Fig. 1: Design of a statistically powered study to determine the impact of 22q11.2 deletion on gene expression.

a Final sample set composed of 20 cell lines with 22q11.2 deletion (brown) and 29 controls (grey), collected at seven locations (MGH: Massachusetts General Hospital, KI: Karolinska Institute, Umea: Umeå University, NFID: Northern Finnish Intellectual Disability Cohort (Institute for Molecular Medicine Finland), GTEx: Genotype-Tissue Expression Project, Mclean: Mclean Hospital). b Pilot study using four hiPSC lines differentiated into neurons through transduction with TetO-Ngn2, Ub-rtTA and TetO-GFP lentivirus and subjected to RNA sequencing. RNA abundances were then used to estimate the appropriate sample size for differential gene expression for the final study. c The final dataset consisted of 49 cell lines that were differentiated and subjected to RNA sequencing. d Provenance. e Diagnosis and (f), Sex of the samples in the final cohort. g Neuronal differentiation protocol (Nehme et al 2018) consisting of the combination of Ngn2 overexpression with forebrain patterning using small molecules (SB431542, LDN193189 and XAV939). Samples were harvested for RNA sequencing at the stem cell (day 0), neuronal progenitor cell (NPCs) (day 4) and neuronal (day 28) stages. h Power estimation in the pilot dataset for median expressed genes (24 read counts) for different fold-changes and sample sizes in neurons. i Principal component analysis (PCA) of RNA sequencing data from the full study.