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 ResearchConceptsNon-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 impactExpanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders
Jurgens J, Barry B, Chan W, MacKinnon S, Whitman M, Ruiz P, Pratt B, England E, Pais L, Lemire G, Groopman E, Glaze C, Russell K, Singer-Berk M, Di Gioia S, Lee A, Andrews C, Shaaban S, Wirth M, Bekele S, Toffoloni M, Bradford V, Foster E, Berube L, Rivera-Quiles C, Mensching F, Sanchis-Juan A, Fu J, Wong I, Zhao X, Wilson M, Weisburd B, Lek M, Consortium O, Abarca-Barriga H, Al-Haddad C, Berman J, Bothun E, Capasso J, Chacon-Camacho O, Chang L, Christiansen S, Ciccarelli M, Cordonnier M, Cox G, Curry C, Dagi L, Dahm T, David K, Davitt B, De Berardinis T, Demer J, Désir J, D’Esposito F, Drack A, Eggenberger E, Elder J, Elliott A, Epley K, Feldman H, Ferreira C, Flaherty M, Fulton A, Gerth-Kahlert C, Gottlob I, Grill S, Halliday D, Hanisch F, Hay E, Heidary G, Holder C, Horton J, Iannaccone A, Isenberg S, Johnston S, Kahana A, Katowitz J, Kazlas M, Kerr N, Kimonis V, Ko M, Koc F, Larsen D, Lay-Son G, Ledoux D, Levin A, Levy R, Lyons C, Mackey D, Magli A, Mantagos I, Marti C, Maystadt I, McKenzie F, Menezes M, Mikail C, Miller D, Miller K, Mills M, Miyana K, Moller H, Mullineaux L, Nishimura J, Noble A, Pandey P, Pavone P, Penzien J, Petersen R, Phalen J, Poduri A, Polo C, Prasov L, Ramos F, Ramos-Caceres M, Robb R, Rossillion B, Sahin M, Singer H, Smith L, Sorkin J, Soul J, Staffieri S, Stalker H, Stasheff S, Strassberg S, Strominger M, Taranath D, Thomas I, Traboulsi E, Ugrin M, VanderVeen D, Vincent A, G M, Wabbels B, Wong A, Woods C, Wu C, Yang E, Yeung A, Young T, Zenteno J, Zubcov-Iwantscheff A, Zwaan J, Brand H, Talkowski M, MacArthur D, O’Donnell-Luria A, Robson C, Hunter D, Engle E. Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders. Genetics In Medicine 2024, 27: 101216. PMID: 39033378, PMCID: PMC11739428, DOI: 10.1016/j.gim.2024.101216.Peer-Reviewed Original ResearchCongenital cranial dysinnervation disordersPrioritized variantsProtein-coding regionsSingle-nucleotide variantsDe novo variantsAnimal model phenotypesGenetically heterogeneous disorderAnalysis of pedigreesGenes associated with syndromesGenome sequenceStructural variantsMendelian conditionsModel phenotypesGenotype/phenotype correlationGenetic etiologyGenotype/phenotype associationsPathogenic variant(sGenesFunctional studiesSyndrome phenotypeSyndrome componentsPhenotypeGeneticsProbandsVariants
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