Supplementary MaterialsSupplementary Information 41467_2017_2330_MOESM1_ESM. fix the smaller effects of common variants within the size of cohorts that can be realistically put together remains uncertain. We recognized and accounted for a variety of technical and biological sources of variance in a large case/control schizophrenia (SZ) hiPSC-derived cohort of neural progenitor cells and neurons. Reducing the stochastic effects of the differentiation process by correcting for cell type composition boosted the SZ signal and increased the concordance with post-mortem data sets. We predict a growing convergence between hiPSC and post-mortem studies as both approaches expand to larger cohort sizes. For studies of complex genetic disorders, to maximize the power of hiPSC cohorts currently feasible, in most cases and whenever possible, we recommend expanding the number of individuals even at the expense of the number of replicate hiPSC clones. Introduction A growing number of studies have demonstrated that human induced pluripotent stem cells (hiPSCs) can serve as cellular models of both syndromic and idiopathic forms of a variety of neurodevelopmental disorders (reviewed in ref. 1). We and others have previously shown that hiPSC-derived neural progenitor cells (NPCs) and neurons generated from patients with schizophrenia (SZ) show altered gene expression2C4, which may underlie observed in vitro phenotypes such as aberrant hiPSC-NPC polarity5 and migration6, as well as deficits in hiPSC-neuron connectivity and function3,7. Altogether, such hiPSC-based approaches seem to capture aspects of SZ biology identified through post-mortem studies and animal models8. Nonetheless, mechanistic studies to date have tended to focus on rare variants3C5; the ability of an hiPSC-based approach to resolve the much smaller effects of common variants remained uncertain. We established a case-control SZ cohort structure designed to capture a broad range of rare and common variants that might underlie SZ risk, in order to address and quantify the intra- and inter-individual variability inherent in this approach and uncover to what extent hiPSC-based models can identify common pathways underlying such different genetic risk factors. Because hiPSC-neurons are likely best suited for the scholarly research of disease predisposition6, we used this strategy to a childhood-onset SZ (COS) cohort, a subset of SZ individuals defined by starting point, prognosis and severity. COS patients possess a far more salient hereditary risk, with an increased price of SZ-associated duplicate number variations (CNVs)9 and Dasatinib ic50 more powerful common SZ polygenic risk ratings10. General, across 94 RNA-Seq examples, we noticed many resources of variant reflecting both natural (i.e., reprogramming and differentiation) and specialized effects. By accounting for Rabbit polyclonal to STK6 covariates and modifying for heterogeneity in neural differentiation systematically, we improved our capability to deal with the disease-relevant sign. Our bioinformatic pipeline decreases the chance of fake positives due to the small test sizes of hiPSC-based techniques and we wish it can benefit guide data evaluation in identical hiPSC-based disease research. Outcomes Transcriptomic profiling of COS hiPSC-neurons and Dasatinib ic50 hiPSC-NPCs People with COS, aswell as unaffected, unrelated healthful controls had been recruited within a longitudinal research conducted in the Country wide Institute of Health9,10 (see Supplementary Data?1 for available clinical information). Dasatinib ic50 This cohort is comprised of nearly equal numbers of cases and controls (Fig.?1aCc); 16 cases were selected representing a range of SZ-relevant CNVs, including 22q11.2 deletion, 16p11.2 duplication, 15q11.2 deletion, and deletion (2p16.3)11 and/or idiopathic genetics with a strong family history of SZ, 12 controls were identified as being most appropriately matched for sex, age, and ethnicity (Fig.?1d; Supplementary Data?1). Open in a separate window Fig. 1 COS hiPSC cohort reprogramming and differentiation. a Validated hiPSCs (from 14 individuals with childhood-onset-schizophrenia (COS) and 12 unrelated healthy controls) and NPCs (12 COS; 12 control individuals) yielded 94 RNA-Seq samples (11 COS; 11 control individuals). b Schematic illustration of the reprogramming and differentiation process, noting the yield at each stage. c Sex breakdown of the COS-control cohort. Dasatinib ic50 d Breakdown of SZ-associated copy number variants in the 11 COS patients with RNA-Seq data. e Representative qPCR validation of expression in hiPSCs (white bar), NPCs (light gray) and 6-week-old neurons (dark gray) from three people..