@article {830,
	title = {Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism.},
	journal = {Cell},
	volume = {180},
	year = {2020},
	month = {2020 02 06},
	pages = {568-584.e23},
	abstract = {<p>We present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n~= 35,584 total samples, 11,986 with ASD). Using an enhanced analytical framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate of 0.1 or less. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained to have severe neurodevelopmental delay, whereas 53 show higher frequencies in individuals ascertained to have ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In cells from the human cortex, expression of risk genes is enriched in excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory-inhibitory imbalance underlying ASD.</p>},
	keywords = {Autistic Disorder, Case-Control Studies, Cell Lineage, Cerebral Cortex, Cohort Studies, Exome, Female, Gene Expression Regulation, Developmental, Gene Frequency, Genetic Predisposition to Disease, Humans, Male, Mutation, Missense, Neurobiology, Neurons, Phenotype, Sex Factors, Single-Cell Analysis, Whole Exome Sequencing},
	issn = {1097-4172},
	doi = {10.1016/j.cell.2019.12.036},
	author = {Satterstrom, F Kyle and Kosmicki, Jack A and Wang, Jiebiao and Breen, Michael S and De Rubeis, Silvia and An, Joon-Yong and Peng, Minshi and Collins, Ryan and Grove, Jakob and Klei, Lambertus and Stevens, Christine and Reichert, Jennifer and Mulhern, Maureen S and Artomov, Mykyta and Gerges, Sherif and Sheppard, Brooke and Xu, Xinyi and Bhaduri, Aparna and Norman, Utku and Brand, Harrison and Schwartz, Grace and Nguyen, Rachel and Guerrero, Elizabeth E and Dias, Caroline and Betancur, Catalina and Cook, Edwin H and Gallagher, Louise and Gill, Michael and Sutcliffe, James S and Thurm, Audrey and Zwick, Michael E and B{\o}rglum, Anders D and State, Matthew W and Cicek, A Ercument and Talkowski, Michael E and Cutler, David J and Devlin, Bernie and Sanders, Stephan J and Roeder, Kathryn and Daly, Mark J and Buxbaum, Joseph D}
}
@article {569,
	title = {Comparative genomic analysis of embryonic, lineage-converted and stem cell-derived motor neurons.},
	journal = {Development},
	volume = {145},
	year = {2018},
	month = {2018 11 21},
	abstract = {<p>Advances in stem cell science allow the production of different cell types  either through the recapitulation of developmental processes, often termed {\textquoteright}directed differentiation{\textquoteright}, or the forced expression of lineage-specific transcription factors. Although cells produced by both approaches are increasingly used in translational applications, their quantitative similarity to their primary counterparts remains largely unresolved. To investigate the similarity between -derived and primary cell types, we harvested and purified mouse spinal motor neurons and compared them with motor neurons produced by transcription factor-mediated lineage conversion of fibroblasts or directed differentiation of pluripotent stem cells. To enable unbiased analysis of these motor neuron types and their cells of origin, we then subjected them to whole transcriptome and DNA methylome analysis by RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS). Despite major differences in methodology, lineage conversion and directed differentiation both produce cells that closely approximate the primary motor neuron state. However, we identify differences in Fas signaling, the Hox code and synaptic gene expression between lineage-converted and directed differentiation motor neurons that affect their utility in translational studies.</p>},
	keywords = {Animals, Cell Lineage, Embryo, Mammalian, Epigenesis, Genetic, Genomics, Mice, Inbred C57BL, Motor Neurons, Pluripotent Stem Cells, Transcription, Genetic},
	issn = {1477-9129},
	doi = {10.1242/dev.168617},
	author = {Ichida, Justin K and Staats, Kim A and Davis-Dusenbery, Brandi N and Clement, Kendell and Galloway, Kate E and Babos, Kimberly N and Shi, Yingxiao and Son, Esther Y and Kiskinis, Evangelos and Atwater, Nicholas and Gu, Hongcang and Gnirke, Andreas and Meissner, Alexander and Eggan, Kevin}
}
