Human embryonic stem cells (hESCs) can be induced and differentiated to form a relatively homogeneous population of neuronal precursors in vitro. We have used this system to screen for genes necessary for neural lineage development by using a pooled human short hairpin RNA (shRNA) library screen and massively parallel sequencing. We confirmed known genes and identified several unpredicted genes with interrelated functions that were specifically required for the formation or survival of neuronal progenitor cells without interfering with the self-renewal capacity of undifferentiated hESCs. Among these are several genes that have been implicated in various neurodevelopmental disorders (i.e., brain malformations, mental retardation, and autism). Unexpectedly, a set of genes mutated in late-onset neurodegenerative disorders and with roles in the formation of RNA granules were also found to interfere with neuronal progenitor cell formation, suggesting their functional relevance in early neurogenesis. This study advances the feasibility and utility of using pooled shRNA libraries in combination with next-generation sequencing for a high-throughput, unbiased functional genomic screen. Our approach can also be used with patient-specific human-induced pluripotent stem cell-derived neural models to obtain unparalleled insights into developmental and degenerative processes in neurological or neuropsychiatric disorders with monogenic or complex inheritance. O ur general aim is to identify genes and pathways of early neural differentiation that are relevant for the development and function of the human nervous system. In vitro differentiation of human embryonic stem cells (hESCs) yielding developmentally competent neuronal progenitors is an attractive model for these studies and several approaches for this have been developed, including those by our group (1).Large-scale loss-of-function analysis by RNA interference (RNAi) using small hairpin (shRNA) or small interfering RNA (siRNA) -mediated knockdown of genes is a powerful screening approach in mammalian cells (2-7). ShRNAs provide the opportunity for long-term silencing by stable infection of cells maintained under selection pressure. Furthermore, pooled libraries of shRNAs can be efficiently used instead of arrayed individual clones. Screening experiments can be designed for detection of shRNAs that produce a desired effect in a cell (positive screens) or for the depletion of shRNA species that silence a necessary gene (dropout screens). The abundance of shRNAs has been measured by using barcodes and array hybridization (8, 9), but this procedure is subject to cross-hybridization and nonlinear responses. Most positive screens have been limited to studies of cellular proliferation or survival because it is easier to analyze the recovered enriched shRNAs (10). For dropout screens it is critical to accurately measure the abundance of shRNAs that are retained in cells at the end of the experiment to determine which shRNAs were depleted (8). In part because of this challenge, ...