymetrix 500K arrays 6, and performed case-control association analysis (Supplementary Table 3), combining these results with the TDT data. Promisingly, we now observed 8 SNPs (in 7 independent regions) with association at P < 10−5(Table 1). Of note, comparing Caucasian with non-Caucasian samples in the AGRE/NIMH dataset, we did not observe significant heterogeneity for top results.
