2024
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders
Lee A, Ayers L, Kosicki M, Chan W, Fozo L, Pratt B, Collins T, Zhao B, Rose M, Sanchis-Juan A, Fu J, Wong I, Zhao X, Tenney A, Lee C, Laricchia K, Barry B, Bradford V, Jurgens J, England E, Lek M, MacArthur D, Lee E, Talkowski M, Brand H, Pennacchio L, Engle E. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. Nature Communications 2024, 15: 8268. PMID: 39333082, PMCID: PMC11436875, DOI: 10.1038/s41467-024-52463-7.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatinEnhancer Elements, GeneticEpigenomicsFemaleHumansMaleMiceMotor NeuronsPedigreeSingle-Cell AnalysisConceptsNon-coding variantsCranial motor neuronsMendelian disordersIn vivo transgenic assayPredictor of enhancer activityCis-regulatory elementsMulti-omic frameworkWhole-genome sequencingEnhanced activityVariant discoveryGenome sequenceChromatin accessibilityPutative enhancersHistone modificationsRegulatory elementsGene expression assaysGene predictionTransgenic assaysEpigenomic profilingMendelian casesExpression assaysMutational enhancementCongenital cranial dysinnervation disordersCell typesFunctional impact
2023
Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis
Tenney A, Di Gioia S, Webb B, Chan W, de Boer E, Garnai S, Barry B, Ray T, Kosicki M, Robson C, Zhang Z, Collins T, Gelber A, Pratt B, Fujiwara Y, Varshney A, Lek M, Warburton P, Van Ryzin C, Lehky T, Zalewski C, King K, Brewer C, Thurm A, Snow J, Facio F, Narisu N, Bonnycastle L, Swift A, Chines P, Bell J, Mohan S, Whitman M, Staffieri S, Elder J, Demer J, Torres A, Rachid E, Al-Haddad C, Boustany R, Mackey D, Brady A, Fenollar-Cortés M, Fradin M, Kleefstra T, Padberg G, Raskin S, Sato M, Orkin S, Parker S, Hadlock T, Vissers L, van Bokhoven H, Jabs E, Collins F, Pennacchio L, Manoli I, Engle E. Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis. Nature Genetics 2023, 55: 1149-1163. PMID: 37386251, PMCID: PMC10335940, DOI: 10.1038/s41588-023-01424-9.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsFacial ParalysisGATA2 Transcription FactorMiceMotor NeuronsNeurogenesisNeurons, EfferentConceptsSingle-nucleotide variantsGATA2 expressionHereditary congenital facial paresisBranchial motor neuronsLoss of GATA3Temporal gene regulationRare Mendelian diseasesChromosome 3q21-q22Autosomal dominant disorderSilencing in vitroNoncoding variationNoncoding variantsFacial paresisMendelian diseasesGene regulationRegulatory regionsHeterozygous duplicationDominant disorderMouse modelReporter expressionType 1Efferent neuronsMotor neuronsGATA2In vivo
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