2017
Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes
Ho S, Hartley B, Flaherty E, Rajarajan P, Abdelaal R, Obiorah I, Barretto N, Muhammad H, Phatnani H, Akbarian S, Brennand K. Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes. Stem Cell Reports 2017, 9: 615-628. PMID: 28757163, PMCID: PMC5550013, DOI: 10.1016/j.stemcr.2017.06.012.Peer-Reviewed Original ResearchConceptsSynthetic activationRisk genesCell typesModulation of transcriptionNeuropsychiatric risk genesCommon single nucleotide variantsCas9 fusion proteinsEndogenous expression levelsNeural cell typesPluripotent stem cell-derived neural progenitor cellsRare copy number variationsCopy number variationsSingle nucleotide variantsNeural progenitor cellsGene functionFunctional annotationGenetic studiesGenesRisk variantsProgenitor cellsExpression levelsTranscriptionRepressionPositional effectsProtein
2015
Effect of predicted protein-truncating genetic variants on the human transcriptome
Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, Consortium T, Consortium T, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG, Segre A, Young T, Gelfand E, Trowbridge C, Ward L, Kheradpour P, Iriarte B, Meng Y, Palmer C, Esko T, Winckler W, Hirschhorn J, Kellis M, Getz G, Shablin A, Li, Zhou Y, Nobel A, Rusyn I, Wright F, Battle A, Mostafavi S, Mele M, Reverter F, Goldmann J, Koller D, Gamazon E, Im H, Konkashbaev A, Nicolae D, Cox N, Flutre T, Wen X, Stephens M, Pritchard J, Tu Z, Zhang B, Huang T, Long Q, Lin L, Yang J, Zhu J, Liu J, Brown A, Mestichelli B, Tidwell D, Lo E, Salvatore M, Shad S, Thomas J, Lonsdale J, Choi R, Karasik E, Ramsey K, Moser M, Foster B, Gillard B, Syron J, Fleming J, Magazine H, Hasz R, Walters G, Bridge J, Miklos M, Sullivan S, Barker L, Traino H, Mosavel M, Siminoff L, Valley D, Rohrer D, Jewel S, Branton P, Sobin L, Barcus M, Qi L, Hariharan P, Wu S, Tabor D, Shive C, Smith A, Buia S, Undale A, Robinson K, Roche N, Valentino K, Britton A, Burges R, Bradbury D, Hambright K, Seleski J, Korzeniewski G, Erickson K, Marcus Y, Tejada J, Taherian M, Lu C, Robles B, Basile M, Mash D, Volpi S, Struewing J, Temple G, Boyer J, Colantuoni D, Little R, Koester S, Carithers L, Moore H, Guan P, Compton C, Sawyer S, Demchok J, Vaught J, Rabiner C, Lockhart N, Friedlander M, Hoen P, Monlong J, Gonzàlez-Porta M, Kurbatova N, Griebel T, Barann M, Wieland T, Greger L, van Iterson M, Almlof J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, Lizano E, Buermans H, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Flicek P, Strom T, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis S, Hasler R, Syvanen A, van Ommen G, Brazma A, Meitinger T, Rosenstiel P, Gut I, Estivill X. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 2015, 348: 666-669. PMID: 25954003, PMCID: PMC4537935, DOI: 10.1126/science.1261877.Peer-Reviewed Original ResearchConceptsGenotype-Tissue ExpressionGenetic variantsProtein-truncating variantsEffects of variantsDosage compensationClass of variantsTranscript decayGene functionTranscriptome dataHuman transcriptomeGenetic variationGEUVADIS projectGene inactivationSplice junctionsGenome interpretationTranscriptome effectsFunctional interpretationClinical genome interpretationFunctional effectsPositional effectsImproved predictive modelVariantsTranscriptomeProfound effectInactivation
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