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Pagnamenta AT, Yu J, Walker S, Noble AJ, Lord J, Dutta P, Hashim M, Camps C, Green H, Devaiah S, Nashef L, Parr J, Fratter C, Ibnouf Hussein R, Lindsay SJ, Lalloo F, Banos-Pinero B, Evans D, Mallin L, Waite A, Evans J, Newman A, Allen Z, Perez-Becerril C, Ryan G, Hart R, Taylor J, Bedenham T, Clement E, Blair E, Hay E, Forzano F, Higgs J, Canham N, Majumdar A, McEntagart M, Lahiri N, Stewart H, Smithson S, Calpena E, Jackson A, Banka S, Titheradge H, McGowan R, Rankin J, Shaw-Smith C, Evans DG, Burghel GJ, Smith MJ, Anderson E, Madhu R, Firth H, Ellard S, Brennan P, Anderson C, Taupin D, Rogers MT, Cook JA, Durkie M, East JE, Fowler D, Wilson L, Igbokwe R, Gardham A, Tomlinson I, Baralle D, Uhlig HH, Taylor JC. The impact of inversions across 33,924 families with rare disease from a national genome sequencing project. Am J Hum Genet 2024; 111:1140-1164. [PMID: 38776926 PMCID: PMC11179413 DOI: 10.1016/j.ajhg.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Detection of structural variants (SVs) is currently biased toward those that alter copy number. The relative contribution of inversions toward genetic disease is unclear. In this study, we analyzed genome sequencing data for 33,924 families with rare disease from the 100,000 Genomes Project. From a database hosting >500 million SVs, we focused on 351 genes where haploinsufficiency is a confirmed disease mechanism and identified 47 ultra-rare rearrangements that included an inversion (24 bp to 36.4 Mb, 20/47 de novo). Validation utilized a number of orthogonal approaches, including retrospective exome analysis. RNA-seq data supported the respective diagnoses for six participants. Phenotypic blending was apparent in four probands. Diagnostic odysseys were a common theme (>50 years for one individual), and targeted analysis for the specific gene had already been performed for 30% of these individuals but with no findings. We provide formal confirmation of a European founder origin for an intragenic MSH2 inversion. For two individuals with complex SVs involving the MECP2 mutational hotspot, ambiguous SV structures were resolved using long-read sequencing, influencing clinical interpretation. A de novo inversion of HOXD11-13 was uncovered in a family with Kantaputra-type mesomelic dysplasia. Lastly, a complex translocation disrupting APC and involving nine rearranged segments confirmed a clinical diagnosis for three family members and resolved a conundrum for a sibling with a single polyp. Overall, inversions play a small but notable role in rare disease, likely explaining the etiology in around 1/750 families across heterogeneous clinical cohorts.
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Affiliation(s)
- Alistair T Pagnamenta
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Jing Yu
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK; Novo Nordisk Oxford Research Centre, Oxford, UK
| | | | - Alexandra J Noble
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK; Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, UK
| | - Prasun Dutta
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Mona Hashim
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Carme Camps
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hannah Green
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Smrithi Devaiah
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lina Nashef
- Department of Neurology, King's College Hospital, London, UK
| | - Jason Parr
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Carl Fratter
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rana Ibnouf Hussein
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Sarah J Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Benito Banos-Pinero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Evans
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Lucy Mallin
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Adrian Waite
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Julie Evans
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Andrew Newman
- The All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Zoe Allen
- North Thames Rare and Inherited Disease Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Cristina Perez-Becerril
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham, UK
| | - Rachel Hart
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - John Taylor
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tina Bedenham
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Clement
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ed Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Eleanor Hay
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Francesca Forzano
- Clinical Genetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jenny Higgs
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Anirban Majumdar
- Department of Paediatric Neurology, Bristol Children's Hospital, Bristol, UK
| | - Meriel McEntagart
- SW Thames Centre for Genomic Medicine, University of London & St George's University Hospitals NHS Foundation Trust, St George's, London, UK
| | - Nayana Lahiri
- SW Thames Centre for Genomic Medicine, University of London & St George's University Hospitals NHS Foundation Trust, St George's, London, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Smithson
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Unidad CIBERER (CB06/07/1030), Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Hannah Titheradge
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Ruth McGowan
- West of Scotland Centre for Genomic Medicine, Glasgow, UK
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - Charles Shaw-Smith
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Miriam J Smith
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Emily Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Rajesh Madhu
- Paediatric Neurosciences Department, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
| | - Helen Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Paul Brennan
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle University, Newcastle, UK
| | - Claire Anderson
- Canberra Clinical Genomics, Canberra Health Services and The Australian National University, Canberra, ACT, Australia
| | - Doug Taupin
- Cancer Research, Canberra Hospital, Canberra, ACT, Australia
| | - Mark T Rogers
- The All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Jackie A Cook
- Department of Clinical Genetics, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, North East and Yorkshire Genomic Laboratory Hub, Sheffield, UK
| | - James E East
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Darren Fowler
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Louise Wilson
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rebecca Igbokwe
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Alice Gardham
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford, UK
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Holm H Uhlig
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Jenny C Taylor
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK.
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Napolitano G, Has C, Schwerk A, Yuan JH, Ullrich C. Potential of Artificial Intelligence to Accelerate Drug Development for Rare Diseases. Pharmaceut Med 2024; 38:79-86. [PMID: 38315404 DOI: 10.1007/s40290-023-00504-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 02/07/2024]
Abstract
The growth in breadth and depth of artificial intelligence (AI) applications has been fast, running hand in hand with the increasing amount of digital data available. Here, we comment on the application of AI in the field of drug development, with a strong focus on the specific achievements and challenges posed by rare diseases. Data paucity and high costs make drug development for rare diseases especially hard. AI can enable otherwise inaccessible approaches based on the large-scale integration of heterogeneous datasets and knowledge bases, guided by expert biological understanding. Obstacles still exist for the routine use of AI in the usually conservative pharmaceutical domain, which can easily become disillusioned. It is crucial to acknowledge that AI is a powerful, supportive tool that can assist but not replace human expertise in the various phases and aspects of drug discovery and development.
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Affiliation(s)
| | - Canan Has
- Centogene GmbH, Alboinstraße 36-42, 12103, Berlin, Germany
| | - Anne Schwerk
- Beriln Institute of Health Center for Regenerative Therapies (BCRT), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jui-Hung Yuan
- Beriln Institute of Health Center for Regenerative Therapies (BCRT), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Carsten Ullrich
- Beriln Institute of Health Center for Regenerative Therapies (BCRT), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
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Pardo LM, Aanicai R, Zonic E, Hakonen AH, Zielske S, Bauer P, Bertoli-Avella AM. Adding to the evidence of gene-disease association of RAP1B and syndromic thrombocytopenia. Clin Genet 2024; 105:196-201. [PMID: 37850357 DOI: 10.1111/cge.14438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023]
Abstract
Syndromic constitutive thrombocytopenia encompasses a heterogeneous group of disorders characterised by quantitative and qualitative defects of platelets while featuring other malformations. Recently, heterozygous, de novo variants in RAP1B were reported in three cases of syndromic thrombocytopenia. Here, we report two additional, unrelated individuals identified retrospectively in our data repository with heterozygous variants in RAP1B: NM_001010942.2(RAP1B):c.35G>A, p.(Gly12Glu) (de novo) and NM_001010942.2(RAP1B):c.178G>A, p.(Gly60Arg). Both individuals had thrombocytopenia, as well as congenital malformations, and neurological, behavioural, and dysmorphic features, in line with previous reports. Our data supports the causal role of monoallelic RAP1B variants that disrupt RAP1B GTPase activity in syndromic congenital thrombocytopenia.
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Affiliation(s)
- Luba M Pardo
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
| | - Ruxandra Aanicai
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
| | - Emir Zonic
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
| | - Anna H Hakonen
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Susan Zielske
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
| | - Peter Bauer
- Medical Genetics, Reporting & Research, CENTOGENE GmbH, Rostock, Germany
- Department of Internal Medicine III - Hematology, Oncology, and Palliative Medicine, University of Rostock, Rostock, Germany
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Crooks KR, Farwell Hagman KD, Mandelker D, Santani A, Schmidt RJ, Temple-Smolkin RL, Lincoln SE. Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors. J Mol Diagn 2023; 25:411-427. [PMID: 37207865 DOI: 10.1016/j.jmoldx.2023.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/27/2023] [Accepted: 03/30/2023] [Indexed: 05/21/2023] Open
Abstract
Clinical laboratory implementation of next-generation sequencing (NGS)-based constitutional genetic testing has been rapid and widespread. In the absence of widely adopted comprehensive guidance, there remains substantial variability among laboratories in the practice of NGS. One issue of sustained discussion in the field is whether and to what extent orthogonal confirmation of genetic variants identified by NGS is necessary or helpful. The Association for Molecular Pathology Clinical Practice Committee convened the NGS Germline Variant Confirmation Working Group to assess current evidence regarding orthogonal confirmation and to establish recommendations for standardizing orthogonal confirmation practices to support quality patient care. On the basis of the results of a survey of the literature, a survey of laboratory practices, and subject expert matter consensus, eight recommendations are presented, providing a common framework for clinical laboratory professionals to develop or refine individualized laboratory policies and procedures regarding orthogonal confirmation of germline variants detected by NGS.
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Affiliation(s)
- Kristy R Crooks
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
| | - Kelly D Farwell Hagman
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California
| | - Diana Mandelker
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Avni Santani
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; LetsGetChecked, PrivaPath Diagnostics, Dublin, Ireland; Veritas Genetics, Danvers, Massachusetts
| | - Ryan J Schmidt
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | | | - Stephen E Lincoln
- NGS Germline Variant Confirmation Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; InVitae, Bethesda, Maryland
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Calì E, Lin SJ, Rocca C, Sahin Y, Al Shamsi A, El Chehadeh S, Chaabouni M, Mankad K, Galanaki E, Efthymiou S, Sudhakar S, Athanasiou-Fragkouli A, Çelik T, Narlı N, Bianca S, Murphy D, De Carvalho Moreira FM, Andrea Accogli, Petree C, Huang K, Monastiri K, Edizadeh M, Nardello R, Ognibene M, De Marco P, Ruggieri M, Zara F, Striano P, Şahin Y, Al-Gazali L, Abi Warde MT, Gerard B, Zifarelli G, Beetz C, Fortuna S, Soler M, Valente EM, Varshney G, Maroofian R, Salpietro V, Houlden H. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genet Med 2022; 24:2194-2203. [PMID: 36001086 PMCID: PMC10519206 DOI: 10.1016/j.gim.2022.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023] Open
Abstract
PURPOSE The mediator (MED) multisubunit-complex modulates the activity of the transcriptional machinery, and genetic defects in different MED subunits (17, 20, 27) have been implicated in neurologic diseases. In this study, we identified a recurrent homozygous variant in MED11 (c.325C>T; p.Arg109Ter) in 7 affected individuals from 5 unrelated families. METHODS To investigate the genetic cause of the disease, exome or genome sequencing were performed in 5 unrelated families identified via different research networks and Matchmaker Exchange. Deep clinical and brain imaging evaluations were performed by clinical pediatric neurologists and neuroradiologists. The functional effect of the candidate variant on both MED11 RNA and protein was assessed using reverse transcriptase polymerase chain reaction and western blotting using fibroblast cell lines derived from 1 affected individual and controls and through computational approaches. Knockouts in zebrafish were generated using clustered regularly interspaced short palindromic repeats/Cas9. RESULTS The disease was characterized by microcephaly, profound neurodevelopmental impairment, exaggerated startle response, myoclonic seizures, progressive widespread neurodegeneration, and premature death. Functional studies on patient-derived fibroblasts did not show a loss of protein function but rather disruption of the C-terminal of MED11, likely impairing binding to other MED subunits. A zebrafish knockout model recapitulates key clinical phenotypes. CONCLUSION Loss of the C-terminal of MED subunit 11 may affect its binding efficiency to other MED subunits, thus implicating the MED-complex stability in brain development and neurodegeneration.
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Affiliation(s)
- Elisa Calì
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Yavuz Sahin
- Department of Medical Genetics, Genoks Genetic Laboratory, Ankara, Turkey
| | | | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Centre de Référence des Déficiences Intellectuelles de Causes Rares, Centre de Recherche en Biomédecine de Strasbourg (CRBS), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | | | - Kshitij Mankad
- Department of Radiology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Evangelia Galanaki
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Sniya Sudhakar
- Department of Radiology, Great Ormond Street Hospital for Children, London, United Kingdom
| | | | - Tamer Çelik
- Department of Pediatric Neurology, Private Practice, Adana, Turkey
| | - Nejat Narlı
- Division of Neonatology, Department of Pediatrics, Medical School, Cukurova University, Adana, Turkey
| | - Sebastiano Bianca
- Medical Genetics, Referral Centre for Rare Genetic Diseases, ARNAS Garibaldi, Catania, Italy
| | - David Murphy
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialities "G. D'Alessandro," University of Palermo, Palermo, Italy
| | | | - Andrea Accogli
- Division of Medical Genetics, Department of Specialized Medicine, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, Quebec, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Kamel Monastiri
- Department of Neonatology, Fattouma Bourguiba Hospital, Monastir, Tunisia
| | - Masoud Edizadeh
- Department of Medical Genetics, Genoks Genetic Laboratory, Ankara, Turkey
| | - Rosaria Nardello
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialities "G. D'Alessandro," University of Palermo, Palermo, Italy
| | - Marzia Ognibene
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Patrizia De Marco
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, AOU "Policlinico," University of Catania, Catania, Italy
| | - Federico Zara
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS "Istituto Giannina Gaslini," Genova, Italy
| | - Yavuz Şahin
- Department of Medical Genetics, Biruni University, İstanbul, Turkey
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | | | - Benedicte Gerard
- Laboratoires de Diagnostic Génétique, Unité de Génétique Moléculaire, Nouvel Hôpital Civil, Strasbourg Cedex, France
| | | | | | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Miguel Soler
- CONCEPT Lab, Italian Institute of Technology (IIT), Genova, Italy
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Gaurav Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Vincenzo Salpietro
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Pediatrics, University of L'Aquila, L'Aquila, Italy.
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
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Musante L, Faletra F, Meier K, Tomoum H, Najarzadeh Torbati P, Blair E, North S, Gärtner J, Diegmann S, Beiraghi Toosi M, Ashrafzadeh F, Ghayoor Karimiani E, Murphy D, Murru FM, Zanus C, Magnolato A, La Bianca M, Feresin A, Girotto G, Gasparini P, Costa P, Carrozzi M. TTC5 syndrome: Clinical and molecular spectrum of a severe and recognizable condition. Am J Med Genet A 2022; 188:2652-2665. [PMID: 35670379 PMCID: PMC9541101 DOI: 10.1002/ajmg.a.62852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/31/2022] [Accepted: 04/30/2022] [Indexed: 01/24/2023]
Abstract
Biallelic mutations in the TTC5 gene have been associated with autosomal recessive intellectual disability (ARID) and subsequently with an ID syndrome including severe speech impairment, cerebral atrophy, and hypotonia as clinical cornerstones. A TTC5 role in IDs has been proposed based on the physical interaction of TTC5 with p300, and possibly reducing p300 co-activator complex activity, similarly to what was observed in Menke-Hennekam 1 and 2 patients (MKHK1 and 2) carrying, respectively, mutations in exon 30 and 31 of CREBBP and EP300, which code for the TTC5-binding region. Recently, TTC5-related brain malformation has been linked to tubulinopathies due to the function of TTC5 in tubulins' dynamics. We reported seven new patients with novel or recurrent TTC5 variants. The deep characterization of the molecular and phenotypic spectrum confirmed TTC5-related disorder as a recognizable, very severe neurodevelopmental syndrome. In addition, other relevant clinical aspects, including a severe pre- and postnatal growth retardation, cryptorchidism, and epilepsy, have emerged from the reversal phenotype approach and the review of already published TTC5 cases. Microcephaly and facial dysmorphism resulted in being less variable than that documented before. The TTC5 clinical features have been compared with MKHK1 published cases in the hypothesis that clinical overlap in some characteristics of the two conditions was related to the common p300 molecular pathway.
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Affiliation(s)
- Luciana Musante
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
| | - Flavio Faletra
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
| | - Kolja Meier
- Department of Pediatrics and Adolescent MedicineUniversity Medical Center GöttingenGöttingenGermany
| | - Hoda Tomoum
- Department of PediatricsAin Shams UniversityCairoEgypt
| | | | - Edward Blair
- Oxford Centre for Genomic MedicineOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Sally North
- Oxford Centre for Genomic MedicineOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Jutta Gärtner
- Department of Pediatrics and Adolescent MedicineUniversity Medical Center GöttingenGöttingenGermany
| | - Susann Diegmann
- Department of Pediatrics and Adolescent MedicineUniversity Medical Center GöttingenGöttingenGermany
| | - Mehran Beiraghi Toosi
- Pediatric Neurology Department, Ghaem HospitalMashhad University of Medical SciencesMashhadIran
| | - Farah Ashrafzadeh
- Department of Pediatrics, Faculty of MedicineMashhad University of Medical SciencesMashhadIran
| | - Ehsan Ghayoor Karimiani
- Department of Molecular GeneticsNext Generation Genetic PolyclinicMashhadIran
- Molecular and Clinical Sciences InstituteSt. George's, University of LondonLondonUK
- Innovative Medical Research Center, Mashhad BranchIslamic Azad UniversityMashhadIran
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
| | - Flora Maria Murru
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
| | - Caterina Zanus
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
| | - Andrea Magnolato
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
| | - Martina La Bianca
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
| | - Agnese Feresin
- Department of Medical, Surgical and Health SciencesUniversity of TriesteTriesteItaly
| | - Giorgia Girotto
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
- Department of Medical, Surgical and Health SciencesUniversity of TriesteTriesteItaly
| | - Paolo Gasparini
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
- Department of Medical, Surgical and Health SciencesUniversity of TriesteTriesteItaly
| | - Paola Costa
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
| | - Marco Carrozzi
- Institute for Maternal and Child Health ‐ IRCCS “Burlo Garofolo”TriesteItaly
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7
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Health technology assessment of whole genome sequencing in the diagnosis of genetic disorders: a scoping review of the literature. Int J Technol Assess Health Care 2022; 38:e71. [PMID: 36016516 DOI: 10.1017/s0266462322000496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE The aim of this scoping review is to map the available evidence about the use of health technology assessment (HTA) in the assessment of whole genome sequencing (WGS). METHODS A scoping review methodology was adopted. The population, concept, and context framework was used to build up the research question and to establish the eligibility criteria. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews was adopted to implement a comprehensive search strategy. Evidence was retrieved from scientific databases and HTA organizations Web sites. Reports were classified as full HTA, mini-HTA, rapid reviews or other. RESULTS The search strategy identified seven reports. Five HTA organizations from five countries elaborated the reports: one full HTA, four rapid reviews, and two classified as others. The reports were mainly focused on the evaluation of the clinical utility and cost-effectiveness of genome-wide sequencing as well as informing policy questions by providing analyses of organizational and ethical considerations. CONCLUSIONS Few HTA organizations are drafting reports for WGS. It is essential to stimulate a critical reflection during the elaboration of HTA reports for WGS to steer choices of decision makers in the establishment of priorities for research and policy and reimbursement rates.
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8
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van der Knoop MM, Maroofian R, Fukata Y, van Ierland Y, Karimiani EG, Lehesjoki AE, Muona M, Paetau A, Miyazaki Y, Hirano Y, Selim L, de França M, Fock RA, Beetz C, Ruivenkamp CAL, Eaton AJ, Morneau-Jacob FD, Sagi-Dain L, Shemer-Meiri L, Peleg A, Haddad-Halloun J, Kamphuis DJ, Peeters-Scholte CMPCD, Kurul SH, Horvath R, Lochmüller H, Murphy D, Waldmüller S, Spranger S, Overberg D, Muir AM, Rad A, Vona B, Abdulwahad F, Maddirevula S, Povolotskaya IS, Voinova VY, Gowda VK, Srinivasan VM, Alkuraya FS, Mefford HC, Alfadhel M, Haack TB, Striano P, Severino M, Fukata M, Hilhorst-Hofstee Y, Houlden H. Biallelic ADAM22 pathogenic variants cause progressive encephalopathy and infantile-onset refractory epilepsy. Brain 2022; 145:2301-2312. [PMID: 35373813 PMCID: PMC9337806 DOI: 10.1093/brain/awac116] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/31/2022] [Accepted: 03/04/2022] [Indexed: 12/03/2022] Open
Abstract
Pathogenic variants in A Disintegrin And Metalloproteinase (ADAM) 22, the postsynaptic cell membrane receptor for the glycoprotein leucine-rich repeat glioma-inactivated protein 1 (LGI1), have been recently associated with recessive developmental and epileptic encephalopathy. However, so far, only two affected individuals have been described and many features of this disorder are unknown. We refine the phenotype and report 19 additional individuals harbouring compound heterozygous or homozygous inactivating ADAM22 variants, of whom 18 had clinical data available. Additionally, we provide follow-up data from two previously reported cases. All affected individuals exhibited infantile-onset, treatment-resistant epilepsy. Additional clinical features included moderate to profound global developmental delay/intellectual disability (20/20), hypotonia (12/20) and delayed motor development (19/20). Brain MRI findings included cerebral atrophy (13/20), supported by post-mortem histological examination in patient-derived brain tissue, cerebellar vermis atrophy (5/20), and callosal hypoplasia (4/20). Functional studies in transfected cell lines confirmed the deleteriousness of all identified variants and indicated at least three distinct pathological mechanisms: (i) defective cell membrane expression; (ii) impaired LGI1-binding; and/or (iii) impaired interaction with the postsynaptic density protein PSD-95. We reveal novel clinical and molecular hallmarks of ADAM22 deficiency and provide knowledge that might inform clinical management and early diagnostics.
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Affiliation(s)
- Marieke M van der Knoop
- Department of Child Neurology, Sophia Children’s Hospital, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Yuko Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yvette van Ierland
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Ehsan G Karimiani
- Next Generation Genetic Polyclinic, Razavi International Hospital, Mashhad, Iran
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George’s University, London SW17 0RE, UK
| | - Anna Elina Lehesjoki
- Folkhälsan Research Center, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki 00290, Finland
| | - Mikko Muona
- Folkhälsan Research Center, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki 00290, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Finland,00100 Helsinki, Finland
- Blueprint Genetics, 02150 Espoo, Finland
| | - Anders Paetau
- Department of Pathology, Medicum, University of Helsinki, 00100 Helsinki, Finland
| | - Yuri Miyazaki
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yoko Hirano
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo 113-8655, Japan
| | - Laila Selim
- Division of Neurology and Metabolism, Kasr Al Ainy School of Medicine, Cairo University Children Hospital, Cairo, Egypt
| | - Marina de França
- Department of Morphology and Genetics, Clinical Center of Medical Genetics Federal, University of São Paulo, São Paulo, Brazil
| | - Rodrigo Ambrosio Fock
- Department of Morphology and Genetics, Clinical Center of Medical Genetics Federal, University of São Paulo, São Paulo, Brazil
| | | | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Alison J Eaton
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | | | - Lena Sagi-Dain
- Affiliated to the Ruth and Bruce Rappaport Faculty of Medicine Technion-Israel Institute of Technology, Genetics Institute, Carmel Medical Center,Haifa, Israel
| | | | - Amir Peleg
- Affiliated to the Ruth and Bruce Rappaport Faculty of Medicine Technion-Israel Institute of Technology, Genetics Institute, Carmel Medical Center,Haifa, Israel
| | - Jumana Haddad-Halloun
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Daan J Kamphuis
- Department of Neurology, Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | | | - Semra Hiz Kurul
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Turkey
- Department of Paediatric Neurology, School of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Hanns Lochmüller
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center–University of Freiburg, Faculty of Medicine, Freiburg, Germany
- Division of Neurology, Department of Medicine, The Ottawa Hospital; and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Stephan Waldmüller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
| | | | - David Overberg
- Department of Pediatrics, Klinikum Bremen-Mitte, Bremen 28205, Germany
| | - Alison M Muir
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, WA 98195, USA
| | - Aboulfazl Rad
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Barbara Vona
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Firdous Abdulwahad
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Victoria Y Voinova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
- Mental Health Research Center, Moscow 107076, Russia
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | | | - Fowzan S Alkuraya
- Department of Translational Genomics, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, WA 98195, USA
| | - Majid Alfadhel
- Genetics and Precision Medicine Department, King Abdullah Specialized Children's Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King AbdulAziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen 72076, Germany
| | - Pasquale Striano
- IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | | | - Masaki Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yvonne Hilhorst-Hofstee
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
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9
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Popescu C. Whole exome sequencing in a juvenile idiopathic arthritis large family with SERPINA1 gene mutations. BMC Rheumatol 2022; 6:39. [PMID: 35786784 PMCID: PMC9251928 DOI: 10.1186/s41927-022-00269-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/29/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Although the underlying mechanisms and mediators of arthritis in juvenile idiopathic arthritis are not well understood, accumulated evidence supports the mixt role of genetic and environmental factors. Few reports of multiplex families with JIA were published until now. The aim of this study was to describe the subjects affected by juvenile idiopathic arthritis and psoriatic features (JIAPs) in a large family. METHODS Here, we characterized an extended multiplex family of 5 patients with juvenile idiopathic arthritis and psoriatic features (PsA) at the clinical and genetic level, using whole exome sequencing. RESULTS We did not confirm in our family the linkage with the genetic factors already described that might be associated with increase susceptibility to JIA. We found a carrier status of siblings who inherited a pathogenic allele of the SERPINA1 gene from their mother who herself has two heterozygous pathogenic variants in the SERPINA1 gene. CONCLUSIONS This study didn't identify genetic contributive factors but highlights potentially environmental associations concerning the siblings of a family with juvenile idiopathic arthritis and psoriatic features (JIAPs). It is difficult to establish that SERPINA1 gene mutation has an etiological role as the levels of AAT are only slightly decreased and all the children harbor heterozygous variants.
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10
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Marais A, Bertoli-Avella AM, Beetz C, Altunoglu U, Alhashem A, Mohamed S, Alghamdi A, Willems P, Tsoutsou E, Fryssira H, Pons R, Almarzooq R, Karatoprak EY, Ayaz A, Ünverengil G, Calvo M, Yüksel Z, Bauer P. Further clinical and genetic evidence of ASC-1 complex dysfunction in congenital neuromuscular disease. Eur J Med Genet 2022; 65:104537. [PMID: 35690317 DOI: 10.1016/j.ejmg.2022.104537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 05/21/2022] [Accepted: 06/06/2022] [Indexed: 11/03/2022]
Abstract
Transcriptional coregulators modulate the efficiency of transcription factors. Bi-allelic variants in TRIP4 and ASCC1, two genes that encode members of the tetrameric coregulator ASC-1, have recently been associated with congenital bone fractures, hypotonia, and muscular dystrophy in a total of 22 unrelated families. Upon exome sequencing and data repository mining, we identified six new patients with pathogenic homozygous variants in either TRIP4 (n = 4, two novel variants) or ASCC1 (n = 2, one novel variant). The associated clinical findings confirm and extend previous descriptions. Considering all patients reported to date, we provide supporting evidence suggesting that ASCC1-related disease has a more severe phenotype compared to TRIP4-related disorder regarding higher incidence of perinatal bone fractures and shorter survival.
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Affiliation(s)
| | | | | | - Umut Altunoglu
- Department of Medical Genetics, Koç University, School of Medicine, 34450, Istanbul, Turkey
| | - Amal Alhashem
- Division of Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City Riyadh, Saudi Arabia; Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Sarar Mohamed
- Division of Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City Riyadh, Saudi Arabia; Prince Abdullah Bin Khaled Coeliac Disease Research Chair, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediarics, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Abdulaziz Alghamdi
- Pediatrics Department, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | | | - Eirini Tsoutsou
- Medical Genetics Department, Choremio Research Laboratory, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Greece
| | - Helena Fryssira
- Medical Genetics Department, Choremio Research Laboratory, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Greece
| | - Roser Pons
- Medical Genetics Department, Choremio Research Laboratory, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Greece
| | - Reem Almarzooq
- Pediatric Department, Salmaniya Medical Complex, Manama, Bahrain
| | - Elif Yüksel Karatoprak
- Departments of Pediatric Neurology, İstanbul Medeniyet University Faculty of Medicine, Göztepe Training and Research Hospital, İstanbul, Turkey
| | - Akif Ayaz
- Istanbul Medipol University Faculty of Medicine, Department of Medical Genetics, Istanbul, Turkey
| | - Gökçen Ünverengil
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
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11
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Almeida LS, Pereira C, Aanicai R, Schröder S, Bochinski T, Kaune A, Urzi A, Spohr TCLS, Viceconte N, Oppermann S, Alasel M, Ebadat S, Iftikhar S, Jasinge E, Elsayed SM, Tomoum H, Marzouk I, Jalan AB, Cerkauskaite A, Cerkauskiene R, Tkemaladze T, Nadeem AM, El Din Mahmoud IG, Mossad FA, Kamel M, Selim LA, Cheema HA, Paknia O, Cozma C, Juaristi-Manrique C, Guatibonza-Moreno P, Böttcher T, Vogel F, Pinto-Basto J, Bertoli-Avella A, Bauer P. An integrated multiomic approach as an excellent tool for the diagnosis of metabolic diseases: our first 3720 patients. Eur J Hum Genet 2022; 30:1029-1035. [PMID: 35614200 PMCID: PMC9437014 DOI: 10.1038/s41431-022-01119-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/11/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
To present our experience using a multiomic approach, which integrates genetic and biochemical testing as a first-line diagnostic tool for patients with inherited metabolic disorders (IMDs). A cohort of 3720 patients from 62 countries was tested using a panel including 206 genes with single nucleotide and copy number variant (SNV/CNV) detection, followed by semi-automatic variant filtering and reflex biochemical testing (25 assays). In 1389 patients (37%), a genetic diagnosis was achieved. Within this cohort, the highest diagnostic yield was obtained for patients from Asia (57.5%, mainly from Pakistan). Overall, 701 pathogenic/likely pathogenic unique SNVs and 40 CNVs were identified. In 620 patients, the result of the biochemical tests guided variant classification and reporting. Top five diagnosed diseases were: Gaucher disease, Niemann-Pick disease type A/B, phenylketonuria, mucopolysaccharidosis type I, and Wilson disease. We show that integrated genetic and biochemical testing facilitated the decision on clinical relevance of the variants and led to a high diagnostic yield (37%), which is comparable to exome/genome sequencing. More importantly, up to 43% of these patients (n = 610) could benefit from medical treatments (e.g., enzyme replacement therapy). This multiomic approach constitutes a unique and highly effective tool for the genetic diagnosis of IMDs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Solaf M Elsayed
- Medical Genetics Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Hoda Tomoum
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Iman Marzouk
- Alexandria University Children Hospital, Alexandria, Egypt
| | - Anil B Jalan
- Navi Mumbai Institute of Research In Mental And Neurological Handicap (NIRMAN) / Pediatric Geneticist, Navi Mumbai, India
| | | | | | - Tinatin Tkemaladze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Anjum Muhammad Nadeem
- Pediatric Gastroenterology, Hepatology and Nutrition, the Children's Hospital and Institute of Child Health, Lahore, Pakistan
| | - Iman Gamal El Din Mahmoud
- Cairo University Children Hospital (Abu El Reesh Children's Hospital), Metabolic, Neurology, Cairo, Egypt
| | - Fawzia Amer Mossad
- Cairo University Children Hospital (Abu El Reesh Children's Hospital), Metabolic, Neurology, Cairo, Egypt
| | - Mona Kamel
- Cairo University Children Hospital (Abu El Reesh Children's Hospital), Metabolic, Neurology, Cairo, Egypt
| | - Laila Abdel Selim
- Cairo University Children Hospital (Abu El Reesh Children's Hospital), Metabolic, Neurology, Cairo, Egypt
| | - Huma Arshad Cheema
- Pediatric Gastroenterology, Hepatology and Nutrition, the Children's Hospital and Institute of Child Health, Lahore, Pakistan
| | | | | | | | | | | | | | | | | | - Peter Bauer
- CENTOGENE GmbH, 18055, Rostock, Germany.,Department of Oncology, University Medical Center Rostock, Rostock, Germany
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12
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PanelDesign: Integrating Epidemiological Information into the Design of Diagnostic NGS Gene Panels. Genes (Basel) 2022; 13:genes13040684. [PMID: 35456490 PMCID: PMC9030971 DOI: 10.3390/genes13040684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022] Open
Abstract
We report upon PanelDesign, a framework to support the design of diagnostic next generation DNA sequencing panels with epidemiological information. Two publicly available resources, namely Genomics England PanelApp and Orphadata, were combined into a single data set to allow genes in a given NGS panel to be ranked according to the frequency of the associated diseases, thereby highlighting potential core genes as defined by the Eurogenetest/ESHG guidelines for diagnostic next generation DNA sequencing. In addition, PanelDesign can be used to evaluate the contribution of different genes to a given disease following ACMG (American College of Medical Genetics) technical standards.
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13
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Alawbathani S, Westenberger A, Ordonez-Herrera N, Al-Hilali M, Al Hebby H, Alabbas F, Alhashem AM, Elyamany G, Megarbane A, Kose M, Alhashmi N, Al Sukaiti N, Al-Raqad M, Al-Tawalbeh S, Abu Adas Blanco O, Alkhattabi F, Sng D, Al-Ali R, Khan S, Tawamie H, Tripolszki K, Karageorgou V, Trunzo R, Al Mutairi F, Reversade B, Bauer P, Bertoli-Avella AM. Biallelic ZNFX1 variants are associated with a spectrum of immuno-hematological abnormalities. Clin Genet 2021; 101:247-254. [PMID: 34708404 DOI: 10.1111/cge.14081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/08/2021] [Accepted: 10/23/2021] [Indexed: 12/27/2022]
Abstract
Biallelic changes in the ZNFX1 gene have been recently reported to cause severe familial immunodeficiency. Through a search of our bio/databank with information from genetic testing of >55 000 individuals, we identified nine additional patients from seven families with six novel homozygous ZNFX1 variants. Consistent with the previously described phenotype, our patients suffered from monocytosis, thrombocytopenia, hepatosplenomegaly, recurrent infections, and lymphadenopathy. The two most severely affected probands also had renal involvement and clinical presentations compatible with hemophagocytic lymphohistiocytosis. The disease was less lethal among our patients than previously reported. We identified two missense changes, two variants predicted to result in complete protein loss through nonsense-mediated decay, and two frameshift changes that likely introduce a truncation. Our findings (i) independently confirm the role of ZNFX1 in primary genetic immunodeficiency, (ii) expand the genetic and clinical spectrum of ZNFX1-related disease, and (iii) illustrate the utility of large, well-curated, and continually updated genotype-phenotype databases in resolving molecular diagnoses of patients with initially negative genetic testing findings.
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Affiliation(s)
- Salem Alawbathani
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | - Ana Westenberger
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany.,Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | | | - Mariam Al-Hilali
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Homoud Al Hebby
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Fahad Alabbas
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Amal M Alhashem
- Division of Pediatric Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ghaleb Elyamany
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - André Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon.,Division of Medical Genetics, Institut Jerome Lejeune, Paris, France
| | - Melis Kose
- Department of Pediatrics, Division of Inborn Errors of Metabolism, Izmir Katip Çelebi University Medical Faculty, Izmir, Turkey.,Ege University Medical Faculty, Department of Pediatrics, Division of Genetics, Izmir, Turkey
| | - Nadia Alhashmi
- Clinical and Biochemical Genetics Department, Child Health Department, Royal Hospital, Muscat, Oman
| | - Nashat Al Sukaiti
- Allergy and Clinical Immunology Department, Child Health Department, Royal Hospital, Muscat, Oman
| | | | - Samah Al-Tawalbeh
- Queen Rania Al-Abdulla Children Hospital, King Hussein Medical Center, Amman, Jordan
| | | | - Fadiah Alkhattabi
- College of Medicine at Alfaisal University, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Danielle Sng
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore
| | - Ruslan Al-Ali
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | - Suliman Khan
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | - Hasan Tawamie
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | | | | | - Roberta Trunzo
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
| | - Fuad Al Mutairi
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia.,Genetics & Precision Medicine Department, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore, A*STAR, Singapore
| | - Peter Bauer
- Genomic Research & Medical Reporting, CENTOGENE GmbH, Rostock, Germany
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14
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Maroofian R, Gubas A, Kaiyrzhanov R, Scala M, Hundallah K, Severino M, Abdel-Hamid MS, Rosenfeld JA, Ebrahimi-Fakhari D, Ali Z, Rahim F, Houlden H, Tooze SA, Alsaleh NS, Zaki MS. Homozygous missense WIPI2 variants cause a congenital disorder of autophagy with neurodevelopmental impairments of variable clinical severity and disease course. Brain Commun 2021; 3:fcab183. [PMID: 34557665 PMCID: PMC8453401 DOI: 10.1093/braincomms/fcab183] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 12/27/2022] Open
Abstract
WIPI2 is a member of the human WIPI protein family (seven-bladed b-propeller proteins binding phosphatidylinositols, PROPPINs), which play a pivotal role in autophagy and has been implicated in the pathogenesis of several neurological conditions. The homozygous WIPI2 variant c.745G>A; p.(Val249Met) (NM_015610.4) has recently been associated with a neurodevelopmental disorder in a single family. Using exome sequencing and Sanger segregation analysis, here, two novel homozygous WIPI2 variants [c.551T>G; p.(Val184Gly) and c.724C>T; p.(Arg242Trp) (NM_015610.4)] were identified in four individuals of two consanguineous families. Additionally, follow-up clinical data were sought from the previously reported family. Three non-ambulant affected siblings of the first family harbouring the p.(Val184Gly) missense variant presented with microcephaly, profound global developmental delay/intellectual disability, refractory infantile/childhood-onset epilepsy, progressive tetraplegia with joint contractures and dyskinesia. In contrast, the proband of the second family carrying the p.(Arg242Trp) missense variant, similar to the initially reported WIPI2 cases, presented with a milder phenotype, encompassing moderate intellectual disability, speech and visual impairment, autistic features, and an ataxic gait. Brain MR imaging in five patients showed prominent white matter involvement with a global reduction in volume, posterior corpus callosum hypoplasia, abnormal dentate nuclei and hypoplasia of the inferior cerebellar vermis. To investigate the functional impact of these novel WIPI2 variants, we overexpressed both in WIPI2-knockout HEK293A cells. In comparison to wildtype, expression of the Val166Gly WIPI2b mutant resulted in a deficient rescue of LC3 lipidation whereas Arg224Trp mutant increased LC3 lipidation, in line with the previously reported Val231Met variant. These findings support a dysregulation of the early steps of the autophagy pathway. Collectively, our findings provide evidence that biallelic WIPI2 variants cause a neurodevelopmental disorder of variable severity and disease course. Our report expands the clinical spectrum and establishes WIPI2-related disorder as a congenital disorders of autophagy.
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Affiliation(s)
- Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London, UK
| | - Andrea Gubas
- Goethe University Medical School, University Hospital, 60590 Frankfurt am Main, Germany
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London, UK
| | - Marcello Scala
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London, UK
| | - Khalid Hundallah
- Division of Neurology, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | | | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Fazal Rahim
- Department of Physiology, Bacha Khan Medical College, Mardan, Pakistan
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London, UK
| | - Sharon A Tooze
- The Francis Crick Institute, Molecular Cell Biology of Autophagy, NW1 1AT London, UK
| | - Norah S Alsaleh
- Division of Medical Genetics and Metabolic Medicine, Department of Pediatrics, Prince Sultan Military Medical City, 11159 Riyadh, Saudi Arabia
| | - Maha S Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, 12311 Cairo, Egypt
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15
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Kovesdi E, Ripszam R, Postyeni E, Horvath EB, Kelemen A, Fabos B, Farkas V, Hadzsiev K, Sumegi K, Magyari L, Moreno PG, Bauer P, Melegh B. Whole Exome Sequencing in a Series of Patients with a Clinical Diagnosis of Tuberous Sclerosis Not Confirmed by Targeted TSC1/TSC2 Sequencing. Genes (Basel) 2021; 12:genes12091401. [PMID: 34573383 PMCID: PMC8471884 DOI: 10.3390/genes12091401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Approximately fifteen percent of patients with tuberous sclerosis complex (TSC) phenotype do not have any genetic disease-causing mutations which could be responsible for the development of TSC. The lack of a proper diagnosis significantly affects the quality of life for these patients and their families. METHODS The aim of our study was to use Whole Exome Sequencing (WES) in order to identify the genes responsible for the phenotype of nine patients with clinical signs of TSC, but without confirmed tuberous sclerosis complex 1/ tuberous sclerosis complex 2 (TSC1/TSC2) mutations using routine molecular genetic diagnostic tools. RESULTS We found previously overlooked heterozygous nonsense mutations in TSC1, and a heterozygous intronic variant in TSC2. In one patient, two heterozygous missense variants were found in polycystic kidney and hepatic disease 1 (PKHD1), confirming polycystic kidney disease type 4. A heterozygous missense mutation in solute carrier family 12 member 5 (SLC12A5) was found in one patient, which is linked to cause susceptibility to idiopathic generalized epilepsy type 14. Heterozygous nonsense variant ring finger protein 213 (RNF213) was identified in one patient, which is associated with susceptibility to Moyamoya disease type 2. In the remaining three patients WES could not reveal any variants clinically relevant to the described phenotypes. CONCLUSION Patients without appropriate diagnosis due to the lack of sensitivity of the currently used routine diagnostic methods can significantly profit from the wider application of next generation sequencing technologies in order to identify genes and variants responsible for their symptoms.
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Affiliation(s)
- Erzsebet Kovesdi
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
- Molecular Neuroendocrinology Research Group, Institute of Physiology, Center for Neuroscience, Szentagothai Research Center, Medical School, University of Pecs, 7624 Pecs, Hungary
- Correspondence:
| | - Reka Ripszam
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
| | - Etelka Postyeni
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
| | - Emese Beatrix Horvath
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary;
| | - Anna Kelemen
- National Institute of Clinical Neurosciences, 1145 Budapest, Hungary;
| | - Beata Fabos
- Somogy County Mor Kaposi Teaching Hospital, 7400 Kaposvar, Hungary;
| | - Viktor Farkas
- Department of Pediatrics, Faculty of Medicine, Semmelweis University, 1085-Budapest, Hungary;
| | - Kinga Hadzsiev
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
| | - Katalin Sumegi
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
- Departments of Biochemistry and Medical Chemistry, Medical School, University of Pecs, 7624 Pecs, Hungary
| | - Lili Magyari
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
| | | | - Peter Bauer
- CENTOGENE GmbH, 18055 Rostock, Germany; (P.B.); (P.G.M.)
| | - Bela Melegh
- Department of Medical Genetics, Medical School, Szentagothai Research Center, University of Pecs, 7624 Pecs, Hungary; (R.R.); (E.P.); (K.H.); (K.S.); (L.M.); (B.M.)
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16
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Pathogenic variants in PIDD1 lead to an autosomal recessive neurodevelopmental disorder with pachygyria and psychiatric features. Eur J Hum Genet 2021; 29:1226-1234. [PMID: 34163010 PMCID: PMC8385073 DOI: 10.1038/s41431-021-00910-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/01/2021] [Accepted: 05/20/2021] [Indexed: 02/02/2023] Open
Abstract
The PIDDosome is a multiprotein complex, composed by the p53-induced death domain protein 1 (PIDD1), the bipartite linker protein CRADD (also known as RAIDD) and the proform of caspase-2 that induces apoptosis in response to DNA damage. In the recent years, biallelic pathogenic variants in CRADD have been associated with a neurodevelopmental disorder (MRT34; MIM 614499) characterized by pachygyria with a predominant anterior gradient, megalencephaly, epilepsy and intellectual disability. More recently, biallelic pathogenic variants in PIDD1 have been described in a few families with apparently nonsydnromic intellectual disability. Here, we aim to delineate the genetic and radio-clinical features of PIDD1-related disorder. Exome sequencing was carried out in six consanguineous families. Thorough clinical and neuroradiological evaluation was performed for all the affected individuals as well as reviewing all the data from previously reported cases. We identified five distinct novel homozygous variants (c.2584C>T p.(Arg862Trp), c.1340G>A p.(Trp447*), c.2116_2120del p.(Val706Hisfs*30), c.1564_1565delCA p.(Gln522fs*44), and c.1804_1805del p.(Gly602fs*26) in eleven subjects displaying intellectual disability, behaviorial and psychiatric features, and a typical anterior-predominant pachygyria, remarkably resembling the CRADD-related neuroimaging pattern. In summary, we outlin`e the phenotypic and molecular spectrum of PIDD1 biallelic variants supporting the evidence that the PIDD1/CRADD/caspase-2 signaling is crucial for normal gyration of the developing human neocortex as well as cognition and behavior.
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17
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Combining exome/genome sequencing with data repository analysis reveals novel gene-disease associations for a wide range of genetic disorders. Genet Med 2021; 23:1551-1568. [PMID: 33875846 PMCID: PMC8354858 DOI: 10.1038/s41436-021-01159-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Within this study, we aimed to discover novel gene-disease associations in patients with no genetic diagnosis after exome/genome sequencing (ES/GS). METHODS We followed two approaches: (1) a patient-centered approach, which after routine diagnostic analysis systematically interrogates variants in genes not yet associated to human diseases; and (2) a gene variant centered approach. For the latter, we focused on de novo variants in patients that presented with neurodevelopmental delay (NDD) and/or intellectual disability (ID), which are the most common reasons for genetic testing referrals. Gene-disease association was assessed using our data repository that combines ES/GS data and Human Phenotype Ontology terms from over 33,000 patients. RESULTS We propose six novel gene-disease associations based on 38 patients with variants in the BLOC1S1, IPO8, MMP15, PLK1, RAP1GDS1, and ZNF699 genes. Furthermore, our results support causality of 31 additional candidate genes that had little published evidence and no registered OMIM phenotype (56 patients). The phenotypes included syndromic/nonsyndromic NDD/ID, oral-facial-digital syndrome, cardiomyopathies, malformation syndrome, short stature, skeletal dysplasia, and ciliary dyskinesia. CONCLUSION Our results demonstrate the value of data repositories which combine clinical and genetic data for discovering and confirming gene-disease associations. Genetic laboratories should be encouraged to pursue such analyses for the benefit of undiagnosed patients and their families.
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18
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Ahmed A, Wang M, Bergant G, Maroofian R, Zhao R, Alfadhel M, Nashabat M, AlRifai MT, Eyaid W, Alswaid A, Beetz C, Qin Y, Zhu T, Tian Q, Xia L, Wu H, Shen L, Dong S, Yang X, Liu C, Ma L, Zhang Q, Khan R, Shah AA, Guo J, Tang B, Leonardis L, Writzl K, Peterlin B, Guo H, Malik S, Xia K, Hu Z. Biallelic loss-of-function variants in NEMF cause central nervous system impairment and axonal polyneuropathy. Hum Genet 2021; 140:579-592. [PMID: 33048237 DOI: 10.1007/s00439-020-02226-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
We aimed to detect the causative gene in five unrelated families with recessive inheritance pattern neurological disorders involving the central nervous system, and the potential function of the NEMF gene in the central nervous system. Exome sequencing (ES) was applied to all families and linkage analysis was performed on family 1. A minigene assay was used to validate the splicing effect of the relevant discovered variants. Immunofluorescence (IF) experiment was performed to investigate the role of the causative gene in neuron development. The large consanguineous family confirms the phenotype-causative relationship with homozygous frameshift variant (NM_004713.6:c.2618del) as revealed by ES. Linkage analysis of the family showed a significant single-point LOD of 4.5 locus. Through collaboration in GeneMatcher, four additional unrelated families' likely pathogenic NEMF variants for a spectrum of central neurological disorders, two homozygous splice-site variants (NM_004713.6:c.574+1G>T and NM_004713.6:c.807-2A>C) and a homozygous frameshift variant (NM_004713.6: c.1234_1235insC) were subsequently identified and segregated with all affected individuals. We further revealed that knockdown (KD) of Nemf leads to impairment of axonal outgrowth and synapse development in cultured mouse primary cortical neurons. Our study demonstrates that disease-causing biallelic NEMF variants result in central nervous system impairment and other variable features. NEMF is an important player in mammalian neuron development.
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Affiliation(s)
- Ashfaque Ahmed
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Meng Wang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Gaber Bergant
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Rongjuan Zhao
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Marwan Nashabat
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Muhammad Talal AlRifai
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Wafaa Eyaid
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre (KAIMRC), King Saud Bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | | | - Yan Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Tengfei Zhu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qi Tian
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Huidan Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Shanshan Dong
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xinyi Yang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Cenying Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Linya Ma
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiumeng Zhang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Rizwan Khan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, 410008, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, 410008, Hunan, China
| | - Lea Leonardis
- Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Karin Writzl
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Borut Peterlin
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, Hunan, China
| | - Sajid Malik
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Chinese Academy of Sciences, Shanghai, China.
- Hunan Key Laboratory of Molecular Precisional Medicine, Central South University, Changsha, China.
| | - Zhengmao Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, Hunan, China.
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19
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Torraco A, Nasca A, Verrigni D, Pennisi A, Zaki MS, Olivieri G, Assouline Z, Martinelli D, Maroofian R, Rizza T, Di Nottia M, Invernizzi F, Lamantea E, Longo D, Houlden H, Prokisch H, Rötig A, Dionisi-Vici C, Bertini E, Ghezzi D, Carrozzo R, Diodato D. Novel NDUFA12 variants are associated with isolated complex I defect and variable clinical manifestation. Hum Mutat 2021; 42:699-710. [PMID: 33715266 DOI: 10.1002/humu.24195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/27/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022]
Abstract
Isolated biochemical deficiency of mitochondrial complex I is the most frequent signature among mitochondrial diseases and is associated with a wide variety of clinical symptoms. Leigh syndrome represents the most frequent neuroradiological finding in patients with complex I defect and more than 80 monogenic causes have been involved in the disease. In this report, we describe seven patients from four unrelated families harboring novel NDUFA12 variants, with six of them presenting with Leigh syndrome. Molecular genetic characterization was performed using next-generation sequencing combined with the Sanger method. Biochemical and protein studies were achieved by enzymatic activities, blue native gel electrophoresis, and western blot analysis. All patients displayed novel homozygous mutations in the NDUFA12 gene, leading to the virtual absence of the corresponding protein. Surprisingly, despite the fact that in none of the analyzed patients, NDUFA12 protein was detected, they present a different onset and clinical course of the disease. Our report expands the array of genetic alterations in NDUFA12 and underlines phenotype variability associated with NDUFA12 defect.
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Affiliation(s)
- Alessandra Torraco
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessia Nasca
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Verrigni
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessandra Pennisi
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Maha S Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Giorgia Olivieri
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Zahra Assouline
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Diego Martinelli
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Teresa Rizza
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Michela Di Nottia
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Invernizzi
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Lamantea
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Longo
- Department of Diagnostic Imaging, Unit of Neuroradiology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Agnès Rötig
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Carlo Dionisi-Vici
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniele Ghezzi
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Rosalba Carrozzo
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daria Diodato
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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20
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Dupont J, Vieira JP, Tavares ALT, Conceição CR, Khan S, Bertoli-Avella AM, Sousa AB. Adding evidence to the role of NEUROG1 in congenital cranial dysinnervation disorders. Clin Genet 2021; 99:588-593. [PMID: 33439489 DOI: 10.1111/cge.13922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 11/28/2022]
Abstract
Congenital cranial dysinnervation disorders (CCDDs) are a heterogeneous group of neurodevelopmental phenotypes caused by a primary disturbance of innervation due to deficient, absent, or misguided cranial nerves. Although some CCDDs genes are known, several clinical phenotypes and their aetiologies remain to be elucidated. We describe a 12-year-old boy with hypotonia, developmental delay, sensorineural hearing loss, and keratoconjunctivitis due to lack of corneal reflex. He had a long expressionless face, severe oromotor dysfunction, bilateral agenesis/severe hypoplasia of the VIII nerve with marked atresia of the internal auditory canals and cochlear labyrinth malformation. Trio-exome sequencing identified a homozygous loss of function variant in the NEUROG1 gene (NM_006161.2: c.202G > T, p.Glu68*). NEUROG1 is considered a causal candidate for CCDDs based on (i) the previous report of a patient with a homozygous gene deletion and developmental delay, deafness due to absent bilateral VIII nerves, and severe oromotor dysfunction; (ii) a second patient with a homozygous NEUROG1 missense variant and corneal opacity, absent corneal reflex and intellectual disability; and (iii) the knockout mouse model phenotype which highly resembles the disorder observed in humans. Our findings support the growing compelling evidence that loss of NEUROG1 leads to a very distinctive disorder of cranial nerves development.
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Affiliation(s)
- Juliette Dupont
- Genetics Department, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, Lisbon, Portugal
| | - José Pedro Vieira
- Neurology Department, Hospital de Dona Estefânia, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Ana Lisa Taylor Tavares
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Health, Genomics England, Queen Mary University of London, Charterhouse Square, London, UK
| | - Carla Ribeiro Conceição
- Neuroradiology Department, Hospital de Dona Estefânia, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Suliman Khan
- Research Data Analysis, CENTOGENE AG, Rostock, Germany
| | | | - Ana Berta Sousa
- Genetics Department, Hospital de Santa Maria, Centro Hospitalar Universitário de Lisboa Norte, Lisbon, Portugal.,Laboratório de Imunologia Básica, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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21
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Abbasi-Moheb L, Westenberger A, Alotaibi M, Alghamdi MA, Hertecant JL, Ariamand A, Beetz C, Rolfs A, Bertoli-Avella AM, Bauer P. Biallelic loss-of-function HACD1 variants are a bona fide cause of congenital myopathy. Clin Genet 2021; 99:513-518. [PMID: 33354762 DOI: 10.1111/cge.13905] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 11/26/2022]
Abstract
Congenital myopathies include a wide range of genetically determined disorders characterized by muscle weakness that usually manifest shortly after birth. To date, two different homozygous loss-of-function variants in the HACD1 gene have been reported to cause congenital myopathy. We identified three patients manifesting with neonatal-onset generalized muscle weakness and motor delay that carried three novel homozygous likely pathogenic HACD1 variants. The two of these changes (c.373_375+2delGAGGT and c.785-1G>T) were predicted to introduce splice site alterations, while one is a nonsense change (c.458G>A). The clinical presentation of our and the previously reported patients was comparable, including the temporally progressive improvement that seems to be characteristic of HACD1-related myopathy. Our findings conclusively confirm the implication of HACD1 in the pathogenesis of congenital myopathies, corroborate the main phenotypic features, and further define the genotypic spectrum of this genetic form of myopathy. Importantly, the genetic diagnosis of HACD1-related myopathy bears impactful prognostic value.
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Affiliation(s)
| | - Ana Westenberger
- CENTOGENE GmbH, Rostock, Germany.,Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Maha Alotaibi
- Department of Genetics and Metabolism, King Saud Medical City, Riyadh, Saudi Arabia
| | - Malak Ali Alghamdi
- Medical Genetic division, Pediatric department, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | | | | | - Arndt Rolfs
- CENTOGENE GmbH, Rostock, Germany.,University of Rostock, Medical Faculty, Rostock, Germany
| | - Aida M Bertoli-Avella
- CENTOGENE GmbH, Rostock, Germany.,University of Rostock, Medical Faculty, Rostock, Germany
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22
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Beetz C, Westenberger A, Al-Ali R, Ameziane N, Alhashmi N, Boustany RM, Al Mutairi F, Alfadhel M, Al-Hassnan Z, AlSayed M, Kandaswamy KK, Paknia O, Skrahina V, Rolfs A, Bauer P. LRRK2 Loss-of-Function Variants in Patients with Rare Diseases: No Evidence for a Phenotypic Impact. Mov Disord 2021; 36:1029-1031. [PMID: 33433017 PMCID: PMC8248088 DOI: 10.1002/mds.28452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
| | - Ana Westenberger
- CENTOGENE GmbH, Rostock, Germany.,Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | | | | | | | - Rose-Mary Boustany
- Neurogenetics Program, AUBMC Special Kids Clinic and Division of Pediatric Neurology, Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon.,Department of Biochemistry and Molecular Genetics, American University of Beirut Medical Center, Beirut, Lebanon
| | - Fuad Al Mutairi
- Genetics and Precision Medicine Department, King Abdullah Specialist Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Genetics and Precision Medicine Department, King Abdullah Specialist Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia
| | - Zuhair Al-Hassnan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Moenaldeen AlSayed
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | | | | | - Arndt Rolfs
- CENTOGENE GmbH, Rostock, Germany.,University of Rostock, Medical Faculty, Rostock, Germany
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23
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Lin YC, Niceta M, Muto V, Vona B, Pagnamenta AT, Maroofian R, Beetz C, van Duyvenvoorde H, Dentici ML, Lauffer P, Vallian S, Ciolfi A, Pizzi S, Bauer P, Grüning NM, Bellacchio E, Del Fattore A, Petrini S, Shaheen R, Tiosano D, Halloun R, Pode-Shakked B, Albayrak HM, Işık E, Wit JM, Dittrich M, Freire BL, Bertola DR, Jorge AAL, Barel O, Sabir AH, Al Tenaiji AMJ, Taji SM, Al-Sannaa N, Al-Abdulwahed H, Digilio MC, Irving M, Anikster Y, Bhavani GSL, Girisha KM, Haaf T, Taylor JC, Dallapiccola B, Alkuraya FS, Yang RB, Tartaglia M. SCUBE3 loss-of-function causes a recognizable recessive developmental disorder due to defective bone morphogenetic protein signaling. Am J Hum Genet 2021; 108:115-133. [PMID: 33308444 PMCID: PMC7820739 DOI: 10.1016/j.ajhg.2020.11.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022] Open
Abstract
Signal peptide-CUB-EGF domain-containing protein 3 (SCUBE3) is a member of a small family of multifunctional cell surface-anchored glycoproteins functioning as co-receptors for a variety of growth factors. Here we report that bi-allelic inactivating variants in SCUBE3 have pleiotropic consequences on development and cause a previously unrecognized syndromic disorder. Eighteen affected individuals from nine unrelated families showed a consistent phenotype characterized by reduced growth, skeletal features, distinctive craniofacial appearance, and dental anomalies. In vitro functional validation studies demonstrated a variable impact of disease-causing variants on transcript processing, protein secretion and function, and their dysregulating effect on bone morphogenetic protein (BMP) signaling. We show that SCUBE3 acts as a BMP2/BMP4 co-receptor, recruits the BMP receptor complexes into raft microdomains, and positively modulates signaling possibly by augmenting the specific interactions between BMPs and BMP type I receptors. Scube3-/- mice showed craniofacial and dental defects, reduced body size, and defective endochondral bone growth due to impaired BMP-mediated chondrogenesis and osteogenesis, recapitulating the human disorder. Our findings identify a human disease caused by defective function of a member of the SCUBE family, and link SCUBE3 to processes controlling growth, morphogenesis, and bone and teeth development through modulation of BMP signaling.
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Affiliation(s)
- Yuh-Charn Lin
- Department of Physiology, School of Medicine, Taipei Medical University, 110301 Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, 115201 Taipei, Taiwan
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Valentina Muto
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; Department of Otolaryngology - Head and Neck Surgery, Eberhard Karls University, 72076 Tübingen, Germany
| | - Alistair T Pagnamenta
- NIHR Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, Cranmer Terrace, SW17 0RE London, UK
| | | | - Hermine van Duyvenvoorde
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Peter Lauffer
- Department of Paediatric Endocrinology, Emma Children's Hospital, Amsterdam University Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Sadeq Vallian
- Department of Cell and Molecular Biology & Microbiology, University of Isfahan, 8174673441 Isfahan, Iran
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Del Fattore
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Research Laboratories, IRCCS Ospedale Pediatrico Bambino Gesù, 00146 Rome, Italy
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, 11211 Riyadh, Saudi Arabia; Qatar Biomedical Research Institute, Hamad Bin Khalifa University, 34110 Doha, Qatar
| | - Dov Tiosano
- Pediatric Endocrinology Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, 352540 Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, 352540 Haifa, Israel
| | - Rana Halloun
- Pediatric Endocrinology Unit, Ruth Rappaport Children's Hospital, Rambam Healthcare Campus, 352540 Haifa, Israel
| | - Ben Pode-Shakked
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, 52621 Tel-Hashomer, Israel; The Sackler Faculty of Medicine, Tel-Aviv University, 6997801 Tel-Aviv, Israel
| | - Hatice Mutlu Albayrak
- Department of Pediatric Endocrinology, Gaziantep Cengiz Gökcek Maternity & Children's Hospital, 27010 Gaziantep, Turkey
| | - Emregül Işık
- Department of Pediatric Endocrinology, Gaziantep Cengiz Gökcek Maternity & Children's Hospital, 27010 Gaziantep, Turkey
| | - Jan M Wit
- Department of Pediatrics, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; Institute of Bioinformatics, Julius Maximilians University, 97070 Würzburg, Germany
| | - Bruna L Freire
- Unidade de Endocrinologia Genética, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, 01246903 Sao Paulo, Brazil
| | - Debora R Bertola
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, 05403000 Sao Paulo, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genética, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, 01246903 Sao Paulo, Brazil
| | - Ortal Barel
- Sheba Cancer Research Center, Sheba Medical Center, 52621 Tel-Hashomer, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, 52621 Tel-Hashomer, Israel
| | - Ataf H Sabir
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, SE1 9RT London, UK; Birmingham Women's and Children's NHS Foundation Trust, University of Birmingham, B4 6NH Birmingham, UK
| | - Amal M J Al Tenaiji
- Department of Paediatrics, Sheikh Khalifa Medical City, 51900 Abu Dhabi, United Arab Emirates
| | - Sulaima M Taji
- Department of Paediatrics, Sheikh Khalifa Medical City, 51900 Abu Dhabi, United Arab Emirates
| | | | | | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Melita Irving
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, SE1 9RT London, UK
| | - Yair Anikster
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, 52621 Tel-Hashomer, Israel; The Sackler Faculty of Medicine, Tel-Aviv University, 6997801 Tel-Aviv, Israel; Wohl Institute for Translational Medicine, Sheba Medical Center, 52621 Tel-Hashomer, Israel
| | - Gandham S L Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Jenny C Taylor
- NIHR Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, 11211 Riyadh, Saudi Arabia
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, 115201 Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, 110301 Taipei, Taiwan; Institute of Pharmacology, School of Medicine, National Yang-Ming University, 112304, Taipei, Taiwan.
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
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24
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Neuray C, Maroofian R, Scala M, Sultan T, Pai GS, Mojarrad M, Khashab HE, deHoll L, Yue W, Alsaif HS, Zanetti MN, Bello O, Person R, Eslahi A, Khazaei Z, Feizabadi MH, Efthymiou S, El-Bassyouni HT, Soliman DR, Tekes S, Ozer L, Baltaci V, Khan S, Beetz C, Amr KS, Salpietro V, Jamshidi Y, Alkuraya FS, Houlden H. Early-infantile onset epilepsy and developmental delay caused by bi-allelic GAD1 variants. Brain 2020; 143:2388-2397. [PMID: 32705143 PMCID: PMC7447512 DOI: 10.1093/brain/awaa178] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 01/31/2023] Open
Abstract
Gamma-aminobutyric acid (GABA) and glutamate are the most abundant amino acid neurotransmitters in the brain. GABA, an inhibitory neurotransmitter, is synthesized by glutamic acid decarboxylase (GAD). Its predominant isoform GAD67, contributes up to ∼90% of base-level GABA in the CNS, and is encoded by the GAD1 gene. Disruption of GAD1 results in an imbalance of inhibitory and excitatory neurotransmitters, and as Gad1-/- mice die neonatally of severe cleft palate, it has not been possible to determine any potential neurological dysfunction. Furthermore, little is known about the consequence of GAD1 disruption in humans. Here we present six affected individuals from six unrelated families, carrying bi-allelic GAD1 variants, presenting with developmental and epileptic encephalopathy, characterized by early-infantile onset epilepsy and hypotonia with additional variable non-CNS manifestations such as skeletal abnormalities, dysmorphic features and cleft palate. Our findings highlight an important role for GAD1 in seizure induction, neuronal and extraneuronal development, and introduce GAD1 as a new gene associated with developmental and epileptic encephalopathy.
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Affiliation(s)
- Caroline Neuray
- UCL Queen Square Institute of Neurology, University College London, London, UK.,Department of Neurology, Christian Doppler Klinik, Paracelsus Medical University, Salzburg, Austria
| | - Reza Maroofian
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Marcello Scala
- UCL Queen Square Institute of Neurology, University College London, London, UK.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Tipu Sultan
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore, Pakistan
| | | | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Genetic Center of Khorasan Razavi, Mashhad, Iran
| | - Heba El Khashab
- Department of Pediatrics, Children's Hospital, Ain Shams University, Cairo, Egypt.,Department of Pediatrics, Dr. Suliman Al Habib Medical Group, Riyadh, Saudi Arabia
| | | | - Wyatt Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, UK
| | - Hessa S Alsaif
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maria N Zanetti
- Department of Clinical and Experimental Epilepsy, University College London, London, UK
| | - Oscar Bello
- Department of Clinical and Experimental Epilepsy, University College London, London, UK
| | | | - Atieh Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Masoumeh H Feizabadi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Stephanie Efthymiou
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | | | | | - Doaa R Soliman
- Department of Pediatrics, Faculty of Medicine, Benha University, Benha, Egypt
| | - Selahattin Tekes
- Dicle University, School of Medicine, Department of Medical Genetics, Diyarbakir, Turkey
| | - Leyla Ozer
- Yuksek Ihtisas University, School of Medicine, Department of Medical Genetics, Ankara, Turkey
| | | | | | | | - Khalda S Amr
- Molecular Genetics Department, National Research Centre, Cairo, Egypt
| | - Vincenzo Salpietro
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Yalda Jamshidi
- Molecular and Clinical Sciences Institute St George's, University of London, UK
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center Riyadh, Saudi Arabia
| | - Henry Houlden
- UCL Queen Square Institute of Neurology, University College London, London, UK
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25
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A novel homozygous variant in the TRAPPC9 gene causing intellectual disability and autism Spectrum disorder. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Genomic testing in 1019 individuals from 349 Pakistani families results in high diagnostic yield and clinical utility. NPJ Genom Med 2020; 5:44. [PMID: 33083013 PMCID: PMC7536406 DOI: 10.1038/s41525-020-00150-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/06/2020] [Indexed: 11/08/2022] Open
Abstract
We implemented a collaborative diagnostic program in Lahore (Pakistan) aiming to establish the genetic diagnosis, and to asses diagnostic yield and clinical impact in patients with suspected genetic diseases. Local physicians ascertained pediatric patients who had no previous access to genetic testing. More than 1586 genetic tests were performed in 1019 individuals (349 index cases, 670 relatives). Most frequently performed tests were exome/genome sequencing (ES/GS, 284/78 index cases) and specific gene panels (55 index cases). In 61.3% of the patients (n = 214) a genetic diagnosis was established based on pathogenic and likely pathogenic variants. Diagnostic yield was higher in consanguineous families (60.1 vs. 39.5%). In 27 patients, genetic diagnosis relied on additional biochemical testing, allowing rapid assessment of the functional effect of the variants. Remarkably, the genetic diagnosis had a direct impact on clinical management. Most relevant consequences were therapy related such as initiation of the appropriated treatment in a timely manner in 51.9% of the patients (n = 111). Finally, we report 12 candidate genes among 66 cases with no genetic diagnosis. Importantly, three of these genes were validated as 'diagnostic' genes given the strong evidence supporting causality derived from our data repository (CAP2-dilated cardiomyopathy, ITFG2-intellectual disability and USP53-liver cholestasis). The high diagnostic yield, clinical impact, and research findings demonstrate the utility of genomic testing, especially when used as first-line genetic test. For patients with suspected genetic diseases from resource-limited regions, ES can be considered as the test of choice to achieve genetic diagnosis.
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27
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A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome. Eur J Hum Genet 2020; 29:271-279. [PMID: 32901138 DOI: 10.1038/s41431-020-00717-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/01/2020] [Accepted: 08/21/2020] [Indexed: 11/08/2022] Open
Abstract
Trafficking protein particle (TRAPP) complexes, which include the TRAPPC4 protein, regulate membrane trafficking between lipid organelles in a process termed vesicular tethering. TRAPPC4 was recently implicated in a recessive neurodevelopmental condition in four unrelated families due to a shared c.454+3A>G splice variant. Here, we report 23 patients from 17 independent families with an early-infantile-onset neurodegenerative presentation, where we also identified the homozygous variant hg38:11:119020256 A>G (NM_016146.5:c.454+3A>G) in TRAPPC4 through exome or genome sequencing. No other clinically relevant TRAPPC4 variants were identified among any of over 10,000 patients with neurodevelopmental conditions. We found the carrier frequency of TRAPPC4 c.454+3A>G was 2.4-5.4 per 10,000 healthy individuals. Affected individuals with the homozygous TRAPPC4 c.454+3A>G variant showed profound psychomotor delay, developmental regression, early-onset epilepsy, microcephaly and progressive spastic tetraplegia. Based upon RNA sequencing, the variant resulted in partial exon 3 skipping and generation of an aberrant transcript owing to use of a downstream cryptic splice donor site, predicting a premature stop codon and nonsense mediated decay. These data confirm the pathogenicity of the TRAPPC4 c.454+3A>G variant, and refine the clinical presentation of TRAPPC4-related encephalopathy.
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28
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Maroofian R, Sedmík J, Mazaheri N, Scala M, Zaki MS, Keegan LP, Azizimalamiri R, Issa M, Shariati G, Sedaghat A, Beetz C, Bauer P, Galehdari H, O'Connell MA, Houlden H. Biallelic variants in ADARB1, encoding a dsRNA-specific adenosine deaminase, cause a severe developmental and epileptic encephalopathy. J Med Genet 2020; 58:495-504. [PMID: 32719099 PMCID: PMC8327408 DOI: 10.1136/jmedgenet-2020-107048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/20/2020] [Accepted: 06/05/2020] [Indexed: 11/08/2022]
Abstract
BACKGROUND Adenosine-to-inosine RNA editing is a co-transcriptional/post-transcriptional modification of double-stranded RNA, catalysed by one of two active adenosine deaminases acting on RNA (ADARs), ADAR1 and ADAR2. ADARB1 encodes the enzyme ADAR2 that is highly expressed in the brain and essential to modulate the function of glutamate and serotonin receptors. Impaired ADAR2 editing causes early onset progressive epilepsy and premature death in mice. In humans, ADAR2 dysfunction has been very recently linked to a neurodevelopmental disorder with microcephaly and epilepsy in four unrelated subjects. METHODS We studied three children from two consanguineous families with severe developmental and epileptic encephalopathy (DEE) through detailed physical and instrumental examinations. Exome sequencing (ES) was used to identify ADARB1 mutations as the underlying genetic cause and in vitro assays with transiently transfected cells were performed to ascertain the impact on ADAR2 enzymatic activity and splicing. RESULTS All patients showed global developmental delay, intractable early infantile-onset seizures, microcephaly, severe-to-profound intellectual disability, axial hypotonia and progressive appendicular spasticity. ES revealed the novel missense c.1889G>A, p.(Arg630Gln) and deletion c.1245_1247+1 del, p.(Leu415PhefsTer14) variants in ADARB1 (NM_015833.4). The p.(Leu415PhefsTer14) variant leads to incorrect splicing resulting in frameshift with a premature stop codon and loss of enzyme function. In vitro RNA editing assays showed that the p.(Arg630Gln) variant resulted in a severe impairment of ADAR2 enzymatic activity. CONCLUSION In conclusion, these data support the pathogenic role of biallelic ADARB1 variants as the cause of a distinctive form of DEE, reinforcing the importance of RNA editing in brain function and development.
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Affiliation(s)
- Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Jiří Sedmík
- CEITEC, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Neda Mazaheri
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Marcello Scala
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genova, Italy
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Liam P Keegan
- CEITEC, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Reza Azizimalamiri
- Department of Paediatric Neurology, Golestan, Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Behbahan, Iran
| | - Mahmoud Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Gholamreza Shariati
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Behbahan, Iran
| | - Alireza Sedaghat
- Health Research Institute, Diabetes Research Center, Ahvaz Jundishapur University of medical Sciences, Ahvaz, Iran
| | | | | | - Hamid Galehdari
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mary A O'Connell
- CEITEC, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
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Massadeh S, Alhashem A, van de Laar IMBH, Alhabshan F, Ordonez N, Alawbathani S, Khan S, Kabbani MS, Chaikhouni F, Sheereen A, Almohammed I, Alghamdi B, Frohn-Mulder I, Ahmad S, Beetz C, Bauer P, Wessels MW, Alaamery M, Bertoli-Avella AM. ADAMTS19-associated heart valve defects: Novel genetic variants consolidating a recognizable cardiac phenotype. Clin Genet 2020; 98:56-63. [PMID: 32323311 DOI: 10.1111/cge.13760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 11/29/2022]
Abstract
Recently, ADAMTS19 was identified as a novel causative gene for autosomal recessive heart valve disease (HVD), affecting mainly the aortic and pulmonary valves. Exome sequencing and data repository (CentoMD) analyses were performed to identify patients with ADAMTS19 variants (two families). A third family was recognized based on cardiac phenotypic similarities and SNP array homozygosity. Three novel loss of function (LoF) variants were identified in six patients from three families. Clinically, all patients presented anomalies of the aortic/pulmonary valves, which included thickening of valve leaflets, stenosis and insufficiency. Three patients had (recurrent) subaortic membrane, suggesting that ADAMTS19 is the first gene identified related to discrete subaortic stenosis. One case presented a bi-commissural pulmonary valve. All patients displayed some degree of atrioventricular valve insufficiency. Other cardiac anomalies included atrial/ventricular septal defects, persistent ductus arteriosus, and mild dilated ascending aorta. Our findings confirm that biallelic LoF variants in ADAMTS19 are causative of a specific and recognizable cardiac phenotype. We recommend considering ADAMTS19 genetic testing in all patients with multiple semilunar valve abnormalities, particularly in the presence of subaortic membrane. ADAMTS19 screening in patients with semilunar valve abnormalities is needed to estimate the frequency of the HVD related phenotype, which might be not so rare.
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Affiliation(s)
- Salam Massadeh
- Department of Developmental Medicine, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,The Joint Center of Excellence for Biomedicine Between King Abdulaziz City for Science and Technology (KACST) and Brigham & Women's Hospital (BWH), Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Amal Alhashem
- Division of Pediatric Genetics, Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.,Department of Anatomy and Cell biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Fahad Alhabshan
- Department of Cardiac Sciences, Ministry of the National Guard-Health Affairs, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | | | | | - Mohamed S Kabbani
- Department of Cardiac Sciences, Ministry of the National Guard-Health Affairs, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Farah Chaikhouni
- Department of Cardiac Sciences, Ministry of the National Guard-Health Affairs, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Atia Sheereen
- Department of Developmental Medicine, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Iman Almohammed
- Department of Developmental Medicine, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,The Joint Center of Excellence for Biomedicine Between King Abdulaziz City for Science and Technology (KACST) and Brigham & Women's Hospital (BWH), Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Bader Alghamdi
- Department of Developmental Medicine, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Ingrid Frohn-Mulder
- Department of Pediatric Cardiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Salim Ahmad
- Prince Sultan Cardiac Center, Prince Sultan Military Medical City, Riyad, Saudi Arabia
| | | | | | - Marja W Wessels
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Manal Alaamery
- Department of Developmental Medicine, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,The Joint Center of Excellence for Biomedicine Between King Abdulaziz City for Science and Technology (KACST) and Brigham & Women's Hospital (BWH), Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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