Browsing by Author "de Vries, Bert B.A."

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    Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome
    (Elsevier, 2021-11) Weerts, Marjolein J.A.; Lanko, Kristina; Guzmán-Vega, Francisco J.; Jackson, Adam; Ramakrishnan, Reshmi; Cardona-Londoño, Kelly J.; Peña-Guerra, Karla A.; van Bever, Yolande; van Paassen, Barbara W.; Kievit, Anneke; van Slegtenhorst, Marjon; Allen, Nicholas M.; Kehoe, Caroline M.; Robinson, Hannah K.; Pang, Lewis; Banu, Selina H.; Zaman, Mashaya; Efthymiou, Stephanie; Houlden, Henry; Järvelä, Irma; Lauronen, Leena; Määttä, Tuomo; Schrauwen, Isabelle; Leal, Suzanne M.; Ruivenkamp, Claudia A.L.; Barge-Schaapveld, Daniela Q.C.M.; Peeters-Scholte, Cacha M.P.C.D.; Galehdari, Hamid; Mazaheri, Neda; Sisodiya, Sanjay M.; Harrison, Victoria; Sun, Angela; Thies, Jenny; Pedroza, Luis Alberto; Lara-Taranchenko, Yana; Chinn, Ivan K.; Lupski, James R.; Garza-Flores, Alexandra; McGlothlin, Jeffery; Yang, Lin; Huang, Shaoping; Wang, Xiaodong; Jewett, Tamison; Rosso, Gretchen; Lin, Xi; Mohammed, Shehla; Merritt, J. Lawrence, II.; Mirzaa, Ghayda M.; Timms, Andrew E.; Scheck, Joshua; Elting, Mariet W.; Polstra, Abeltje M.; Schenck, Lauren; Ruzhnikov, Maura R.Z.; Vetro, Annalisa; Montomoli, Martino; Guerrini, Renzo; Koboldt, Daniel C.; Mihalic Mosher, Theresa; Pastore, Matthew T.; McBride, Kim L.; Peng, Jing; Pan, Zou; Willemsen, Marjolein; Koning, Susanne; Turnpenny, Peter D.; de Vries, Bert B.A.; Gilissen, Christian; Pfundt, Rolph; Lees, Melissa; Braddock, Stephen R.; Klemp, Kara C.; Vansenne, Fleur; van Gijn, Marielle E.; Quindipan, Catherine; Deardorff, Matthew A.; Hamm, J. Austin; Putnam, Abbey M.; Baud, Rebecca; Walsh, Laurence; Lynch, Sally A.; Baptista, Julia; Person, Richard E.; Monaghan, Kristin G.; Crunk, Amy; Keller-Ramey, Jennifer; Reich, Adi; Elloumi, Houda Zghal; Alders, Marielle; Kerkhof, Jennifer; McConkey, Haley; Haghshenas, Sadegheh; Maroofian, Reza; Sadikovic, Bekim; Banka, Siddharth; Arold, Stefan T.; Barakat, Tahsin Stefan; Medical and Molecular Genetics, School of Medicine
    Purpose: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort. Methods: We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays. Results: Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants. Conclusion: Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome.
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    Disruption of RFX family transcription factors causes autism, attention-deficit/hyperactivity disorder, intellectual disability, and dysregulated behavior
    (Elsevier, 2021) Harris, Holly K.; Nakayama, Tojo; Lai, Jenny; Zhao, Boxun; Argyrou, Nikoleta; Gubbels, Cynthia S.; Soucy, Aubrie; Genetti, Casie A.; Suslovitch, Victoria; Rodan, Lance H.; Tiller, George E.; Lesca, Gaetan; Gripp, Karen W.; Asadollahi, Reza; Hamosh, Ada; Applegate, Carolyn D.; Turnpenny, Peter D.; Simon, Marleen E.H.; Volker-Touw, Catharina M.L.; van Gassen, Koen L.I.; van Binsbergen, Ellen; Pfundt, Rolph; Gardeitchik, Thatjana; de Vries, Bert B.A.; Immken, LaDonna L.; Buchanan, Catherine; Willing, Marcia; Toler, Tomi L.; Fassi, Emily; Baker, Laura; Vansenne, Fleur; Wang, Xiadong; Ambrus, Julian L., Jr.; Fannemel, Madeleine; Posey, Jennifer E.; Agolini, Emanuele; Novelli, Antonio; Rauch, Anita; Boonsawat, Paranchai; Fagerberg, Christina R.; Larsen, Martin J.; Kibaek, Maria; Labalme, Audrey; Poisson, Alice; Payne, Katelyn K.; Walsh, Laurence E.; Aldinger, Kimberly A.; Balciuniene, Jorune; Skraban, Cara; Gray, Christopher; Murrell, Jill; Bupp, Caleb P.; Pascolini, Giulia; Grammatico, Paola; Broly, Martin; Küry, Sébastien; Nizon, Mathilde; Rasool, Iqra Ghulam; Zahoor, Muhammad Yasir; Kraus, Cornelia; Reis, André; Iqbal, Muhammad; Uguen, Kevin; Audebert-Bellanger, Severine; Ferec, Claude; Redon, Sylvia; Baker, Janice; Wu, Yunhong; Zampino, Guiseppe; Syrbe, Steffan; Brosse, Ines; Jamra, Rami Abou; Dobyns, William B.; Cohen, Lilian L.; Blomhoff, Anne; Mignot, Cyril; Keren, Boris; Courtin, Thomas; Agrawal, Pankaj B.; Beggs, Alan H.; Yu, Timothy W.; Neurology, School of Medicine
    Purpose: We describe a novel neurobehavioral phenotype of autism spectrum disorder (ASD), intellectual disability, and/or attention-deficit/hyperactivity disorder (ADHD) associated with de novo or inherited deleterious variants in members of the RFX family of genes. RFX genes are evolutionarily conserved transcription factors that act as master regulators of central nervous system development and ciliogenesis. Methods: We assembled a cohort of 38 individuals (from 33 unrelated families) with de novo variants in RFX3, RFX4, and RFX7. We describe their common clinical phenotypes and present bioinformatic analyses of expression patterns and downstream targets of these genes as they relate to other neurodevelopmental risk genes. Results: These individuals share neurobehavioral features including ASD, intellectual disability, and/or ADHD; other frequent features include hypersensitivity to sensory stimuli and sleep problems. RFX3, RFX4, and RFX7 are strongly expressed in developing and adult human brain, and X-box binding motifs as well as RFX ChIP-seq peaks are enriched in the cis-regulatory regions of known ASD risk genes. Conclusion: These results establish a likely role of deleterious variation in RFX3, RFX4, and RFX7 in cases of monogenic intellectual disability, ADHD and ASD, and position these genes as potentially critical transcriptional regulators of neurobiological pathways associated with neurodevelopmental disease pathogenesis.
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    The Human Phenotype Ontology in 2017
    (Oxford Journals, 2016-11-24) Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin D.; McMurry, Julie A.; Aymé, Ségolène; Baynam, Gareth; Bello, Susan M.; Boerkoel, Cornelius F.; Boycott, Kym M.; Brudno, Michael; Buske, Orion J.; Chinnery, Patrick F.; Cipriani, Valentina; Connell, Laureen E.; Dawkins, Hugh J.S.; DeMare, Laura E.; Devereau, Andrew D.; de Vries, Bert B.A.; Firth, Helen V.; Freson, Kathleen; Greene, Daniel; Hamosh, Ada; Helbig, Ingo; Hum, Courtney; Jähn, Johanna A.; James, Roger; Krause, Roland; Laulederkind, Stanley J. F.; Lochmüller, Hanns; Lyon, Gholson J.; Ogishima, Soichi; Olry, Annie; Ouwehand, Willem H.; Pontikos, Nikolas; Rath, Ana; Schaefer, Franz; Scott, Richard H.; Segal, Michael; Sergouniotis, Panagiotis I.; Sever, Richard; Smith, Cynthia L.; Straub, Volker; Thompson, Rachel; Turner, Catherine; Turro, Ernest; Veltman, Marijcke W.M.; Vulliamy, Tom; Yu, Jing; von Ziegenweidt, Julie; Zankl, Andreas; Züchner, Stephan; Zemojtel, Tomasz; Jacobsen, Julius O.B.; Groza, Tudor; Smedley, Damian; Mungall, Christopher J.; Haendel, Melissa A.; Robinson, Peter N.
    Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
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    De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder
    (Elsevier, 2018-06-07) Reijnders, Margot R.F.; Miller, Kerry A.; Alvi, Mohsan; Goos, Jacqueline A.C.; Lees, Melissa M.; de Burca, Anna; Henderson, Alex; Kraus, Alison; Mikat, Barbara; de Vries, Bert B.A.; Isidor, Bertrand; Kerr, Bronwyn; Marcelis, Carlo; Schluth-Bolard, Caroline; Deshpande, Charu; Ruivenkamp, Claudia A.L.; Wieczorek, Dagmar; Baralle, Diana; Blair, Edward M.; Engels, Hartmut; Lüdecke, Hermann-Josef; Eason, Jacqueline; Santen, Gijs W.E.; Clayton-Smith, Jill; Chandler, Kate; Tatton-Brown, Katrina; Payne, Katelyn; Helbig, Katherine; Radtke, Kelly; Nugent, Kimberly M.; Cremer, Kirsten; Strom, Tim M.; Bird, Lynne M.; Sinnema, Margje; Bitner-Glindzicz, Maria; van Dooren, Marieke F.; Alders, Marielle; Koopmans, Marije; Brick, Lauren; Kozenko, Mariya; Harline, Megan L.; Klaassens, Merel; Steinraths, Michelle; Cooper, Nicola S.; Edery, Patrick; Yap, Patrick; Terhal, Paulien A.; van der Spek, Peter J.; Lakeman, Phillis; Taylor, Rachel L.; Littlejohn, Rebecca O.; Pfundt, Rolph; Mercimek-Andrews, Saadet; Stegmann, Alexander P.A.; Kant, Sarina G.; McLean, Scott; Joss, Shelagh; Swagemakers, Sigrid M.A.; Douzgou, Sofia; Wall, Steven A.; Küry, Sebastian; Calpena, Eduardo; Koelling, Nils; McGowan, Simon J.; Twigg, Stephen R.F.; Mathijssen, Irene M.J.; Nellaker, Christoffer; Brunner, Han G.; Wilkie, Andrew O.M.; Medical and Molecular Genetics, School of Medicine
    Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2.