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1. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders

Author

Michael A. Levy, Haley McConkey, Jennifer Kerkhof, Mouna Barat-Houari, Sara Bargiacchi, Elisa Biamino, María Palomares Bralo, Gerarda Cappuccio, Andrea Ciolfi, Angus Clarke, Barbara R. DuPont, Mariet W. Elting, Laurence Faivre, Timothy Fee, Robin S. Fletcher, Florian Cherik, Aidin Foroutan, Michael J. Friez, Cristina Gervasini, Sadegheh Haghshenas, Benjamin A. Hilton, Zandra Jenkins, Simranpreet Kaur, Suzanne Lewis, Raymond J. Louie, Silvia Maitz, Donatella Milani, Angela T. Morgan, Renske Oegema, Elsebet Østergaard, Nathalie Ruiz Pallares, Maria Piccione, Simone Pizzi, Astrid S. Plomp, Cathryn Poulton, Jack Reilly, Raissa Relator, Rocio Rius, Stephen Robertson, Kathleen Rooney, Justine Rousseau, Gijs W.E. Santen, Fernando Santos-Simarro, Josephine Schijns, Gabriella Maria Squeo, Miya St John, Christel Thauvin-Robinet, Giovanna Traficante, Pleuntje J. van der Sluijs, Samantha A. Vergano, Niels Vos, Kellie K. Walden, Dimitar Azmanov, Tugce Balci, Siddharth Banka, Jozef Gecz, Peter Henneman, Jennifer A. Lee, Marcel M.A.M. Mannens, Tony Roscioli, Victoria Siu, David J. Amor, Gareth Baynam, Eric G. Bend, Kym Boycott, Nicola Brunetti-Pierri, Philippe M. Campeau, John Christodoulou, David Dyment, Natacha Esber, Jill A. Fahrner, Mark D. Fleming, David Genevieve, Kristin D. Kerrnohan, Alisdair McNeill, Leonie A. Menke, Giuseppe Merla, Paolo Prontera, Cheryl Rockman-Greenberg, Charles Schwartz, Steven A. Skinner, Roger E. Stevenson, Antonio Vitobello, Marco Tartaglia, Marielle Alders, Matthew L. Tedder, and Bekim Sadikovic

Subjects
Episignatures, Neurodevelopmental disorders, DNA methylation, Epigenetics, Clinical diagnostics, Genetics, QH426-470
Abstract

Summary: Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.

Published
2022
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2. Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort

Author

Pleuntje J. van der Sluijs, Marieke Joosten, Caroline Alby, Tania Attié-Bitach, Kelly Gilmore, Christele Dubourg, Mélanie Fradin, Tianyun Wang, Evangeline C. Kurtz-Nelson, Kaitlyn P. Ahlers, Peer Arts, Christopher P. Barnett, Myla Ashfaq, Anwar Baban, Myrthe van den Born, Sarah Borrie, Tiffany Busa, Alicia Byrne, Miriam Carriero, Claudia Cesario, Karen Chong, Anna Maria Cueto-González, Jennifer C. Dempsey, Karin E.M. Diderich, Dan Doherty, Stense Farholt, Erica H. Gerkes, Svetlana Gorokhova, Lutgarde C.P. Govaerts, Pernille A. Gregersen, Scott E. Hickey, Mathilde Lefebvre, Francesca Mari, Jelena Martinovic, Hope Northrup, Melanie O’Leary, Kareesma Parbhoo, Sophie Patrier, Bernt Popp, Fernando Santos-Simarro, Corinna Stoltenburg, Christel Thauvin-Robinet, Elisabeth Thompson, Anneke T. Vulto-van Silfhout, Farah R. Zahir, Hamish S. Scott, Rachel K. Earl, Evan E. Eichler, Neeta L. Vora, Yael Wilnai, Jessica L. Giordano, Ronald J. Wapner, Jill A. Rosenfeld, Monique C. Haak, Gijs W.E. Santen, Leiden University Medical Center (LUMC), Universiteit Leiden, Erasmus University Medical Center [Rotterdam] (Erasmus MC), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), 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], Hôpital de la Timone [CHU - APHM] (TIMONE), Marseille medical genetics - Centre de génétique médicale de Marseille (MMG), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Agro Dijon, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CHU Rouen, Normandie Université (NU), Columbia University Medical Center (CUMC), Columbia University [New York], Baylor College of Medicine (BCM), Baylor University, This work was supported, in part, by grants from the National Institutes of Health (Grant No. R01 MH101221 [to E.E.E.]). E.E.E. is an investigator of the Howard Hughes Medical Institute.Sequencing and analysis for individual 30 was provided by the Broad Institute of MIT and Harvard Center for Mendelian Genomics and was funded by the National Human Genome Research Institute, the National Eye Institute, and the National Heart, Lung, and Blood Institute (Grant Nos. UM1 HG008900 and R01 HG009141).Sequencing and analysis of cases 5 and 18 was funded by the National Institute of Child Human Development (Grant Nos. K23 HD088742 and R01 HD105868 [to N.L.V.])., Emergency Medicine, Clinical Genetics, van der Sluijs, Pleuntje J, Joosten, Marieke, Alby, Caroline, Attié-Bitach, Tania, Arts, Peer, Byrne, Alicia, Scott, Hamish S, and Santen, Gijs WE

Subjects
prenatal, genetic association, Chromosomal Proteins, Non-Histone, Micrognathism, SMARCB1, genetic vulnerability, Article, Fetal, SMARCA4, Intellectual Disability, Humans, Coffin-Siris syndrome, Abnormalities, Multiple, Genetic Association Studies, Genetics (clinical), Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], BAF-complex, SMARCB, ARID1A, ARID1B BAFopathy, Phenotype, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Face, abnormalities, Hand Deformities, Congenital, Neck
Abstract

Purpose: Genome-wide sequencing is increasingly being performed during pregnancy to identify the genetic cause of congenital anomalies. The interpretation of prenatally identified variants can be challenging and is hampered by our often limited knowledge of prenatal phenotypes. To better delineate the prenatal phenotype of Coffin-Siris syndrome (CSS), we collected clinical data from patients with a prenatal phenotype and a pathogenic variant in one of the CSS-associated genes. Methods: Clinical data was collected through an extensive web-based survey. Results: We included 44 patients with a variant in a CSS-associated gene and a prenatal phenotype; 9 of these patients have been reported before. Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction. Anal anomalies were frequently identified after birth in patients with ARID1A variants (6/14, 43%). Interestingly, pathogenic ARID1A variants were much more frequently identified in the current prenatal cohort (16/44, 36%) than in postnatal CSS cohorts (5%-9%). Conclusion: Our data shed new light on the prenatal phenotype of patients with pathogenic variants in CSS genes. (C) 2022 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.

Published
2022

3. Elucidating the clinical and molecular spectrum ofSMARCC2-associated NDD in a cohort of 65 affected individuals

Author

Elisabeth Bosch, Bernt Popp, Esther Güse, Cindy Skinner, Pleuntje J. van der Sluijs, Isabelle Maystadt, Anna Maria Pinto, Alessandra Renieri, Lucia Pia Bruno, Stefania Granata, Carlo Marcelis, Özlem Baysal, Dewi Hartwich, Laura Holthöfer, Bertrand Isidor, Benjamin Cogne, Dagmar Wieczorek, Valeria Capra, Marcello Scala, Patrizia De Marco, Marzia Ognibene, Rami Abou Jamra, Konrad Platzer, Lauren B. Carter, Outi Kuismin, Arie van Haeringen, Reza Maroofian, Irene Valenzuela, Ivon Cuscò, Julian A. Martinez-Agosto, Ahna M. Rabani, Heather C. Mefford, Elaine M. Pereira, Charlotte Close, Kwame Anyane-Yeboa, Mallory Wagner, Mark C. Hannibal, Pia Zacher, Isabelle Thiffault, Gea Beunders, Muhammad Umair, Priya T. Bhola, Erin McGinnis, John Millichap, Jiddeke M van de Kamp, Eloise J. Prijoles, Amy Dobson, Amelle Shillington, Brett H. Graham, Evan-Jacob Garcia, Maureen Kelly Galindo, Fabienne G. Ropers, Esther AR Nibbeling, Gail Hubbard, Catherine Karimov, Guido Goj, Renee Bend, Julie Rath, Michelle M Morrow, Francisca Millan, Vincenzo Salpietro, Annalaura Torella, Vincenzo Nigro, Mitja Kurki, Roger E Stevenson, Gijs W.E. Santen, Markus Zweier, Philippe M. Campeau, Mariasavina Severino, André Reis, Andrea Accogli, and Georgia Vasileiou

Abstract

PURPOSECoffin-Siris and Nicolaides-Baraitser syndromes, are recognisable neurodevelopmental disorders caused by germline variants in BAF complex subunits. TheSMARCC2BAFopathy was recently reported. Herein, we present clinical and molecular data on a large cohort.METHODSClinical symptoms for 41 novel and 24 previously published cases were analyzed using the Human Phenotype Ontology. For genotype-phenotype correlation, molecular data were standardized and grouped into non-truncating and likely gene-disrupting variants (LGD). Missense variant protein expression and BAF subunit interactions were examined using 3D protein modeling, co-immunoprecipitation, and proximity-ligation assays.RESULTSNeurodevelopmental delay with intellectual disability, muscular hypotonia and behavioral disorders were the major manifestations. Clinical hallmarks of BAFopathies were rare. Clinical presentation differed significantly, with LGD variants being predominantly inherited and associated with mildly reduced or normal cognitive development, while non-truncating variants were mostlyde novoand presented with severe developmental delay. These distinct manifestations and non-truncating variant clustering in functional domains suggest different pathomechanisms.In vitrotesting showed decreased protein expression for N-terminal missense variants similar to LGD.CONCLUSIONThis study improvedSMARCC2variant classification and identified discernibleSMARCC2-associated phenotypes for LGD and non-truncating variants, which were distinct from other BAFopathies. The pathomechanism of most non-truncating variants has yet to be investigated.

Published
2023

4. Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders

Author

Michael A. Levy, Raissa Relator, Haley McConkey, Erinija Pranckeviciene, Jennifer Kerkhof, Mouna Barat‐Houari, Sara Bargiacchi, Elisa Biamino, María Palomares Bralo, Gerarda Cappuccio, Andrea Ciolfi, Angus Clarke, Barbara R. DuPont, Mariet W. Elting, Laurence Faivre, Timothy Fee, Marco Ferilli, Robin S. Fletcher, Florian Cherick, Aidin Foroutan, Michael J. Friez, Cristina Gervasini, Sadegheh Haghshenas, Benjamin A. Hilton, Zandra Jenkins, Simranpreet Kaur, Suzanne Lewis, Raymond J. Louie, Silvia Maitz, Donatella Milani, Angela T. Morgan, Renske Oegema, Elsebet Østergaard, Nathalie R. Pallares, Maria Piccione, Astrid S. Plomp, Cathryn Poulton, Jack Reilly, Rocio Rius, Stephen Robertson, Kathleen Rooney, Justine Rousseau, Gijs W. E. Santen, Fernando Santos‐Simarro, Josephine Schijns, Gabriella M. Squeo, Miya St John, Christel Thauvin‐Robinet, Giovanna Traficante, Pleuntje J. van der Sluijs, Samantha A. Vergano, Niels Vos, Kellie K. Walden, Dimitar Azmanov, Tugce B. Balci, Siddharth Banka, Jozef Gecz, Peter Henneman, Jennifer A. Lee, Marcel M. A. M. Mannens, Tony Roscioli, Victoria Siu, David J. Amor, Gareth Baynam, Eric G. Bend, Kym Boycott, Nicola Brunetti‐Pierri, Philippe M. Campeau, Dominique Campion, John Christodoulou, David Dyment, Natacha Esber, Jill A. Fahrner, Mark D. Fleming, David Genevieve, Delphine Heron, Thomas Husson, Kristin D. Kernohan, Alisdair McNeill, Leonie A. Menke, Giuseppe Merla, Paolo Prontera, Cheryl Rockman‐Greenberg, Charles Schwartz, Steven A. Skinner, Roger E. Stevenson, Marie Vincent, Antonio Vitobello, Marco Tartaglia, Marielle Alders, Matthew L. Tedder, Bekim Sadikovic, Human genetics, Amsterdam Reproduction & Development (AR&D), Pediatrics, Levy M.A., Relator R., McConkey H., Pranckeviciene E., Kerkhof J., Barat-Houari M., Bargiacchi S., Biamino E., Palomares Bralo M., Cappuccio G., Ciolfi A., Clarke A., DuPont B.R., Elting M.W., Faivre L., Fee T., Ferilli M., Fletcher R.S., Cherick F., Foroutan A., Friez M.J., Gervasini C., Haghshenas S., Hilton B.A., Jenkins Z., Kaur S., Lewis S., Louie R.J., Maitz S., Milani D., Morgan A.T., Oegema R., Ostergaard E., Pallares N.R., Piccione M., Plomp A.S., Poulton C., Reilly J., Rius R., Robertson S., Rooney K., Rousseau J., Santen G.W.E., Santos-Simarro F., Schijns J., Squeo G.M., John M.S., Thauvin-Robinet C., Traficante G., van der Sluijs P.J., Vergano S.A., Vos N., Walden K.K., Azmanov D., Balci T.B., Banka S., Gecz J., Henneman P., Lee J.A., Mannens M.M.A.M., Roscioli T., Siu V., Amor D.J., Baynam G., Bend E.G., Boycott K., Brunetti-Pierri N., Campeau P.M., Campion D., Christodoulou J., Dyment D., Esber N., Fahrner J.A., Fleming M.D., Genevieve D., Heron D., Husson T., Kernohan K.D., McNeill A., Menke L.A., Merla G., Prontera P., Rockman-Greenberg C., Schwartz C., Skinner S.A., Stevenson R.E., Vincent M., Vitobello A., Tartaglia M., Alders M., Tedder M.L., Sadikovic B., Levy, Michael A, Relator, Raissa, Mcconkey, Haley, Pranckeviciene, Erinija, Kerkhof, Jennifer, Barat-Houari, Mouna, Bargiacchi, Sara, Biamino, Elisa, Bralo, María Palomare, Cappuccio, Gerarda, Ciolfi, Andrea, Clarke, Angu, Dupont, Barbara R, Elting, Mariet W, Faivre, Laurence, Fee, Timothy, Ferilli, Marco, Fletcher, Robin S, Cherick, Florian, Foroutan, Aidin, Friez, Michael J, Gervasini, Cristina, Haghshenas, Sadegheh, Hilton, Benjamin A, Jenkins, Zandra, Kaur, Simranpreet, Lewis, Suzanne, Louie, Raymond J, Maitz, Silvia, Milani, Donatella, Morgan, Angela T, Oegema, Renske, Østergaard, Elsebet, Pallares, Nathalie Ruiz, Piccione, Maria, Plomp, Astrid S, Poulton, Cathryn, Reilly, Jack, Rius, Rocio, Robertson, Stephen, Rooney, Kathleen, Rousseau, Justine, Santen, Gijs W E, Santos-Simarro, Fernando, Schijns, Josephine, Squeo, Gabriella Maria, John, Miya St, Thauvin-Robinet, Christel, Traficante, Giovanna, van der Sluijs, Pleuntje J, Vergano, Samantha A, Vos, Niel, Walden, Kellie K, Azmanov, Dimitar, Balci, Tugce B, Banka, Siddharth, Gecz, Jozef, Henneman, Peter, Lee, Jennifer A, Mannens, Marcel M A M, Roscioli, Tony, Siu, Victoria, Amor, David J, Baynam, Gareth, Bend, Eric G, Boycott, Kym, Brunetti-Pierri, Nicola, Campeau, Philippe M, Campion, Dominique, Christodoulou, John, Dyment, David, Esber, Natacha, Fahrner, Jill A, Fleming, Mark D, Genevieve, David, Heron, Delphine, Husson, Thoma, Kernohan, Kristin D, Mcneill, Alisdair, Menke, Leonie A, Merla, Giuseppe, Prontera, Paolo, Rockman-Greenberg, Cheryl, Schwartz, Charle, Skinner, Steven A, Stevenson, Roger E, Vincent, Marie, Vitobello, Antonio, Tartaglia, Marco, Alders, Marielle, Tedder, Matthew L, Sadikovic, Bekim, Human Genetics, General Paediatrics, Graduate School, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, ARD - Amsterdam Reproduction and Development, ANS - Cellular & Molecular Mechanisms, ANS - Complex Trait Genetics, and ACS - Pulmonary hypertension & thrombosis

Subjects
DNA methylation, clinical diagnostics, Syndrome, DNA methylation, clinical diagnostics, episignatures, neurodevelopmental syndromes, neurodevelopmental syndromes, Epigenesis, Genetic, Neurodevelopmental Disorders, Genetics, Humans, CpG Islands, DNA, Intergenic, episignatures, Episignature, Genetics (clinical)
Abstract

An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes which can share significant overlap amongst different conditions. In this study we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders. This article is protected by copyright. All rights reserved.

Published
2022

5. PhenoScore: AI-based phenomics to quantify rare disease and genetic variation

Author

Alexander J M Dingemans, Max Hinne, Kim M G Truijen, Lia Goltstein, Jeroen van Reeuwijk, Nicole de Leeuw, Janneke Schuurs-Hoeijmakers, Rolph Pfundt, Illja J Diets, Joery den Hoed, Elke de Boer, Jet Coenen-van der Spek, Sandra Jansen, Bregje W van Bon, Noraly Jonis, Charlotte Ockeloen, Anneke T Vulto-van Silfhout, Tjitske Kleefstra, David A Koolen, Hilde Van Esch, Gholson J Lyon, Fowzan S Alkuraya, Anita Rauch, Ronit Marom, Diana Baralle, Pleuntje J van der Sluijs, Gijs W E Santen, R Frank Kooy, Marcel A J van Gerven, Lisenka E L M Vissers, and Bert B A de Vries

Abstract

While both molecular and phenotypic data are essential when interpreting genetic variants, prediction scores (CADD, PolyPhen, and SIFT) have focused on molecular details to evaluate pathogenicity — omitting phenotypic features. To unlock the full potential of phenotypic data, we developed PhenoScore: an open source, artificial intelligence-based phenomics framework. PhenoScore combines facial recognition technology with Human Phenotype Ontology (HPO) data analysis to quantify phenotypic similarity at both the level of individual patients as well as of cohorts. We prove PhenoScore’s ability to recognize distinct phenotypic entities by establishing recognizable phenotypes for 25 out of 26 investigated genetic syndromes against clinical features observed in individuals with other neurodevelopmental disorders. Moreover, PhenoScore was able to provide objective clinical evidence for two distinctADNP-related phenotypes, that had already been established functionally, but not yet phenotypically. Hence, PhenoScore will not only be of use to unbiasedly quantify phenotypes to assist genomic variant interpretation at the individual level, such as for reclassifying variants of unknown clinical significance, but is also of importance for detailed genotype-phenotype studies.

Published
2022

6. A Case Series of Familial ARID1B Variants Illustrating Variable Expression and Suggestions to Update the ACMG Criteria

Author

Claudia A. L. Ruivenkamp, Isabelle Maystadt, Scott E. Hickey, Bert B.A. de Vries, Marielle Alders, Stéphanie Moortgat, Bregje W.M. van Bon, Jill A. Rosenfeld, Kareesma Parbhoo, Catherine Vincent-Delorme, Johan T. den Dunnen, Thomas Smol, Debra S. Regier, Pleuntje J. van der Sluijs, Gijs W. E. Santen, Alexander J. M. Dingemans, Betsy Schmalz, Erica H. Gerkes, Bekim Sadikovic, Kyra E. Stuurman, Dan Doherty, Jennifer C. Dempsey, Ilana M. Milller, Human Genetics, ACS - Pulmonary hypertension & thrombosis, ARD - Amsterdam Reproduction and Development, and Clinical Genetics

Subjects
Male, Inherited, Coffin–Siris syndrome, Intellectual disability, QH426-470, PHENOTYPE, Variable Expression, Familial, non-pathogenic, ARID1B, Loss of Function Mutation, Child, Genetics (clinical), Genetics, RISK, familial, Middle Aged, ACMG guidelines, DNA-Binding Proteins, intellectual disability, DNA methylation, Medical genetics, Female, Haploinsufficiency, Hand Deformities, Congenital, Adult, medicine.medical_specialty, GENES, Adolescent, Genomics, Biology, Non-pathogenic, Article, Young Adult, All institutes and research themes of the Radboud University Medical Center, medicine, Humans, Abnormalities, Multiple, Genetic Predisposition to Disease, AUTISM, Gene, Loss function, Sequence (medicine), COMPLEX, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], DISABILITY, COFFIN-SIRIS SYNDROME, Variable expression, DNA Methylation, inherited, variable expression, Gene Expression Regulation, Face, Transcription Factors
Abstract

ARID1B is one of the most frequently mutated genes in intellectual disability (~1%). Most variants are readily classified, since they are de novo and are predicted to lead to loss of function, and therefore classified as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines for the interpretation of sequence variants. However, familial loss-of-function variants can also occur and can be challenging to interpret. Such variants may be pathogenic with variable expression, causing only a mild phenotype in a parent. Alternatively, since some regions of the ARID1B gene seem to be lacking pathogenic variants, loss-of-function variants in those regions may not lead to ARID1B haploinsufficiency and may therefore be benign. We describe 12 families with potential loss-of-function variants, which were either familial or with unknown inheritance and were in regions where pathogenic variants have not been described or are otherwise challenging to interpret. We performed detailed clinical and DNA methylation studies, which allowed us to confidently classify most variants. In five families we observed transmission of pathogenic variants, confirming their highly variable expression. Our findings provide further evidence for an alternative translational start site and we suggest updates for the ACMG guidelines for the interpretation of sequence variants to incorporate DNA methylation studies and facial analyses.

Published
2021
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7. Correction: Putting genome-wide sequencing in neonates into perspective

Author

Regina Bökenkamp-Gramann, Daniela Q.C.M. Barge-Schaapveld, Monique Williams, Julie W. Rutten, Karin van der Tuin, Esther A. R. Nibbeling, Claudia A. L. Ruivenkamp, Sylke J. Steggerda, Laura Donker Kaat, Dietje E. Fransen van de Putte, Remco van Doorn, Marjolein Kriek, Ruben S G M Witlox, Maartje van Rij, Cacha M.P.C.D. Peeters-Scholte, Arie van Haeringen, Thomas P. Potjer, Emilia K. Bijlsma, Setareh Moghadasi, Yvette van Ierland, Manon Suerink, Emmelien Aten, Gijs W. E. Santen, Remco Visser, Anne Sophie van der Werf–t Lam, Mariëtte J.V. Hoffer, Marije Koopmans, Pleuntje J. van der Sluijs, Ratna N G B Tan, Nicolette S. den Hollander, Arend D. J. ten Harkel, and Yvonne Hilhorst-Hofstee

Subjects
Published Erratum, Perspective (graphical), Psychology, Genome, Genetics (clinical), Genealogy, Human genetics, Spelling
Abstract

The original version of this Article contained an error in the spelling of the author Pleuntje J. van der Sluijs, which was incorrectly given as Eline (P. J.) van der Sluijs. This has now been corrected in both the PDF and HTML versions of the Article.

Published
2019

8. The ARID1B spectrum in 143 patients

Author

Catherine Vincent-Delorme, Claudia A. L. Ruivenkamp, Marjan De Rademaeker, Francisco Martínez, Tracy Dudding-Byth, Marianne McGuire, Bert B.A. de Vries, Mitsuhiro Kato, Levinus A. Bok, Hülya Kayserili, Jeff M. Milunsky, Suzanne C E H Sallevelt, Alwin F. J. Brouwer, Jill Clayton-Smith, Emilia K. Bijlsma, Miranda Splitt, Patricia G. Wheeler, Philippe M. Campeau, Fatma Mujgan Sonmez, Kylin Lammers, Stefanie Beck-Wödl, Caroline Rooryck, Louise C. Wilson, Evan E. Eichler, Sarina G. Kant, Johanna C. Herkert, Karin R. Heitink, Eyyup Uctepe, Pleuntje J. van der Sluijs, Miho Adachi-Fukuda, Lone W. Laulund, Sandra Jansen, Nicolette S. den Hollander, Damien Lederer, Tomoki Kosho, Constance T. R. M. Stumpel, Saskia M. Maas, Esra Kılıç, Erica H. Gerkes, Duco Steenbeek, Melissa Lees, Kay Metcalfe, Karin Dahan, Ineke van der Burgt, Isabelle Maystadt, Christian Netzer, Ute Grasshoff, Carmen Orellana, Mahmut Şamil Sağıroğlu, Gijs W. E. Santen, Pelin Ozlem Simsek-Kiper, Mónica Roselló, Gabriela Soares, Alexander P.A. Stegmann, Stephen P. Robertson, Adila Al-Kindy, Maian Roifman, Saori Tanabe, Vera Riehmer, Brain H Y Chung, Arie van Haeringen, G. Eda Utine, Yasemin Alanay, Rogier Kersseboom, John B. Moeschler, Barbara Oehl-Jaschkowitz, Katherine Berry, Denise Horn, Alice Gardham, Shane McKee, Anwar Baban, Amparo Sanchis Calvo, Golder N. Wilson, Krystyna H. Chrzanowska, G. M. S. Mancini, Ellen R. Elias, Małgorzata Krajewska-Walasek, Rolph Pfundt, Sarju G. Mehta, Fabienne G. Ropers, Seiji Mizuno, David Hunt, Caroline Pottinger, Dagmar Wieczorek, Yoyo W. Y. Chu, Laurent Pasquier, Bernd Wollnik, Nobuhiko Okamoto, Sunita Venkateswaran, Vanesa López-González, Natalie Canham, Blanca Gener, Anne Destree, Christina Fagerberg, Rachel K. Earl, Sharon N M Olminkhof, Nursel Elcioglu, Charlotte W. Ockeloen, Carlo Marcelis, Samantha A. Vergano, Hermine E. Veenstra-Knol, Anneke T. Vulto-van Silfhout, Allan Bayat, Catheline Vilain, Lucia Solaeche, MUMC+: DA KG Polikliniek (9), RS: GROW - R4 - Reproductive and Perinatal Medicine, Genetica & Celbiologie, MUMC+: DA KG Lab Centraal Lab (9), MUMC+: DA Pat Cytologie (9), Klinische Genetica, van der Sluijs, Pleuntje J., Jansen, Sandra, Vergano, Samantha A., Adachi-Fukuda, Miho, Alanay, Yasemin, AlKindy, Adila, Baban, Anwar, Bayat, Allan, Beck-Woedl, Stefanie, Berry, Katherine, Bijlsma, Emilia K., Bok, Levinus A., Brouwer, Alwin F. J., van der Burgt, Ineke, Campeau, Philippe M., Canham, Natalie, Chrzanowska, Krystyna, Chu, Yoyo W. Y., Chung, Brain H. Y., Dahan, Karin, De Rademaeker, Marjan, Destree, Anne, Dudding-Byth, Tracy, Earl, Rachel, Elcioglu, Nursel, Elias, Ellen R., Fagerberg, Christina, Gardham, Alice, Gener, Blanca, Gerkes, Erica H., Grasshoff, Ute, van Haeringen, Arie, Heitink, Karin R., Herkert, Johanna C., den Hollander, Nicolette S., Horn, Denise, Hunt, David, Kant, Sarina G., Kato, Mitsuhiro, Kayserili, Hulya, Kersseboom, Rogier, Kilic, Esra, Krajewska-Walasek, Malgorzata, Lammers, Kylin, Laulund, Lone W., Lederer, Damien, Lees, Melissa, Lopez-Gonzalez, Vanesa, Maas, Saskia, Mancini, Grazia M. S., Marcelis, Carlo, Martinez, Francisco, Maystadt, Isabelle, McGuire, Marianne, McKee, Shane, Mehta, Sarju, Metcalfe, Kay, Milunsky, Jeff, Mizuno, Seiji, Moeschler, John B., Netzer, Christian, Ockeloen, Charlotte W., Oehl-Jaschkowitz, Barbara, Okamoto, Nobuhiko, Olminkhof, Sharon N. M., Orellana, Carmen, Pasquier, Laurent, Pottinger, Caroline, Riehmer, Vera, Robertson, Stephen P., Roifman, Maian, Rooryck, Caroline, Ropers, Fabienne G., Rosello, Monica, Ruivenkamp, Claudia A. L., Sagiroglu, Mahmut S., Sallevelt, Suzanne C. E. H., Sanchis Calvo, Amparo, Simsek-Kiper, Pelin O., Soares, Gabriela, Solaeche, Lucia, Sonmez, Fatma Mujgan, Splitt, Miranda, Steenbeek, Duco, Stegmann, Alexander P. A., Stumpel, Constance T. R. M., Tanabe, Saori, Uctepe, Eyyup, Utine, G. Eda, Veenstra-Knol, Hermine E., Venkateswaran, Sunita, Vilain, Catheline, Vincent-Delorme, Catherine, Vulto-van Silfhout, Anneke T., Wheeler, Patricia, Wilson, Golder N., Wilson, Louise C., Wollnik, Bernd, Kosho, Tomoki, Wieczorek, Dagmar, Eichler, Evan, Pfundt, Rolph, de Vries, Bert B. A., Clayton-Smith, Jill, Santen, Gijs W. E., Erasmus MC other, Clinical Genetics, Human Genetics, and Acibadem University Dspace

Subjects
Male, 0301 basic medicine, Hypertrichosis, Pediatrics, cuello, bias, Coffin–Siris syndrome, Chromosomal Proteins, Non-Histone, humanos, adolescente, Penetrance, PHENOTYPE, 0302 clinical medicine, Genotype, Intellectual disability, Exome, Coffin-Siris syndrome, Child, mediana edad, Genetics (clinical), Exome sequencing, factores de transcripción, adulto, Middle Aged, estudios de asociación genética, 3. Good health, DNA-Binding Proteins, intellectual disability, Child, Preschool, discapacidad intelectual, penetrancia, Female, Hand Deformities, Congenital, Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Adult, medicine.medical_specialty, Adolescent, Micrognathism, Article, CHROMATIN-REMODELING COMPLEX, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, cara, micrognatismo, Human Phenotype Ontology, medicine, Humans, Abnormalities, Multiple, mutación, Long eyelashes, Genetic Association Studies, lactante, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], business.industry, MUTATIONS, proteínas de unión al ADN, Infant, Newborn, Genetic Variation, Infant, ARID1B, Hand Deformities, Phalanx, medicine.disease, variación genética, deformidades de la mano, exoma, 030104 developmental biology, Face, Mutation, business, Neck, 030217 neurology & neurosurgery, Transcription Factors
Abstract

Purpose: Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin-Siris patients (ARID1BCSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods: Clinicians entered clinical data in an extensive webbased survey. Results: 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion: There are only minor differences between ARID1BID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features., We are grateful for the assistance of Pepijn Cox in setting up the website www.arid1bgene.com. This study has made use of data generated by the Human Disease Genes website series, www.humandiseasegenes.com. This work was financially supported by grants from the Netherlands Organisation for Health Research and Development (917-86-319 to B.B.A.d.V., 912-12-109 to B.B.A.d.V.)

Published
2019

9. Putting genome-wide sequencing in neonates into perspective

Author

Setareh Moghadasi, Emilia K. Bijlsma, Remco van Doorn, Monique Williams, Maartje van Rij, Remco Visser, Thomas P. Potjer, Arend D. J. ten Harkel, Yvette van Ierland, Laura Donker Kaat, Emmelien Aten, Daniela Q.C.M. Barge-Schaapveld, Cacha M.P.C.D. Peeters-Scholte, Nicolette S. den Hollander, Ratna N G B Tan, Ruben S G M Witlox, Regina Bökenkamp-Gramann, Julie W. Rutten, Manon Suerink, Marjolein Kriek, Yvonne Hilhorst-Hofstee, Sylke J. Steggerda, Mariëtte J.V. Hoffer, Marije Koopmans, Pleuntje J. van der Sluijs, Anne-Sophie van der Werf –’t Lam, Gijs W. E. Santen, Claudia A. L. Ruivenkamp, Dietje E. Fransen van de Putte, Arie van Haeringen, Karin van der Tuin, Esther A. R. Nibbeling, Neurology, and Graduate School

Subjects
0301 basic medicine, NICU, Male, Pediatrics, medicine.medical_specialty, Neonatal intensive care unit, health care facilities, manpower, and services, Population, clinical geneticists, 030105 genetics & heredity, Genome, Infant, Newborn, Diseases, Single test, 03 medical and health sciences, Exome Sequencing, Clinical genetic, medicine, Humans, Exome, Genetic Testing, Medical diagnosis, education, Genetics (clinical), Exome sequencing, Retrospective Studies, education.field_of_study, business.industry, Infant, Newborn, Chromosome Mapping, sequencing, rapid, 030104 developmental biology, ES, Intensive Care, Neonatal, Female, business, Genome-Wide Association Study
Abstract

Purpose: Several studies have reported diagnostic yields up to 57% for rapid exome or genome sequencing (rES/GS) as a single test in neonatal intensive care unit (NICU) patients, but the additional yield of rES/GS compared with other available diagnostic options still remains unquantified in this population. Methods: We retrospectively evaluated all genetic NICU consultations in a 2-year period. Results: In 132 retrospectively evaluated NICU consultations 27 of 32 diagnoses (84.4%) were made using standard genetic workup. Most diagnoses (65.6%) were made within 16 days. Diagnostic ES yield was 5/29 (17.2%). Genetic diagnoses had a direct effect on clinical management in 90.6% (29/32) of patients. Conclusions: Our study shows that exome sequencing has a place in NICU diagnostics, but given the associated costs and the high yield of alternative diagnostic strategies, we recommend to first perform clinical genetic consultation.

Published
2019

10. A case series of familial ARID1B variants illustrating variable expression and suggestions to update the ACMG criteria

Author

Pleuntje J. van der Sluijs, Mariëlle Alders, Alexander J.M. Dingemans, Kareesma Parbhoo, Bregje W. van Bon, Jennifer C. Dempsey, Dan Doherty, Johan T. Den Dunnen, Erica H. Gerkes, Ilana M. Milller, Stephanie Moortgat, Debra S. Regier, Claudia Ruivenkamp, Betsy Schmalz, Thomas Smol, K.E. (Kyra) Stuurman, Catherine Vincent-Delorme, Bert B.A. de Vries, Bekim Sadikovic, Scott E. Hickey, Jill A. Rosenfeld, Isabelle Maystadt, Gijs W.E. Santen, Pleuntje J. van der Sluijs, Mariëlle Alders, Alexander J.M. Dingemans, Kareesma Parbhoo, Bregje W. van Bon, Jennifer C. Dempsey, Dan Doherty, Johan T. Den Dunnen, Erica H. Gerkes, Ilana M. Milller, Stephanie Moortgat, Debra S. Regier, Claudia Ruivenkamp, Betsy Schmalz, Thomas Smol, K.E. (Kyra) Stuurman, Catherine Vincent-Delorme, Bert B.A. de Vries, Bekim Sadikovic, Scott E. Hickey, Jill A. Rosenfeld, Isabelle Maystadt, and Gijs W.E. Santen

Abstract

ARID1B is one of the most frequently mutated genes in intellectual disability (~1%). Most variants are readily classified, since they are de novo and are predicted to lead to loss of function, and therefore classified as pathogenic according to the American College of Medical Genetics and Genomics (ACMG) guidelines for the interpretation of sequence variants. However, familial loss-of-function variants can also occur and can be challenging to interpret. Such variants may be pathogenic with variable expression, causing only a mild phenotype in a parent. Alternatively, since some regions of the ARID1B gene seem to be lacking pathogenic variants, loss-of-function variants in those regions may not lead to ARID1B haploinsufficiency and may therefore be benign. We describe 12 families with potential loss-of-function variants, which were either familial or with unknown inheritance and were in regions where pathogenic variants have not been described or are otherwise challenging to interpret. We performed detailed clinical and DNA methylation studies, which allowed us to confidently classify most variants. In five families we observed transmission of pathogenic variants, confirming their highly variable expression. Our findings provide further evidence for an alternative translational start site and we suggest updates for the ACMG guidelines for the interpretation of seque

Published
2021
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11. Correction: The ARID1B spectrum in 143 patients

Author

Mitsuhiro Kato, Grazia M.S. Mancini, Krystyna H. Chrzanowska, Alexander P.A. Stegmann, Stephen P. Robertson, Suzanne C E H Sallevelt, Yasemin Alanay, Melissa Lees, Sarju G. Mehta, Anne Destree, Emilia K. Bijlsma, Seiji Mizuno, David Hunt, Laurent Pasquier, H. lya Kayserili, Karin R. Heitink, Ineke van der Burgt, Christian Netzer, Duco Steenbeek, Mónica Roselló, Rachel K. Earl, Sharon N. M. Olminkhof, Arie van Haeringen, Katherine Berry, Ute Grasshoff, Francisco Martínez, Alwin F. J. Brouwer, Nursel Elcioglu, Patricia G. Wheeler, Rolph Pfundt, Shane McKee, Maian Roifman, Yoyo W. Y. Chu, Brain H. Y. Chung, John B. Moeschler, Barbara Oehl-Jaschkowitz, Denise Horn, Karin Dahan, Ellen R. Elias, Natalie Canham, Pelin Ozlem Simsek-Kiper, Vanesa López-González, Samantha A. Vergano, Tracy Dudding-Byth, Esra Kılıç, Charlotte W. Ockeloen, Carlo Marcelis, Levinus A. Bok, Gijs W. E. Santen, Philippe M. Campeau, Kylin Lammers, Anneke T. Vulto-van Silfhout, Stefanie Beck-Wödl, Allan Bayat, Eyyup Uctepe, Louise C. Wilson, Sarina G. Kant, Pleuntje J. van der Sluijs, Fatma Mujgan Sonmez, Tomoki Kosho, Marianne McGuire, Evan E. Eichler, Mahmut Şamil Sağıroğlu, Vera Riehmer, Caroline Rooryck, Miho Adachi-Fukuda, Rogier Kersseboom, Saskia M. Maas, Jeff M. Milunsky, Johanna C. Herkert, Anwar Baban, Nicolette S. den Hollander, Amparo Sanchis Calvo, Lone W. Laulund, Sandra Jansen, Golder N. Wilson, Kay Metcalfe, Fabienne G. Ropers, Caroline Pottinger, Gabriela Soares, Isabelle Maystadt, Miranda Splitt, Constance T. R. M. Stumpel, Catherine Vincent-Delorme, Bert B.A. de Vries, Jill Clayton-Smith, Claudia A. L. Ruivenkamp, Marjan De Rademaeker, Bernd Wollnik, Nobuhiko Okamoto, Christina Fagerberg, Erica H. Gerkes, Damien Lederer, Carmen Orellana, Alice Gardham, Saori Tanabe, Małgorzata Krajewska-Walasek, Adila Al-Kindy, Catheline Vilain, Dagmar Wieczorek, G. Eda Utine, Sunita Venkateswaran, Blanca Gener, Lucia Solaeche, and Hermine E. Veenstra-Knol

Subjects
0303 health sciences, Coffin–Siris syndrome, Correction, medicine.disease, Genealogy, Spelling, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Intellectual disability, medicine, Psychology, 030217 neurology & neurosurgery, Genetics (clinical), 030304 developmental biology
Abstract

The original version of this Article contained an error in the spelling of the author Pleuntje J. van der Sluijs, which was incorrectly given as Eline (P. J.) van der Sluijs. This has now been corrected in both the PDF and HTML versions of the Article.

Published
2019

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