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1. Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses

Author

German Demidov, Burcu Yaldiz, José Garcia-Pelaez, Elke de Boer, Nika Schuermans, Liedewei Van de Vondel, Ida Paramonov, Lennart F. Johansson, Francesco Musacchia, Elisa Benetti, Gemma Bullich, Karolis Sablauskas, Sergi Beltran, Christian Gilissen, Alexander Hoischen, Stephan Ossowski, Richarda de Voer, Katja Lohmann, Carla Oliveira, Ana Topf, Lisenka E. L. M. Vissers, Solve-RD Consortium, and Steven Laurie

Subjects
Medicine, Genetics, QH426-470
Abstract

Abstract We report the results of a comprehensive copy number variant (CNV) reanalysis of 9171 exome sequencing datasets from 5757 families affected by a rare disease (RD). The data reanalysed was extremely heterogeneous, having been generated using 28 different enrichment kits by 42 different research groups across Europe partnering in the Solve-RD project. Each research group had previously undertaken their own analysis of the data but failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity, and rare CNVs overlapping genes of interest, provided by four partner European Reference Networks, were taken forward for interpretation by clinical experts. This reanalysis has resulted in a molecular diagnosis being provided to 51 families in this sample, with ClinCNV performing the best of the three algorithms. We also identified partially explanatory pathogenic CNVs in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs.

Published
2024
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2. A complex structural variant near SOX3 causes X-linked split-hand/foot malformation

Author

Elke de Boer, Carlo Marcelis, Kornelia Neveling, Ellen van Beusekom, Alexander Hoischen, Willemijn M. Klein, Nicole de Leeuw, Tuomo Mantere, Uirá S. Melo, Jeroen van Reeuwijk, Dominique Smeets, Malte Spielmann, Tjitske Kleefstra, Hans van Bokhoven, and Lisenka E.L.M. Vissers

Subjects
SOX3, X-linked split-hand/foot malformation, SHFM2, Structural variation, Whole genome sequencing, Optical genome mapping, Genetics, QH426-470
Abstract

Summary: Split-hand/foot malformation (SHFM) is a congenital limb defect most typically presenting with median clefts in hands and/or feet, that can occur in a syndromic context as well as in isolated form. SHFM is caused by failure to maintain normal apical ectodermal ridge function during limb development. Although several genes and contiguous gene syndromes are implicated in the monogenic etiology of isolated SHFM, the disorder remains genetically unexplained for many families and associated genetic loci. We describe a family with isolated X-linked SHFM, for which the causative variant could be detected after a diagnostic journey of 20 years. We combined well-established approaches including microarray-based copy number variant analysis and fluorescence in situ hybridization coupled with optical genome mapping and whole genome sequencing. This strategy identified a complex structural variant (SV) comprising a 165-kb gain of 15q26.3 material ([GRCh37/hg19] chr15:99795320-99960362dup) inserted in inverted position at the site of a 38-kb deletion on Xq27.1 ([GRCh37/hg19] chrX:139481061-139518989del). In silico analysis suggested that the SV disrupts the regulatory framework on the X chromosome and may lead to SOX3 misexpression. We hypothesize that SOX3 dysregulation in the developing limb disturbed the fine balance between morphogens required for maintaining AER function, resulting in SHFM in this family.

Published
2023
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3. Clinical, genetic, epidemiologic, evolutionary, and functional delineation of TSPEAR-related autosomal recessive ectodermal dysplasia 14

Author

Adam Jackson, Sheng-Jia Lin, Elizabeth A. Jones, Kate E. Chandler, David Orr, Celia Moss, Zahra Haider, Gavin Ryan, Simon Holden, Mike Harrison, Nigel Burrows, Wendy D. Jones, Mary Loveless, Cassidy Petree, Helen Stewart, Karen Low, Deirdre Donnelly, Simon Lovell, Konstantina Drosou, Gaurav K. Varshney, Siddharth Banka, J.C. Ambrose, P. Arumugam, R. Bevers, M. Bleda, F. Boardman-Pretty, C.R. Boustred, H. Brittain, M.A. Brown, M.J. Caulfield, G.C. Chan, A. Giess, J.N. Griffin, A. Hamblin, S. Henderson, T.J.P. Hubbard, R. Jackson, L.J. Jones, D. Kasperaviciute, M. Kayikci, A. Kousathanas, L. Lahnstein, A. Lakey, S.E.A. Leigh, I.U.S. Leong, F.J. Lopez, F. Maleady-Crowe, M. McEntagart, F. Minneci, J. Mitchell, L. Moutsianas, M. Mueller, N. Murugaesu, A.C. Need, P. O‘Donovan, C.A. Odhams, C. Patch, D. Perez-Gil, M.B. Pereira, J. Pullinger, T. Rahim, A. Rendon, T. Rogers, K. Savage, K. Sawant, R.H. Scott, A. Siddiq, A. Sieghart, S.C. Smith, A. Sosinsky, A. Stuckey, M. Tanguy, A.L. Taylor Tavares, E.R.A. Thomas, S.R. Thompson, A. Tucci, M.J. Welland, E. Williams, K. Witkowska, S.M. Wood, M. Zarowiecki, Olaf Riess, Tobias B. Haack, Holm Graessner, Birte Zurek, Kornelia Ellwanger, Stephan Ossowski, German Demidov, Marc Sturm, Julia M. Schulze-Hentrich, Rebecca Schüle, Christoph Kessler, Melanie Wayand, Matthis Synofzik, Carlo Wilke, Andreas Traschütz, Ludger Schöls, Holger Hengel, Peter Heutink, Han Brunner, Hans Scheffer, Nicoline Hoogerbrugge, Alexander Hoischen, Peter A.C. ’t Hoen, Lisenka E.L.M. Vissers, Christian Gilissen, Wouter Steyaert, Karolis Sablauskas, Richarda M. de Voer, Erik-Jan Kamsteeg, Bart van de Warrenburg, Nienke van Os, Iris te Paske, Erik Janssen, Elke de Boer, Marloes Steehouwer, Burcu Yaldiz, Tjitske Kleefstra, Anthony J. Brookes, Colin Veal, Spencer Gibson, Marc Wadsley, Mehdi Mehtarizadeh, Umar Riaz, Greg Warren, Farid Yavari Dizjikan, Thomas Shorter, Ana Töpf, Volker Straub, Chiara Marini Bettolo, Sabine Specht, Jill Clayton-Smith, Elizabeth Alexander, Laurence Faivre, Christel Thauvin, Antonio Vitobello, Anne-Sophie Denommé-Pichon, Yannis Duffourd, Emilie Tisserant, Ange-Line Bruel, Christine Peyron, Aurore Pélissier, Sergi Beltran, Ivo Glynne Gut, Steven Laurie, Davide Piscia, Leslie Matalonga, Anastasios Papakonstantinou, Gemma Bullich, Alberto Corvo, Carles Garcia, Marcos Fernandez-Callejo, Carles Hernández, Daniel Picó, Ida Paramonov, Hanns Lochmüller, Gulcin Gumus, Virginie Bros-Facer, Ana Rath, Marc Hanauer, Annie Olry, David Lagorce, Svitlana Havrylenko, Katia Izem, Fanny Rigour, Giovanni Stevanin, Alexandra Durr, Claire-Sophie Davoine, Léna Guillot-Noel, Anna Heinzmann, Giulia Coarelli, Gisèle Bonne, Teresinha Evangelista, Valérie Allamand, Isabelle Nelson, Rabah Ben Yaou, Corinne Metay, Bruno Eymard, Enzo Cohen, Antonio Atalaia, Tanya Stojkovic, Milan Macek, Jr., Marek Turnovec, Dana Thomasová, Radka Pourová Kremliková, Vera Franková, Markéta Havlovicová, Vlastimil Kremlik, Helen Parkinson, Thomas Keane, Dylan Spalding, Alexander Senf, Peter Robinson, Daniel Danis, Glenn Robert, Alessia Costa, Christine Patch, Mike Hanna, Henry Houlden, Mary Reilly, Jana Vandrovcova, Francesco Muntoni, Irina Zaharieva, Anna Sarkozy, Vincent Timmerman, Jonathan Baets, Liedewei Van de Vondel, Danique Beijer, Peter de Jonghe, Vincenzo Nigro, Sandro Banfi, Annalaura Torella, Francesco Musacchia, Giulio Piluso, Alessandra Ferlini, Rita Selvatici, Rachele Rossi, Marcella Neri, Stefan Aretz, Isabel Spier, Anna Katharina Sommer, Sophia Peters, Carla Oliveira, Jose Garcia Pelaez, Ana Rita Matos, Celina São José, Marta Ferreira, Irene Gullo, Susana Fernandes, Luzia Garrido, Pedro Ferreira, Fátima Carneiro, Morris A. Swertz, Lennart Johansson, Joeri K. van der Velde, Gerben van der Vries, Pieter B. Neerincx, Dieuwke Roelofs-Prins, Sebastian Köhler, Alison Metcalfe, Alain Verloes, Séverine Drunat, Caroline Rooryck, Aurelien Trimouille, Raffaele Castello, Manuela Morleo, Michele Pinelli, Alessandra Varavallo, Manuel Posada De la Paz, Eva Bermejo Sánchez, Estrella López Martín, Beatriz Martínez Delgado, F. Javier Alonso García de la Rosa, Andrea Ciolfi, Bruno Dallapiccola, Simone Pizzi, Francesca Clementina Radio, Marco Tartaglia, Alessandra Renieri, Elisa Benetti, Peter Balicza, Maria Judit Molnar, Ales Maver, Borut Peterlin, Alexander Münchau, Katja Lohmann, Rebecca Herzog, Martje Pauly, Alfons Macaya, Anna Marcé-Grau, Andres Nascimiento Osorio, Daniel Natera de Benito, Rachel Thompson, Kiran Polavarapu, David Beeson, Judith Cossins, Pedro M. Rodriguez Cruz, Peter Hackman, Mridul Johari, Marco Savarese, Bjarne Udd, Rita Horvath, Gabriel Capella, Laura Valle, Elke Holinski-Feder, Andreas Laner, Verena Steinke-Lange, Evelin Schröck, and Andreas Rump

Subjects
TSPEAR, Ectodermal dysplasia, Enamel knot, WNT10A, Hypodontia, Conical teeth, Genetics, QH426-470
Abstract

Summary: TSPEAR variants cause autosomal recessive ectodermal dysplasia (ARED) 14. The function of TSPEAR is unknown. The clinical features, the mutation spectrum, and the underlying mechanisms of ARED14 are poorly understood. Combining data from new and previously published individuals established that ARED14 is primarily characterized by dental anomalies such as conical tooth cusps and hypodontia, like those seen in individuals with WNT10A-related odontoonychodermal dysplasia. AlphaFold-predicted structure-based analysis showed that most of the pathogenic TSPEAR missense variants likely destabilize the β-propeller of the protein. Analysis of 100000 Genomes Project (100KGP) data revealed multiple founder TSPEAR variants across different populations. Mutational and recombination clock analyses demonstrated that non-Finnish European founder variants likely originated around the end of the last ice age, a period of major climatic transition. Analysis of gnomAD data showed that the non-Finnish European population TSPEAR gene-carrier rate is ∼1/140, making it one of the commonest AREDs. Phylogenetic and AlphaFold structural analyses showed that TSPEAR is an ortholog of drosophila Closca, an extracellular matrix-dependent signaling regulator. We, therefore, hypothesized that TSPEAR could have a role in enamel knot, a structure that coordinates patterning of developing tooth cusps. Analysis of mouse single-cell RNA sequencing (scRNA-seq) data revealed highly restricted expression of Tspear in clusters representing enamel knots. A tspeara−/−;tspearb−/− double-knockout zebrafish model recapitulated the clinical features of ARED14 and fin regeneration abnormalities of wnt10a knockout fish, thus suggesting interaction between tspear and wnt10a. In summary, we provide insights into the role of TSPEAR in ectodermal development and the evolutionary history, epidemiology, mechanisms, and consequences of its loss of function variants.

Published
2023
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4. History and highlights of the teratological collection in the Narrenturm, Vienna (Austria)

Author

Lucas L. Boer, Susanne Gerit Kircher, Helga Rehder, Jana Behunova, Eduard Winter, Helmut Ringl, Anke Scharrer, Elke de Boer, Roelof‐Jan Oostra, Medical Biology, ACS - Amsterdam Cardiovascular Sciences, and ARD - Amsterdam Reproduction and Development

Subjects
All institutes and research themes of the Radboud University Medical Center, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], congenital anomalies, Narrenturm, museum, syndromes, Other Research Radboud Institute for Health Sciences [Radboudumc 0], Genetics, historical collections, Genetics (clinical), teratology
Abstract

Contains fulltext : 291894.pdf (Publisher’s version ) (Open Access) The collection of the Narrenturm in Vienna houses and maintains more than 50,000 objects including approximately 1200 teratological specimens; making it one of the biggest collections of specimens from human origin in Europe. The existence of this magnificent collection-representing an important resource for dysmorphology research, mostly awaiting contemporary diagnoses-is not widely known in the scientific community. Here, we show that the Narrenturm harbors a wealth of specimens with (exceptionally) rare congenital anomalies. These museums can be seen as physical repositories of human malformation, covering hundreds of years of dedicated collecting and preserving, thereby creating unique settings that can be used to expand our knowledge of developmental conditions that have to be preserved for future generations of scientists.

Published
2023

5. Genome-wide variant calling in reanalysis of exome sequencing data uncovered a pathogenic TUBB3 variant

Author

Elke de Boer, Burcu Yaldiz, Anne-Sophie Denommé-Pichon, Leslie Matalonga, Steve Laurie, Wouter Steyaert, Rick de Reuver, Christian Gilissen, Michael Kwint, Rolph Pfundt, Alain Verloes, Michèl A.A.P. Willemsen, Bert B.A. de Vries, A. Vitobello, Tjitske Kleefstra, Lisenka E.L.M. Vissers, Enzo Cohen, Isabel Cuesta, Daniel Danis, Fei Gao, Rita Horvath, Mridul Johari, Lennart Johanson, Shuang Li, Heba Morsy, Isabelle Nelson, Ida Paramonov, Iris B.A.W. te Paske, Peter Robinson, Marco Savarese, Ana Töpf, Aurélien Trimouille, Joeri K. van der Velde, Jana Vandrovcova, Antonio Vitobello, Birte Zurek, Kristin M. Abbot, Siddharth Banka, Elisa Benetti, Giorgio Casari, Andrea Ciolfi, Jill Clayton-Smith, Bruno Dallapiccola, Kornelia Ellwanger, Laurence Faivre, Holm Graessner, Tobias B. Haack, Anna Hammarsjö, Marketa Havlovicova, Alexander Hoischen, Anne Hugon, Adam Jackson, Mieke Kerstjens, Anna Lindstrand, Estrella López Martín, Milan Macek, Isabelle Maystadt, Manuela Morleo, Vicenzo Nigro, Ann Nordgren, Maria Pettersson, Michele Pinelli, Simone Pizzi, Manuel Posada, Francesca C. Radio, Alessandra Renieri, Caroline Rooryck, Lukas Ryba, Gijs W.E. Santen, Martin Schwarz, Marco Tartaglia, Christel Thauvin, Annalaura Torella, Lisenka Vissers, Pavel Votypka, Klea Vyshka, Kristina Zguro, Dutch Research Council (Holanda), Unión Europea. Comisión Europea. H2020, Netherlands Organisation for Health Research and Development, de Boer, E., Yaldiz, B., Denomme-Pichon, A. -S., Matalonga, L., Laurie, S., Steyaert, W., de Reuver, R., Gilissen, C., Kwint, M., Pfundt, R., Verloes, A., Willemsen, M. A. A. P., de Vries, B. B. A., Vitobello, A., Kleefstra, T., Vissers, L. E. L. M., Nigro, V., Torella, A., and Banfi, S.

Subjects
Proband, Exome sequencing, Adolescent, Developmental Disabilities, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Mutation, Missense, Computational biology, Biology, Genome, Exon, All institutes and research themes of the Radboud University Medical Center, Tubulin, Intellectual Disability, Solve-RD, Exome Sequencing, Genetics, Coding region, Missense mutation, Humans, TUBB3, Gene, Genetics (clinical), Sequence (medicine), Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], ERN ITHACA, Brain, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], General Medicine, Genome-wide variant calling, Strabismus, Face, Microcephaly, Female
Abstract

Almost half of all individuals affected by intellectual disability (ID) remain undiagnosed. In the Solve-RD project, exome sequencing (ES) datasets from unresolved individuals with (syndromic) ID (n = 1,472 probands) are systematically reanalyzed, starting from raw sequencing files, followed by genome-wide variant calling and new data interpretation. This strategy led to the identification of a disease-causing de novo missense variant in TUBB3 in a girl with severe developmental delay, secondary microcephaly, brain imaging abnormalities, high hypermetropia, strabismus and short stature. Interestingly, the TUBB3 variant could only be identified through reanalysis of ES data using a genome-wide variant calling approach, despite being located in protein coding sequence. More detailed analysis revealed that the position of the variant within exon 5 of TUBB3 was not targeted by the enrichment kit, although consistent high-quality coverage was obtained at this position, resulting from nearby targets that provide off-target coverage. In the initial analysis, variant calling was restricted to the exon targets ± 200 bases, allowing the variant to escape detection by the variant calling algorithm. This phenomenon may potentially occur more often, as we determined that 36 established ID genes have robust off-target coverage in coding sequence. Moreover, within these regions, for 17 genes (likely) pathogenic variants have been identified before. Therefore, this clinical report highlights that, although compute-intensive, performing genome-wide variant calling instead of target-based calling may lead to the detection of diagnostically relevant variants that would otherwise remain unnoticed. This work was financially supported by Aspasia grants of the Dutch Research Council (015.014.036 to TK and 015.014.066 to LELMV) and Netherlands Organization for Health Research and Development (917.183.10 to TK). The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 779257. Sí

Published
2021

6. SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females

Author

Gilles Morin, Krista Bluske, Nathaniel H. Robin, Laurence Faivre, Manuela Priolo, Dihong Zhou, Evangeline Kurtz-Nelson, Tianyun Wang, Omar Sherbini, Daryl A. Scott, Karen Stals, Fabíola Paoli Monteiro, Kaifang Pang, Sara Cabet, Francesca Clementina Radio, Bruno Dallapiccola, Marjon van Slegtenhorst, Rachel K. Earl, Katheryn Grand, Maria Iascone, Alice S. Brooks, Angelo Selicorni, July K. Jean Cuevas, Paolo Gasparini, Maria Lisa Dentici, Marialetizia Motta, Britt-Marie Anderlid, Kristin Lindstrom, Berrin Monteleone, Andrea Ciolfi, Karin Weiss, Katharina Steindl, Kirsty McWalter, Rosalba Carrozzo, Ruben Boers, Helen Kingston, Kym M. Boycott, Bekim Sadikovic, Laura Schultz-Rogers, Evan E. Eichler, Laura A Cross, Alison M R Castle, Louisa Kalsner, Lucia Pedace, Marijke R. Wevers, John M. Graham, Jessica Sebastian, Antonio Vitobello, Gaetan Lesca, Alexander P.A. Stegmann, Suneeta Madan-Khetarpal, Tahsin Stefan Barakat, Abdallah F. Elias, Teresa Robert Finestra, Adeline Vanderver, Peter D. Turnpenny, Bregje W.M. van Bon, Aida Telegrafi, David J. Amor, Deepali N. Shinde, Pedro A. Sanchez-Lara, Lisenka E.L.M. Vissers, Adam Jackson, Rolph Pfundt, Alessandro Bruselles, Andres Hernandez-Garcia, Karin E. M. Diderich, Flavio Faletra, Dana H. Goodloe, Joanne Baez, Sarit Ravid, Romano Tenconi, Sarah L. Sawyer, Lynn Pais, Bronwyn Kerr, Joost Gribnau, Lauren Carter, Melissa T. Carter, Zhandong Liu, Jennifer L. Kemppainen, Jennifer MacKenzie, Jimmy Holder, Elke de Boer, Margaret Au, Taila Hartley, Carol J Saunders, Luciana Musante, Bert B.A. de Vries, Tania Vertemati Secches, Haley McConkey, Willow Sheehan, Francesca Pantaleoni, Caterina Zanus, Christophe Philippe, Chelsea Roadhouse, Stefania Lo Cicero, Sian Ellard, R. Tanner Hagelstrom, Megha Desai, Fernando Kok, Joset Pascal, Marco Tartaglia, Eric W. Klee, Eva Morava, Michael A. Levy, Peggy Kulch, Lyndon Gallacher, Erica L. Macke, Emilia Stellacci, Siddharth Banka, Kristin G. Monaghan, Anita Rauch, Meghan C. Towne, Kate Chandler, Clinical Genetics, Developmental Biology, Radio, F. C., Pang, K., Ciolfi, A., Levy, M. A., Hernandez-Garcia, A., Pedace, L., Pantaleoni, F., Liu, Z., de Boer, E., Jackson, A., Bruselles, A., Mcconkey, H., Stellacci, E., Lo Cicero, S., Motta, M., Carrozzo, R., Dentici, M. L., Mcwalter, K., Desai, M., Monaghan, K. G., Telegrafi, A., Philippe, C., Vitobello, A., Au, M., Grand, K., Sanchez-Lara, P. A., Baez, J., Lindstrom, K., Kulch, P., Sebastian, J., Madan-Khetarpal, S., Roadhouse, C., Mackenzie, J. J., Monteleone, B., Saunders, C. J., Jean Cuevas, J. K., Cross, L., Zhou, D., Hartley, T., Sawyer, S. L., Monteiro, F. P., Secches, T. V., Kok, F., Schultz-Rogers, L. E., Macke, E. L., Morava, E., Klee, E. W., Kemppainen, J., Iascone, M., Selicorni, A., Tenconi, R., Amor, D. J., Pais, L., Gallacher, L., Turnpenny, P. D., Stals, K., Ellard, S., Cabet, S., Lesca, G., Pascal, J., Steindl, K., Ravid, S., Weiss, K., Castle, A. M. R., Carter, M. T., Kalsner, L., de Vries, B. B. A., van Bon, B. W., Wevers, M. R., Pfundt, R., Stegmann, A. P. A., Kerr, B., Kingston, H. M., Chandler, K. E., Sheehan, W., Elias, A. F., Shinde, D. N., Towne, M. C., Robin, N. H., Goodloe, D., Vanderver, A., Sherbini, O., Bluske, K., Hagelstrom, R. T., Zanus, C., Faletra, F., Musante, L., Kurtz-Nelson, E. C., Earl, R. K., Anderlid, B. -M., Morin, G., van Slegtenhorst, M., Diderich, K. E. M., Brooks, A. S., Gribnau, J., Boers, R. G., Finestra, T. R., Carter, L. B., Rauch, A., Gasparini, P., Boycott, K. M., Barakat, T. S., Graham, J. M., Faivre, L., Banka, S., Wang, T., Eichler, E. E., Priolo, M., Dallapiccola, B., Vissers, L. E. L. M., Sadikovic, B., Scott, D. A., Holder, J. L., Tartaglia, M., MUMC+: DA KG Lab Centraal Lab (9), and RS: FHML non-thematic output

Subjects
0301 basic medicine, SHARP, Male, obesity, genotype-phenotype correlations, Autism Spectrum Disorder, PROTEIN, Chromosome Disorders, Haploinsufficiency, RNA-Binding Protein, PHENOTYPE CORRELATIONS, 1p36, distal 1p36 deletion syndrome, DNA methylome analysis, episignature, neurodevelopmental disorder, proximal 1p36 deletion syndrome, SPEN, X chromosome, Adolescent, Child, Child, Preschool, Chromosome Deletion, Chromosomes, Human, Pair 1, Chromosomes, Human, X, DNA Methylation, DNA-Binding Proteins, Epigenesis, Genetic, Female, Humans, Intellectual Disability, Neurodevelopmental Disorders, Phenotype, RNA-Binding Proteins, Young Adult, 0302 clinical medicine, Neurodevelopmental disorder, Neurodevelopmental Disorder, Intellectual disability, MOLECULAR CHARACTERIZATION, Genetics (clinical), Genetics, DNA methylome analysi, SPLIT-ENDS, Hypotonia, Autism spectrum disorder, MONOSOMY 1P36, Pair 1, medicine.symptom, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Human, DNA-Binding Protein, Biology, genotype-phenotype correlation, Chromosomes, 03 medical and health sciences, Genetic, SDG 3 - Good Health and Well-being, Report, REVEALS, medicine, Epigenetics, Preschool, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], 1p36 deletion syndrome, IDENTIFICATION, MUTATIONS, medicine.disease, GENE, 030104 developmental biology, Chromosome Disorder, 030217 neurology & neurosurgery, Epigenesis
Abstract

Contains fulltext : 231702.pdf (Publisher’s version ) (Closed access) Deletion 1p36 (del1p36) syndrome is the most common human disorder resulting from a terminal autosomal deletion. This condition is molecularly and clinically heterogeneous. Deletions involving two non-overlapping regions, known as the distal (telomeric) and proximal (centromeric) critical regions, are sufficient to cause the majority of the recurrent clinical features, although with different facial features and dysmorphisms. SPEN encodes a transcriptional repressor commonly deleted in proximal del1p36 syndrome and is located centromeric to the proximal 1p36 critical region. Here, we used clinical data from 34 individuals with truncating variants in SPEN to define a neurodevelopmental disorder presenting with features that overlap considerably with those of proximal del1p36 syndrome. The clinical profile of this disease includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females. SPEN also emerges as a relevant gene for del1p36 syndrome by co-expression analyses. Finally, we show that haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females, providing further evidence of a specific contribution of the protein to the epigenetic control of this chromosome, and a paradigm of an X chromosome-specific episignature that classifies syndromic traits. We conclude that SPEN is required for multiple developmental processes and SPEN haploinsufficiency is a major contributor to a disorder associated with deletions centromeric to the previously established 1p36 critical regions.

Published
2021

7. Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome

Author

Sixto Garcia Minaur, Pankaj B. Agrawal, A. Micheil Innes, Catherine A. Brownstein, David S. Wargowski, Brenda McInnes, Isaac Wong, Albert E. Chudley, Jennifer E. Posey, Francesc López-Giráldez, Ping-Yee B Au, Alper Gezdirici, Kyrieckos A. Aleck, Eric Boerwinkle, Paolo Prontera, Bilgen Bilge Geçkinli, Yeting Zhang, An Nguyen, David A. Dyment, Jukka S. Moilanen, Alan H. Beggs, Nara Sobreira, Hatip Aydin, Elizabeth E. Blue, Kathryn Dunn, Gerald F. Cox, Bernard N. Chodirker, Harrison Brand, Jinchuan Xing, Hind Al Sharhan, Bert B.A. de Vries, Maria Juliana Rodovalho Doriqui, Davut Pehlivan, Shalini N. Jhangiani, Centers for Mendelian Genomics, Katrin Õunap, Cheryl R. Greenberg, Kaya Bilguvar, Carol L. Clericuzio, Cynthia J. Curry, Taila Hartley, Julie Lauzon, Michael J. Bamshad, Timothy Poterba, R. Brian Lowry, Jill A. Fahrner, Cullen M. Dutmer, M. E. Suzanne Lewis, Steve Buyske, Ender Karaca, Aziz Mhanni, William T. Gibson, Valentina Stanley, April Hall, Elke de Boer, Kristin D. Kernohan, Joseph G. Gleeson, P. Dane Witmer, Jungmin Choi, Danny Antaki, Małgorzata J.M. Nowaczyk, Sander Pajusalu, Anne H. O’Donnell-Luria, Sarah L. Sawyer, Zeynep Coban Akdemir, Tara C. Matise, Jennifer McEvoy-Venneri, Casie A. Genetti, Kym M. Boycott, Lynette S. Penney, Ada Hamosh, Eleina M. England, Deniz Torun, Maha S. Zaki, Deborah A. Nickerson, Dyment, David A., O'Donnell-Luria, Anne, Agrawal, Pankaj B., Coban Akdemir, Zeynep, Aleck, Kyrieckos A., Antaki, Danny, Al Sharhan, Hind, Au, Ping-Yee B., Aydin, Hatip, Beggs, Alan H., Bilguvar, Kaya, Boerwinkle, Eric, Brand, Harrison, Brownstein, Catherine A., Buyske, Steve, Chodirker, Bernard, Choi, Jungmin, Chudley, Albert E., Clericuzio, Carol L., Cox, Gerald F., Curry, Cynthia, de Boer, Elke, de Vries, Bert B. A., Dunn, Kathryn, Dutmer, Cullen M., England, Eleina M., Fahrner, Jill A., Geckinli, Bilgen B., Genetti, Casie A., Gezdirici, Alper, Gibson, William T., Gleeson, Joseph G., Greenberg, Cheryl R., Hall, April, Hamosh, Ada, Hartley, Taila, Jhangiani, Shalini N., Karaca, Ender, Kernohan, Kristin, Lauzon, Julie L., Lewis, M. E. Suzanne, Lowry, R. Brian, Lopez-Giraldez, Francesc, Matise, Tara C., McEvoy-Venneri, Jennifer, McInnes, Brenda, Mhanni, Aziz, Garcia Minaur, Sixto, Moilanen, Jukka, Nguyen, An, Nowaczyk, Malgorzata J. M., Posey, Jennifer E., Ounap, Katrin, Pehlivan, Davut, Pajusalu, Sander, Penney, Lynette S., Poterba, Timothy, Prontera, Paolo, Doriqui, Maria Juliana Rodovalho, Sawyer, Sarah L., Sobreira, Nara, Stanley, Valentina, Torun, Deniz, Wargowski, David, Witmer, P. Dane, Wong, Isaac, Xing, Jinchuan, Zaki, Maha S., Zhang, Yeting, Boycott, Kym M., Bamshad, Michael J., Nickerson, Deborah A., Blue, Elizabeth E., and Innes, A. Micheil

Subjects
0301 basic medicine, Male, ANOMALIES, INTELLECTUAL DISABILITY, Eczema, 030105 genetics & heredity, PHENOTYPE, genetic heterogeneity, Locus heterogeneity, Dubowitz syndrome, Exome, Child, Genetics (clinical), Exome sequencing, Growth Disorders, Genetics, FRAMESHIFT, Genomics, 3. Good health, VPS13B, genome sequencing, LOSS-OF-FUNCTION, Child, Preschool, symbols, Microcephaly, Female, microarray, Adolescent, DNA Copy Number Variations, Biology, NSUN2, PATIENT, DNA sequencing, Histone Deacetylases, Article, 03 medical and health sciences, symbols.namesake, medicine, Humans, Genetic Predisposition to Disease, ANEMIA, Genetic heterogeneity, Genome, Human, MUTATIONS, Facies, Infant, PLATFORM, medicine.disease, Repressor Proteins, 030104 developmental biology, Mendelian inheritance, exome sequencing
Abstract

Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported with Dubowitz or a "Dubowitz-like" condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome-wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy-number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next-generation sequencing. Overall, the DubS-like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype.

Published
2021

8. De Novo Variants in CNOT1, a Central Component of the CCR4-NOT Complex Involved in Gene Expression and RNA and Protein Stability, Cause Neurodevelopmental Delay

Author

Paul Kruszka, Sreehari Kalvakuri, Austin Larson, Dong Li, Inge van Outersterp, Florence Demurger, Ian Hayes, F. Lucy Raymond, Lauren J. Massingham, Claudia A. L. Ruivenkamp, Ian D. Krantz, Kendra Brunet, Nicole Revencu, Maaike Vreeburg, Donatella Milani, Tjitske Kleefstra, Lisenka E.L.M. Vissers, Maximilian Muenke, Sinje Geuer, Candace Gamble, Rolf Bodmer, Hanka Venselaar, Elke de Boer, Sarina G. Kant, Dilys Weijers, Arjan P.M. de Brouwer, Machteld M. Oud, Maria Iascone, Christopher C. Griffith, Frédéric Tran Mau-Them, Karin Weiss, Megan T. Cho, Ayesha Ahmad, James A. Bartley, Nina Powell Hamilton, Lenika De Simone, George E. Hoganson, Lucie Evenepoel, Simone Kersten, Daniel L. Polla, Himanshu Goel, Antonio Vitobello, Rachel Fisher, Arthur Sorlin, Sébastien Moutton, Myrthe van den Born, Hilary J. Vernon, Michael Kwint, Kaitlyn Burns, Anna Ruiz, Kirsty McWalter, Jenny Morton, Jennifer Schwab, Elizabeth J. Bhoj, Philippe Christophe, Hans van Bokhoven, Elisabeth Gabau, Kimberly M. Nugent, Jill R. Murrell, Thierry Billette de Villemeur, Kathleen Wood, Alexandra Afenjar, Amber Begtrup, Chanika Phornphutkul, Sarah E. Raible, Melde Witmond, Perrine Charles, Claudia Soler-Alfonso, D. Isum Ward, Marjolaine Willems, Boris Keren, Julian Delanne, UCL - SSS/IREC/SLUC - Pôle St.-Luc, UCL - (SLuc) Centre de génétique médicale UCL, Clinical Genetics, Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, and MUMC+: DA KG Polikliniek (9)

Subjects
Male, DYRK1A, Developmental Disabilities, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Gene Expression, de novo mutations, Haploinsufficiency, 0302 clinical medicine, Gene expression, Nuclear Receptor Subfamily 4, Group A, Member 2, Genetics (clinical), Genetics, 0303 health sciences, Gene knockdown, repressor, neurodevelopment, Protein Stability, CCR4-NOT complex, Phenotype, developmental delay, intellectual disability, Drosophila, deadenylase complex, Female, regulators, Heterozygote, Receptors, CCR4, Biology, Nervous System Malformations, 03 medical and health sciences, Report, genomics, Humans, Gene, Alleles, 030304 developmental biology, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Genetic Variation, Protein ubiquitination, Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11], Neurodevelopmental Disorders, SUBUNIT, RNA, CNOT1, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], exome sequencing, 030217 neurology & neurosurgery, Transcription Factors
Abstract

Contains fulltext : 220423.pdf (Publisher’s version ) (Closed access) CNOT1 is a member of the CCR4-NOT complex, which is a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. We report on 39 individuals with heterozygous de novo CNOT1 variants, including missense, splice site, and nonsense variants, who present with a clinical spectrum of intellectual disability, motor delay, speech delay, seizures, hypotonia, and behavioral problems. To link CNOT1 dysfunction to the neurodevelopmental phenotype observed, we generated variant-specific Drosophila models, which showed learning and memory defects upon CNOT1 knockdown. Introduction of human wild-type CNOT1 was able to rescue this phenotype, whereas mutants could not or only partially, supporting our hypothesis that CNOT1 impairment results in neurodevelopmental delay. Furthermore, the genetic interaction with autism-spectrum genes, such as ASH1L, DYRK1A, MED13, and SHANK3, was impaired in our Drosophila models. Molecular characterization of CNOT1 variants revealed normal CNOT1 expression levels, with both mutant and wild-type alleles expressed at similar levels. Analysis of protein-protein interactions with other members indicated that the CCR4-NOT complex remained intact. An integrated omics approach of patient-derived genomics and transcriptomics data suggested only minimal effects on endonucleolytic nonsense-mediated mRNA decay components, suggesting that de novo CNOT1 variants are likely haploinsufficient hypomorph or neomorph, rather than dominant negative. In summary, we provide strong evidence that de novo CNOT1 variants cause neurodevelopmental delay with a wide range of additional co-morbidities. Whereas the underlying pathophysiological mechanism warrants further analysis, our data demonstrate an essential and central role of the CCR4-NOT complex in human brain development.

Published
2020

9. Integrating healthcare and research genetic data empowers the discovery of 49 novel developmental disorders

Author

Joanna Kaplanis, Kaitlin E. Samocha, Laurens Wiel, Zhancheng Zhang, Kevin J. Arvai, Ruth Y. Eberhardt, Giuseppe Gallone, Stefan H. Lelieveld, Hilary C. Martin, Jeremy F. McRae, Patrick J. Short, Rebecca I. Torene, Elke de Boer, Petr Danecek, Eugene J. Gardner, Ni Huang, Jenny Lord, Iñigo Martincorena, Rolph Pfundt, Margot R. F. Reijnders, Alison Yeung, Helger G. Yntema, DDD Study, Lisenka E. L. M. Vissers, Jane Juusola, Caroline F. Wright, Han G. Brunner, Helen V. Firth, David R. FitzPatrick, Jeffrey C. Barrett, Matthew E. Hurles, Christian Gilissen, and Kyle Retterer

Subjects
Genetics, 0303 health sciences, biology, Variant type, Genomics, 3. Good health, 03 medical and health sciences, chemistry.chemical_compound, Negative selection, 0302 clinical medicine, chemistry, biology.protein, Missense mutation, Exome, Gene, 030217 neurology & neurosurgery, Polymerase, DNA, 030304 developmental biology
Abstract

Approximately 2% of de novo single nucleotide variants (SNVs) appear as part of clustered mutations that create multinucleotide variants (MNVs). MNVs are an important source of genomic variability as they are more likely to alter an encoded protein than a SNV, which has important implications in disease as well as evolution. Previous studies of MNVs have focused on their mutational origins and have not systematically evaluated their functional impact and contribution to disease. We identified 69,940 MNVs and 106 de novo MNVs in 6,688 exome sequenced parent-offspring trios from the Deciphering Developmental Disorders Study comprising families with severe developmental disorders. We replicated the previously described MNV mutational signatures associated with DNA polymerase zeta, an error-prone translesion polymerase, and the APOBEC family of DNA deaminases. We found that most MNVs within a single codon create a missense change that could not have been created by a SNV. MNV-induced missense changes were, on average, more physico-chemically divergent, more depleted in highly constrained genes (pLI>=0.9) and were under stronger purifying selection compared to SNV-induced missense changes. We found that de novo MNVs were significantly enriched in genes previously associated with developmental disorders in affected children. This demonstrates that MNVs can be more damaging than SNVs even when both induce missense changes and are an important variant type to consider in relation to human disease.

Published
2018
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10. Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction

Author

Antonio Vitobello, Christel Depienne, Kelly Radtke, Bruria Ben-Zeev, Vaidutis Kučinskas, Hirofumi Kashii, Leslie Granger, Florence Demurger, Adi Vaknin-Dembinsky, Androu Waheeb, Takeshi Mizuguchi, Lip H. Moey, Urania Kotzaeridou, Frédérique Béna, Fernando Kok, Timothy Blake Palculict, Yasmin Hamzavi Abedi, Satoko Miyatake, Anne-Sophie Denommé-Pichon, Linda Manwaring, Laura Elena Orec, Laurens Wiel, Han G. Brunner, Sylvie Odent, Eric Vilain, Linh Tran, Simon E. Fisher, Emmanuèlle C. Délot, Vidya Krishnamurthy, Rebecca C. Spillmann, Hilary Coon, Shelagh Joss, Hui B. Chew, Matias Wagner, David A. Dyment, Kirsty McWalter, Michael W. Parker, Adam Jackson, Margje Sinnema, Pengfei Liu, Elke de Boer, Alma Kuechler, Christoffer Nellåker, Christian Gilissen, Yasuo Hachiya, Marcia C. Willing, Shivarajan M. Amudhavalli, Alexander P.A. Stegmann, Ange-Line Bruel, Siddharth Banka, Joery den Hoed, Vardiella Meiner, Rosalyn Jewell, Britton D Zuccarelli, Alexander J. M. Dingemans, Kelly L. Jones, Anja A. Kattentidt-Mouravieva, Matthew Osmond, Orly Elpeleg, Andrea K. Petersen, Nicolas Guex, Dianne F. Newbury, Jill A. Rosenfeld, Alexandre Reymond, Mohamad A. Mikati, Tjitske Kleefstra, Lisenka E.L.M. Vissers, Naomichi Matsumoto, Vincent R. Bonagura, Loreta Cimbalistienė, Benoît Mazel, Hayley S. Mountford, Isabelle Thiffault, Rolph Pfundt, Ruth Newbury-Ecob, Teresa Santiago-Sim, Alinoë Lavillaureix, Eglė Preikšaitienė, Jacqueline Chrast, Toshiyuki Itai, Norine Voisin, Usha Kini, Emmanuelle Ranza, Caitlin Schwager, Brooke Horist, Samantha A. Schrier Vergano, Jennifer Hanebeck, Juliana H. Vedovato-dos-Santos, Mitsuhiro Kato, Theresa Brunet, Lot Snijders Blok, Jayne Y. Hehir-Kwa, Shehla Mohammed, Benjamin Haber, Hagar Mor-Shaked, Laurence Faivre, Dian Donnai, Max Planck Institute for Psycholinguistics, Max-Planck-Gesellschaft, Université de Lausanne = University of Lausanne (UNIL), Children's Mercy Hospital [Kansas City], University of Manchester [Manchester], Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), CHU Pontchaillou [Rennes], Centre de référence Maladies Rares CLAD-Ouest [Rennes], Radboud University [Nijmegen], Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Nederlandse Organisatie voor Wetenschappelijk Onderzoek, University of Lausanne (UNIL), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Radboud university [Nijmegen], The DDD study, RS: GROW - R4 - Reproductive and Perinatal Medicine, Klinische Genetica, and MUMC+: DA Klinische Genetica (5)

Subjects
0301 basic medicine, Male, Models, Molecular, MISSENSE MUTATIONS, CHROMATIN, Transcription, Genetic, Cell, Medizin, Disease, Haploinsufficiency, medicine.disease_cause, 0302 clinical medicine, Missense mutation, de novo variants, Genetics (clinical), INTERLEUKIN-2, seizures, Genetics, 0303 health sciences, Mutation, Chromatin binding, neurodevelopmental disorders, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], SATB1, Phenotype, medicine.anatomical_structure, intellectual disability, Female, teeth abnormalities, Protein Binding, Neuroinformatics, EXPRESSION, GENES, Mutation, Missense, Biology, BINDING PROTEIN, REGION, 03 medical and health sciences, Protein Domains, Report, medicine, HPO-based analysis, Humans, Genetic Association Studies, Hpo-based Analysis, Satb1, Cell-based Functional Assays, De Novo Variants, Intellectual Disability, Neurodevelopmental Disorders, Seizures, Teeth Abnormalities, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Matrix Attachment Region Binding Proteins, 030104 developmental biology, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], 030217 neurology & neurosurgery, cell-based functional assays
Abstract

Whereas large-scale statistical analyses can robustly identify disease-gene relationships, they do not accurately capture genotype-phenotype correlations or disease mechanisms. We use multiple lines of independent evidence to show that different variant types in a single gene,SATB1, cause clinically overlapping but distinct neurodevelopmental disorders. Clinical evaluation of 42 individuals carryingSATB1variants identified overt genotype-phenotype relationships, associated with different pathophysiological mechanisms, established by functional assays. Missense variants in the CUT1 and CUT2 DNA-binding domains result in stronger chromatin binding, increased transcriptional repression and a severe phenotype. Contrastingly, variants predicted to result in haploinsufficiency are associated with a milder clinical presentation. A similarly mild phenotype is observed for individuals with premature protein truncating variants that escape nonsense-mediated decay and encode truncated proteins, which are transcriptionally active but mislocalized in the cell. Our results suggest that in-depth mutation-specific genotype-phenotype studies are essential to capture full disease complexity and to explain phenotypic variability.

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