endophenotypes associated with 22q11.2DS (DGCR8, DGCR2, RANBP1, RTN4R, and COMT, for example) showed a significant decrease (~2-fold reduction, FDR < 0.05) in the patient samples compared with controls. One exception is CLDN5, which also showed larger than 2-fold difference in expression between conditions, but failed to reach statistical significance because of large intragroup variability and relatively lower expression. Another exception is TBX1. Its expression in the neuronal differentiation method we used is even lower (mean FPKM ~0.6 in control and 22q11.2 del neurons), so accurate quantitation is difficult. The other differentially expressing genes passing FDR <0.05 but not in the 22q11.2 region are DDX11, PDK3, PCIF1, FAM103A1, TMSB4X and HLA-A.
