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Riess O, Sturm M, Menden B, Liebmann A, Demidov G, Witt D, Casadei N, Admard J, Schütz L, Ossowski S, Taylor S, Schaffer S, Schroeder C, Dufke A, Haack T. Genomes in clinical care. NPJ Genom Med 2024; 9:20. [PMID: 38485733 PMCID: PMC10940576 DOI: 10.1038/s41525-024-00402-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/07/2024] [Indexed: 03/18/2024] Open
Abstract
In the era of precision medicine, genome sequencing (GS) has become more affordable and the importance of genomics and multi-omics in clinical care is increasingly being recognized. However, how to scale and effectively implement GS on an institutional level remains a challenge for many. Here, we present Genome First and Ge-Med, two clinical implementation studies focused on identifying the key pillars and processes that are required to make routine GS and predictive genomics a reality in the clinical setting. We describe our experience and lessons learned for a variety of topics including test logistics, patient care processes, data reporting, and infrastructure. Our model of providing clinical care and comprehensive genomic analysis from a single source may be used by other centers with a similar structure to facilitate the implementation of omics-based personalized health concepts in medicine.
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Affiliation(s)
- Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- NGS Competence Center Tübingen, University of Tübingen, Tübingen, Germany.
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany.
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Benita Menden
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Alexandra Liebmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Dennis Witt
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Leon Schütz
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | | | | | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Center for Rare Diseases Tübingen, University of Tübingen, Tübingen, Germany
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2
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Lischka A, Eggermann K, Record CJ, Dohrn MF, Laššuthová P, Kraft F, Begemann M, Dey D, Eggermann T, Beijer D, Šoukalová J, Laura M, Rossor AM, Mazanec R, Van Lent J, Tomaselli PJ, Ungelenk M, Debus KY, Feely SME, Gläser D, Jagadeesh S, Martin M, Govindaraj GM, Singhi P, Baineni R, Biswal N, Ibarra-Ramírez M, Bonduelle M, Gess B, Romero Sánchez J, Suthar R, Udani V, Nalini A, Unnikrishnan G, Marques W, Mercier S, Procaccio V, Bris C, Suresh B, Reddy V, Skorupinska M, Bonello-Palot N, Mochel F, Dahl G, Sasidharan K, Devassikutty FM, Nampoothiri S, Rodovalho Doriqui MJ, Müller-Felber W, Vill K, Haack TB, Dufke A, Abele M, Stucka R, Siddiqi S, Ullah N, Spranger S, Chiabrando D, Bolgül BS, Parman Y, Seeman P, Lampert A, Schulz JB, Wood JN, Cox JJ, Auer-Grumbach M, Timmerman V, de Winter J, Themistocleous AC, Shy M, Bennett DL, Baets J, Hübner CA, Leipold E, Züchner S, Elbracht M, Çakar A, Senderek J, Hornemann T, Woods CG, Reilly MM, Kurth I. Genetic landscape of congenital insensitivity to pain and hereditary sensory and autonomic neuropathies. Brain 2023; 146:4880-4890. [PMID: 37769650 PMCID: PMC10689924 DOI: 10.1093/brain/awad328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/16/2023] [Accepted: 09/03/2023] [Indexed: 10/02/2023] Open
Abstract
Congenital insensitivity to pain (CIP) and hereditary sensory and autonomic neuropathies (HSAN) are clinically and genetically heterogeneous disorders exclusively or predominantly affecting the sensory and autonomic neurons. Due to the rarity of the diseases and findings based mainly on single case reports or small case series, knowledge about these disorders is limited. Here, we describe the molecular workup of a large international cohort of CIP/HSAN patients including patients from normally under-represented countries. We identify 80 previously unreported pathogenic or likely pathogenic variants in a total of 73 families in the >20 known CIP/HSAN-associated genes. The data expand the spectrum of disease-relevant alterations in CIP/HSAN, including novel variants in previously rarely recognized entities such as ATL3-, FLVCR1- and NGF-associated neuropathies and previously under-recognized mutation types such as larger deletions. In silico predictions, heterologous expression studies, segregation analyses and metabolic tests helped to overcome limitations of current variant classification schemes that often fail to categorize a variant as disease-related or benign. The study sheds light on the genetic causes and disease-relevant changes within individual genes in CIP/HSAN. This is becoming increasingly important with emerging clinical trials investigating subtype or gene-specific treatment strategies.
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Affiliation(s)
- Annette Lischka
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Katja Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Christopher J Record
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Maike F Dohrn
- Department of Neurology, Medical Faculty of the RWTH Aachen University, 52074 Aachen, Germany
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Petra Laššuthová
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06 Praha, Czechia
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Daniela Dey
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Danique Beijer
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Jana Šoukalová
- Department of Medical Genetics, University Hospital Brno, 625 00 Brno, Czechia
| | - Matilde Laura
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Alexander M Rossor
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Radim Mazanec
- Department of Neurology, Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06 Prague, Czechia
| | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, 2160 Antwerp, Belgium
| | - Pedro J Tomaselli
- Department of Neurosciences and Behaviour Sciences, Clinical Hospital of Ribeirão Preto, University of São Paulo, Ribeirão Preto, 14015-130, Brazil
| | - Martin Ungelenk
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Karlien Y Debus
- Center for Molecular Biomedicine Institute for Biophysics, Friedrich-Schiller Universität Jena, 07745 Jena, Germany
| | - Shawna M E Feely
- Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Division of Pediatric Neurology, Seattle Children’s Hospital, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Dieter Gläser
- Center for Human Genetics, Genetikum®, 89231 Neu-Ulm, Germany
| | - Sujatha Jagadeesh
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai 600032, Tamilnadu, India
| | - Madelena Martin
- Davis and Davis Children's Hospital, University of California, Sacramento, CA 95817, USA
| | - Geeta M Govindaraj
- Department of Pediatrics, Government Medical College, Kozhikode, Kerala 673 008, India
| | - Pratibha Singhi
- Pediatric Neurology and Neurodevelopment, Medanta, The Medicity, Gurgaon, Haryana 122 001, India
| | - Revanth Baineni
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605 006, India
| | - Niranjan Biswal
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605 006, India
| | - Marisol Ibarra-Ramírez
- Genetics Department, Hospital Universitario Dr. José Eleuterio González Universidad Autónoma de Nuevo León, 64460 Monterrey, Nuevo León, México
| | - Maryse Bonduelle
- Centre for Medical Genetics, Universitair Ziekenhuis Brussel, 1090 Jette, Brussels, Belgium
| | - Burkhard Gess
- Department of Neurology, Medical Faculty of the RWTH Aachen University, 52074 Aachen, Germany
- Department of Neurology, University Hospital, Evangelisches Klinikum Bethel, University of Bielefeld, 33617 Bielefeld, Germany
| | | | - Renu Suthar
- Pediatric Neurology and Neurodevelopment Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160 012, India
| | - Vrajesh Udani
- Department of Child Neurology, PD Hinduja Hospital and Medical Research Centre, Mumbai, Maharashtra 400 016, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru 560 029, India
| | - Gopikrishnan Unnikrishnan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru 560 029, India
| | - Wilson Marques
- Department of Neurosciences and Behaviour Sciences, Clinical Hospital of Ribeirão Preto, University of São Paulo, Ribeirão Preto, 14015-130, Brazil
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, Centre de Référence des Maladies Neuromusculaires AOC, 44000 Nantes, France
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, 49055 Angers, France
| | - Céline Bris
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, 49055 Angers, France
| | - Beena Suresh
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai 600032, Tamilnadu, India
| | - Vaishnavi Reddy
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai 600032, Tamilnadu, India
| | - Mariola Skorupinska
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Fanny Mochel
- Genetics Department, Sorbonne Université, Paris Brain Institute, APHP, INSERM, CNRS, 75013 Paris, France
| | - Georg Dahl
- Pediatric Neurology, Children’s Hospital of the King’s Daughters in Norfolk, Norfolk, VA 23507, USA
| | - Karthika Sasidharan
- Department of Pediatrics, Government Medical College, Kozhikode, Kerala 673 008, India
| | - Fiji M Devassikutty
- Department of Pediatrics, Government Medical College, Kozhikode, Kerala 673 008, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, Cochin, Kerala 682 041, India
| | - Maria J Rodovalho Doriqui
- Department of Genetics, Hospital Infantil Doutor Juvêncio Mattos, São Luis, Maranhão 65015-460, Brazil
| | - Wolfgang Müller-Felber
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, LMU Campus Innenstadt, University of Munich, 80337 Munich, Germany
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, 80337 Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Abele
- Neurologie, Praxis für Neurologie und Schlafmedizin, 53359 Rheinbach, Germany
| | - Rolf Stucka
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Saima Siddiqi
- Genomics Group, Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 44000, Pakistan
| | - Noor Ullah
- Institute for Paramedical Sciences, Khyber Medical University, Peshawar, KPK 25100, Pakistan
| | | | - Deborah Chiabrando
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center ‘Guido Tarone’, University of Torino, 10124 Turin, Italy
| | - Behiye S Bolgül
- Department of Pedodontics, Faculty of Dentistry, Dicle University, 21200 Diyarbakir, Turkey
| | - Yesim Parman
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Pavel Seeman
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06 Praha, Czechia
| | - Angelika Lampert
- Institute of Neurophysiology, Medical Faculty, Uniklinik RWTH Aachen University, 52074 Aachen, Germany
| | - Jörg B Schulz
- Department of Neurology, Medical Faculty of the RWTH Aachen University, 52074 Aachen, Germany
- JARA-BRAIN Institute Molecular Neuroscience and Neuroimaging, Research Centre Jülich GmbH, and RWTH Aachen University, 52056 Aachen, Germany
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Michaela Auer-Grumbach
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, 2160 Antwerp, Belgium
| | - Jonathan de Winter
- Translational Neurosciences and Institute Born Bunge, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, 2610 Antwerp, Belgium
| | | | - Michael Shy
- Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX3 9DU, UK
| | - Jonathan Baets
- Translational Neurosciences and Institute Born Bunge, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, 2610 Antwerp, Belgium
| | - Christian A Hübner
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Enrico Leipold
- Department of Anesthesiology and Intensive Care and CBBM—Center of Brain, Behavior and Metabolism, University of Luebeck, 23562 Luebeck, Germany
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Arman Çakar
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Jan Senderek
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Thorsten Hornemann
- Department of Clinical Chemistry, University Hospital Zurich, University of Zurich, 8006 Zurich, Switzerland
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
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Schroeder C, Faust U, Krauße L, Liebmann A, Abele M, Demidov G, Schütz L, Kelemen O, Pohle A, Gauß S, Sturm M, Roggia C, Streiter M, Buchert R, Armenau-Ebinger S, Nann D, Beschorner R, Handgretinger R, Ebinger M, Lang P, Holzer U, Skokowa J, Ossowski S, Haack TB, Mau-Holzmann UA, Dufke A, Riess O, Brecht IB. Clinical trio genome sequencing facilitates the interpretation of variants in cancer predisposition genes in paediatric tumour patients. Eur J Hum Genet 2023; 31:1139-1146. [PMID: 37507557 PMCID: PMC10545765 DOI: 10.1038/s41431-023-01423-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The prevalence of pathogenic and likely pathogenic (P/LP) variants in genes associated with cancer predisposition syndromes (CPS) is estimated to be 8-18% for paediatric cancer patients. In more than half of the carriers, the family history is unsuspicious for CPS. Therefore, broad genetic testing could identify germline predisposition in additional children with cancer resulting in important implications for themselves and their families. We thus evaluated clinical trio genome sequencing (TGS) in a cohort of 72 paediatric patients with solid cancers other than retinoblastoma or CNS-tumours. The most prevalent cancer types were sarcoma (n = 26), neuroblastoma (n = 15), and nephroblastoma (n = 10). Overall, P/LP variants in CPS genes were identified in 18.1% of patients (13/72) and P/LP variants in autosomal-dominant CPS genes in 9.7% (7/72). Genetic evaluation would have been recommended for the majority of patients with P/LP variants according to the Jongmans criteria. Four patients (5.6%, 4/72) carried P/LP variants in autosomal-dominant genes known to be associated with their tumour type. With the immediate information on variant inheritance, TGS facilitated the identification of a de novo P/LP in NF1, a gonadosomatic mosaic in WT1 and two pathogenic variants in one patient (DICER1 and PALB2). TGS allows a more detailed characterization of structural variants with base-pair resolution of breakpoints which can be relevant for the interpretation of copy number variants. Altogether, TGS allows comprehensive identification of children with a CPS and supports the individualised clinical management of index patients and high-risk relatives.
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Affiliation(s)
- Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
- Centre for Personalized Cancer Prevention, University Hospital Tübingen, Tübingen, Germany
| | - Ulrike Faust
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Luisa Krauße
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Alexandra Liebmann
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Michael Abele
- Department of Paediatric Haematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Leon Schütz
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Olga Kelemen
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Alexandra Pohle
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Silja Gauß
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Cristiana Roggia
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Monika Streiter
- Department of Paediatric Haematology and Oncology, Children's Hospital Heilbronn, Heilbronn, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Sorin Armenau-Ebinger
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Dominik Nann
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Rudi Beschorner
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Rupert Handgretinger
- Department of Paediatric Haematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Martin Ebinger
- Department of Paediatric Haematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Peter Lang
- Department of Paediatric Haematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Ursula Holzer
- Department of Paediatric Haematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Julia Skokowa
- Department of Oncology, Haematology, Immunology, Rheumatology, and Pulmonology, University Hospital Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Ulrike A Mau-Holzmann
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
- Centre for Personalized Cancer Prevention, University Hospital Tübingen, Tübingen, Germany
- NGS Core Centre Tübingen, University Tübingen, Tübingen, Germany
| | - Ines B Brecht
- Department of Paediatric Haematology and Oncology, University Children's Hospital Tübingen, Tübingen, Germany.
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Dufke A, Eggermann T, Kagan KO, Hoopmann M, Elbracht M. Prenatal testing for imprinting disorders: A clinical perspective. Prenat Diagn 2023. [PMID: 37341686 DOI: 10.1002/pd.6400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/02/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023]
Abstract
Imprinting Disorders (ImpDis) are a group of congenital conditions caused by aberrant imprinting resulting in disturbed expression of parentally imprinted genes. ImpDis are rarely associated with major malformations, but pre- and/or postnatal growth and nutrition are often affected. In some ImpDis, behavioral, developmental, metabolic and neurological symptoms might present in the perinatal context or later in life, and in single ImpDis there is a higher risk of tumors in childhood. Prognosis depends in part on the molecular cause of each ImpDis, but due to high clinical variability and (epi)genetic mosaicism, predicting the clinical outcome of a pregnancy solely based on the underlying molecular disturbance is difficult. Therefore, interdisciplinary care and treatment approaches play an important role in the management and decision making of affected pregnancies, especially taking into account fetal imaging in addition to genetic findings. Prenatal findings influence perinatal management, and thereby improve the prognosis of ImpDis associated with severe but sometimes transient clinical complications in the neonatal period. Therefore, prenatal diagnosis can be crucial for appropriate management not only of the pregnancy itself but might also have a life-long effect. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Karl Oliver Kagan
- Department for women's health, University Hospital of Tübingen, Tübingen, Germany
| | - Markus Hoopmann
- Department for women's health, University Hospital of Tübingen, Tübingen, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
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Beygo J, Russo S, Tannorella P, Santen GWE, Dufke A, Schlaich E, Eggermann T. Prenatal testing for imprinting disorders: A laboratory perspective. Prenat Diagn 2023. [PMID: 37340544 DOI: 10.1002/pd.6398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023]
Abstract
OBJECTIVE Imprinting Disorders (ImpDis) are a group of congenital syndromes associated with up to four different types of molecular disturbances affecting the monoallelic and parent-of-origin specific expression of genomically imprinted genes. Though each ImpDis is characterised by aberrations at a distinct genetic site and a specific set of postnatal clinical signs, there is a broad overlap between several of them. In particular, the prenatal features of ImpDis are non-specific. Therefore, the decision on the appropriate molecular testing strategy is difficult. A further molecular characteristic of ImpDis is (epi)genetic mosaicism, which makes prenatal testing for ImpDis challenging. Accordingly, sampling and diagnostic workup has to consider the methodological limitations. Furthermore, the prediction of the clinical outcome of a pregnancy can be difficult. False-negative results can occur, and therefore fetal imaging should be the diagnostic tool on which decisions on the management of the pregnancy should be based. CONCLUSION In summary, the decision for molecular prenatal testing for ImpDis should be based on close exchanges between clinicians, geneticists, and the families before the initiation of the test. These discussions should weigh the chances and challenges of the prenatal test, with focus on the need of the family. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jasmin Beygo
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Silvia Russo
- Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Pierpaola Tannorella
- Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andreas Dufke
- Medical Faculty, Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Elia Schlaich
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Medical Faculty, Institute for Human Genetics and Genome Medicine, RWTH Aachen University, Aachen, Germany
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6
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Rots D, Jakub TE, Keung C, Jackson A, Banka S, Pfundt R, de Vries BBA, van Jaarsveld RH, Hopman SMJ, van Binsbergen E, Valenzuela I, Hempel M, Bierhals T, Kortüm F, Lecoquierre F, Goldenberg A, Hertz JM, Andersen CB, Kibæk M, Prijoles EJ, Stevenson RE, Everman DB, Patterson WG, Meng L, Gijavanekar C, De Dios K, Lakhani S, Levy T, Wagner M, Wieczorek D, Benke PJ, Lopez Garcia MS, Perrier R, Sousa SB, Almeida PM, Simões MJ, Isidor B, Deb W, Schmanski AA, Abdul-Rahman O, Philippe C, Bruel AL, Faivre L, Vitobello A, Thauvin C, Smits JJ, Garavelli L, Caraffi SG, Peluso F, Davis-Keppen L, Platt D, Royer E, Leeuwen L, Sinnema M, Stegmann APA, Stumpel CTRM, Tiller GE, Bosch DGM, Potgieter ST, Joss S, Splitt M, Holden S, Prapa M, Foulds N, Douzgou S, Puura K, Waltes R, Chiocchetti AG, Freitag CM, Satterstrom FK, De Rubeis S, Buxbaum J, Gelb BD, Branko A, Kushima I, Howe J, Scherer SW, Arado A, Baldo C, Patat O, Bénédicte D, Lopergolo D, Santorelli FM, Haack TB, Dufke A, Bertrand M, Falb RJ, Rieß A, Krieg P, Spranger S, Bedeschi MF, Iascone M, Josephi-Taylor S, Roscioli T, Buckley MF, Liebelt J, Dagli AI, Aten E, Hurst ACE, Hicks A, Suri M, Aliu E, Naik S, Sidlow R, Coursimault J, Nicolas G, Küpper H, Petit F, Ibrahim V, Top D, Di Cara F, Louie RJ, Stolerman E, Brunner HG, Vissers LELM, Kramer JM, Kleefstra T. The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder. Am J Hum Genet 2023; 110:963-978. [PMID: 37196654 PMCID: PMC10257005 DOI: 10.1016/j.ajhg.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
De novo variants are a leading cause of neurodevelopmental disorders (NDDs), but because every monogenic NDD is different and usually extremely rare, it remains a major challenge to understand the complete phenotype and genotype spectrum of any morbid gene. According to OMIM, heterozygous variants in KDM6B cause "neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities." Here, by examining the molecular and clinical spectrum of 85 reported individuals with mostly de novo (likely) pathogenic KDM6B variants, we demonstrate that this description is inaccurate and potentially misleading. Cognitive deficits are seen consistently in all individuals, but the overall phenotype is highly variable. Notably, coarse facies and distal skeletal anomalies, as defined by OMIM, are rare in this expanded cohort while other features are unexpectedly common (e.g., hypotonia, psychosis, etc.). Using 3D protein structure analysis and an innovative dual Drosophila gain-of-function assay, we demonstrated a disruptive effect of 11 missense/in-frame indels located in or near the enzymatic JmJC or Zn-containing domain of KDM6B. Consistent with the role of KDM6B in human cognition, we demonstrated a role for the Drosophila KDM6B ortholog in memory and behavior. Taken together, we accurately define the broad clinical spectrum of the KDM6B-related NDD, introduce an innovative functional testing paradigm for the assessment of KDM6B variants, and demonstrate a conserved role for KDM6B in cognition and behavior. Our study demonstrates the critical importance of international collaboration, sharing of clinical data, and rigorous functional analysis of genetic variants to ensure correct disease diagnosis for rare disorders.
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Affiliation(s)
- Dmitrijs Rots
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Taryn E Jakub
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Crystal Keung
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Adam Jackson
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Rolph Pfundt
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | | | | | - Saskia M J Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Irene Valenzuela
- Hospital Universitari Vall D'Hebron, Clinical and Molecular Genetics Unit, Barcelona, Catalonia, Spain
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Francois Lecoquierre
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Alice Goldenberg
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Jens Michael Hertz
- Odense University Hospital, Department of Clinical Genetics, Odense, Denmark; University of Southern Denmark, Department of Clinical Research, Odense, Denmark
| | | | - Maria Kibæk
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | | | | | | | | | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Charul Gijavanekar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Karl De Dios
- Division of Medical Genetics, Dayton Children's Hospital, Dayton, OH, USA
| | - Shenela Lakhani
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Tess Levy
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany; Division of Pediatric Neurology, Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, Munich, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Paul J Benke
- Division of Genetics, Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | | | - Renee Perrier
- Department of Medical Genetics, Alberta Children's Hospital and Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sergio B Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Pedro M Almeida
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria José Simões
- CBR Genomics, Cantanhede, Portugal; Genoinseq, Next-Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Wallid Deb
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Andrew A Schmanski
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Laurence Faivre
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Christel Thauvin
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Jeroen J Smits
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Stefano G Caraffi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Francesca Peluso
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Laura Davis-Keppen
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Dylan Platt
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Erin Royer
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Lisette Leeuwen
- University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Margje Sinnema
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Alexander P A Stegmann
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Constance T R M Stumpel
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Reproduction, Maastricht, the Netherlands
| | - George E Tiller
- Kaiser Permanente, Department of Genetics, Los Angeles, CA, USA
| | | | | | - Shelagh Joss
- West of Scotland Regional Genetics Service, Laboratory Medicine Building, Queen Elizabeth University Hospital, Glasgow, UK
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, International Centre for Life, Newcastle Upon Tyne NE1 3BZ, UK
| | - Simon Holden
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Matina Prapa
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton SO16 5YA, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kaija Puura
- Department of Child Psychiatry, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Regina Waltes
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvia De Rubeis
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph Buxbaum
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksic Branko
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Jennifer Howe
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Alessia Arado
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Chiara Baldo
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Olivier Patat
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Demeer Bénédicte
- Service de Génétique Clinique, Centre de référence maladies rares, CHU d'Amiens-site Sud, Amiens, France
| | - Diego Lopergolo
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 2, 53100 Siena, Italy; IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Filippo M Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Angelika Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Peter Krieg
- Department of Pediatrics, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | | | - Maria Iascone
- Laboratory of Medical Genetics, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, University of New South Wales, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW 2031, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2031, Australia
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Aditi I Dagli
- Orlando Health Arnold Palmer Hospital for Children, Division of Genetics, Orlando, FL, USA
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alesha Hicks
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, City Hospital Campus, Nottingham, UK
| | - Ermal Aliu
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Sunil Naik
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Richard Sidlow
- Valley Children's Hospital, Valley Children's Place, Madera, CA 93636, USA
| | - Juliette Coursimault
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Gaël Nicolas
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Hanna Küpper
- Neuropediatric Department, University Hospital Tübingen, Tübingen, Germany
| | - Florence Petit
- Centre Hospitalier Universitaire de Lille, Clinique de Génétique Guy Fontaine, Lille, France
| | - Veyan Ibrahim
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Deniz Top
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Francesca Di Cara
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | | | | | - Han G Brunner
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | | | - Jamie M Kramer
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada.
| | - Tjitske Kleefstra
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Center for Neuropsychiatry, Vincent van Gogh, Venray, the Netherlands; Department of Clinical Genetics, ErasmusMC, Rotterdam, the Netherlands.
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Falb RJ, Müller AJ, Klein W, Grimmel M, Grasshoff U, Spranger S, Stöbe P, Gauck D, Kuechler A, Dikow N, Schwaibold EMC, Schmidt C, Averdunk L, Buchert R, Heinrich T, Prodan N, Park J, Kehrer M, Sturm M, Kelemen O, Hartmann S, Horn D, Emmerich D, Hirt N, Neumann A, Kristiansen G, Gembruch U, Haen S, Siebert R, Hentze S, Hoopmann M, Ossowski S, Waldmüller S, Beck-Wödl S, Gläser D, Tekesin I, Distelmaier F, Riess O, Kagan KO, Dufke A, Haack TB. Bi-allelic loss-of-function variants in KIF21A cause severe fetal akinesia with arthrogryposis multiplex. J Med Genet 2023; 60:48-56. [PMID: 34740919 PMCID: PMC9811090 DOI: 10.1136/jmedgenet-2021-108064] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/14/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Fetal akinesia (FA) results in variable clinical presentations and has been associated with more than 166 different disease loci. However, the underlying molecular cause remains unclear in many individuals. We aimed to further define the set of genes involved. METHODS We performed in-depth clinical characterisation and exome sequencing on a cohort of 23 FA index cases sharing arthrogryposis as a common feature. RESULTS We identified likely pathogenic or pathogenic variants in 12 different established disease genes explaining the disease phenotype in 13 index cases and report 12 novel variants. In the unsolved families, a search for recessive-type variants affecting the same gene was performed; and in five affected fetuses of two unrelated families, a homozygous loss-of-function variant in the kinesin family member 21A gene (KIF21A) was found. CONCLUSION Our study underlines the broad locus heterogeneity of FA with well-established and atypical genotype-phenotype associations. We describe KIF21A as a new factor implicated in the pathogenesis of severe neurogenic FA sequence with arthrogryposis of multiple joints, pulmonary hypoplasia and facial dysmorphisms. This hypothesis is further corroborated by a recent report on overlapping phenotypes observed in Kif21a null piglets.
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Affiliation(s)
- Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Amelie J Müller
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | - Petra Stöbe
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Darja Gauck
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | | | - Luisa Averdunk
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University Dusseldorf, Dusseldorf, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Tilman Heinrich
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Natalia Prodan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Martin Kehrer
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Olga Kelemen
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | - Denise Horn
- Institute of Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dirk Emmerich
- Practice for Ultrasound and Prenatal Medicine, Freiburg, Germany
| | - Nina Hirt
- Institute of Human Genetics, University Medical Center Freiburg, Freiburg, Germany
| | | | - Glen Kristiansen
- Institute of Pathology, Center for Integrated Oncology, University of Bonn, Bonn, Germany
| | - Ulrich Gembruch
- Department of Obstetrics and Prenatal Medicine, University Hospital Bonn, Bonn, Germany
| | - Susanne Haen
- Institute of Pathology and Neuropathology, University of Tuebingen, Tuebingen, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | | | - Markus Hoopmann
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Stephan Waldmüller
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Stefanie Beck-Wödl
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | | | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University Dusseldorf, Dusseldorf, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany,Centre for Rare Diseases, University of Tuebingen, Tuebingen, Germany
| | - Karl-Oliver Kagan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany,Centre for Rare Diseases, University of Tuebingen, Tuebingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany,Centre for Rare Diseases, University of Tuebingen, Tuebingen, Germany
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8
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Brar BK, Thompson MG, Vora NL, Gilmore K, Blakemore K, Miller KA, Giordano J, Dufke A, Wong B, Stover S, Lianoglou B, Van den Veyver I, Dempsey E, Rosner M, Chong K, Chitayat D, Sparks TN, Norton ME, Wapner R, Baranano K, Jelin AC. Prenatal phenotyping of fetal tubulinopathies: A multicenter retrospective case series. Prenat Diagn 2022; 42:1686-1693. [PMID: 36403095 PMCID: PMC9805891 DOI: 10.1002/pd.6269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Tubulinopathies refer to conditions caused by genetic variants in isotypes of tubulin resulting in defective neuronal migration. Historically, diagnosis was primarily via postnatal imaging. Our objective was to establish the prenatal phenotype/genotype correlations of tubulinopathies identified by fetal imaging. METHODS A large, multicenter retrospective case series was performed across nine institutions in the Fetal Sequencing Consortium. Demographics, fetal imaging reports, genetic screening and diagnostic testing results, delivery reports, and neonatal imaging reports were extracted for pregnancies with a confirmed molecular diagnosis of a tubulinopathy. RESULTS Nineteen pregnancies with a fetal tubulinopathy were identified. The most common prenatal imaging findings were cerebral ventriculomegaly (15/19), cerebellar hypoplasia (13/19), absence of the cavum septum pellucidum (6/19), abnormalities of the corpus callosum (6/19), and microcephaly (3/19). Fetal MRI identified additional central nervous system features that were not appreciated on neurosonogram in eight cases. Single gene variants were reported in TUBA1A (13), TUBB (1), TUBB2A (1), TUBB2B (2), and TUBB3 (2). CONCLUSION The presence of ventriculomegaly with cerebellar abnormalities in conjunction with additional prenatal neurosonographic findings warrants additional evaluation for a tubulinopathy. Conclusive diagnosis can be achieved by molecular sequencing, which may assist in coordination, prognostication, and reproductive planning.
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Affiliation(s)
- Bobby K Brar
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | | | - Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal - Fetal Medicine, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal - Fetal Medicine, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Karin Blakemore
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Kristen A Miller
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Jessica Giordano
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Beatrix Wong
- Division of Human Genetics, Cincinnati Children's Hospital Center, Cincinnati, Ohio, USA
| | - Samantha Stover
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Billie Lianoglou
- Department of Surgery, University of California, San Francisco, California, USA
| | - Ignatia Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA
| | - Esther Dempsey
- St George's University of London, Molecular and Clinical Sciences Research Institute, London, UK
| | - Mara Rosner
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Karen Chong
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Teresa N Sparks
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California, USA
| | - Mary E Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
| | - Kristin Baranano
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Angie C Jelin
- Department of Gynecology and Obstetrics, Division of Maternal-Fetal Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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9
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Dhombres F, Morgan P, Chaudhari BP, Filges I, Sparks TN, Lapunzina P, Roscioli T, Agarwal U, Aggarwal S, Beneteau C, Cacheiro P, Carmody LC, Collardeau‐Frachon S, Dempsey EA, Dufke A, Duyzend MH, el Ghosh M, Giordano JL, Glad R, Grinfelde I, Iliescu DG, Ladewig MS, Munoz‐Torres MC, Pollazzon M, Radio FC, Rodo C, Silva RG, Smedley D, Sundaramurthi JC, Toro S, Valenzuela I, Vasilevsky NA, Wapner RJ, Zemet R, Haendel MA, Robinson PN. Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology. Am J Med Genet C Semin Med Genet 2022; 190:231-242. [PMID: 35872606 PMCID: PMC9588534 DOI: 10.1002/ajmg.c.31989] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/01/2022] [Indexed: 01/07/2023]
Abstract
Technological advances in both genome sequencing and prenatal imaging are increasing our ability to accurately recognize and diagnose Mendelian conditions prenatally. Phenotype-driven early genetic diagnosis of fetal genetic disease can help to strategize treatment options and clinical preventive measures during the perinatal period, to plan in utero therapies, and to inform parental decision-making. Fetal phenotypes of genetic diseases are often unique and at present are not well understood; more comprehensive knowledge about prenatal phenotypes and computational resources have an enormous potential to improve diagnostics and translational research. The Human Phenotype Ontology (HPO) has been widely used to support diagnostics and translational research in human genetics. To better support prenatal usage, the HPO consortium conducted a series of workshops with a group of domain experts in a variety of medical specialties, diagnostic techniques, as well as diseases and phenotypes related to prenatal medicine, including perinatal pathology, musculoskeletal anomalies, neurology, medical genetics, hydrops fetalis, craniofacial malformations, cardiology, neonatal-perinatal medicine, fetal medicine, placental pathology, prenatal imaging, and bioinformatics. We expanded the representation of prenatal phenotypes in HPO by adding 95 new phenotype terms under the Abnormality of prenatal development or birth (HP:0001197) grouping term, and revised definitions, synonyms, and disease annotations for most of the 152 terms that existed before the beginning of this effort. The expansion of prenatal phenotypes in HPO will support phenotype-driven prenatal exome and genome sequencing for precision genetic diagnostics of rare diseases to support prenatal care.
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Affiliation(s)
- Ferdinand Dhombres
- Sorbonne University, GRC26, INSERM, Limics, Armand Trousseau Hospital, Fetal Medicine Department, APHPParisFrance
| | - Patricia Morgan
- American College of Medical Genetics and Genomics, Newborn Screening Translational Research NetworkBethesdaMarylandUSA
| | - Bimal P. Chaudhari
- Institute for Genomic MedicineNationwide Children's HospitalColumbusOhioUSA
| | - Isabel Filges
- University Hospital Basel and University of Basel, Medical GeneticsBaselSwitzerland
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, & Reproductive SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Pablo Lapunzina
- CIBERER and Hospital Universitario La Paz, INGEMM‐Institute of Medical and Molecular GeneticsMadridSpain
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), University of New South WalesSydneyNew South WalesAustralia
| | - Umber Agarwal
- Department of Maternal and Fetal MedicineLiverpool Women's NHS Foundation TrustLiverpoolUK
| | - Shagun Aggarwal
- Department of Medical GeneticsNizam's Institute of Medical SciencesHyderabadTelanganaIndia
| | - Claire Beneteau
- Service de Génétique Médicale, UF 9321 de Fœtopathologie et Génétique, CHU de NantesNantesFrance
| | - Pilar Cacheiro
- William Harvey Research InstituteQueen Mary University of LondonLondonUK
| | - Leigh C. Carmody
- Department of Genomic MedicineThe Jackson LaboratoryFarmingtonConnecticutUSA
| | | | - Esther A. Dempsey
- St George's University of London, Molecular and Clinical Sciences Research InstituteLondonUK
| | - Andreas Dufke
- University of Tübingen, Institute of Medical Genetics and Applied GenomicsTübingenGermany
| | | | | | - Jessica L. Giordano
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Ragnhild Glad
- Department of Obstetrics and GynecologyUniversity Hospital of North NorwayTromsøNorway
| | - Ieva Grinfelde
- Department of Medical Genetics and Prenatal diagnosisChildren's University HospitalRigaLatvia
| | - Dominic G. Iliescu
- Department of Obstetrics and GynecologyUniversity of Medicine and Pharmacy CraiovaCraiovaDoljRomania
| | - Markus S. Ladewig
- Department of OphthalmologyKlinikum SaarbrückenSaarbrückenSaarlandGermany
| | - Monica C. Munoz‐Torres
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Marzia Pollazzon
- Azienda USL‐IRCCS di Reggio EmiliaMedical Genetics UnitReggio EmiliaItaly
| | | | - Carlota Rodo
- Vall d'Hebron Hospital Campus, Maternal & Fetal MedicineBarcelonaSpain
| | - Raquel Gouveia Silva
- Hospital Santa Maria, Serviço de Genética, Departamento de PediatriaHospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Centro Académico de Medicina de LisboaLisboaPortugal
| | - Damian Smedley
- William Harvey Research InstituteQueen Mary University of LondonLondonUK
| | | | - Sabrina Toro
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Irene Valenzuela
- Hospital Vall d'Hebron, Clinical and Molecular Genetics AreaBarcelonaSpain
| | - Nicole A. Vasilevsky
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Ronald J. Wapner
- Department of Obstetrics and GynecologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Roni Zemet
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Melissa A Haendel
- Department of Biochemistry and Molecular GeneticsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Peter N. Robinson
- Department of Genomic MedicineThe Jackson LaboratoryFarmingtonConnecticutUSA
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10
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Scholz T, Dufke A, Haack T, Elbracht M, Eggermann T, Roggia C, Riess O, Kurth I, Hempel M. Exomsequenzierung bei Kindern und Jugendlichen mit seltenen Erkrankungen. Monatsschr Kinderheilkd 2021. [DOI: 10.1007/s00112-021-01352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Singer S, Gazou A, Sturm M, Demidov G, Mazzola P, Riess O, Ossowski S, Dufke A. New euchromatic variant dup(11)(p15.3p15.1) transmitted through two generations defined by low coverage whole genome sequencing. Am J Med Genet A 2021; 185:3053-3056. [PMID: 34042264 DOI: 10.1002/ajmg.a.62357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/17/2021] [Accepted: 04/30/2021] [Indexed: 11/06/2022]
Abstract
We report on a 14-year old boy, his father, and his paternal uncle, all three carriers of a duplication of chromosomal region 11p15.3-p15.1. The aberration was transmitted by the grandmother, who is carrier of a balanced insertion 46,XX,ins(14;11)(q32.1;p15.3p15.1). In order to determine the precise molecular basis of this structural variant, we performed low-coverage whole genome sequencing on the boy's father. This approach allowed precise determination of the genomic breakpoints and revealed a duplication of 6.9 Mb, centromeric to the Beckwith-Wiedemann/Silver-Russell syndrome critical region in 11p15.5, that inserted in inverse orientation into 14q32.12 (according to HGVS nomenclature: NC_000014.8:g.92871000_92871001ins[NC_000011.9:g.12250642_19165928inv;T]). To our knowledge, this is the first report of a duplication of 11p15.3-p15.1 involving more than 40 genes and transmitted through two generations without apparent clinical effects.
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Affiliation(s)
- Sylke Singer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Anastasia Gazou
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - German Demidov
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Pascale Mazzola
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Center for Rare Diseases, University of Tübingen, Tübingen, Germany
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12
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Kagan KO, Hoopmann M, Pfaff T, Prodan N, Wagner P, Schmid M, Dufke A, Mau-Holzmann U, Brucker S, Marcato L, Malvestiti B, Grati FR. First Trimester Screening for Common Trisomies and Microdeletion 22q11.2 Syndrome Using Cell-Free DNA: A Prospective Clinical Study. Fetal Diagn Ther 2020; 47:841-852. [PMID: 32877902 DOI: 10.1159/000510069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/08/2020] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The aims of the study were to assess the false-positive and uninformative test rate with first trimester cell-free DNA (cfDNA) screening for common trisomies and microdeletion 22q11.2 (22q11.2DS) and to examine women's attitudes toward such an approach. METHODS This is a prospective study at the Prenatal Medicine Department of the University of Tübingen, Germany, at 11-13 weeks. In all pregnancies, a detailed ultrasound examination was carried out, followed by a cfDNA analysis for common trisomies and 22q11.2DS. In cases where the cfDNA analysis indicated 22q11.2DS, invasive prenatal diagnostic testing and parental testing were performed. After delivery, a detailed neonatal clinical examination was carried out including further genetic testing. Prior to counselling about the study, we asked the pregnant women who were potentially eligible for the study to anonymously report on their knowledge about 22q11.2DS. RESULTS A total of 1,127 pregnancies were included in the final analysis of the study. The first cfDNA test was uninformative in 15 (1.33%) pregnancies. In 10 (0.89%) cases, the test remained uninformative, even after the second blood sample. There were 3 (0.27%) cases with a positive cfDNA test for 22q11.2DS. In all, 983 women returned the anonymous questionnaire prior to study participation. Only 80 (8.1%) women responded that they felt familiar or very familiar with 22q11.2DS. CONCLUSION The addition of 22q11.2DS in first trimester cfDNA screening for common trisomies is feasible. The uninformative test rate for common trisomies and 22q11.2DS is 0.9%, and the false-positive rate for 22q11.2DS is 0.3%. Awareness and education around 22q11.2DS should be improved.
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Affiliation(s)
- Karl Oliver Kagan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany,
| | - Markus Hoopmann
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Theresa Pfaff
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Natalia Prodan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Philipp Wagner
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Maximilian Schmid
- Roche Sequencing Solutions Inc., Ariosa Diagnostics Inc., San Jose, California, USA
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Ulrike Mau-Holzmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Sara Brucker
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Livia Marcato
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
| | - Barbara Malvestiti
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
| | - Francesca Romana Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
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13
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Habhab W, Mau-Holzmann U, Singer S, Rieß A, Kagan KO, Gerbig I, Schäferhoff K, Dufke A, Kehrer M. Pre- and postnatal findings in a patient with a recombinant chromosome rec(8)(qter→q21.11::p23.3→qter) due to a paternal pericentric inversion inv(8)(p23.3q21.11) and review of the literature. Am J Med Genet A 2020; 182:2680-2684. [PMID: 32803851 DOI: 10.1002/ajmg.a.61804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/22/2020] [Accepted: 07/13/2020] [Indexed: 11/06/2022]
Abstract
Recombinant chromosome 8 (Rec8) syndrome (San Luis Valley [SLV] syndrome; OMIM #179613) is a rare chromosome disorder associated with intellectual disability, congenital heart defects, variable skeletal and urogenital anomalies, and dysmorphic features. It is characterized by a partial terminal deletion of 8p and a partial terminal duplication of 8q, which is usually due to meiotic recombination of a pericentric inversion of chromosome 8 of a healthy carrier parent. There are only few reports of cases with breakpoints defined at the molecular level by molecular karyotyping. We report on a case of Rec8 syndrome with previously unreported breakpoints in a male fetus with intrauterine growth restriction, hypogenesis of the corpus callosum, bilateral cleft lip/palate, and congenital heart defect. Cytogenetic analysis revealed a recombinant chromosome 8 [46,XY,rec(8)(qter→q21.11::p23.3→qter)] secondary to a paternal pericentric inversion [46,XY,inv(8)(p23.3q21.11)]. Molecular karyotyping correspondingly showed a terminal copy number loss of 1.4 Mb (arr[hg19] 8p23.3(158048_1514749)×1) and a terminal copy number gain of chromosome band 8q21.11q24.3 of 69.8 Mb (arr[hg19] 8q21.11q24.3(76477367_146295771)×3). To our knowledge, this is the fourth reported case diagnosed prenatally. We describe the postnatal clinical course of the male newborn. Furthermore, we review and compare the phenotypic features and breakpoints of 74 reported Rec8/SLV cases.
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Affiliation(s)
- Wisam Habhab
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ulrike Mau-Holzmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Sylke Singer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Angelika Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Karl-Oliver Kagan
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
| | - Ines Gerbig
- University Children's Hospital, University of Tübingen, Tübingen, Germany
| | - Karin Schäferhoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Martin Kehrer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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14
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Melo US, Schöpflin R, Acuna-Hidalgo R, Mensah MA, Fischer-Zirnsak B, Holtgrewe M, Klever MK, Türkmen S, Heinrich V, Pluym ID, Matoso E, Bernardo de Sousa S, Louro P, Hülsemann W, Cohen M, Dufke A, Latos-Bieleńska A, Vingron M, Kalscheuer V, Quintero-Rivera F, Spielmann M, Mundlos S. Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases. Am J Hum Genet 2020; 106:872-884. [PMID: 32470376 PMCID: PMC7273525 DOI: 10.1016/j.ajhg.2020.04.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
Genome-wide analysis methods, such as array comparative genomic hybridization (CGH) and whole-genome sequencing (WGS), have greatly advanced the identification of structural variants (SVs) in the human genome. However, even with standard high-throughput sequencing techniques, complex rearrangements with multiple breakpoints are often difficult to resolve, and predicting their effects on gene expression and phenotype remains a challenge. Here, we address these problems by using high-throughput chromosome conformation capture (Hi-C) generated from cultured cells of nine individuals with developmental disorders (DDs). Three individuals had previously been identified as harboring duplications at the SOX9 locus and six had been identified with translocations. Hi-C resolved the positions of the duplications and was instructive in interpreting their distinct pathogenic effects, including the formation of new topologically associating domains (neo-TADs). Hi-C was very sensitive in detecting translocations, and it revealed previously unrecognized complex rearrangements at the breakpoints. In several cases, we observed the formation of fused-TADs promoting ectopic enhancer-promoter interactions that were likely to be involved in the disease pathology. In summary, we show that Hi-C is a sensible method for the detection of complex SVs in a clinical setting. The results help interpret the possible pathogenic effects of the SVs in individuals with DDs.
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Affiliation(s)
- Uirá Souto Melo
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Rocio Acuna-Hidalgo
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Martin Atta Mensah
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Björn Fischer-Zirnsak
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Manuel Holtgrewe
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin Institute of Health (BIH), Core Unit Bioinformatics, 10117 Berlin, Germany
| | - Marius-Konstantin Klever
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Seval Türkmen
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Verena Heinrich
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 13353 Berlin, Germany
| | - Ilina Datkhaeva Pluym
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Eunice Matoso
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal; Center of Investigation on Environment Genetics and Oncobiology (iCBR-CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | | | - Pedro Louro
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal; Familial Risk Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, 1099-023 Lisboa, Portugal; Faculty of Health Sciences, Universidade da Beira Interior, 6201-001 Covilhã, Portugal
| | - Wiebke Hülsemann
- Handchirurgie Kinderkrankenhaus Wilhelmstift, 22149 Hamburg, Germany
| | - Monika Cohen
- kbo-Kinderzentrum München, 81377 München, Germany
| | - Andreas Dufke
- Institut für Medizinische Genetik und Angewandte Genomik, 72076 Tübingen, Germany
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, University of Medical Sciences in Poznan, 60-806 Poznan, Poland; Centers for Medical Genetics GENESIS, Grudzieniec st, 60-601 Poznan, Poland
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 13353 Berlin, Germany
| | - Vera Kalscheuer
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Human Molecular Genomics Group, 13353 Berlin, Germany; Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany.
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany.
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15
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Frints SGM, Ozanturk A, Rodríguez Criado G, Grasshoff U, de Hoon B, Field M, Manouvrier-Hanu S, E Hickey S, Kammoun M, Gripp KW, Bauer C, Schroeder C, Toutain A, Mihalic Mosher T, Kelly BJ, White P, Dufke A, Rentmeester E, Moon S, Koboldt DC, van Roozendaal KEP, Hu H, Haas SA, Ropers HH, Murray L, Haan E, Shaw M, Carroll R, Friend K, Liebelt J, Hobson L, De Rademaeker M, Geraedts J, Fryns JP, Vermeesch J, Raynaud M, Riess O, Gribnau J, Katsanis N, Devriendt K, Bauer P, Gecz J, Golzio C, Gontan C, Kalscheuer VM. Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder. Mol Psychiatry 2019; 24:1748-1768. [PMID: 29728705 DOI: 10.1038/s41380-018-0065-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/28/2018] [Indexed: 12/25/2022]
Abstract
RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations. In contrast, 44 heterozygous female carriers have normal cognition and behavior, but eight showed mild physical features. All RLIM variants identified are missense changes co-segregating with the phenotype and predicted to affect protein function. Eight of the nine altered amino acids are conserved and lie either within a domain essential for binding interacting proteins or in the C-terminal RING finger catalytic domain. In vitro experiments revealed that these amino acid changes in the RLIM RING finger impaired RLIM ubiquitin ligase activity. In vivo experiments in rlim mutant zebrafish showed that wild type RLIM rescued the zebrafish rlim phenotype, whereas the patient-specific missense RLIM variants failed to rescue the phenotype and thus represent likely severe loss-of-function mutations. In summary, we identified a spectrum of RLIM missense variants causing syndromic XLID and affecting the ubiquitin ligase activity of RLIM, suggesting that enzymatic activity of RLIM is required for normal development, cognition and behavior.
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Affiliation(s)
- Suzanna G M Frints
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands. .,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands.
| | - Aysegul Ozanturk
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | | | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Bas de Hoon
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands.,Department of Gynaecology and Obstetrics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Michael Field
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Sylvie Manouvrier-Hanu
- Clinique de Génétique médicale Guy Fontaine, Centre de référence maladies rares Anomalies du développement Hôpital Jeanne de Flandre, Lille, 59000, France.,EA 7364 RADEME Maladies Rares du Développement et du Métabolisme, Faculté de Médecine, Université de Lille, Lille, 59000, France
| | - Scott E Hickey
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA
| | - Molka Kammoun
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Karen W Gripp
- Alfred I. duPont Hospital for Children Nemours, Wilmington, DE, 19803, USA
| | - Claudia Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Theresa Mihalic Mosher
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Benjamin J Kelly
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Eveline Rentmeester
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Sungjin Moon
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Daniel C Koboldt
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Kees E P van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Lucinda Murray
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Eric Haan
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Renee Carroll
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Lynne Hobson
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Marjan De Rademaeker
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, 1090, Brussels, Belgium
| | - Joep Geraedts
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Jean-Pierre Fryns
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Joris Vermeesch
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Martine Raynaud
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Nicholas Katsanis
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Christelle Golzio
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics; Centre National de la Recherche Scientifique, UMR7104; Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, 67400, Illkirch, France
| | - Cristina Gontan
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany.
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16
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Park J, Colombo R, Schäferhoff K, Janiri L, Grimmel M, Sturm M, Grasshoff U, Dufke A, Haack TB, Kehrer M. Novel HIVEP2 Variants in Patients with Intellectual Disability. Mol Syndromol 2019; 10:195-201. [PMID: 31602191 DOI: 10.1159/000499060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2019] [Indexed: 12/31/2022] Open
Abstract
Intellectual disability (ID) occurs in approximately 1% of the population. Over the last years, broad sequencing approaches such as whole exome sequencing (WES) substantially contributed to the definition of the molecular defects underlying nonsyndromic ID. Pathogenic variants in HIVEP2, which encodes the human immunodeficiency virus type I enhancer binding protein 2, have recently been reported as a cause of ID, developmental delay, behavioral disorders, and dysmorphic features. HIVEP2 serves as a transcriptional factor regulating NF-ĸB and diverse genes that are essential in neural development. To date, only 8 patients with pathogenic de novo nonsense or frameshift variants and 1 patient with a pathogenic missense variant in HIVEP2 have been reported. By WES, we identified 2 novel truncating HIVEP2 variants, c.6609_6616delTGAGGGTC (p.Glu2204*) and c.6667C>T (p.Arg2223*), in 2 young adults presenting with developmental delay and mild ID without any dysmorphic features, systemic malformations, or behavioral issues.
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Affiliation(s)
- Joohyun Park
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Roberto Colombo
- Institute of Clinical Biochemistry, Faculty of Medicine, Catholic University, Rome, Italy.,Institute of IRCCS Policlinico Gemelli, Rome, Italy
| | - Karin Schäferhoff
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Luigi Janiri
- Institute of Psychiatry and Psychology, Faculty of Medicine, Catholic University, Rome, Italy.,Institute of IRCCS Policlinico Gemelli, Rome, Italy
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Martin Kehrer
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
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17
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Bosse K, Oberlechner E, Hoffmann A, Fugunt R, Böer B, Gruber I, Helms G, Hoopmann U, Röhm C, Hartkopf A, Komoss S, Faust U, Pohle A, Dufke A, Nguyen H, Kehrer M, Schroeder C, Heinrich T, Rieß O, Staebler A, Vogel U, Taran FA, Brucker SY, Marx M, Wallwiener D, Hahn M. Prädiktive Testung bei Familienangehörigen von BRCA1, BRCA2 und CHEK2 Mutationsträgerinnen am Universitätsbrustzentrum Tübingen – eine klinische retrospektive unizentrische Kohortenstudie. Geburtshilfe Frauenheilkd 2018. [DOI: 10.1055/s-0038-1671360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- K Bosse
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - E Oberlechner
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - A Hoffmann
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - R Fugunt
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - B Böer
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - I Gruber
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - G Helms
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - U Hoopmann
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - C Röhm
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - A Hartkopf
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - S Komoss
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - U Faust
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - A Pohle
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - A Dufke
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - H Nguyen
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - M Kehrer
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - C Schroeder
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - T Heinrich
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - O Rieß
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - A Staebler
- Institut für Pathologie und Neuropathologie, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - U Vogel
- Institut für Pathologie und Neuropathologie, Universitätsklinikum Tübingen, Tübingen, Deutschland
| | - FA Taran
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - SY Brucker
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - M Marx
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - D Wallwiener
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
| | - M Hahn
- Department für Frauengesundheit, Universitätsfauenklinik Tübingen, Tübingen, Deutschland
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18
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Charzewska A, Maiwald R, Kahrizi K, Oehl-Jaschkowitz B, Dufke A, Lemke J, Enders H, Najmabadi H, Tzschach A, Hachmann W, Jensen C, Bienek M, Poznański J, Nawara M, Chilarska T, Obersztyn E, Hoffman-Zacharska D, Gos M, Bal J, Kalscheuer V. The power of the Mediator complex-Expanding the genetic architecture and phenotypic spectrum of MED12
-related disorders. Clin Genet 2018; 94:450-456. [DOI: 10.1111/cge.13412] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/27/2018] [Accepted: 07/03/2018] [Indexed: 01/22/2023]
Affiliation(s)
- A. Charzewska
- Department of Medical Genetics; Institute of Mother and Child; Warsaw Poland
| | - R. Maiwald
- MVZ für Medizinische Genetik und Molekulare Medizin; Cologne Germany
| | - K. Kahrizi
- Genetics Research Center; University of Social Welfare and Rehabilitation Sciences; Tehran Iran
| | - B. Oehl-Jaschkowitz
- Gemeinschaftspraxis für Humangenetik, Biomedizinisches Zentrum; Homburg Germany
| | - A. Dufke
- Institut für Medizinische Genetik und Angewandte Genomik; Tübingen Germany
| | - J.R. Lemke
- Institut für Medizinische Genetik und Angewandte Genomik; Tübingen Germany
- Institut für Humangenetik am Universitätsklinikum Leipzig AöR; Leipzig Germany
| | - H. Enders
- Institut für Medizinische Genetik und Angewandte Genomik; Tübingen Germany
- MVZ Humangenetik Ulm; Ulm Germany
| | - H. Najmabadi
- Genetics Research Center; University of Social Welfare and Rehabilitation Sciences; Tehran Iran
| | - A. Tzschach
- Institut für Medizinische Genetik und Angewandte Genomik; Tübingen Germany
- Institut für Klinische Genetik, Medizinische Fakultät CGC; Technische Universität Dresden; Dresden Germany
| | - W. Hachmann
- Elisabeth-Krankenhaus Rheydt, Klinik für Kinder und Jugendliche; Mönchengladbach Germany
| | - C. Jensen
- Department of Human Molecular Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
- Abteilung Funktionelle Genomforschung, Universitätsmedizin; Greifswald Germany
| | - M. Bienek
- Department of Human Molecular Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - J. Poznański
- Department of Biophysics; Polish Academy of Sciences, Institute of Biochemistry and Biophysics; Warsaw Poland
| | - M. Nawara
- Department of Medical Genetics; Institute of Mother and Child; Warsaw Poland
| | - T. Chilarska
- Department of Genetics; Polish Mother's Memorial Hospital Research Institute; Łódź Poland
| | - E. Obersztyn
- Department of Medical Genetics; Institute of Mother and Child; Warsaw Poland
| | | | - M. Gos
- Department of Medical Genetics; Institute of Mother and Child; Warsaw Poland
| | - J. Bal
- Department of Medical Genetics; Institute of Mother and Child; Warsaw Poland
| | - V.M. Kalscheuer
- Max Planck Institute for Molecular Genetics, Research Group Development and Disease; Berlin Germany
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19
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Liehr T, Schreyer I, Kuechler A, Manolakos E, Singer S, Dufke A, Wilhelm K, Jančušková T, Čmejla R, Othman MAK, Al-Rikabi AH, Mrasek K, Ziegler M, Kankel S, Kreskowski K, Weise A. Parental origin of deletions and duplications - about the necessity to check for cryptic inversions. Mol Cytogenet 2018. [PMID: 29541160 PMCID: PMC5845138 DOI: 10.1186/s13039-018-0369-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Copy number variants (CNVs) are the genetic bases for microdeletion/ microduplication syndromes (MMSs). Couples with an affected child and desire to have further children are routinely tested for a potential parental origin of a specific CNV either by molecular karyotyping or by two color fluorescence in situ hybridization (FISH), yet. In the latter case a critical region probe (CRP) is combined with a control probe for identification of the chromosome in question. However, CNVs can arise also due to other reasons, like a recombination-event based on a submicroscopic, cryptic inversion in one of the parents. Results Seventy-four patients with different MMSs and overall 81 CNVs were studied here by a novel three color FISH approach. The way how three locus-specific probes are selected (one is the CRP and two are flanking it in a distance of 5-10 Mb) enables to detect or exclude two possible parental conditions as origins of the CNV seen in the index: (i) direct parental origin of the CNV (deletion or duplication) or (ii) a parental cryptic inversion. Thus, for overall 51/81 CNVs (63%) a parental origin could be determined. 36/51 (70.5%) inherited the CNV directly from one of the parents, but 15/51 (29.5%) were due to an exclusively by three color FISH detectable parental inversion. A 2:1 ratio of maternal versus paternal inheritance was found. Also almost two times more male than female were among the index patients. Conclusion The new, here suggested three color FISH approach is suited for more comprehensive parental studies of patients with MMS. The detection rate for parental origin was increased by 140% in this study. Still, for 30/81 cases (37%) no reason for the ‘de novo’ MMS in the affected index patient could be found by the here suggested FISH-probe set. Electronic supplementary material The online version of this article (10.1186/s13039-018-0369-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Liehr
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany
| | - Isolde Schreyer
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany.,2Center for Ambulant Medicine, Jena University Hospital, Jena, Germany
| | - Alma Kuechler
- 3Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | | | - Sylke Singer
- Institut für Medizinische Genetik und angewandte Genomik, Tübingen, Germany
| | - Andreas Dufke
- Institut für Medizinische Genetik und angewandte Genomik, Tübingen, Germany
| | - Kathleen Wilhelm
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany
| | | | - Radek Čmejla
- 6Synlab czech s.r.o., synlab genetics s.r.o, Praha, Czech Republic
| | - Moneeb A K Othman
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany
| | - Ahmed H Al-Rikabi
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany
| | - Kristin Mrasek
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany
| | - Monika Ziegler
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany
| | - Stefanie Kankel
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany
| | - Katharina Kreskowski
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany
| | - Anja Weise
- 1Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Postfach D-07740, Jena, Germany
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20
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Rath M, Najm J, Sirb H, Kentouche K, Dufke A, Pauli S, Hackmann K, Liehr T, Hübner CA, Felbor U. Large deletions play a minor but essential role in congenital coagulation factor VII and X deficiencies. Hamostaseologie 2017. [DOI: 10.1055/s-0037-1619821] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
SummaryCongenital factor VII (FVII) and factor X (FX) deficiencies belong to the group of rare bleeding disorders which may occur in separate or combined forms since both the F7 and F10 genes are located in close proximity on the distal long arm of chromosome 13 (13q34). We here present data of 192 consecutive index cases with FVII and/or FX deficiency. 10 novel and 53 recurrent sequence alterations were identified in the F7 gene and 5 novel as well as 11 recurrent in the F10 gene including one homozygous 4.35 kb deletion within F7 (c.64+430_131–6delins - TCGTAA) and three large heterozygous deletions involving both the F7 and F10 genes. One of the latter proved to be cytogenetically visible as a chromosome 13q34 deletion and associated with agenesis of the corpus callosum and psychomotor retardation.ConclusionsLarge deletions play a minor but essential role in the mutational spectrum of the F7 and F10 genes. Copy number analyses (e. g. MLPA) should be considered if sequencing cannot clarify the underlying reason of an observed coagulopathy. Of note, in cases of combined FVII/FX deficiency, a deletion of the two contiguous genes might be part of a larger chromosomal rearrangement.
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21
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Telegrafi A, Webb BD, Robbins SM, Speck-Martins CE, FitzPatrick D, Fleming L, Redett R, Dufke A, Houge G, van Harssel JJT, Verloes A, Robles A, Manoli I, Engle EC, Jabs EW, Valle D, Carey J, Hoover-Fong JE, Sobreira NLM. Identification of STAC3 variants in non-Native American families with overlapping features of Carey-Fineman-Ziter syndrome and Moebius syndrome. Am J Med Genet A 2017; 173:2763-2771. [PMID: 28777491 DOI: 10.1002/ajmg.a.38375] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/26/2017] [Accepted: 07/01/2017] [Indexed: 11/07/2022]
Abstract
Horstick et al. (2013) previously reported a homozygous p.Trp284Ser variant in STAC3 as the cause of Native American myopathy (NAM) in 5 Lumbee Native American families with congenital hypotonia and weakness, cleft palate, short stature, ptosis, kyphoscoliosis, talipes deformities, and susceptibility to malignant hyperthermia (MH). Here we present two non-Native American families, who were found to have STAC3 pathogenic variants. The first proband and her affected older sister are from a consanguineous Qatari family with a suspected clinical diagnosis of Carey-Fineman-Ziter syndrome (CFZS) based on features of hypotonia, myopathic facies with generalized weakness, ptosis, normal extraocular movements, cleft palate, growth delay, and kyphoscoliosis. We identified the homozygous c.851G>C;p.Trp284Ser variant in STAC3 in both sisters. The second proband and his affected sister are from a non-consanguineous, Puerto Rican family who was evaluated for a possible diagnosis of Moebius syndrome (MBS). His features included facial and generalized weakness, minimal limitation of horizontal gaze, cleft palate, and hypotonia, and he has a history of MH. The siblings were identified to be compound heterozygous for STAC3 variants c.851G>C;p.Trp284Ser and c.763_766delCTCT;p.Leu255IlefsX58. Given the phenotypic overlap of individuals with CFZS, MBS, and NAM, we screened STAC3 in 12 individuals diagnosed with CFZS and in 50 individuals diagnosed with MBS or a congenital facial weakness disorder. We did not identify any rare coding variants in STAC3. NAM should be considered in patients presenting with facial and generalized weakness, normal or mildly abnormal extraocular movement, hypotonia, cleft palate, and scoliosis, particularly if there is a history of MH.
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Affiliation(s)
| | - Bryn D Webb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sarah M Robbins
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - David FitzPatrick
- Human Genetics Unit, Medical and Developmental Genetics, University of Edinburgh Western General Hospital, Edinburgh, United Kingdom
| | - Leah Fleming
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Richard Redett
- Department of Plastic & Reconstructive Surgery, Johns Hopkins Hospital University School of Medicine, Baltimore, Maryland
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Jeske J T van Harssel
- Department of Clinical Genetics, University Medical Center, University of Utrecht, Utrecht, The Netherlands
| | - Alain Verloes
- Department of Genetics-Hospital Robert DEBRE, Paris, France
| | - Angela Robles
- Dr. Angela Robles Pediatrics Private Practice, San Sebastian, Puerto Rico
| | - Irini Manoli
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts.,Howard Hughes Medical Institution, Chevy Chase, Maryland
| | | | - Ethylin W Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John Carey
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Julie E Hoover-Fong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Greenberg Center for Skeletal Dysplasias, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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22
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Acuna-Hidalgo R, Deriziotis P, Steehouwer M, Gilissen C, Graham SA, van Dam S, Hoover-Fong J, Telegrafi AB, Destree A, Smigiel R, Lambie LA, Kayserili H, Altunoglu U, Lapi E, Uzielli ML, Aracena M, Nur BG, Mihci E, Moreira LMA, Borges Ferreira V, Horovitz DDG, da Rocha KM, Jezela-Stanek A, Brooks AS, Reutter H, Cohen JS, Fatemi A, Smitka M, Grebe TA, Di Donato N, Deshpande C, Vandersteen A, Marques Lourenço C, Dufke A, Rossier E, Andre G, Baumer A, Spencer C, McGaughran J, Franke L, Veltman JA, De Vries BBA, Schinzel A, Fisher SE, Hoischen A, van Bon BW. Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies. PLoS Genet 2017; 13:e1006683. [PMID: 28346496 PMCID: PMC5386295 DOI: 10.1371/journal.pgen.1006683] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 04/10/2017] [Accepted: 03/10/2017] [Indexed: 11/18/2022] Open
Abstract
Schinzel-Giedion syndrome (SGS) is a rare developmental disorder characterized by multiple malformations, severe neurological alterations and increased risk of malignancy. SGS is caused by de novo germline mutations clustering to a 12bp hotspot in exon 4 of SETBP1. Mutations in this hotspot disrupt a degron, a signal for the regulation of protein degradation, and lead to the accumulation of SETBP1 protein. Overlapping SETBP1 hotspot mutations have been observed recurrently as somatic events in leukemia. We collected clinical information of 47 SGS patients (including 26 novel cases) with germline SETBP1 mutations and of four individuals with a milder phenotype caused by de novo germline mutations adjacent to the SETBP1 hotspot. Different mutations within and around the SETBP1 hotspot have varying effects on SETBP1 stability and protein levels in vitro and in in silico modeling. Substitutions in SETBP1 residue I871 result in a weak increase in protein levels and mutations affecting this residue are significantly more frequent in SGS than in leukemia. On the other hand, substitutions in residue D868 lead to the largest increase in protein levels. Individuals with germline mutations affecting D868 have enhanced cell proliferation in vitro and higher incidence of cancer compared to patients with other germline SETBP1 mutations. Our findings substantiate that, despite their overlap, somatic SETBP1 mutations driving malignancy are more disruptive to the degron than germline SETBP1 mutations causing SGS. Additionally, this suggests that the functional threshold for the development of cancer driven by the disruption of the SETBP1 degron is higher than for the alteration in prenatal development in SGS. Drawing on previous studies of somatic SETBP1 mutations in leukemia, our results reveal a genotype-phenotype correlation in germline SETBP1 mutations spanning a molecular, cellular and clinical phenotype.
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MESH Headings
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Abnormalities, Multiple/pathology
- Blotting, Western
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Line
- Cell Proliferation/genetics
- Cell Transformation, Neoplastic/genetics
- Child
- Child, Preschool
- Craniofacial Abnormalities/genetics
- Craniofacial Abnormalities/metabolism
- Craniofacial Abnormalities/pathology
- Female
- Gene Expression Profiling
- Genetic Association Studies
- Genetic Predisposition to Disease/genetics
- Germ-Line Mutation
- HEK293 Cells
- Hand Deformities, Congenital/genetics
- Hand Deformities, Congenital/metabolism
- Hand Deformities, Congenital/pathology
- Hematologic Neoplasms/genetics
- Hematologic Neoplasms/metabolism
- Hematologic Neoplasms/pathology
- Humans
- Infant
- Infant, Newborn
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Male
- Mutation
- Nails, Malformed/genetics
- Nails, Malformed/metabolism
- Nails, Malformed/pathology
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phenotype
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Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pelagia Deriziotis
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah A. Graham
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Sipko van Dam
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Julie Hoover-Fong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | | | - Anne Destree
- Institute of Pathology and Genetics (IPG), Gosselies, Belgium
| | - Robert Smigiel
- Department of Pediatrics and Rare Disorders, Medical University, Wroclaw, Poland
| | - Lindsday A. Lambie
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine (KUSOM), İstanbul, Turkey
| | - Umut Altunoglu
- Medical Genetics Department, İstanbul Medical Faculty, İstanbul University, İstanbul, Turkey
| | - Elisabetta Lapi
- Medical Genetics Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | | | - Mariana Aracena
- División de Pediatría, Pontificia Universidad Católica de Chile and Unidad de Genética, Hospital Dr. Luis Calvo Mackenna, Santiago Chile
| | - Banu G. Nur
- Department of Pediatric Genetics, Akdeniz University Medical School, Antalya, Turkey
| | - Ercan Mihci
- Department of Pediatric Genetics, Akdeniz University Medical School, Antalya, Turkey
| | - Lilia M. A. Moreira
- Laboratory of Human Genetics, Biology Institute, Federal University of Bahia (UFBA), Bahia, Brazil
| | | | - Dafne D. G. Horovitz
- CERES-Genetica Reference Center and Studies in Medical Genetics and Instituto Fernandes Figueira / Fiocruz, Rio de Janeiro, Brazil
| | - Katia M. da Rocha
- Center for Human Genome Studies, Institute of Biosciences, USP, Sao Paulo, Brazil
| | | | - Alice S. Brooks
- Department of Clinical Genetics, Sophia Children's Hospital, Erasmus MC, Rotterdam, The Netherlands
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany and Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
| | - Julie S. Cohen
- Division of Neurogenetics, Kennedy Krieger Institute, Departments of Neurology and Pediatrics, The Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Ali Fatemi
- Division of Neurogenetics, Kennedy Krieger Institute, Departments of Neurology and Pediatrics, The Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Martin Smitka
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Theresa A. Grebe
- Division of Genetics & Metabolism, Phoenix Children’s Hospital, Phoenix, Arizona, United States of America
| | | | - Charu Deshpande
- Department of Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Anthony Vandersteen
- North West Thames Regional Genetics Unit, Kennedy Galton Centre, North West London Hospitals NHS Trust, Northwick Park & St Marks Hospital, Harrow, Middlesex, United Kingdom
| | - Charles Marques Lourenço
- Neurogenetics Unit, Department of Medical Genetics School of Medicine of Ribeirao Preto, University of Sao Paulo, Sao Paulo, Brazil
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Eva Rossier
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Gwenaelle Andre
- Unité de foetopathologie, Hôpital Pellegrin, Place Amélie Raba Léon, Bordeaux, France
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Careni Spencer
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland and School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bert B. A. De Vries
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Simon E. Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail: (BWvB); (AH)
| | - Bregje W. van Bon
- Department of Human Genetics, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail: (BWvB); (AH)
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23
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Kagan KO, Hoopmann M, Singer S, Schaeferhoff K, Dufke A, Mau-Holzmann UA. Discordance between ultrasound and cell free DNA screening for monosomy X. Arch Gynecol Obstet 2016; 294:219-24. [DOI: 10.1007/s00404-016-4077-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/14/2016] [Indexed: 01/26/2023]
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24
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Hu H, Haas SA, Chelly J, Van Esch H, Raynaud M, de Brouwer APM, Weinert S, Froyen G, Frints SGM, Laumonnier F, Zemojtel T, Love MI, Richard H, Emde AK, Bienek M, Jensen C, Hambrock M, Fischer U, Langnick C, Feldkamp M, Wissink-Lindhout W, Lebrun N, Castelnau L, Rucci J, Montjean R, Dorseuil O, Billuart P, Stuhlmann T, Shaw M, Corbett MA, Gardner A, Willis-Owen S, Tan C, Friend KL, Belet S, van Roozendaal KEP, Jimenez-Pocquet M, Moizard MP, Ronce N, Sun R, O'Keeffe S, Chenna R, van Bömmel A, Göke J, Hackett A, Field M, Christie L, Boyle J, Haan E, Nelson J, Turner G, Baynam G, Gillessen-Kaesbach G, Müller U, Steinberger D, Budny B, Badura-Stronka M, Latos-Bieleńska A, Ousager LB, Wieacker P, Rodríguez Criado G, Bondeson ML, Annerén G, Dufke A, Cohen M, Van Maldergem L, Vincent-Delorme C, Echenne B, Simon-Bouy B, Kleefstra T, Willemsen M, Fryns JP, Devriendt K, Ullmann R, Vingron M, Wrogemann K, Wienker TF, Tzschach A, van Bokhoven H, Gecz J, Jentsch TJ, Chen W, Ropers HH, Kalscheuer VM. X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Mol Psychiatry 2016; 21:133-48. [PMID: 25644381 PMCID: PMC5414091 DOI: 10.1038/mp.2014.193] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/17/2014] [Accepted: 12/08/2014] [Indexed: 12/27/2022]
Abstract
X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4(-/-) mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.
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Affiliation(s)
- H Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - S A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - J Chelly
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - H Van Esch
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - M Raynaud
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France,Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - A P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - S Weinert
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - G Froyen
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium,Human Genome Laboratory, Department of Human Genetics, K.U. Leuven, Leuven, Belgium
| | - S G M Frints
- Department of Clinical Genetics, Maastricht University Medical Center, azM, Maastricht, The Netherlands,School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - F Laumonnier
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France
| | - T Zemojtel
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M I Love
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - H Richard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A-K Emde
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M Bienek
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - C Jensen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M Hambrock
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - U Fischer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - C Langnick
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - M Feldkamp
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - W Wissink-Lindhout
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - N Lebrun
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - L Castelnau
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - J Rucci
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - R Montjean
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - O Dorseuil
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - P Billuart
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - T Stuhlmann
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - M Shaw
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - M A Corbett
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - A Gardner
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - S Willis-Owen
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,National Heart and Lung Institute, Imperial College London, London, UK
| | - C Tan
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia
| | - K L Friend
- SA Pathology, Women's and Children's Hospital, Adelaide, SA, Australia
| | - S Belet
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium,Human Genome Laboratory, Department of Human Genetics, K.U. Leuven, Leuven, Belgium
| | - K E P van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center, azM, Maastricht, The Netherlands,School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - M Jimenez-Pocquet
- Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - M-P Moizard
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France,Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - N Ronce
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France,Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - R Sun
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - S O'Keeffe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - R Chenna
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A van Bömmel
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - J Göke
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A Hackett
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - M Field
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - L Christie
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - J Boyle
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - E Haan
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,SA Pathology, Women's and Children's Hospital, Adelaide, SA, Australia
| | - J Nelson
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia
| | - G Turner
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - G Baynam
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia,Telethon Kids Institute, Perth, WA, Australia
| | | | - U Müller
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany,bio.logis Center for Human Genetics, Frankfurt a. M., Germany
| | - D Steinberger
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany,bio.logis Center for Human Genetics, Frankfurt a. M., Germany
| | - B Budny
- Chair and Department of Endocrinology, Metabolism and Internal Diseases, Ponzan University of Medical Sciences, Poznan, Poland
| | - M Badura-Stronka
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - A Latos-Bieleńska
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - L B Ousager
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - P Wieacker
- Institut für Humangenetik, Universitätsklinikum Münster, Muenster, Germany
| | | | - M-L Bondeson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - G Annerén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - A Dufke
- Institut für Medizinische Genetik und Angewandte Genomik, Tübingen, Germany
| | - M Cohen
- Kinderzentrum München, München, Germany
| | - L Van Maldergem
- Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France
| | - C Vincent-Delorme
- Service de Génétique, Hôpital Jeanne de Flandre CHRU de Lilles, Lille, France
| | - B Echenne
- Service de Neuro-Pédiatrie, CHU Montpellier, Montpellier, France
| | - B Simon-Bouy
- Laboratoire SESEP, Centre hospitalier de Versailles, Le Chesnay, France
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - M Willemsen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - J-P Fryns
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - K Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - R Ullmann
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - K Wrogemann
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - T F Wienker
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A Tzschach
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - H van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - J Gecz
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - T J Jentsch
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - W Chen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany,Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - H-H Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - V M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany,Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany. E-mail:
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25
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Tzschach A, Grasshoff U, Beck-Woedl S, Dufke C, Bauer C, Kehrer M, Evers C, Moog U, Oehl-Jaschkowitz B, Di Donato N, Maiwald R, Jung C, Kuechler A, Schulz S, Meinecke P, Spranger S, Kohlhase J, Seidel J, Reif S, Rieger M, Riess A, Sturm M, Bickmann J, Schroeder C, Dufke A, Riess O, Bauer P. Next-generation sequencing in X-linked intellectual disability. Eur J Hum Genet 2015; 23:1513-8. [PMID: 25649377 DOI: 10.1038/ejhg.2015.5] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 01/02/2014] [Accepted: 01/07/2015] [Indexed: 12/11/2022] Open
Abstract
X-linked intellectual disability (XLID) is a genetically heterogeneous disorder with more than 100 genes known to date. Most genes are responsible for a small proportion of patients only, which has hitherto hampered the systematic screening of large patient cohorts. We performed targeted enrichment and next-generation sequencing of 107 XLID genes in a cohort of 150 male patients. Hundred patients had sporadic intellectual disability, and 50 patients had a family history suggestive of XLID. We also analysed a sporadic female patient with severe ID and epilepsy because she had strongly skewed X-inactivation. Target enrichment and high parallel sequencing allowed a diagnostic coverage of >10 reads for ~96% of all coding bases of the XLID genes at a mean coverage of 124 reads. We found 18 pathogenic variants in 13 XLID genes (AP1S2, ATRX, CUL4B, DLG3, IQSEC2, KDM5C, MED12, OPHN1, SLC9A6, SMC1A, UBE2A, UPF3B and ZDHHC9) among the 150 male patients. Thirteen pathogenic variants were present in the group of 50 familial patients (26%), and 5 pathogenic variants among the 100 sporadic patients (5%). Systematic gene dosage analysis for low coverage exons detected one pathogenic hemizygous deletion. An IQSEC2 nonsense variant was detected in the female ID patient, providing further evidence for a role of this gene in encephalopathy in females. Skewed X-inactivation was more frequently observed in mothers with pathogenic variants compared with those without known X-linked defects. The mutation rate in the cohort of sporadic patients corroborates previous estimates of 5-10% for X-chromosomal defects in male ID patients.
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Affiliation(s)
- Andreas Tzschach
- Institute of Clinical Genetics, Technische Universität Dresden, Dresden, Germany.,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stefanie Beck-Woedl
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Claudia Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Claudia Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Martin Kehrer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Christina Evers
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Ute Moog
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | | | - Nataliya Di Donato
- Institute of Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | | | | | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Solveig Schulz
- Center of Human Genetics, Jena University Hospital, Jena, Germany
| | - Peter Meinecke
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Silke Reif
- Practice of Medical Genetics, Dresden, Germany
| | | | - Angelika Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Julia Bickmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
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26
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Kagan KO, Berg C, Dufke A, Geipel A, Hoopmann M, Abele H. Novel fetal and maternal sonographic findings in confirmed cases of Beckwith-Wiedemann syndrome. Prenat Diagn 2015; 35:394-9. [PMID: 25641174 DOI: 10.1002/pd.4555] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 12/26/2014] [Accepted: 12/26/2014] [Indexed: 11/10/2022]
Abstract
OBJECTIVE The objective of the study was to examine the prenatal anomalies in fetuses with Beckwith-Wiedemann syndrome (BWS). METHODS The study included a retrospective assessment of 12 pregnancies that were seen at three tertiary referral centres (Universities of Tübingen, Bonn, and Cologne/Germany). The genetic mutation, the results of the second trimester ultrasound examination, and the outcome of the pregnancies are shown. Biometric data were transformed into z-values. RESULTS Median gestational age at the time of examination was 22.6 (range 19.0-29.7) weeks of gestation. In all cases, the head circumference (HC) and the femur length (FL) were within the normal range, but the HC-FL ratio was above the 95th centile in 75% of the cases. An exomphalos, macroglossia, and visceromegaly were observed in 67%, 50%, and 83% of the cases, and in 58% and 83%, there were polyhydramnios and placentamegaly respectively. The fetal pancreas was identified in three quarters of the cases. A third of the women had large, overstimulation-like ovaries, although each pregnancy was conceived naturally. In four cases, beta-human chorionic gonadotropin (hCG) levels were measured and mean hCG levels were 498 106 IU/L. DISCUSSION Besides exomphalos, BWS should be considered if there is macroglossia, a distinct growth pattern, pancreatic hyperplasia, placentamegaly, and substantially increased levels of beta-hCG. © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Karl Oliver Kagan
- Department of Obstetrics and Gynaecology, University of Tübingen, Tübingen, Germany
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27
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Rath M, Najm J, Sirb H, Kentouche K, Dufke A, Pauli S, Hackmann K, Liehr T, Hübner CA, Felbor U. Large deletions play a minor but essential role in congenital coagulation factor VII and X deficiencies. Hamostaseologie 2015; 35 Suppl 1:S36-S42. [PMID: 26540129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 10/16/2015] [Indexed: 06/05/2023] Open
Abstract
UNLABELLED Congenital factor VII (FVII) and factor X (FX) deficiencies belong to the group of rare bleeding disorders which may occur in separate or combined forms since both the F7 and F10 genes are located in close proximity on the distal long arm of chromosome 13 (13q34). We here present data of 192 consecutive index cases with FVII and/or FX deficiency. 10 novel and 53 recurrent sequence alterations were identified in the F7 gene and 5 novel as well as 11 recurrent in the F10 gene including one homozygous 4.35 kb deletion within F7 (c.64+430_131-6delinsTCGTAA) and three large heterozygous deletions involving both the F7 and F10 genes. One of the latter proved to be cytogenetically visible as a chromosome 13q34 deletion and associated with agenesis of the corpus callosum and psychomotor retardation. CONCLUSIONS Large deletions play a minor but essential role in the mutational spectrum of the F7 and F10 genes. Copy number analyses (e. g. MLPA) should be considered if sequencing cannot clarify the underlying reason of an observed coagulopathy. Of note, in cases of combined FVII/FX deficiency, a deletion of the two contiguous genes might be part of a larger chromosomal rearrangement.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - U Felbor
- Prof. Dr. med. Ute Felbor, Department of Human Genetics, University Medicine Greifswald, Fleischmannstr. 42-44, 17475 Greifswald, Germany, Tel. +49/(0)38 34/86 53 71, Fax +49/(0)38 34/86 53 69,
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28
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Dufke A, Riess O. Präkonzeptionelle und vorgeburtliche klinische Genomsequenzierung. MED GENET-BERLIN 2014. [DOI: 10.1007/s11825-014-0023-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Zusammenfassung
Hintergrund
Innerhalb kürzester Zeit haben Hochdurchsatzanalysen von Exomen und Genomen Eingang in die postnatale klinisch-diagnostische Anwendung gefunden. Bei hoher technischer Analysezuverlässigkeit, sinkenden Kosten und kurzen Analysezeiten ist das Potenzial, welches sich für diese Anwendung auch für das präkonzeptionelle Screening und die Pränataldiagnostik ergeben könnte, offensichtlich. Insbesondere diese beiden Anwendungsgebiete erfordern eine sehr hohe Sicherheit in der klinischen Befundinterpretation. Eine weitere Herausforderung gegenüber der postnatalen diagnostischen Anwendung wird die Beurteilung des klinischen Manifestationsspektrums präklinisch oder pränatal erhobener genomischer Sequenzdaten sein.
Material und Methoden
Abgeleitet von den Erfahrungen mit NGS-Analysen im postnatalen diagnostischen Ansatz erfolgen eine Übertragung und ein Ausblick auf die Anwendung der Methode im Kontext der Familienplanung.
Diskussion und Ergebnisse
Der Beitrag beschränkt sich auf die technische und klinische Anwendbarkeit. Diskutiert werden der Einsatz von NGS als umfassende Screeningmethode von Populationen, Niedrigrisikokollektiven und die Beschränkung auf ausgewählte, dem individuellen Risikoprofil angepasste Analysen. Letztere könnten kurz- bis mittelfristig Eingang in die präkonzeptionelle und auch vorgeburtliche Diagnostik finden.
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Affiliation(s)
- Andreas Dufke
- Aff1 grid.411544.1 0000000101968249 Institut für Medizinische Genetik und Angewandte Genomik Universitätsklinikum Tübingen Calwerstr. 7 72076 Tübingen Deutschland
| | - Olaf Riess
- Aff1 grid.411544.1 0000000101968249 Institut für Medizinische Genetik und Angewandte Genomik Universitätsklinikum Tübingen Calwerstr. 7 72076 Tübingen Deutschland
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Schroeder C, Ekici AB, Moog U, Grasshoff U, Mau-Holzmann U, Sturm M, Vosseler V, Poths S, Rappold G, Riess A, Riess O, Dufke A, Bonin M. Genome-wide UPD screening in patients with intellectual disability. Eur J Hum Genet 2014; 22:1233-5. [PMID: 24801762 DOI: 10.1038/ejhg.2014.63] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/28/2014] [Accepted: 03/13/2014] [Indexed: 12/18/2022] Open
Abstract
Uniparental disomy (UPD) describes the inheritance of a pair of chromosomes from only one parent. It may occur as isodisomy, heterodisomy or a combination of both and may involve only chromosome segments. UPD can affect each chromosome. The incidence is estimated to be around 1:3500 in live births. Some parts of chromosomes are subject to 'parent-of-origin imprinting' and the phenotypic effect in UPD syndromes is mainly due to functional imbalance of imprinted genes. Isodisomy can result in mutation homozygosity in autosomal-recessive inherited diseases. UPD causes several well-defined imprinting syndromes associated with intellectual disability (ID). Although knowledge on frequency and size of UPDs in patients with unexplained ID remains largely unknown as no efficient genome-wide screening technique was available for detection of both isodisomic and heterodisomic UPDs. SNP microarrays have been proven to be capable to detect UPDs through Mendelian errors. The correct subclassification of UPD requires child-parent trio experiments. To further elucidate the role of UPD in patients with unexplained ID, we analyzed a total of 322 child-parent trios. We were not able to detect UPDs (isodisomies and heterodisomies) within our cohort spanning whole chromosomes or chromosomal segments. We conclude that UPD is rare in patients with unexplained ID.
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Affiliation(s)
- Christopher Schroeder
- 1] Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany [2] Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Arif Bülent Ekici
- Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ute Grasshoff
- 1] Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany [2] Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Ulrike Mau-Holzmann
- 1] Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany [2] Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- 1] Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany [2] Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Vanessa Vosseler
- 1] Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany [2] Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Sven Poths
- 1] Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany [2] Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Gudrun Rappold
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Angelika Riess
- Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Olaf Riess
- 1] Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany [2] Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Andreas Dufke
- 1] Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany [2] Rare Disease Center, University of Tübingen, Tübingen, Germany
| | - Michael Bonin
- 1] Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany [2] Rare Disease Center, University of Tübingen, Tübingen, Germany
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30
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Krieger M, Roos A, Stendel C, Claeys KG, Sonmez FM, Baudis M, Bauer P, Bornemann A, de Goede C, Dufke A, Finkel RS, Goebel HH, Häussler M, Kingston H, Kirschner J, Medne L, Muschke P, Rivier F, Rudnik-Schöneborn S, Spengler S, Inzana F, Stanzial F, Benedicenti F, Synofzik M, Lia Taratuto A, Pirra L, Tay SKH, Topaloglu H, Uyanik G, Wand D, Williams D, Zerres K, Weis J, Senderek J. SIL1 mutations and clinical spectrum in patients with Marinesco-Sjogren syndrome. ACTA ACUST UNITED AC 2013; 136:3634-44. [PMID: 24176978 DOI: 10.1093/brain/awt283] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Marinesco-Sjögren syndrome is a rare autosomal recessive multisystem disorder featuring cerebellar ataxia, early-onset cataracts, chronic myopathy, variable intellectual disability and delayed motor development. More recently, mutations in the SIL1 gene, which encodes an endoplasmic reticulum resident co-chaperone, were identified as the main cause of Marinesco-Sjögren syndrome. Here we describe the results of SIL1 mutation analysis in 62 patients presenting with early-onset ataxia, cataracts and myopathy or combinations of at least two of these. We obtained a mutation detection rate of 60% (15/25) among patients with the characteristic Marinesco-Sjögren syndrome triad (ataxia, cataracts, myopathy) whereas the detection rate in the group of patients with more variable phenotypic presentation was below 3% (1/37). We report 16 unrelated families with a total of 19 different SIL1 mutations. Among these mutations are 15 previously unreported changes, including single- and multi-exon deletions. Based on data from our screening cohort and data compiled from the literature we found that SIL1 mutations are invariably associated with the combination of a cerebellar syndrome and chronic myopathy. Cataracts were observed in all patients beyond the age of 7 years, but might be missing in infants. Six patients with SIL1 mutations had no intellectual disability, extending the known wide range of cognitive capabilities in Marinesco-Sjögren syndrome to include normal intelligence. Modestly constant features were somatic growth retardation, skeletal abnormalities and pyramidal tract signs. Examination of mutant SIL1 expression in cultured patient lymphoblasts suggested that SIL1 mutations result in severely reduced SIL1 protein levels irrespective of the type and position of mutations. Our data broaden the SIL1 mutation spectrum and confirm that SIL1 is the major Marinesco-Sjögren syndrome gene. SIL1 patients usually present with the characteristic triad but cataracts might be missing in young children. As cognitive impairment is not obligatory, patients without intellectual disability but a Marinesco-Sjögren syndrome-compatible phenotype should receive SIL1 mutation analysis. Despite allelic heterogeneity and many families with private mutations, the phenotype related to SIL1 mutations is relatively homogenous. Based on SIL1 expression studies we speculate that this may arise from a uniform effect of different mutations on protein expression.
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Affiliation(s)
- Michael Krieger
- 1 Institute of Human Genetics, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, 52074 Aachen, Germany
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31
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Kehrer M, Beckmann A, Wyduba J, Finckh U, Dufke A, Gaiser U, Tzschach A. Floating-Harbor syndrome: SRCAP mutations are not restricted to exon 34. Clin Genet 2013; 85:498-9. [PMID: 23763483 DOI: 10.1111/cge.12199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/17/2013] [Accepted: 05/17/2013] [Indexed: 11/29/2022]
Affiliation(s)
- M Kehrer
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
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32
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Schroeder C, Sturm M, Dufke A, Mau-Holzmann U, Eggermann T, Poths S, Riess O, Bonin M. UPDtool: a tool for detection of iso- and heterodisomy in parent-child trios using SNP microarrays. ACTA ACUST UNITED AC 2013; 29:1562-4. [PMID: 23589652 DOI: 10.1093/bioinformatics/btt174] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
UNLABELLED UPDtool is a computational tool for detection and classification of uniparental disomy (UPD) in trio SNP-microarray experiments. UPDs are rare events of chromosomal malsegregation and describe the condition of two homologous chromosomes or homologous chromosomal segments that were inherited from one parent. The occurrence of UPD can be of major clinical relevance. Though high-throughput molecular screening techniques are widely used, detection of UPDs and especially the subclassification remains complex. We developed UPDtool to detect and classify UPDs from SNP microarray data of parent-child trios. The algorithm was tested using five positive controls including both iso- and heterodisomic segmental UPDs and 30 trios from the HapMap project as negative controls. With UPDtool, we were able to correctly identify all occurrences of non-mosaic UPD within our positive controls, whereas no occurrence of UPD was found within our negative controls. In addition, the chromosomal breakage points could be determined more precisely than by microsatellite analysis. Our results were compared with both the gold standard, microsatellite analysis and SNPtrio, another program available for UPD detection. UPDtool is platform independent, light weight and flexible. Because of its simple input format, UPDtool may also be used with other high-throughput technologies (e.g., next-generation sequencing). AVAILABILITY AND IMPLEMENTATION UPDtool executables, documentation and examples can be downloaded from http://www.uni-tuebingen.de/uni/thk/de/f-genomik-software.html.
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Affiliation(s)
- Christopher Schroeder
- Department of Medical Genetics, University of Tübingen, Calwerstr. 7, 72076 Tübingen, Germany.
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Hoopmann M, Sonek J, Schramm T, Zubke W, Dufke A, Kagan KO. Position of the conus medullaris in fetuses with skeletal dysplasia. Prenat Diagn 2012; 32:1313-7. [DOI: 10.1002/pd.4005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Markus Hoopmann
- Department of Obstetrics and Gynaecology; University of Tuebingen; Tuebingen Germany
| | - Jiri Sonek
- Fetal Medicine Foundation USA; Dayton OH USA
- Division of Maternal Fetal Medicine; Wright State University; Dayton OH USA
| | | | - Wolfgang Zubke
- Department of Obstetrics and Gynaecology; University of Tuebingen; Tuebingen Germany
| | - Andreas Dufke
- Institute of Human Genetics; University of Tuebingen; Tuebingen Germany
| | - Karl Oliver Kagan
- Department of Obstetrics and Gynaecology; University of Tuebingen; Tuebingen Germany
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34
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Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, Albrecht B, Bartholdi D, Beygo J, Di Donato N, Dufke A, Cremer K, Hempel M, Horn D, Hoyer J, Joset P, Röpke A, Moog U, Riess A, Thiel CT, Tzschach A, Wiesener A, Wohlleber E, Zweier C, Ekici AB, Zink AM, Rump A, Meisinger C, Grallert H, Sticht H, Schenck A, Engels H, Rappold G, Schröck E, Wieacker P, Riess O, Meitinger T, Reis A, Strom TM. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 2012; 380:1674-82. [PMID: 23020937 DOI: 10.1016/s0140-6736(12)61480-9] [Citation(s) in RCA: 754] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND The genetic cause of intellectual disability in most patients is unclear because of the absence of morphological clues, information about the position of such genes, and suitable screening methods. Our aim was to identify de-novo variants in individuals with sporadic non-syndromic intellectual disability. METHODS In this study, we enrolled children with intellectual disability and their parents from ten centres in Germany and Switzerland. We compared exome sequences between patients and their parents to identify de-novo variants. 20 children and their parents from the KORA Augsburg Diabetes Family Study were investigated as controls. FINDINGS We enrolled 51 participants from the German Mental Retardation Network. 45 (88%) participants in the case group and 14 (70%) in the control group had de-novo variants. We identified 87 de-novo variants in the case group, with an exomic mutation rate of 1·71 per individual per generation. In the control group we identified 24 de-novo variants, which is 1·2 events per individual per generation. More participants in the case group had loss-of-function variants than in the control group (20/51 vs 2/20; p=0·022), suggesting their contribution to disease development. 16 patients carried de-novo variants in known intellectual disability genes with three recurrently mutated genes (STXBP1, SYNGAP1, and SCN2A). We deemed at least six loss-of-function mutations in six novel genes to be disease causing. We also identified several missense alterations with potential pathogenicity. INTERPRETATION After exclusion of copy-number variants, de-novo point mutations and small indels are associated with severe, sporadic non-syndromic intellectual disability, accounting for 45-55% of patients with high locus heterogeneity. Autosomal recessive inheritance seems to contribute little in the outbred population investigated. The large number of de-novo variants in known intellectual disability genes is only partially attributable to known non-specific phenotypes. Several patients did not meet the expected syndromic manifestation, suggesting a strong bias in present clinical syndrome descriptions. FUNDING German Ministry of Education and Research, European Commission 7th Framework Program, and Swiss National Science Foundation.
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Affiliation(s)
- Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schwerzenbach-Zurich, Switzerland
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Riess A, Rossier E, Krüger R, Dufke A, Beck-Woedl S, Horber V, Alber M, Gläser D, Riess O, Tzschach A. Novel SLC9A6 mutations in two families with Christianson syndrome. Clin Genet 2012; 83:596-7. [PMID: 22931061 DOI: 10.1111/j.1399-0004.2012.01948.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 07/24/2012] [Accepted: 08/02/2012] [Indexed: 11/28/2022]
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Begemann M, Spengler S, Gogiel M, Grasshoff U, Bonin M, Betz RC, Dufke A, Spier I, Eggermann T. Clinical significance of copy number variations in the 11p15.5 imprinting control regions: new cases and review of the literature. J Med Genet 2012; 49:547-53. [PMID: 22844132 PMCID: PMC3439641 DOI: 10.1136/jmedgenet-2012-100967] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Among the clusters of imprinted genes in humans, one of the most relevant regions involved in human growth is localised in 11p15. Opposite epigenetic and genomic disturbances in this chromosomal region contribute to two distinct imprinting disorders associated with disturbed growth, Silver-Russell and Beckwith-Wiedemann syndromes. Due to the complexity of the 11p15 imprinting regions and their interactions, the interpretation of the copy number variations in that region is complicated. The clinical outcome in case of microduplications or microdeletions is therefore influenced by the size, the breakpoint positions and the parental inheritance of the imbalance as well as by the imprinting status of the affected genes. Based on their own new cases and those from the literature, the authors give an overview on the genotype-phenotype correlation in chromosomal rearrangements in 11p15 as the basis for a directed genetic counselling. The detailed characterisation of patients and families helps to further delineate risk figures for syndromes associated with 11p15 disturbances. Furthermore, these cases provide us with profound insights in the complex regulation of the (imprinted) factors localised in 11p15.
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37
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Riess A, Dufke A, Riess O, Beck-Woedl S, Fode B, Skladny H, Klaes R, Tzschach A. Mirror-image asymmetry in monozygotic twins with kabuki syndrome. Mol Syndromol 2012; 3:94-7. [PMID: 23326255 DOI: 10.1159/000341251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2012] [Indexed: 01/10/2023] Open
Abstract
Kabuki syndrome (OMIM 147920) is a rare disorder characterised by moderate intellectual disability, growth retardation, microcephaly and characteristic facial dysmorphic features which comprise long palpebral fissures, eversion of the lateral third of the eyelids and arched eyebrows with lateral sparseness. Mutations in MLL2 are the most frequent cause of this disorder. More than 100 MLL2 point mutations have been reported, but large intragenic deletions comprising one or more exons have not yet been identified. We report on a pair of monozygotic twin brothers in whom a deletion of 2 neighbouring exons was detected. The twins had the characteristic facial features of Kabuki syndrome, and they suffered from microcephaly, cleft lip and palate and congenital heart disease. Cleft lip and palate were left-sided in the first twin and right-sided in the second twin, i.e. they represented a mirror-image asymmetry. The intragenic deletion in these brothers broadens the spectrum of MLL2 mutations, and they provide a rare example of mirror-image asymmetry of congenital malformations in monozygotic twins.
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Affiliation(s)
- A Riess
- Institute of Human Genetics, University of Tuebingen, Tuebingen, Germany
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38
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Tzschach A, Grasshoff U, Schäferhoff K, Bonin M, Dufke A, Wolff M, Haas-Lude K, Bevot A, Riess O. Interstitial 9q34.11-q34.13 deletion in a patient with severe intellectual disability, hydrocephalus, and cleft lip/palate. Am J Med Genet A 2012; 158A:1709-12. [PMID: 22639460 DOI: 10.1002/ajmg.a.35398] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/14/2012] [Indexed: 11/08/2022]
Abstract
Interstitial deletions of chromosome bands 9q34.11-q34.13 are rare. We report on a 16-year-old female patient with severe intellectual disability, congenital hydrocephalus, cleft lip and palate, talipes equinovarus, epilepsy, kyphoscoliosis, convergent strabismus, severe short stature, dystrophy, and facial dysmorphic signs. Array analysis revealed a 3.7 Mb interstitial deletion in 9q34.11-q34.13. The deletion harbors more than 60 genes, including SPTAN1, DYT1/TOR1A, ABL1, ASS1, LAMC3, POMT1, DOLK, and GLE1, mutations in which have previously been associated with monogenic disorders. This is the first patient with a deletion of this size and position in 9q34.11-q34.13. Reports of additional patients with aberrations in this region will be needed to establish karyotype-phenotype correlations and to gain information on the contribution of individual genes for the clinical manifestations.
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Affiliation(s)
- Andreas Tzschach
- Institute of Human Genetics, University of Tuebingen, Tuebingen, Germany.
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39
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Höckner M, Spreiz A, Frühmesser A, Tzschach A, Dufke A, Rittinger O, Kalscheuer V, Singer S, Erdel M, Fauth C, Grossmann V, Utermann G, Zschocke J, Kotzot D. Parental origin of de novo cytogenetically balanced reciprocal non-Robertsonian translocations. Cytogenet Genome Res 2012; 136:242-5. [PMID: 22516930 DOI: 10.1159/000337923] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2012] [Indexed: 11/19/2022] Open
Abstract
De novo cytogenetically balanced reciprocal non-Robertsonian translocations are rare findings in clinical cytogenetics and might be associated with an abnormal phenotype. Knowledge of the parental origin and mechanisms of formation is still limited. By microdissection of the derivative chromosomes and their normal homologs from metaphases followed by microsatellite-mediated marker analysis we identified 7 cases of paternal and 3 cases of maternal origin in a cohort of 10 patients with de novo cytogenetically balanced reciprocal non-Robertsonian translocations. Neither in the maternal nor in the paternal group of our study parental age seems to be increased. Together with the data from the literature our results confirm that the majority of de novo cytogenetically balanced reciprocal translocations are of paternal origin, but the preponderance does not appear to be as distinct as previously thought and the paternal age does not seem to be necessarily a major contributing factor.
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Affiliation(s)
- M Höckner
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Austria
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40
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Hoyer J, Ekici AB, Endele S, Popp B, Zweier C, Wiesener A, Wohlleber E, Dufke A, Rossier E, Petsch C, Zweier M, Göhring I, Zink AM, Rappold G, Schröck E, Wieczorek D, Riess O, Engels H, Rauch A, Reis A. Haploinsufficiency of ARID1B, a member of the SWI/SNF-a chromatin-remodeling complex, is a frequent cause of intellectual disability. Am J Hum Genet 2012; 90:565-72. [PMID: 22405089 DOI: 10.1016/j.ajhg.2012.02.007] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 01/24/2012] [Accepted: 02/07/2012] [Indexed: 11/17/2022] Open
Abstract
Intellectual disability (ID) is a clinically and genetically heterogeneous common condition that remains etiologically unresolved in the majority of cases. Although several hundred diseased genes have been identified in X-linked, autosomal-recessive, or syndromic types of ID, the establishment of an etiological basis remains a difficult task in unspecific, sporadic cases. Just recently, de novo mutations in SYNGAP1, STXBP1, MEF2C, and GRIN2B were reported as relatively common causes of ID in such individuals. On the basis of a patient with severe ID and a 2.5 Mb microdeletion including ARID1B in chromosomal region 6q25, we performed mutational analysis in 887 unselected patients with unexplained ID. In this cohort, we found eight (0.9%) additional de novo nonsense or frameshift mutations predicted to cause haploinsufficiency. Our findings indicate that haploinsufficiency of ARID1B, a member of the SWI/SNF-A chromatin-remodeling complex, is a common cause of ID, and they add to the growing evidence that chromatin-remodeling defects are an important contributor to neurodevelopmental disorders.
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Affiliation(s)
- Juliane Hoyer
- Institute of Human Genetics, University of Erlangen-Nuremberg, Germany
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Grasshoff U, Bonin M, Goehring I, Ekici A, Dufke A, Cremer K, Wagner N, Rossier E, Jauch A, Walter M, Bauer C, Bauer P, Horber K, Beck-Woedl S, Wieczorek D. De novo MECP2 duplication in two females with random X-inactivation and moderate mental retardation. Eur J Hum Genet 2011; 19:507-12. [PMID: 21326285 DOI: 10.1038/ejhg.2010.226] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Xq28 duplications including MECP2 are a well-known cause of severe mental retardation in males with seizures, muscular hypotonia, progressive spasticity, poor speech and recurrent infections that often lead to early death. Female carriers usually show a normal intellectual performance due to skewed X-inactivation (XCI). We report on two female patients with a de novo MECP2 duplication associated with moderate mental retardation. In both patients, the de novo duplication occurred on the paternal allele, and both patients show a random XCI, which can be assumed as the triggering factor for the phenotype. Furthermore, we describe the phenotype that might be restricted to unspecific mild-to -moderate mental retardation with neurological features in early adulthood.
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Affiliation(s)
- Ute Grasshoff
- Department of Medical Genetics, University of Tübingen, Tübingen, Germany.
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Hoopmann M, Abele H, Dufke A, Kagan K. Pränatale Diagnostik des Smith-Lemli-Opitz-Syndroms. Geburtshilfe Frauenheilkd 2011. [DOI: 10.1055/s-0030-1270726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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43
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Allanson JE, Bohring A, Dörr HG, Dufke A, Gillessen-Kaesbach G, Horn D, König R, Kratz CP, Kutsche K, Pauli S, Raskin S, Rauch A, Turner A, Wieczorek D, Zenker M. The face of Noonan syndrome: Does phenotype predict genotype. Am J Med Genet A 2010; 152A:1960-6. [PMID: 20602484 DOI: 10.1002/ajmg.a.33518] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The facial photographs of 81 individuals with Noonan syndrome, from infancy to adulthood, have been evaluated by two dysmorphologists (JA and MZ), each of whom has considerable experience with disorders of the Ras/MAPK pathway. Thirty-two of this cohort have PTPN11 mutations, 21 SOS1 mutations, 11 RAF1 mutations, and 17 KRAS mutations. The facial appearance of each person was judged to be typical of Noonan syndrome or atypical. In each gene category both typical and unusual faces were found. We determined that some individuals with mutations in the most commonly affected gene, PTPN11, which is correlated with the cardinal physical features, may have a quite atypical face. Conversely, some individuals with KRAS mutations, which may be associated with a less characteristic intellectual phenotype and a resemblance to Costello and cardio-facio-cutaneous syndromes, can have a very typical face. Thus, the facial phenotype, alone, is insufficient to predict the genotype, but certain facial features may facilitate an educated guess in some cases.
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Behnecke A, Hinderhofer K, Bartsch O, Nümann A, Ipach ML, Damatova N, Haaf T, Dufke A, Riess O, Moog U. Intragenic deletions of IL1RAPL1: Report of two cases and review of the literature. Am J Med Genet A 2010; 155A:372-9. [PMID: 21271657 DOI: 10.1002/ajmg.a.33656] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 07/11/2010] [Indexed: 01/28/2023]
Abstract
IL1RAPL1 (interleukin-1 receptor accessory protein-like 1) located at Xp21.3-22.1 has repeatedly been shown to be deleted in patients with a contiguous gene syndrome also affecting neighboring genes, in particular DMD (dystrophin), DAX-1 (NR0B1, nuclear receptor subfamily 0, group B, member 1), and GK (glycerol kinase). In contrast, intragenic deletions of IL1RAPL1 or other mutations or cytogenetic aberrations affecting IL1RAPL1 have only rarely been identified. Up to date, they have mostly been associated with nonspecific mental retardation (MRX). We report on two nonrelated patients with MR and additional dysmorphic features who both show intragenic deletions of IL1RAPL1, one of them being de novo (exon 2) and the other one being inherited from his mother (exons 3-5). Deletions were identified by microarray-based chromosome analysis and confirmed by multiplex PCR and FISH, respectively. These data, along with recent functional studies indicating its role in neuronal development, provide further evidence for the relevance of IL1RAPL1 in the pathogenesis of X-linked MR and add knowledge to the phenotypic spectrum of IL1RAPL1 mutations.
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Affiliation(s)
- Anne Behnecke
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
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45
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46
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McMullan DJ, Bonin M, Hehir-Kwa JY, de Vries BBA, Dufke A, Rattenberry E, Steehouwer M, Moruz L, Pfundt R, de Leeuw N, Riess A, Altug-Teber O, Enders H, Singer S, Grasshoff U, Walter M, Walker JM, Lamb CV, Davison EV, Brueton L, Riess O, Veltman JA. Molecular karyotyping of patients with unexplained mental retardation by SNP arrays: a multicenter study. Hum Mutat 2009; 30:1082-92. [PMID: 19388127 DOI: 10.1002/humu.21015] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Genomic microarrays have been implemented in the diagnosis of patients with unexplained mental retardation. This method, although revolutionizing cytogenetics, is still limited to the detection of rare de novo copy number variants (CNVs). Genome-wide single nucleotide polymorphism (SNP) microarrays provide high-resolution genotype as well as CNV information in a single experiment. We hypothesize that the widespread use of these microarray platforms can be exploited to greatly improve our understanding of the genetic causes of mental retardation and many other common disorders, while already providing a robust platform for routine diagnostics. Here we report a detailed validation of Affymetrix 500k SNP microarrays for the detection of CNVs associated to mental retardation. After this validation we applied the same platform in a multicenter study to test a total of 120 patients with unexplained mental retardation and their parents. Rare de novo CNVs were identified in 15% of cases, showing the importance of this approach in daily clinical practice. In addition, much more genomic variation was observed in these patients as well as their parents. We provide all of these data for the scientific community to jointly enhance our understanding of these genomic variants and their potential role in this common disorder.
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Affiliation(s)
- Dominic J McMullan
- West Midlands Regional Genetics Laboratory and Clinical Genetics Unit, Birmingham Women's Hospital, Birmingham, United Kingdom
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47
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Nguyen HP, Riess A, Krüger M, Bauer P, Singer S, Schneider M, Enders H, Dufke A. Mosaic trisomy 21/monosomy 21 in a living female infant. Cytogenet Genome Res 2009; 125:26-32. [PMID: 19617693 DOI: 10.1159/000218745] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2009] [Indexed: 11/19/2022] Open
Abstract
Many autosomal monosomies are presumed to end in arrested growth in the first few mitoses, prior even to the time of implantation, with possibly some proceeding to the stage of occult abortion. The single exception may be monosomy 21, although this has been questioned, with most earlier reports of monosomy 21 recently re-interpreted as being due to an unbalanced translocation involving chromosome 21. Here we report a female infant with a mosaic trisomy 21/monosomy 21 karyotype. While the karyotype 46,XX,i(21)(q10) is detected in all metaphases investigated in lymphocytes, mosaicism with the karyotype 46,XX,i(21)(q10)[31]/45,XX, -21[12] is seen in fibroblasts from a skin biopsy. Dysmorphic facial features and multiple malformations remarkably resemble cases of monosomy 21 that have been described in the literature. This suggests a dominant phenotypic effect of loss of one chromosome 21. Detailed clinical description, results of gene dosage studies, and cytogenetic analysis will be presented.
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Affiliation(s)
- H P Nguyen
- Department of Medical Genetics, University of Tuebingen, Tuebingen, Germany.
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Manvelyan M, Riegel M, Santos M, Fuster C, Pellestor F, Mazaurik ML, Schulze B, Polityko A, Tittelbach H, Reising-Ackermann G, Belitz B, Hehr U, Kelbova C, Volleth M, Gödde E, Anderson J, Küpferling P, Köhler S, Duba HC, Dufke A, Aktas D, Martin T, Schreyer I, Ewers E, Reich D, Mrasek K, Weise A, Liehr T. Thirty-two new cases with small supernumerary marker chromosomes detected in connection with fertility problems: Detailed molecular cytogenetic characterization and review of the literature. Int J Mol Med 2008. [DOI: 10.3892/ijmm.21.6.705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Manvelyan M, Riegel M, Santos M, Fuster C, Pellestor F, Mazaurik ML, Schulze B, Polityko A, Tittelbach H, Reising-Ackermann G, Belitz B, Hehr U, Kelbova C, Volleth M, Gödde E, Anderson J, Küpferling P, Köhler S, Duba HC, Dufke A, Aktas D, Martin T, Schreyer I, Ewers E, Reich D, Mrasek K, Weise A, Liehr T. Thirty-two new cases with small supernumerary marker chromosomes detected in connection with fertility problems: detailed molecular cytogenetic characterization and review of the literature. Int J Mol Med 2008; 21:705-714. [PMID: 18506363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Thirty-two patients with fertility problems were identified as carriers of small supernumerary marker chromosomes (sSMC). Molecular cytogenetic techniques were used to characterize their chromosomal origin. Together with the other cases available in the literature 111 sSMC cases have now been detected in connection with fertility problems in otherwise clinically healthy persons and characterized for their genetic content. According to this study, in 60% of the cases the sSMC originated from chromosomes 14 or 15. Euchromatic imbalances were caused by the sSMC presence in 30% of the cases. Notably, in 53% of infertile sSMC carriers, the sSMC was parentally transmitted. As we found indications of an as yet unknown mechanism for the elimination of sSMC from the human gene pool, sSMC could also play a role in elucidating the process of chromosome gain and loss during evolution. Nonetheless, further detailed molecular analysis will be necessary in the future to characterize the mechanisms and genetic basis for this phenomenon.
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Affiliation(s)
- Marina Manvelyan
- Institute of Human Genetics and Anthropology, Kollegiengasse 10, D-07743 Jena, Germany
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50
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Kuçi S, Kuçi Z, Schmid S, Seitz G, Müller I, Dufke A, Leimig T, Murti G, Jurecic R, Schumm M, Lang P, Bruchelt G, Bader P, Klingebiel T, Niethammer D, Handgretinger R. Efficient in vitro generation of adult multipotent cells from mobilized peripheral blood CD133+ cells. Cell Prolif 2008; 41:12-27. [PMID: 18211283 DOI: 10.1111/j.1365-2184.2007.00502.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVES To generate non-haematopoietic tissues from mobilized haematopoietic CD133(+) stem cells. MATERIALS AND METHODS Mobilized peripheral blood CD133(+) cells from adult healthy donors were used. In vitro ability of highly enriched CD133(+) cells from mobilized peripheral blood to generate multipotent cells, and their potential to give rise to cells with characteristics of neuroectoderm, endoderm and mesoderm layers was investigated. RESULTS We found that a recently identified population of CD45(+) adherent cells generated in vitro after culture of highly purified CD133(+) cells for 3-5 weeks with Flt3/Flk2 ligand and interleukin-6 can, in presence of the appropriate microenvironmental cues, differentiate into neural progenitor-like cells (NPLCs), hepatocyte-like cells and skeletal muscle-like cells. We have termed them to be adult multipotent haematopoietic cells (AMHCs). AMHC-derived NPLCs expressed morphological, phenotypic and molecular markers associated with primary neural progenitor cells. They can differentiate into astrocyte-like cells, neuronal-like cells and oligodendrocyte-like cells. Moreover, AMHC-derived NPLCs produced 3,4-dihydrophenylalanine and dopamine and expressed voltage-activated ion channels, suggesting their functional maturation. In addition, AMHC-derived hepatocyte-like cells and skeletal muscle-like cells, showed typical morphological features and expressed primary tissue-associated proteins. CONCLUSION Our data demonstrate that AMHCs may therefore serve as a novel source of adult multipotent cells for autologous replacement cell therapies.
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Affiliation(s)
- S Kuçi
- University Children's Hospital, Department of Hematology/Oncology, University of Tübingen, Tübingen, Germany.
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