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To facilitate cellular and molecular investigations into these phenotypes, 65 clones of human induced pluripotent stem cells (hiPSCs) were generated from 13 individuals with 16p11.2 copy number variations (CNVs). To ensure these cell lines were suitable for downstream mechanistic investigations, a customizable bioinformatic strategy for the detection of random integration and expression of reprogramming vectors was developed and leveraged towards identifying a subset of \u2018footprint\u2019-free hiPSC clones. Transcriptomic profiling of cortical neural progenitor cells derived from these hiPSCs identified alterations in gene expression patterns which precede morphological abnormalities reported at later neurodevelopmental stages. Interpreting clinical information\u2014available with the cell lines by request from the Simons Foundation Autism Research Initiative\u2014with this transcriptional data revealed disruptions in gene programs related to both nervous system function and cellular metabolism. As demonstrated by these analyses, this publicly available resource has the potential to serve as a powerful medium for probing the etiology of developmental disorders associated with 16p11.2 CNVs.<\/jats:p>","DOI":"10.7554\/elife.58178","type":"journal-article","created":{"date-parts":[[2020,11,10]],"date-time":"2020-11-10T08:05:20Z","timestamp":1604995520000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.58178","source":"Crossref","is-referenced-by-count":50,"title":["16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural development"],"prefix":"10.7554","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7560-3258","authenticated-orcid":true,"given":"Julien G","family":"Roth","sequence":"first","affiliation":[{"name":"Department of Neurosurgery and The Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United 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