1
|
Mitscherling J, Sczakiel HL, Kiskemper-Nestorjuk O, Winterhalter S, Mundlos S, Bartzela T, Mensah MA. Whole genome sequencing in families with oligodontia. Oral Dis 2024; 30:3935-3950. [PMID: 38071191 DOI: 10.1111/odi.14816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/22/2023] [Accepted: 11/10/2023] [Indexed: 09/03/2024]
Abstract
BACKGROUND/OBJECTIVES Tooth agenesis (TA) is among the most common malformations in humans. Although several causative mutations have been described, the genetic cause often remains elusive. Here, we test whether whole genome sequencing (WGS) could bridge this diagnostic gap. METHODS In four families with TA, we assessed the dental phenotype using the Tooth Agenesis Code after intraoral examination and radiographic and photographic documentation. We performed WGS of index patients and subsequent segregation analysis. RESULTS We identified two variants of uncertain significance (a potential splice variant in PTH1R, and a 2.1 kb deletion abrogating a non-coding element in FGF7) and three pathogenic variants: a novel frameshift in the final exon of PITX2, a novel deletion in PAX9, and a known nonsense variant in WNT10A. Notably, the FGF7 variant was found in the patient, also featuring the WNT10A variant. While mutations in PITX2 are known to cause Axenfeld-Rieger syndrome 1 (ARS1) predominantly featuring ocular findings, accompanied by dental malformations, we found the PITX2 frameshift in a family with predominantly dental and varying ocular findings. CONCLUSION Severe TA predicts a genetic cause identifiable by WGS. Final exon PITX2 frameshifts can cause a predominantly dental form of ARS1.
Collapse
Affiliation(s)
- Janna Mitscherling
- Department of Orthodontics and Dentofacial Orthopedics, Charité - Centrum 03 für Zahn-, Mund- und Kieferheilkunde, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, und Berlin Institute of Health, Berlin, Germany
| | - Henrike L Sczakiel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Junior Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Olga Kiskemper-Nestorjuk
- Department of Orthodontics and Dentofacial Orthopedics, Charité - Centrum 03 für Zahn-, Mund- und Kieferheilkunde, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, und Berlin Institute of Health, Berlin, Germany
| | - Sibylle Winterhalter
- Department of Ophthalmology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Theodosia Bartzela
- Department of Orthodontics and Dentofacial Orthopedics, Charité - Centrum 03 für Zahn-, Mund- und Kieferheilkunde, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, und Berlin Institute of Health, Berlin, Germany
- Department of Orthodontics, Technische Universität Dresden, Dresden, Germany
| | - Martin A Mensah
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- BIH Biomedical Innovation Academy, Digital Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
2
|
Arlt A, Knaus A, Hsieh TC, Klinkhammer H, Bhasin MA, Hustinx A, Moosa S, Krawitz P, Ekure E. Next-generation phenotyping in Nigerian children with Cornelia de Lange syndrome. Am J Med Genet A 2024; 194:e63641. [PMID: 38725242 DOI: 10.1002/ajmg.a.63641] [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: 02/08/2024] [Revised: 03/29/2024] [Accepted: 04/11/2024] [Indexed: 08/10/2024]
Abstract
Next-generation phenotyping (NGP) can be used to compute the similarity of dysmorphic patients to known syndromic diseases. So far, the technology has been evaluated in variant prioritization and classification, providing evidence for pathogenicity if the phenotype matched with other patients with a confirmed molecular diagnosis. In a Nigerian cohort of individuals with facial dysmorphism, we used the NGP tool GestaltMatcher to screen portraits prior to genetic testing and subjected individuals with high similarity scores to exome sequencing (ES). Here, we report on two individuals with global developmental delay, pulmonary artery stenosis, and genital and limb malformations for whom GestaltMatcher yielded Cornelia de Lange syndrome (CdLS) as the top hit. ES revealed a known pathogenic nonsense variant, NM_133433.4: c.598C>T; p.(Gln200*), as well as a novel frameshift variant c.7948dup; p.(Ile2650Asnfs*11) in NIPBL. Our results suggest that NGP can be used as a screening tool and thresholds could be defined for achieving high diagnostic yields in ES. Training the artificial intelligence (AI) with additional cases of the same ethnicity might further increase the positive predictive value of GestaltMatcher.
Collapse
Affiliation(s)
- Annabelle Arlt
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Meghna Ahuja Bhasin
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Alexander Hustinx
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Stellenbosch University and Medical Genetics, Tygerberg Hospital, Cape Town, South Africa
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - Ekanem Ekure
- Faculty of Clinical Sciences, Department of Pediatrics, College of Medicine, University of Lagos, Lagos, Nigeria
| |
Collapse
|
3
|
Schmidt A, Danyel M, Grundmann K, Brunet T, Klinkhammer H, Hsieh TC, Engels H, Peters S, Knaus A, Moosa S, Averdunk L, Boschann F, Sczakiel HL, Schwartzmann S, Mensah MA, Pantel JT, Holtgrewe M, Bösch A, Weiß C, Weinhold N, Suter AA, Stoltenburg C, Neugebauer J, Kallinich T, Kaindl AM, Holzhauer S, Bührer C, Bufler P, Kornak U, Ott CE, Schülke M, Nguyen HHP, Hoffjan S, Grasemann C, Rothoeft T, Brinkmann F, Matar N, Sivalingam S, Perne C, Mangold E, Kreiss M, Cremer K, Betz RC, Mücke M, Grigull L, Klockgether T, Spier I, Heimbach A, Bender T, Brand F, Stieber C, Morawiec AM, Karakostas P, Schäfer VS, Bernsen S, Weydt P, Castro-Gomez S, Aziz A, Grobe-Einsler M, Kimmich O, Kobeleva X, Önder D, Lesmann H, Kumar S, Tacik P, Basin MA, Incardona P, Lee-Kirsch MA, Berner R, Schuetz C, Körholz J, Kretschmer T, Di Donato N, Schröck E, Heinen A, Reuner U, Hanßke AM, Kaiser FJ, Manka E, Munteanu M, Kuechler A, Cordula K, Hirtz R, Schlapakow E, Schlein C, Lisfeld J, Kubisch C, Herget T, Hempel M, Weiler-Normann C, Ullrich K, Schramm C, Rudolph C, Rillig F, Groffmann M, Muntau A, Tibelius A, Schwaibold EMC, Schaaf CP, Zawada M, Kaufmann L, Hinderhofer K, Okun PM, Kotzaeridou U, Hoffmann GF, Choukair D, Bettendorf M, Spielmann M, Ripke A, Pauly M, Münchau A, Lohmann K, Hüning I, Hanker B, Bäumer T, Herzog R, Hellenbroich Y, Westphal DS, Strom T, Kovacs R, Riedhammer KM, Mayerhanser K, Graf E, Brugger M, Hoefele J, Oexle K, Mirza-Schreiber N, Berutti R, Schatz U, Krenn M, Makowski C, Weigand H, Schröder S, Rohlfs M, Vill K, Hauck F, Borggraefe I, Müller-Felber W, Kurth I, Elbracht M, Knopp C, Begemann M, Kraft F, Lemke JR, Hentschel J, Platzer K, Strehlow V, Abou Jamra R, Kehrer M, Demidov G, Beck-Wödl S, Graessner H, Sturm M, Zeltner L, Schöls LJ, Magg J, Bevot A, Kehrer C, Kaiser N, Turro E, Horn D, Grüters-Kieslich A, Klein C, Mundlos S, Nöthen M, Riess O, Meitinger T, Krude H, Krawitz PM, Haack T, Ehmke N, Wagner M. Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings. Nat Genet 2024; 56:1644-1653. [PMID: 39039281 PMCID: PMC11319204 DOI: 10.1038/s41588-024-01836-1] [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: 07/19/2023] [Accepted: 06/18/2024] [Indexed: 07/24/2024]
Abstract
Individuals with ultrarare disorders pose a structural challenge for healthcare systems since expert clinical knowledge is required to establish diagnoses. In TRANSLATE NAMSE, a 3-year prospective study, we evaluated a novel diagnostic concept based on multidisciplinary expertise in Germany. Here we present the systematic investigation of the phenotypic and molecular genetic data of 1,577 patients who had undergone exome sequencing and were partially analyzed with next-generation phenotyping approaches. Molecular genetic diagnoses were established in 32% of the patients totaling 370 distinct molecular genetic causes, most with prevalence below 1:50,000. During the diagnostic process, 34 novel and 23 candidate genotype-phenotype associations were identified, mainly in individuals with neurodevelopmental disorders. Sequencing data of the subcohort that consented to computer-assisted analysis of their facial images with GestaltMatcher could be prioritized more efficiently compared with approaches based solely on clinical features and molecular scores. Our study demonstrates the synergy of using next-generation sequencing and phenotyping for diagnosing ultrarare diseases in routine healthcare and discovering novel etiologies by multidisciplinary teams.
Collapse
Affiliation(s)
- Axel Schmidt
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Magdalena Danyel
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kathrin Grundmann
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
- Institut für Medizinische Biometrie, Informatik und Epidemiologie, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Shahida Moosa
- Institute for Medical Genetics, Stellenbosch University, Cape Town, South Africa
| | - Luisa Averdunk
- Department of Pediatrics, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Felix Boschann
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Henrike Lisa Sczakiel
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sarina Schwartzmann
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Atta Mensah
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jean Tori Pantel
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Manuel Holtgrewe
- Core Uni Bioinformatics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Annemarie Bösch
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Weiß
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Weinhold
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Aude-Annick Suter
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Corinna Stoltenburg
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Neugebauer
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tillmann Kallinich
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Angela M Kaindl
- Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute of Cell and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Holzhauer
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Bührer
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philip Bufler
- Department of Pediatrics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Uwe Kornak
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Claus-Eric Ott
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Schülke
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Sabine Hoffjan
- Department of Human Genetics, Ruhr University Bochum, Bochum, Germany
| | - Corinna Grasemann
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Tobias Rothoeft
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Folke Brinkmann
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Nora Matar
- Department of Pediatrics Bochum and CeSER, Ruhr University Bochum, Bochum, Germany
| | - Sugirthan Sivalingam
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Claudia Perne
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Martina Kreiss
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Martin Mücke
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Lorenz Grigull
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Thomas Klockgether
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Tim Bender
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Fabian Brand
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Christiane Stieber
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Alexandra Marzena Morawiec
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Pantelis Karakostas
- Clinic for Internal Medicine III, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Valentin S Schäfer
- Clinic for Internal Medicine III, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sarah Bernsen
- Center for Rare Diseases, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Patrick Weydt
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sergio Castro-Gomez
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Ahmad Aziz
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Marcus Grobe-Einsler
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Okka Kimmich
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Xenia Kobeleva
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Demet Önder
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Hellen Lesmann
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Sheetal Kumar
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Pawel Tacik
- Department of Neurology, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Meghna Ahuja Basin
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Pietro Incardona
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Min Ae Lee-Kirsch
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Reinhard Berner
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Catharina Schuetz
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Julia Körholz
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Tanita Kretschmer
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Nataliya Di Donato
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Evelin Schröck
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - André Heinen
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Ulrike Reuner
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
- Department of Neurology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Amalia-Mihaela Hanßke
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Eva Manka
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - Martin Munteanu
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Kiewert Cordula
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - Raphael Hirtz
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - Elena Schlapakow
- Department of Neurology, University Hospital Halle, Halle, Germany
| | - Christian Schlein
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Jasmin Lisfeld
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Christina Weiler-Normann
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Kurt Ullrich
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Schramm
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Cornelia Rudolph
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Franziska Rillig
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Groffmann
- Martin Zeitz Center for Rare Diseases, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Ania Muntau
- Department of Pediatrics, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Michal Zawada
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Pamela M Okun
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Urania Kotzaeridou
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Center for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Annekatrin Ripke
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Martje Pauly
- Department of Neurology, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute for Neurogenetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Alexander Münchau
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Systems Motor Science, University of Lübeck, Lübeck, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Irina Hüning
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Britta Hanker
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Tobias Bäumer
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Systems Motor Science, University of Lübeck, Lübeck, Germany
| | - Rebecca Herzog
- Center for Rare Diseases, University Hospital Schleswig-Holstein, Lübeck, Germany
- Department of Neurology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Yorck Hellenbroich
- Department of Human Genetics, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Dominik S Westphal
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Tim Strom
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Reka Kovacs
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
- Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Konrad Oexle
- Institute of Neurogenomics, Helmholtz Zentrum München, München, Germany
| | | | - Riccardo Berutti
- Institute of Neurogenomics, Helmholtz Zentrum München, München, Germany
| | - Ulrich Schatz
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Martin Krenn
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
- Department of Neurology, Medical University of Vienna, Wien, Austria
| | - Christine Makowski
- Department of Paediatrics, Adolescent Medicine and Neonatology, München, Germany
| | - Heike Weigand
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Sebastian Schröder
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Meino Rohlfs
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Katharina Vill
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Fabian Hauck
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Ingo Borggraefe
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | | | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Cordula Knopp
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Martin Kehrer
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - German Demidov
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stefanie Beck-Wödl
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Holm Graessner
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Lena Zeltner
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Ludger J Schöls
- Department of Neurology, University of Tübingen, Tübingen, Germany
| | - Janine Magg
- Center for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Andrea Bevot
- Department of Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | - Christiane Kehrer
- Department of Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | - Nadja Kaiser
- Department of Pediatric Neurology and Developmental Medicine, University of Tübingen, Tübingen, Germany
| | - Ernest Turro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Christoph Klein
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Olaf Riess
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
| | - Heiko Krude
- Berlin Centre for Rare Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany.
| | - Tobias Haack
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nadja Ehmke
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
- BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, München, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, München, Germany
- Dr. von Hauner Children's Hospital, University Hospital Munich, München, Germany
| |
Collapse
|
4
|
Pozojevic J, Sivaprasad R, Laß J, Haarich F, Trinh J, Kakar N, Schulz K, Händler K, Verrijn Stuart AA, Giltay JC, van Gassen KL, Caliebe A, Holterhus PM, Spielmann M, Hornig NC. LINE1-mediated epigenetic repression of androgen receptor transcription causes androgen insensitivity syndrome. Sci Rep 2024; 14:16302. [PMID: 39009627 PMCID: PMC11251026 DOI: 10.1038/s41598-024-65439-w] [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: 03/11/2024] [Accepted: 06/20/2024] [Indexed: 07/17/2024] Open
Abstract
Androgen insensitivity syndrome (AIS) is a difference of sex development (DSD) characterized by different degrees of undervirilization in individuals with a 46,XY karyotype despite normal to high gonadal testosterone production. Classically, AIS is explained by hemizygous mutations in the X-chromosomal androgen receptor (AR) gene. Nevertheless, the majority of individuals with clinically diagnosed AIS do not carry an AR gene mutation. Here, we present a patient with a 46,XY karyotype, born with undervirilized genitalia, age-appropriate testosterone levels and no uterus, characteristic for AIS. Diagnostic whole exome sequencing (WES) showed a maternally inherited LINE1 (L1) retrotransposon insertion in the 5' untranslated region (5'UTR) of the AR gene. Long-read nanopore sequencing confirmed this as an insertion of a truncated L1 element of ≈ 2.7 kb and showed an increased DNA methylation at the L1 insertion site in patient-derived genital skin fibroblasts (GSFs) compared to healthy controls. The insertion coincided with reduced AR transcript and protein levels in patient-derived GSFs confirming the clinical diagnosis AIS. Our results underline the relevance of retrotransposons in human disease, and expand the growing list of human diseases associated with them.
Collapse
Affiliation(s)
- Jelena Pozojevic
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany.
| | - Radhika Sivaprasad
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Joshua Laß
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Franziska Haarich
- Institute of Cardiogenetics, University of Lübeck and German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Naseebullah Kakar
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Department of Biotechnology, FLS&I, BUITEMS, Quetta, Pakistan
| | - Kristin Schulz
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Kristian Händler
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Annemarie A Verrijn Stuart
- Department of Pediatric Endocrinology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jacques C Giltay
- Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen L van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Almuth Caliebe
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Paul-Martin Holterhus
- Division of Paediatric Endocrinology and Diabetes, Department of Paediatrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Nadine C Hornig
- Institute of Human Genetics, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany.
| |
Collapse
|
5
|
Hramyka D, Sczakiel HL, Zhao MX, Stolpe O, Nieminen M, Adam R, Danyel M, Einicke L, Hägerling R, Knaus A, Mundlos S, Schwartzmann S, Seelow D, Ehmke N, Mensah M, Boschann F, Beule D, Holtgrewe M. REEV: review, evaluate and explain variants. Nucleic Acids Res 2024; 52:W148-W158. [PMID: 38769069 PMCID: PMC11223839 DOI: 10.1093/nar/gkae366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/07/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In the era of high throughput sequencing, special software is required for the clinical evaluation of genetic variants. We developed REEV (Review, Evaluate and Explain Variants), a user-friendly platform for clinicians and researchers in the field of rare disease genetics. Supporting data was aggregated from public data sources. We compared REEV with seven other tools for clinical variant evaluation. REEV (semi-)automatically fills individual ACMG criteria facilitating variant interpretation. REEV can store disease and phenotype data related to a case to use these for phenotype similarity measures. Users can create public permanent links for individual variants that can be saved as browser bookmarks and shared. REEV may help in the fast diagnostic assessment of genetic variants in a clinical as well as in a research context. REEV (https://reev.bihealth.org/) is free and open to all users and there is no login requirement.
Collapse
Affiliation(s)
- Dzmitry Hramyka
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Henrike Lisa Sczakiel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Max Xiaohang Zhao
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Oliver Stolpe
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Mikko Nieminen
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Ronja Adam
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Magdalena Danyel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lara Einicke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - René Hägerling
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health, BIH Center for Regenerative Therapies, Berlin, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sarina Schwartzmann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Martin Atta Mensah
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Digital Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| |
Collapse
|
6
|
Kopp J, Koch LA, Lyubenova H, Küchler O, Holtgrewe M, Ivanov A, Dubourg C, Launay E, Brachs S, Mundlos S, Ehmke N, Seelow D, Fradin M, Kornak U, Fischer-Zirnsak B. Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy. Hum Genet 2024; 143:683-694. [PMID: 38592547 PMCID: PMC11098864 DOI: 10.1007/s00439-024-02669-y] [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: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
Generalized lipodystrophy is a feature of various hereditary disorders, often leading to a progeroid appearance. In the present study we identified a missense and a frameshift variant in a compound heterozygous state in SUPT7L in a boy with intrauterine growth retardation, generalized lipodystrophy, and additional progeroid features. SUPT7L encodes a component of the transcriptional coactivator complex STAGA. By transcriptome sequencing, we showed the predicted missense variant to cause aberrant splicing, leading to exon truncation and thereby to a complete absence of SUPT7L in dermal fibroblasts. In addition, we found altered expression of genes encoding DNA repair pathway components. This pathway was further investigated and an increased rate of DNA damage was detected in proband-derived fibroblasts and genome-edited HeLa cells. Finally, we performed transient overexpression of wildtype SUPT7L in both cellular systems, which normalizes the number of DNA damage events. Our findings suggest SUPT7L as a novel disease gene and underline the link between genome instability and progeroid phenotypes.
Collapse
Affiliation(s)
- Johannes Kopp
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Leonard A Koch
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
| | - Hristiana Lyubenova
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Oliver Küchler
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andranik Ivanov
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christele Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, F-35033, France
- Univercity Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, F-35000, France
| | - Erika Launay
- Service de Cytogénétique et Biologie cellulaire, Hôpital Pontchaillou - CHU Rennes, 2 rue Henri Le Guilloux - Rennes cedex 9, France, Rennes, F-35033, France
| | - Sebastian Brachs
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
- German Centre for Cardiovascular Research, partner site Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Exploratory Diagnostic Sciences, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mélanie Fradin
- Service de Génétique Clinique, Centre Référence Déficiences Intellectuelles CRDI, Hôpital Sud - CHU Rennes, 16 boulevard de Bulgarie - BP 90347, Rennes cedex 2, Rennes, F-35203, France
- Service de Génétique, CH Saint Brieuc, St Brieuc, 22000, France
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, 13353, Berlin, Germany.
- Max Planck Institute for Molecular Genetics, FG Development and Disease, Berlin, Germany.
| |
Collapse
|
7
|
Schwartzmann S, Zhao M, Sczakiel HL, Hildebrand G, Ehmke N, Horn D, Mensah MA, Boschann F. RNA analysis and computer-aided facial phenotyping help to classify a novel TRIO splice site variant. Am J Med Genet A 2024:e63599. [PMID: 38517182 DOI: 10.1002/ajmg.a.63599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/26/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Pathogenic variants in TRIO, encoding the guanine nucleotide exchange factor, are associated with two distinct neurodevelopmental delay phenotypes: gain-of-function missense mutations within the spectrin repeats are causative for a severe developmental delay with macrocephaly (MIM: 618825), whereas loss-of-function missense variants in the GEF1 domain and truncating variants throughout the gene lead to a milder developmental delay and microcephaly (MIM: 617061). In three affected family members with mild intellectual disability/NDD and microcephaly, we detected a novel heterozygous TRIO variant at the last coding base of exon 31 (NM_007118.4:c.4716G>A). RNA analysis from patient-derived lymphoblastoid cells confirmed aberrant splicing resulting in the skipping of exon 31 (r.4615_4716del), leading to an in-frame deletion in the first Pleckstrin homology subdomain of the GEF1 domain: p.(Thr1539_Lys1572del). To test for a distinct gestalt, facial characteristics of the family members and 41 previously published TRIO cases were systematically evaluated via GestaltMatcher. Computational analysis of the facial gestalt suggests a distinguishable facial TRIO-phenotype not outlined in the existing literature.
Collapse
Affiliation(s)
- Sarina Schwartzmann
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Max Zhao
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Henrike Lisa Sczakiel
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Berlin, Germany
| | - Gabriele Hildebrand
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Nadja Ehmke
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Denise Horn
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Martin A Mensah
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Berlin, Germany
| | - Felix Boschann
- Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité, Clinician Scientist Program, Berlin, Germany
| |
Collapse
|
8
|
Bhasin MA, Knaus A, Incardona P, Schmid A, Holtgrewe M, Elbracht M, Krawitz PM, Hsieh TC. Enhancing Variant Prioritization in VarFish through On-Premise Computational Facial Analysis. Genes (Basel) 2024; 15:370. [PMID: 38540429 PMCID: PMC10969976 DOI: 10.3390/genes15030370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/03/2024] [Accepted: 03/13/2024] [Indexed: 06/14/2024] Open
Abstract
Genomic variant prioritization is crucial for identifying disease-associated genetic variations. Integrating facial and clinical feature analyses into this process enhances performance. This study demonstrates the integration of facial analysis (GestaltMatcher) and Human Phenotype Ontology analysis (CADA) within VarFish, an open-source variant analysis framework. Challenges related to non-open-source components were addressed by providing an open-source version of GestaltMatcher, facilitating on-premise facial analysis to address data privacy concerns. Performance evaluation on 163 patients recruited from a German multi-center study of rare diseases showed PEDIA's superior accuracy in variant prioritization compared to individual scores. This study highlights the importance of further benchmarking and future integration of advanced facial analysis approaches aligned with ACMG guidelines to enhance variant classification.
Collapse
Affiliation(s)
- Meghna Ahuja Bhasin
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
| | - Pietro Incardona
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Alexander Schmid
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
| | - Manuel Holtgrewe
- CUBI—Core Unit Bioinformatics, Berlin Institute of Health, 10117 Berlin, Germany;
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, 52062 Aachen, Germany;
| | - Peter M. Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany; (M.A.B.); (A.K.); (P.I.); (A.S.); (P.M.K.)
| |
Collapse
|
9
|
Koparir A, Lekszas C, Keseroglu K, Rose T, Rappl L, Rad A, Maroofian R, Narendran N, Hasanzadeh A, Karimiani EG, Boschann F, Kornak U, Klopocki E, Özbudak EM, Vona B, Haaf T, Liedtke D. Zebrafish as a model to investigate a biallelic gain-of-function variant in MSGN1, associated with a novel skeletal dysplasia syndrome. Hum Genomics 2024; 18:23. [PMID: 38448978 PMCID: PMC10916241 DOI: 10.1186/s40246-024-00593-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND/OBJECTIVES Rare genetic disorders causing specific congenital developmental abnormalities often manifest in single families. Investigation of disease-causing molecular features are most times lacking, although these investigations may open novel therapeutic options for patients. In this study, we aimed to identify the genetic cause in an Iranian patient with severe skeletal dysplasia and to model its molecular function in zebrafish embryos. RESULTS The proband displays short stature and multiple skeletal abnormalities, including mesomelic dysplasia of the arms with complete humero-radio-ulna synostosis, arched clavicles, pelvic dysplasia, short and thin fibulae, proportionally short vertebrae, hyperlordosis and mild kyphosis. Exome sequencing of the patient revealed a novel homozygous c.374G > T, p.(Arg125Leu) missense variant in MSGN1 (NM_001105569). MSGN1, a basic-Helix-Loop-Helix transcription factor, plays a crucial role in formation of presomitic mesoderm progenitor cells/mesodermal stem cells during early developmental processes in vertebrates. Initial in vitro experiments show protein stability and correct intracellular localization of the novel variant in the nucleus and imply retained transcription factor function. To test the pathogenicity of the detected variant, we overexpressed wild-type and mutant msgn1 mRNA in zebrafish embryos and analyzed tbxta (T/brachyury/ntl). Overexpression of wild-type or mutant msgn1 mRNA significantly reduces tbxta expression in the tailbud compared to control embryos. Mutant msgn1 mRNA injected embryos depict a more severe effect, implying a gain-of-function mechanism. In vivo analysis on embryonic development was performed by clonal msgn1 overexpression in zebrafish embryos further demonstrated altered cell compartments in the presomitic mesoderm, notochord and pectoral fin buds. Detection of ectopic tbx6 and bmp2 expression in these embryos hint to affected downstream signals due to Msgn1 gain-of-function. CONCLUSION In contrast to loss-of-function effects described in animal knockdown models, gain-of-function of MSGN1 explains the only mildly affected axial skeleton of the proband and rather normal vertebrae. In this context we observed notochord bending and potentially disruption of pectoral fin buds/upper extremity after overexpression of msgn1 in zebrafish embryos. The latter might result from Msgn1 function on mesenchymal stem cells or on chondrogenesis in these regions. In addition, we detected ectopic tbx6 and bmp2a expression after gain of Msgn1 function in zebrafish, which are interconnected to short stature, congenital scoliosis, limb shortening and prominent skeletal malformations in patients. Our findings highlight a rare, so far undescribed skeletal dysplasia syndrome associated with a gain-of-function mutation in MSGN1 and hint to its molecular downstream effectors.
Collapse
Affiliation(s)
- Asuman Koparir
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Caroline Lekszas
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Kemal Keseroglu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Thalia Rose
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Lena Rappl
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Aboulfazl Rad
- Cellular and Molecular Research Centre, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Nakul Narendran
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Atefeh Hasanzadeh
- Cellular and Molecular Research Centre, Sabzevar University of Medical Sciences, Sabzevar, 009851, Iran
| | | | - Felix Boschann
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Uwe Kornak
- Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Eva Klopocki
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Ertuğrul M Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany
| | - Daniel Liedtke
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Biozentrum, Am Hubland, 97074, Würzburg, Germany.
| |
Collapse
|
10
|
Wolf C, Lim EL, Mokhtari M, Kind B, Odainic A, Lara-Villacanas E, Koss S, Mages S, Menzel K, Engel K, Dückers G, Bernbeck B, Schneider DT, Siepermann K, Niehues T, Goetzke CC, Durek P, Minden K, Dörner T, Stittrich A, Szelinski F, Guerra GM, Massoud M, Bieringer M, de Oliveira Mann CC, Beltrán E, Kallinich T, Mashreghi MF, Schmidt SV, Latz E, Klughammer J, Majer O, Lee-Kirsch MA. UNC93B1 variants underlie TLR7-dependent autoimmunity. Sci Immunol 2024; 9:eadi9769. [PMID: 38207055 DOI: 10.1126/sciimmunol.adi9769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024]
Abstract
UNC93B1 is critical for trafficking and function of nucleic acid-sensing Toll-like receptors (TLRs) TLR3, TLR7, TLR8, and TLR9, which are essential for antiviral immunity. Overactive TLR7 signaling induced by recognition of self-nucleic acids has been implicated in systemic lupus erythematosus (SLE). Here, we report UNC93B1 variants (E92G and R336L) in four patients with early-onset SLE. Patient cells or mouse macrophages carrying the UNC93B1 variants produced high amounts of TNF-α and IL-6 and upon stimulation with TLR7/TLR8 agonist, but not with TLR3 or TLR9 agonists. E92G causes UNC93B1 protein instability and reduced interaction with TLR7, leading to selective TLR7 hyperactivation with constitutive type I IFN signaling. Thus, UNC93B1 regulates TLR subtype-specific mechanisms of ligand recognition. Our findings establish a pivotal role for UNC93B1 in TLR7-dependent autoimmunity and highlight the therapeutic potential of targeting TLR7 in SLE.
Collapse
Affiliation(s)
- Christine Wolf
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Ee Lyn Lim
- Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Mohammad Mokhtari
- Gene Center, Systems Immunology, Ludwig-Maximilians-Universität Munich, Munich 81377, Germany
| | - Barbara Kind
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Alexandru Odainic
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Eusebia Lara-Villacanas
- Department of Pediatrics, Klinikum Dortmund, University Witten/Herdecke, Dortmund 44145, Germany
| | - Sarah Koss
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Simon Mages
- Gene Center, Systems Immunology, Ludwig-Maximilians-Universität Munich, Munich 81377, Germany
| | - Katharina Menzel
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Kerstin Engel
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Gregor Dückers
- Department of Pediatrics, Helios Klinik Krefeld, Krefeld 47805, Germany
| | - Benedikt Bernbeck
- Department of Pediatrics, Klinikum Dortmund, University Witten/Herdecke, Dortmund 44145, Germany
| | - Dominik T Schneider
- Department of Pediatrics, Klinikum Dortmund, University Witten/Herdecke, Dortmund 44145, Germany
| | | | - Tim Niehues
- Department of Pediatrics, Helios Klinik Krefeld, Krefeld 47805, Germany
| | - Carl Christoph Goetzke
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin 10178, Germany
| | - Pawel Durek
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Kirsten Minden
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Thomas Dörner
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
- Department of Medicine, Rheumatology and Clinical Immunology, Charite-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Anna Stittrich
- Labor Berlin Charité-Vivantes GmbH, Department of Human Genetics, Berlin 13353, Germany
| | - Franziska Szelinski
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
- Department of Medicine, Rheumatology and Clinical Immunology, Charite-Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Gabriela Maria Guerra
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Mona Massoud
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Markus Bieringer
- Department of Cardiology and Nephrology, HELIOS Klinikum Berlin-Buch, Berlin 13125, Germany
| | | | - Eduardo Beltrán
- Institute for Clinical Neuroimmunology, BioMedizinisches Zentrum, Ludwig-Maximilians-Universität Munich, Munich 82152, Germany
| | - Tilmann Kallinich
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin 10117, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin 10178, Germany
| | - Mir-Farzin Mashreghi
- Deutsches Rheuma-Forschungszentrum (DRFZ), an institute of the Leibniz Association, Berlin 10117, Germany
| | - Susanne V Schmidt
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University of Bonn, Bonn 53127, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn 53175, Germany
| | - Johanna Klughammer
- Gene Center, Systems Immunology, Ludwig-Maximilians-Universität Munich, Munich 81377, Germany
| | - Olivia Majer
- Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
- University Center for Rare Diseases, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| |
Collapse
|
11
|
Boschann F, Kosmehl S, Bloching M, Grünhagen J, Hildebrand G, Horn D, Lyutenski S. Novel noncanonical splice site variant causes mild CHD7-related disorder with variable intrafamilial expressivity. Am J Med Genet A 2023; 191:1128-1132. [PMID: 36708132 DOI: 10.1002/ajmg.a.63122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/29/2023]
Abstract
The clinical diagnosis criteria for CHARGE syndrome have been revised several times in the last 25 years. Variable expressivity and reduced penetrance are known, particularly in mild and familial cases. Therefore, it has been proposed to include the detection of a pathogenic CHD7 variant as a major diagnostic criterion. However, intronic variants not located at the canonical splice site are still underrepresented in mutation databases, often because functional analysis is not performed in the diagnostic setting. Here, we report a two-generation family that did not meet the criteria for CHARGE syndrome, until the molecular findings were taken into account. By exome sequencing, we detected an intronic variant in a male individual, who presented with unilateral external ear malformation, bilateral semicircular canal aplasia, polydactyly, vertebral body fusion and a heart defect. The variant was inherited by his mother, who also had bilateral semicircular canal aplasia additionally to unilateral sensorineural hearing impairment, unilateral mandibular palpebral synkinesia, orofacial cleft, and dysphagia. Using RNA studies, we were able to demonstrate that aberrant splicing occurs at an upstream cryptic splice acceptor site, resulting in a frameshift and premature stop of translation. Our data show causality of the noncanonical intronic CHD7 variant and end the diagnostic odyssey of this unsolved phenotype of the family.
Collapse
Affiliation(s)
- Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Sabine Kosmehl
- Department of Otorhinolaryngology, Helios Hospital Berlin-Buch, Berlin, Germany
| | - Marc Bloching
- Department of Otorhinolaryngology, Helios Hospital Berlin-Buch, Berlin, Germany
| | - Johannes Grünhagen
- Labor Berlin Charité Vivantes GmbH-Corporate Member of Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriele Hildebrand
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Lyutenski
- Department of Otorhinolaryngology, Helios Hospital Berlin-Buch, Berlin, Germany
| |
Collapse
|
12
|
Horn S, Danyel M, Erdmann N, Boschann F, Gunnarsson C, Biskup S, Juengling J, Potratz C, Prager C, Kaindl AM. Case report: KPTN gene-related syndrome associated with a spectrum of neurodevelopmental anomalies including severe epilepsy. Front Neurol 2023; 13:1113811. [PMID: 36703628 PMCID: PMC9871926 DOI: 10.3389/fneur.2022.1113811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Biallelic variants in the kaptin gene KPTN were identified recently in individuals with a novel syndrome referred to as autosomal recessive intellectual developmental disorder 41 (MRT41). MRT41 is characterized by developmental delay, predominantly in language development, behavioral abnormalities, and epilepsy. Only about 15 affected individuals have been described in the literature, all with primary or secondary macrocephaly. Using exome sequencing, we identified three different biallelic variants in KPTN in five affected individuals from three unrelated families. In total, two KPTN variants were already reported as a loss of function variants. A novel splice site variant in KPTN was detected in two unrelated families of this study. The core phenotype with neurodevelopment delay was present in all patients. However, macrocephaly was not present in at least one patient. In total, two patients exhibited developmental and epileptic encephalopathies with generalized tonic-clonic seizures that were drug-resistant in one of them. Thus, we further delineate the KPTN-related syndrome, especially emphasizing the severity of epilepsy phenotypes and difficulties in treatment in patients of our cohort.
Collapse
Affiliation(s)
- Svea Horn
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Magdalena Danyel
- Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, Berlin, Germany,BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Nina Erdmann
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, Berlin, Germany,BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Cecilia Gunnarsson
- Department of Clinical Genetics, Linköping University, Linköping, Sweden,Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden,Centre for Rare Diseases in South East Region of Sweden, Linköping University, Linköping, Sweden
| | | | | | - Cornelia Potratz
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Christine Prager
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Angela M. Kaindl
- Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, Berlin, Germany,Center for Chronically Sick Children, Charité–Universitätsmedizin Berlin, Berlin, Germany,Institute for Cell Biology and Neurobiology, Charité–Universitätsmedizin Berlin, Berlin, Germany,*Correspondence: Angela M. Kaindl ✉
| |
Collapse
|
13
|
Nieminen M, Stolpe O, Kuhring M, Weiner J, Pett P, Beule D, Holtgrewe M. SODAR: managing multiomics study data and metadata. Gigascience 2022; 12:giad052. [PMID: 37498129 PMCID: PMC10373112 DOI: 10.1093/gigascience/giad052] [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: 07/22/2022] [Revised: 03/30/2023] [Accepted: 06/27/2023] [Indexed: 07/28/2023] Open
Abstract
Scientists employing omics in life science studies face challenges such as the modeling of multiassay studies, recording of all relevant parameters, and managing many samples with their metadata. They must manage many large files that are the results of the assays or subsequent computation. Users with diverse backgrounds, ranging from computational scientists to wet-lab scientists, have dissimilar needs when it comes to data access, with programmatic interfaces being favored by the former and graphical ones by the latter. We introduce SODAR, the system for omics data access and retrieval. SODAR is a software package that addresses these challenges by providing a web-based graphical user interface for managing multiassay studies and describing them using the ISA (Investigation, Study, Assay) data model and the ISA-Tab file format. Data storage is handled using the iRODS data management system, which handles large quantities of files and substantial amounts of data. SODAR also offers programmable APIs and command-line access for metadata and file storage. SODAR supports complex omics integration studies and can be easily installed. The software is written in Python 3 and freely available at https://github.com/bihealth/sodar-server under the MIT license.
Collapse
Affiliation(s)
- Mikko Nieminen
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Unit Bioinformatics (CUBI), Berlin 10117 , Germany
| | - Oliver Stolpe
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Unit Bioinformatics (CUBI), Berlin 10117 , Germany
| | - Mathias Kuhring
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Unit Bioinformatics (CUBI), Berlin 10117 , Germany
| | - January Weiner
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Unit Bioinformatics (CUBI), Berlin 10117 , Germany
| | - Patrick Pett
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Unit Bioinformatics (CUBI), Berlin 10117 , Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Unit Bioinformatics (CUBI), Berlin 10117 , Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Core Unit Bioinformatics (CUBI), Berlin 10117 , Germany
| |
Collapse
|
14
|
Phenotype-aware prioritisation of rare Mendelian disease variants. Trends Genet 2022; 38:1271-1283. [PMID: 35934592 PMCID: PMC9950798 DOI: 10.1016/j.tig.2022.07.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 01/24/2023]
Abstract
A molecular diagnosis from the analysis of sequencing data in rare Mendelian diseases has a huge impact on the management of patients and their families. Numerous patient phenotype-aware variant prioritisation (VP) tools have been developed to help automate this process, and shorten the diagnostic odyssey, but performance statistics on real patient data are limited. Here we identify, assess, and compare the performance of all up-to-date, freely available, and programmatically accessible tools using a whole-exome, retinal disease dataset from 134 individuals with a molecular diagnosis. All tools were able to identify around two-thirds of the genetic diagnoses as the top-ranked candidate, with LIRICAL performing best overall. Finally, we discuss the challenges to overcome most cases remaining undiagnosed after current, state-of-the-art practices.
Collapse
|
15
|
Bögershausen N, Krawczyk HE, Jamra RA, Lin SJ, Yigit G, Hüning I, Polo AM, Vona B, Huang K, Schmidt J, Altmüller J, Luppe J, Platzer K, Dörgeloh BB, Busche A, Biskup S, Mendes MI, Smith DEC, Salomons GS, Zibat A, Bültmann E, Nürnberg P, Spielmann M, Lemke JR, Li Y, Zenker M, Varshney GK, Hillen HS, Kratz CP, Wollnik B. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Hum Mutat 2022; 43:1454-1471. [PMID: 35790048 DOI: 10.1002/humu.24430] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023]
Abstract
Aminoacylation of transfer RNA (tRNA) is a key step in protein biosynthesis, carried out by highly specific aminoacyl-tRNA synthetases (ARSs). ARSs have been implicated in autosomal dominant and autosomal recessive human disorders. Autosomal dominant variants in tryptophanyl-tRNA synthetase 1 (WARS1) are known to cause distal hereditary motor neuropathy and Charcot-Marie-Tooth disease, but a recessively inherited phenotype is yet to be clearly defined. Seryl-tRNA synthetase 1 (SARS1) has rarely been implicated in an autosomal recessive developmental disorder. Here, we report five individuals with biallelic missense variants in WARS1 or SARS1, who presented with an overlapping phenotype of microcephaly, developmental delay, intellectual disability, and brain anomalies. Structural mapping showed that the SARS1 variant is located directly within the enzyme's active site, most likely diminishing activity, while the WARS1 variant is located in the N-terminal domain. We further characterize the identified WARS1 variant by showing that it negatively impacts protein abundance and is unable to rescue the phenotype of a CRISPR/Cas9 wars1 knockout zebrafish model. In summary, we describe two overlapping autosomal recessive syndromes caused by variants in WARS1 and SARS1, present functional insights into the pathogenesis of the WARS1-related syndrome and define an emerging disease spectrum: ARS-related developmental disorders with or without microcephaly.
Collapse
Affiliation(s)
- Nina Bögershausen
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Hannah E Krawczyk
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Rami A Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Irina Hüning
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Anna M Polo
- MVZ Labor Krone, Filialpraxis für Humangenetik, Bielefeld, Germany
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Kevin Huang
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Julia Schmidt
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Johannes Luppe
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Beate B Dörgeloh
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Andreas Busche
- Institut für Humangenetik, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Saskia Biskup
- CeGaT GmbH, Center for Genomics and Transcriptomics, Tübingen, Germany
| | - Marisa I Mendes
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Desiree E C Smith
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Gajja S Salomons
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, Netherlands
| | - Arne Zibat
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Eva Bültmann
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Malte Spielmann
- Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Martin Zenker
- Institute of Human Genetics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Hauke S Hillen
- Research Group Structure and Function of Molecular Machines, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable cells" (MBExC), University of Göttingen, Göttingen, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
| |
Collapse
|
16
|
Liu Y, Yeung WSB, Chiu PCN, Cao D. Computational approaches for predicting variant impact: An overview from resources, principles to applications. Front Genet 2022; 13:981005. [PMID: 36246661 PMCID: PMC9559863 DOI: 10.3389/fgene.2022.981005] [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: 06/29/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
One objective of human genetics is to unveil the variants that contribute to human diseases. With the rapid development and wide use of next-generation sequencing (NGS), massive genomic sequence data have been created, making personal genetic information available. Conventional experimental evidence is critical in establishing the relationship between sequence variants and phenotype but with low efficiency. Due to the lack of comprehensive databases and resources which present clinical and experimental evidence on genotype-phenotype relationship, as well as accumulating variants found from NGS, different computational tools that can predict the impact of the variants on phenotype have been greatly developed to bridge the gap. In this review, we present a brief introduction and discussion about the computational approaches for variant impact prediction. Following an innovative manner, we mainly focus on approaches for non-synonymous variants (nsSNVs) impact prediction and categorize them into six classes. Their underlying rationale and constraints, together with the concerns and remedies raised from comparative studies are discussed. We also present how the predictive approaches employed in different research. Although diverse constraints exist, the computational predictive approaches are indispensable in exploring genotype-phenotype relationship.
Collapse
Affiliation(s)
- Ye Liu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - William S. B. Yeung
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Philip C. N. Chiu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Dandan Cao
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| |
Collapse
|
17
|
Seidel F, Laser KT, Klingel K, Dartsch J, Theisen S, Pickardt T, Holtgrewe M, Gärtner A, Berger F, Beule D, Milting H, Schubert S, Klaassen S, Kühnisch J. Pathogenic Variants in Cardiomyopathy Disorder Genes Underlie Pediatric Myocarditis—Further Impact of Heterozygous Immune Disorder Gene Variants? J Cardiovasc Dev Dis 2022; 9:jcdd9070216. [PMID: 35877578 PMCID: PMC9321514 DOI: 10.3390/jcdd9070216] [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: 05/19/2022] [Revised: 06/23/2022] [Accepted: 07/01/2022] [Indexed: 12/04/2022] Open
Abstract
Myocarditis is an inflammatory disease of the heart. Pediatric myocarditis with the dilated cardiomyopathy (DCM) phenotype may be caused by likely pathogenic or pathogenic genetic variants [(L)P] in cardiomyopathy (CMP) genes. Systematic analysis of immune disorder gene defects has not been performed so far. We analyzed 12 patients with biopsy-proven myocarditis and the DCM phenotype together with their parents using whole-exome sequencing (WES). The WES data were filtered for rare pathogenic variants in CMP (n = 89) and immune disorder genes (n = 631). Twelve children with a median age of 2.9 (1.0–6.8) years had a mean left ventricular ejection fraction of 28% (22–32%) and myocarditis was confirmed by endomyocardial biopsy. Patients with primary immunodeficiency were excluded from the study. Four patients underwent implantation of a ventricular assist device and subsequent heart transplantation. Genetic analysis of the 12 families revealed an (L)P variant in the CMP gene in 8/12 index patients explaining DCM. Screening of recessive immune disorder genes identified a heterozygous (L)P variant in 3/12 index patients. This study supports the genetic impact of CMP genes for pediatric myocarditis with the DCM phenotype. Piloting the idea that additional immune-related genetic defects promote myocarditis suggests that the presence of heterozygous variants in these genes needs further investigation. Altered cilium function might play an additional role in inducing inflammation in the context of CMP.
Collapse
Affiliation(s)
- Franziska Seidel
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (F.S.); (J.D.); (S.T.); (D.B.)
- Department of Congenital Heart Disease and Pediatric Cardiology, German Heart Center Berlin, 13353 Berlin, Germany;
- Experimental and Clinical Research Center, A Cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Department of Pediatric Cardiology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Kai Thorsten Laser
- Center for Congenital Heart Disease/Pediatric Cardiology, Heart-and Diabetescenter NRW, University Clinic of Ruhr University Bochum, 32545 Bad Oeynhausen, Germany; (K.T.L.); (S.S.)
| | - Karin Klingel
- Cardiopathology, Institute for Pathology and Neuropathology, University Hospital Tübingen, 72016 Tübingen, Germany;
| | - Josephine Dartsch
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (F.S.); (J.D.); (S.T.); (D.B.)
- Experimental and Clinical Research Center, A Cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Simon Theisen
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (F.S.); (J.D.); (S.T.); (D.B.)
- Experimental and Clinical Research Center, A Cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
| | - Thomas Pickardt
- National Register for Congenital Heart Defects, 13353 Berlin, Germany;
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), 10117 Berlin, Germany;
- Core Facility Bioinformatik, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Anna Gärtner
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development & Clinic for Thoracic and Cardiovascular Surgery, Heart-and Diabetescenter NRW, University Hospital of the Ruhr University Bochum, 32545 Bad Oeynhausen, Germany; (A.G.); (H.M.)
| | - Felix Berger
- Department of Congenital Heart Disease and Pediatric Cardiology, German Heart Center Berlin, 13353 Berlin, Germany;
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Department of Pediatric Cardiology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Dieter Beule
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (F.S.); (J.D.); (S.T.); (D.B.)
- Core Unit Bioinformatics, Berlin Institute of Health (BIH), 10117 Berlin, Germany;
| | - Hendrik Milting
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development & Clinic for Thoracic and Cardiovascular Surgery, Heart-and Diabetescenter NRW, University Hospital of the Ruhr University Bochum, 32545 Bad Oeynhausen, Germany; (A.G.); (H.M.)
| | - Stephan Schubert
- Department of Congenital Heart Disease and Pediatric Cardiology, German Heart Center Berlin, 13353 Berlin, Germany;
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Center for Congenital Heart Disease/Pediatric Cardiology, Heart-and Diabetescenter NRW, University Clinic of Ruhr University Bochum, 32545 Bad Oeynhausen, Germany; (K.T.L.); (S.S.)
| | - Sabine Klaassen
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (F.S.); (J.D.); (S.T.); (D.B.)
- Experimental and Clinical Research Center, A Cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Department of Pediatric Cardiology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Correspondence: (S.K.); (J.K.); Tel.: +49-30-9406-3319 (S.K. & J.K.); Fax: +49-30-9406-3358 (S.K. & J.K.)
| | - Jirko Kühnisch
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; (F.S.); (J.D.); (S.T.); (D.B.)
- Experimental and Clinical Research Center, A Cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Correspondence: (S.K.); (J.K.); Tel.: +49-30-9406-3319 (S.K. & J.K.); Fax: +49-30-9406-3358 (S.K. & J.K.)
| |
Collapse
|
18
|
Lischka A, Lassuthova P, Çakar A, Record CJ, Van Lent J, Baets J, Dohrn MF, Senderek J, Lampert A, Bennett DL, Wood JN, Timmerman V, Hornemann T, Auer-Grumbach M, Parman Y, Hübner CA, Elbracht M, Eggermann K, Geoffrey Woods C, Cox JJ, Reilly MM, Kurth I. Genetic pain loss disorders. Nat Rev Dis Primers 2022; 8:41. [PMID: 35710757 DOI: 10.1038/s41572-022-00365-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 01/05/2023]
Abstract
Genetic pain loss includes congenital insensitivity to pain (CIP), hereditary sensory neuropathies and, if autonomic nerves are involved, hereditary sensory and autonomic neuropathy (HSAN). This heterogeneous group of disorders highlights the essential role of nociception in protecting against tissue damage. Patients with genetic pain loss have recurrent injuries, burns and poorly healing wounds as disease hallmarks. CIP and HSAN are caused by pathogenic genetic variants in >20 genes that lead to developmental defects, neurodegeneration or altered neuronal excitability of peripheral damage-sensing neurons. These genetic variants lead to hyperactivity of sodium channels, disturbed haem metabolism, altered clathrin-mediated transport and impaired gene regulatory mechanisms affecting epigenetic marks, long non-coding RNAs and repetitive elements. Therapies for pain loss disorders are mainly symptomatic but the first targeted therapies are being tested. Conversely, chronic pain remains one of the greatest unresolved medical challenges, and the genes and mechanisms associated with pain loss offer new targets for analgesics. Given the progress that has been made, the coming years are promising both in terms of targeted treatments for pain loss disorders and the development of innovative pain medicines based on knowledge of these genetic diseases.
Collapse
Affiliation(s)
- Annette Lischka
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Petra Lassuthova
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Arman Çakar
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Christopher J Record
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Jonathan Baets
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Maike F Dohrn
- Department of Neurology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.,Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Jan Senderek
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-University, Munich, Germany
| | - Angelika Lampert
- Institute of Physiology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, Oxford University, Oxford, UK
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Thorsten Hornemann
- Department of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michaela Auer-Grumbach
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, Vienna, Austria
| | - Yesim Parman
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Katja Eggermann
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Mary M Reilly
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.
| |
Collapse
|
19
|
Pietzsch L, Körholz J, Boschann F, Sergon M, Dorjbal B, Yee D, Gilly V, Kämmerer E, Paul D, Kastl C, Laass MW, Berner R, Jacobsen EM, Roesler J, Aust D, Lee-Kirsch MA, Snow AL, Schuetz C. Hyper-IgE and Carcinoma in CADINS Disease. Front Immunol 2022; 13:878989. [PMID: 35651609 PMCID: PMC9149281 DOI: 10.3389/fimmu.2022.878989] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background Atopic dermatitis (AD) affects up to 25% of children and 10% of adults in Western countries. When severe or recurrent infections and exceedingly elevated serum IgE levels occur in AD patients, an inborn error of immunity (IEI) may be suspected. The International Union of Immunological Societies classification lists variants in different genes responsible for so-called Hyper-IgE syndromes. Diagnosing an underlying IEI may influence treatment strategies. Methods Clinical and diagnostic workup of family members are presented including a detailed immunological description and histology of the carcinoma. Functional testing of the novel variant in CARD11 underlying ‘CARD11-associated atopy with dominant interference of NF-kB signaling’ (CADINS) was performed. Results We report on an 18-year-old patient with a long-standing history of infections, accompanied by hypogammaglobulinemia, intermittent agranulocytosis, atopy, eosinophilia and colitis. The working diagnosis of common variable immunodeficiency was revised when a novel heterozygous CARD11 variant [c.223C>T; p.(Arg75Trp)] was identified. Functional studies confirmed this variant to have a dominant negative (DN) effect, as previously described in patients with CADINS. Five other family members were affected by severe atopy associated with the above variant, but not hypogammaglobulinemia. Malignancies occurred in two generations: an HPV-positive squamous cell carcinoma and a cutaneous T-cell lymphoma. So far, one patient is under treatment with dupilumab, which has shown marked benefit in controlling severe eczema. Conclusion The phenotypic spectrum associated with heterozygous CARD11 DN mutations is broad. Partial T-cell deficiency, diminished IFN-γ cytokine and increased IL-4 production, were identified as disease-causing mechanisms. Malignant disease associated with germline CARD11 DN variants has only been reported sporadically. HPV vaccination in teenage years, and cytology screening analogous with routine cervical swabs may be recommended. Treatment with dupilumab, a monoclonal antibody blocking interleukin-4- and interleukin-13 signaling, may be of benefit in controlling severe and extended AD for some patients as reported for STAT3 loss-of-function.
Collapse
Affiliation(s)
- Leonora Pietzsch
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Julia Körholz
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Berlin Institute of Health, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mildred Sergon
- Department of Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Batsukh Dorjbal
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Debra Yee
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Vanessa Gilly
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Diana Paul
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Clemens Kastl
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Martin W Laass
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Reinhard Berner
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Universitäts Centrum für Seltene Erkrankungen, University Hospital Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Joachim Roesler
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Daniela Aust
- Department of Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT) Dresden, Dresden, Germany.,Nationales Centrum für Tumorerkrankungen (NCT)/Universitäts KrebsCentrum (UCC) Biobank Dresden, National Center for Tumor Diseases (NCT) Dresden and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Min A Lee-Kirsch
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Universitäts Centrum für Seltene Erkrankungen, University Hospital Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Andrew L Snow
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Catharina Schuetz
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Universitäts Centrum für Seltene Erkrankungen, University Hospital Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
20
|
van der Velde KJ, Singh G, Kaliyaperumal R, Liao X, de Ridder S, Rebers S, Kerstens HHD, de Andrade F, van Reeuwijk J, De Gruyter FE, Hiltemann S, Ligtvoet M, Weiss MM, van Deutekom HWM, Jansen AML, Stubbs AP, Vissers LELM, Laros JFJ, van Enckevort E, Stemkens D, 't Hoen PAC, Beliën JAM, van Gijn ME, Swertz MA. FAIR Genomes metadata schema promoting Next Generation Sequencing data reuse in Dutch healthcare and research. Sci Data 2022; 9:169. [PMID: 35418585 PMCID: PMC9008059 DOI: 10.1038/s41597-022-01265-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/25/2022] [Indexed: 11/08/2022] Open
Abstract
The genomes of thousands of individuals are profiled within Dutch healthcare and research each year. However, this valuable genomic data, associated clinical data and consent are captured in different ways and stored across many systems and organizations. This makes it difficult to discover rare disease patients, reuse data for personalized medicine and establish research cohorts based on specific parameters. FAIR Genomes aims to enable NGS data reuse by developing metadata standards for the data descriptions needed to FAIRify genomic data while also addressing ELSI issues. We developed a semantic schema of essential data elements harmonized with international FAIR initiatives. The FAIR Genomes schema v1.1 contains 110 elements in 9 modules. It reuses common ontologies such as NCIT, DUO and EDAM, only introducing new terms when necessary. The schema is represented by a YAML file that can be transformed into templates for data entry software (EDC) and programmatic interfaces (JSON, RDF) to ease genomic data sharing in research and healthcare. The schema, documentation and MOLGENIS reference implementation are available at https://fairgenomes.org .
Collapse
Affiliation(s)
- K Joeri van der Velde
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Gurnoor Singh
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Rajaram Kaliyaperumal
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - XiaoFeng Liao
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Sander de Ridder
- Amsterdam University Medical Center, University of Amsterdam, Department of Pathology, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Susanne Rebers
- The Netherlands Cancer Institute, Division of Molecular Pathology, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Hindrik H D Kerstens
- Prinses Máxima Center for Pediatric Oncology, Kemmeren group, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
| | - Fernanda de Andrade
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Jeroen van Reeuwijk
- Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Fini E De Gruyter
- University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Saskia Hiltemann
- Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Maarten Ligtvoet
- Nictiz - Dutch competence centre for electronic exchange of health and care information, Oude Middenweg 55, 2491 AC, The Hague, The Netherlands
| | - Marjan M Weiss
- Radboud University Medical Center, Department of Human Genetics, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Hanneke W M van Deutekom
- University Medical Center Utrecht, Department of Genetics, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Anne M L Jansen
- University Medical Center Utrecht, Department of Pathology, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Andrew P Stubbs
- Erasmus Medical Center, Department of Pathology, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Lisenka E L M Vissers
- Radboud University Medical Center, Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Jeroen F J Laros
- Leiden University Medical Center, Department of Human Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Leiden University Medical Center, Department of Clinical Genetics, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Rijksinstituut voor Volksgezondheid en Milieu, Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands
| | - Esther van Enckevort
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Daphne Stemkens
- VSOP - Patient Alliance for Rare and Genetic Diseases The Netherlands, Koninginnelaan 23, 3762 DA, Soest, The Netherlands
| | - Peter A C 't Hoen
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Jeroen A M Beliën
- Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Department of Pathology, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Mariëlle E van Gijn
- University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Morris A Swertz
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
- University of Groningen and University Medical Center Groningen, Department of Genetics, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
| |
Collapse
|
21
|
Manshaei R, DeLong S, Andric V, Joshi E, Okello JBA, Dhir P, Somerville C, Farncombe KM, Kalbfleisch K, Jobling RK, Scherer SW, Kim RH, Hosseini SM. GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation. BMC Med Genomics 2022; 15:31. [PMID: 35180879 PMCID: PMC8857790 DOI: 10.1186/s12920-022-01166-3] [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: 08/17/2021] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Background Variant interpretation is the main bottleneck in medical genomic sequencing efforts. This usually involves genome analysts manually searching through a multitude of independent databases, often with the aid of several, mostly independent, computational tools. To streamline variant interpretation, we developed the GeneTerpret platform which collates data from current interpretation tools and databases, and applies a phenotype-driven query to categorize the variants identified in the genome(s). The platform assigns quantitative validity scores to genes by query and assembly of the genotype–phenotype data, sequence homology, molecular interactions, expression data, and animal models. It also uses the American College of Medical Genetics and Genomics (ACMG) criteria to categorize variants into five tiers of pathogenicity. The final output is a prioritized list of potentially causal variants/genes.
Results We tested GeneTerpret by comparing its performance to expert-curated genes (ClinGen’s gene-validity database) and variant pathogenicity reports (DECIPHER database). Output from GeneTerpret was 97.2% and 83.5% concordant with the expert-curated sources, respectively. Additionally, similar concordance was observed when GeneTerpret’s performance was compared with our internal expert-interpreted clinical datasets. Conclusions GeneTerpret is a flexible platform designed to streamline the genome interpretation process, through a unique interface, with improved ease, speed and accuracy. This modular and customizable system allows the user to tailor the component-programs in the analysis process to their preference. GeneTerpret is available online at https://geneterpret.com. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01166-3.
Collapse
Affiliation(s)
- Roozbeh Manshaei
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sean DeLong
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Electrical Engineering and Computer Science, York University, Toronto, ON, Canada
| | - Veronica Andric
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Esha Joshi
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - John B A Okello
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,MIT Sloan School of Management, Massachusetts Institute of Technology, 100 Main Street, Cambridge, MA, 02142, USA
| | - Priya Dhir
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Cherith Somerville
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kirsten M Farncombe
- Ted Rogers Centre for Heart Research, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Kelsey Kalbfleisch
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rebekah K Jobling
- Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.,Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Raymond H Kim
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada. .,Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Department of Medicine, University of Toronto, Toronto, ON, Canada.
| | - S Mohsen Hosseini
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
22
|
Samuels DC, Yu H, Guo Y. Is it time to reassess variant annotation? Trends Genet 2022; 38:521-523. [DOI: 10.1016/j.tig.2022.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 11/25/2022]
|
23
|
Boschann F, Moreno DA, Mensah MA, Sczakiel HL, Skipalova K, Holtgrewe M, Mundlos S, Fischer-Zirnsak B. Xq27.1 palindrome mediated interchromosomal insertion likely causes familial congenital bilateral laryngeal abductor paralysis (Plott syndrome). J Hum Genet 2022; 67:405-410. [PMID: 35095096 PMCID: PMC9233990 DOI: 10.1038/s10038-022-01018-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 01/27/2023]
Abstract
Bilateral laryngeal abductor paralysis is a rare entity and the second most common cause of stridor in newborns. So far, no conclusive genetic or chromosomal aberration has been reported for X-linked isolated bilateral vocal cord paralysis, also referred to as Plott syndrome. Via whole genome sequencing (WGS), we identified a complex interchromosomal insertion in a large family with seven affected males. The 404 kb inserted fragment originates from chromosome 10q21.3, contains no genes and is inserted inversionally into the intergenic chromosomal region Xq27.1, 82 kb centromeric to the nearest gene SOX3. The patterns found at the breakpoint junctions resemble typical characteristics that arise in replication-based mechanisms with long-distance template switching. Non protein-coding insertions into the same genomic region have been described to result in different phenotypes, indicating that the phenotypic outcome likely depends on the introduction of regulatory elements. In conclusion, our data adds Plott syndrome as another entity, likely caused by the insertion of non-coding DNA into the intergenic chromosomal region Xq27.1. In this regard, we demonstrate the importance of WGS as a powerful diagnostic test in unsolved genetic diseases, as this genomic rearrangement has not been detected by current first-line diagnostic tests, i.e., exome sequencing and chromosomal microarray analysis.
Collapse
|
24
|
Schutz S, Monod-Broca C, Bourneuf L, Marijon P, Montier T. Cutevariant: a standalone GUI-based desktop application to explore genetic variations from an annotated VCF file. BIOINFORMATICS ADVANCES 2021; 2:vbab028. [PMID: 36699349 PMCID: PMC9710699 DOI: 10.1093/bioadv/vbab028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/21/2021] [Accepted: 10/25/2021] [Indexed: 01/28/2023]
Abstract
Summary Cutevariant is a graphical user interface (GUI)-based desktop application designed to filter variations from annotated VCF file. The application imports data into a local SQLite database where complex filter queries can be built either from GUI controllers or using a domain-specific language called Variant Query Language. Cutevariant provides more features than existing applications and is fully customizable thanks to a complete plugins architecture. Availability and implementation Cutevariant is distributed as a multiplatform client-side software under an open source license and is available at https://github.com/labsquare/cutevariant.
Collapse
Affiliation(s)
- Sacha Schutz
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest 29200, France,CHRU Brest, Brest 29200, France,To whom correspondence should be addressed.
| | | | - Lucas Bourneuf
- Univ Rennes, Inria, CNRS, IRISA—UMR 6074, Rennes F-35000, France
| | - Pierre Marijon
- Heinrich-Heine-Universität Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | - Tristan Montier
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest 29200, France,CHRU Brest, Brest 29200, France
| |
Collapse
|
25
|
An Introductory Overview of Open-Source and Commercial Software Options for the Analysis of Forensic Sequencing Data. Genes (Basel) 2021; 12:genes12111739. [PMID: 34828345 PMCID: PMC8618049 DOI: 10.3390/genes12111739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022] Open
Abstract
The top challenges of adopting new methods to forensic DNA analysis in routine laboratories are often the capital investment and the expertise required to implement and validate such methods locally. In the case of next-generation sequencing, in the last decade, several specifically forensic commercial options became available, offering reliable and validated solutions. Despite this, the readily available expertise to analyze, interpret and understand such data is still perceived to be lagging behind. This review gives an introductory overview for the forensic scientists who are at the beginning of their journey with implementing next-generation sequencing locally and because most in the field do not have a bioinformatics background may find it difficult to navigate the new terms and analysis options available. The currently available open-source and commercial software for forensic sequencing data analysis are summarized here to provide an accessible starting point for those fairly new to the forensic application of massively parallel sequencing.
Collapse
|
26
|
Kim SY, Lee S, Seo GH, Kim BJ, Oh DY, Han JH, Park MK, Lee SM, Kim B, Yi N, Kim NJ, Koh DH, Hwang S, Keum C, Choi BY. Powerful use of automated prioritization of candidate variants in genetic hearing loss with extreme etiologic heterogeneity. Sci Rep 2021; 11:19476. [PMID: 34593925 PMCID: PMC8484668 DOI: 10.1038/s41598-021-99007-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/17/2021] [Indexed: 01/02/2023] Open
Abstract
Variant prioritization of exome sequencing (ES) data for molecular diagnosis of sensorineural hearing loss (SNHL) with extreme etiologic heterogeneity poses a significant challenge. This study used an automated variant prioritization system (“EVIDENCE”) to analyze SNHL patient data and assess its diagnostic accuracy. We performed ES of 263 probands manifesting mild to moderate or higher degrees of SNHL. Candidate variants were classified according to the 2015 American College of Medical Genetics guidelines, and we compared the accuracy, call rates, and efficiency of variant prioritizations performed manually by humans or using EVIDENCE. In our in silico panel, 21 synthetic cases were successfully analyzed by EVIDENCE. In our cohort, the ES diagnostic yield for SNHL by manual analysis was 50.19% (132/263) and 50.95% (134/263) by EVIDENCE. EVIDENCE processed ES data 24-fold faster than humans, and the concordant call rate between humans and EVIDENCE was 97.72% (257/263). Additionally, EVIDENCE outperformed human accuracy, especially at discovering causative variants of rare syndromic deafness, whereas flexible interpretations that required predefined specific genotype–phenotype correlations were possible only by manual prioritization. The automated variant prioritization system remarkably facilitated the molecular diagnosis of hearing loss with high accuracy and efficiency, fostering the popularization of molecular genetic diagnosis of SNHL.
Collapse
Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Seungmin Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.,R&D Center, ENCell Co. Ltd, Seoul, Republic of Korea
| | - Go Hun Seo
- 3billion, Inc., Seoul, Republic of Korea
| | - Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University Sejong Hospital, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Doo Yi Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Moo Kyun Park
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - So Min Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
| | - Bonggi Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Nayoung Yi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Namju Justin Kim
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Doo Hyun Koh
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam, Republic of Korea
| | - Sohyun Hwang
- Department of Biomedical Science, The Graduate School, CHA University, Seongnam, Republic of Korea.,Department of Pathology, CHA University, CHA Bundang Medical Center, Seongnam, Republic of Korea
| | | | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.
| |
Collapse
|
27
|
Richter GM, Wagner G, Reichenmiller K, Staufenbiel I, Martins O, Löscher BS, Holtgrewe M, Jepsen S, Dommisch H, Schaefer AS. Exome Sequencing of 5 Families with Severe Early-Onset Periodontitis. J Dent Res 2021; 101:151-157. [PMID: 34515563 PMCID: PMC8807999 DOI: 10.1177/00220345211029266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Periodontitis is characterized by alveolar bone loss leading to tooth loss. A small proportion of patients develop severe periodontitis at the juvenile or adolescent age without exposure to the main risk factors of the disease. It is considered that these cases carry rare variants with large causal effects, but the specific variants are largely unknown. In this study, we performed exome sequencing of 5 families with children who developed stage IV, grade C, periodontitis between 3 and 18 y of age. In 1 family, we found compound heterozygous variants in the gene CTSC (p.R272H, p.G139R), 1 of which was previously identified in a family with prepubertal periodontitis. Subsequent targeted resequencing of the CTSC gene in 24 patients <25 y of age (stage IV, grade C) identified the known mutation p.I453V (odds ratio = 4.06, 95% CI = 1.6 to 10.3, P = 0.001), which was previously reported to increase the risk for adolescent periodontitis. An affected sibling of another family carried a homozygous deleterious mutation in the gene TUT7 (p.R560Q, CADD score >30 [Combined Annotation Dependent Depletion]), which is implicated in regulation of interleukin 6 expression. Two other affected siblings shared heterozygous deleterious mutations in the interacting genes PADI1 and FLG (both CADD = 36), which contribute to the integrity of the environment-tissue barrier interface. Additionally, we found predicted deleterious mutations in the periodontitis risk genes ABCA1, GLT6D1, and SIGLEC5. We conclude that the CTSC variants p.R272H and p.I453V have different expressivity and diagnostic relevance for prepubertal and adolescent periodontitis, respectively. We propose additional causal variants for early-onset periodontitis, which also locate within genes that carry known susceptibility variants for common forms. However, the genetic architecture of juvenile periodontitis is complex and differs among the affected siblings of the sequenced families.
Collapse
Affiliation(s)
- G M Richter
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Charité-University Medicine Berlin, Berlin, Germany
| | - G Wagner
- Department of Periodontology, Operative and Preventive Dentistry, University of Bonn, Bonn, Germany
| | | | - I Staufenbiel
- Department of Conservative Dentistry, Periodontology and Preventive Dentistry, Hannover Medical School, Hannover, Germany
| | - O Martins
- Institute of Periodontology, Department of Dentistry, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - B S Löscher
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - M Holtgrewe
- Core Unit Bioinformatics-CUBI, Berlin Institute of Health, Charité-University Medicine Berlin, Berlin, Germany
| | - S Jepsen
- Department of Periodontology, Operative and Preventive Dentistry, University of Bonn, Bonn, Germany
| | - H Dommisch
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Charité-University Medicine Berlin, Berlin, Germany
| | - A S Schaefer
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Charité-University Medicine Berlin, Berlin, Germany
| |
Collapse
|
28
|
Umlai UKI, Bangarusamy DK, Estivill X, Jithesh PV. Genome sequencing data analysis for rare disease gene discovery. Brief Bioinform 2021; 23:6366880. [PMID: 34498682 DOI: 10.1093/bib/bbab363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/24/2021] [Accepted: 08/17/2021] [Indexed: 12/14/2022] Open
Abstract
Rare diseases occur in a smaller proportion of the general population, which is variedly defined as less than 200 000 individuals (US) or in less than 1 in 2000 individuals (Europe). Although rare, they collectively make up to approximately 7000 different disorders, with majority having a genetic origin, and affect roughly 300 million people globally. Most of the patients and their families undergo a long and frustrating diagnostic odyssey. However, advances in the field of genomics have started to facilitate the process of diagnosis, though it is hindered by the difficulty in genome data analysis and interpretation. A major impediment in diagnosis is in the understanding of the diverse approaches, tools and datasets available for variant prioritization, the most important step in the analysis of millions of variants to select a few potential variants. Here we present a review of the latest methodological developments and spectrum of tools available for rare disease genetic variant discovery and recommend appropriate data interpretation methods for variant prioritization. We have categorized the resources based on various steps of the variant interpretation workflow, starting from data processing, variant calling, annotation, filtration and finally prioritization, with a special emphasis on the last two steps. The methods discussed here pertain to elucidating the genetic basis of disease in individual patient cases via trio- or family-based analysis of the genome data. We advocate the use of a combination of tools and datasets and to follow multiple iterative approaches to elucidate the potential causative variant.
Collapse
Affiliation(s)
- Umm-Kulthum Ismail Umlai
- Division of Genomics & Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, B-147, Penrose House, PO Box 34110, Education City, Doha, Qatar
| | - Dhinoth Kumar Bangarusamy
- Division of Genomics & Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, B-147, Penrose House, PO Box 34110, Education City, Doha, Qatar
| | - Xavier Estivill
- Quantitative Genomics Laboratories (qGenomics), Barcelona, Catalonia, Spain
| | - Puthen Veettil Jithesh
- Division of Genomics & Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, B-147, Penrose House, PO Box 34110, Education City, Doha, Qatar
| |
Collapse
|
29
|
Körholz J, Gabrielyan A, Sowerby JM, Boschann F, Chen LS, Paul D, Brandt D, Kleymann J, Kolditz M, Toepfner N, Knöfler R, Jacobsen EM, Wolf C, Conrad K, Röber N, Lee-Kirsch MA, Smith KGC, Mundlos S, Berner R, Dalpke AH, Schuetz C, Rae W. One Gene, Many Facets: Multiple Immune Pathway Dysregulation in SOCS1 Haploinsufficiency. Front Immunol 2021; 12:680334. [PMID: 34421895 PMCID: PMC8375263 DOI: 10.3389/fimmu.2021.680334] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/13/2021] [Indexed: 01/25/2023] Open
Abstract
Background Inborn errors of immunity (IEI) present with a large phenotypic spectrum of disease, which can pose diagnostic and therapeutic challenges. Suppressor of cytokine signaling 1 (SOCS1) is a key negative regulator of cytokine signaling, and has recently been associated with a novel IEI. Of patients described to date, it is apparent that SOCS1 haploinsufficiency has a pleiotropic effect in humans. Objective We sought to investigate whether dysregulation of immune pathways, in addition to STAT1, play a role in the broad clinical manifestations of SOCS1 haploinsufficiency. Methods We assessed impacts of reduced SOCS1 expression across multiple immune cell pathways utilizing patient cells and CRISPR/Cas9 edited primary human T cells. Results SOCS1 haploinsufficiency phenotypes straddled across the International Union of Immunological Societies classifications of IEI. We found that reduced SOCS1 expression led to dysregulation of multiple intracellular pathways in immune cells. STAT1 phosphorylation is enhanced, comparably with STAT1 gain-of-function mutations, and STAT3 phosphorylation is similarly reduced with concurrent reduction of Th17 cells. Furthermore, reduced SOCS1 E3 ligase function was associated with increased FAK1 in immune cells, and increased AKT and p70 ribosomal protein S6 kinase phosphorylation. We also found Toll-like receptor responses are increased in SOCS1 haploinsufficiency patients. Conclusions SOCS1 haploinsufficiency is a pleiotropic monogenic IEI. Dysregulation of multiple immune cell pathways may explain the variable clinical phenotype associated with this new condition. Knowledge of these additional dysregulated immune pathways is important when considering the optimum management for SOCS1 haploinsufficient patients.
Collapse
Affiliation(s)
- Julia Körholz
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany.,UniversitätsCentrum für seltene Erkrankungen, Medizinische Fakultät Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Anastasia Gabrielyan
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - John M Sowerby
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Lan-Sun Chen
- Institute of Medical Microbiology and Virology, Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Diana Paul
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - David Brandt
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Janina Kleymann
- Department of Internal Medicine, Pneumology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Martin Kolditz
- Department of Internal Medicine, Pneumology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nicole Toepfner
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Ralf Knöfler
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Christine Wolf
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Karsten Conrad
- Institute of Immunology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nadja Röber
- Institute of Immunology, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany.,UniversitätsCentrum für seltene Erkrankungen, Medizinische Fakultät Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Mundlos
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Research Group (RG) Development and Disease, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Reinhard Berner
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany.,UniversitätsCentrum für seltene Erkrankungen, Medizinische Fakultät Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Alexander H Dalpke
- Institute of Medical Microbiology and Virology, Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - Catharina Schuetz
- Department of Pediatrics, University Hospital and Medical Faculty Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany.,UniversitätsCentrum für seltene Erkrankungen, Medizinische Fakultät Carl-Gustav-Carus, Technische Universität Dresden, Dresden, Germany
| | - William Rae
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
30
|
Steinhaus R, Proft S, Schuelke M, Cooper DN, Schwarz JM, Seelow D. MutationTaster2021. Nucleic Acids Res 2021; 49:W446-W451. [PMID: 33893808 PMCID: PMC8262698 DOI: 10.1093/nar/gkab266] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 01/13/2023] Open
Abstract
Here we present an update to MutationTaster, our DNA variant effect prediction tool. The new version uses a different prediction model and attains higher accuracy than its predecessor, especially for rare benign variants. In addition, we have integrated many sources of data that only became available after the last release (such as gnomAD and ExAC pLI scores) and changed the splice site prediction model. To more easily assess the relevance of detected known disease mutations to the clinical phenotype of the patient, MutationTaster now provides information on the diseases they cause. Further changes represent a major overhaul of the interfaces to increase user-friendliness whilst many changes under the hood have been designed to accelerate the processing of uploaded VCF files. We also offer an API for the rapid automated query of smaller numbers of variants from within other software. MutationTaster2021 integrates our disease mutation search engine, MutationDistiller, to prioritise variants from VCF files using the patient's clinical phenotype. The novel version is available at https://www.genecascade.org/MutationTaster2021/. This website is free and open to all users and there is no login requirement.
Collapse
Affiliation(s)
- Robin Steinhaus
- Berliner Institut für Gesundheitsforschung in der Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Sebastian Proft
- Berliner Institut für Gesundheitsforschung in der Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Markus Schuelke
- Klinik für Pädiatrie m.S. Neurologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany.,NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XW, UK
| | - Jana Marie Schwarz
- Klinik für Pädiatrie m.S. Neurologie, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Dominik Seelow
- Berliner Institut für Gesundheitsforschung in der Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.,Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| |
Collapse
|
31
|
Seidel F, Holtgrewe M, Al-Wakeel-Marquard N, Opgen-Rhein B, Dartsch J, Herbst C, Beule D, Pickardt T, Klingel K, Messroghli D, Berger F, Schubert S, Kühnisch J, Klaassen S. Pathogenic Variants Associated With Dilated Cardiomyopathy Predict Outcome in Pediatric Myocarditis. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003250. [PMID: 34213952 PMCID: PMC8373449 DOI: 10.1161/circgen.120.003250] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Myocarditis is one of the most common causes leading to heart failure in children and a possible genetic background has been postulated. We sought to characterize the clinical and genetic characteristics in patients with myocarditis ≤18 years of age to predict outcome. METHODS A cohort of 42 patients (Genetics in Pediatric Myocarditis) with biopsy-proven myocarditis underwent genetic testing with targeted panel sequencing of cardiomyopathy-associated genes. Genetics in Pediatric Myocarditis patients were divided into subgroups according to the phenotype of dilated cardiomyopathy (DCM) at presentation, resulting in 22 patients without DCM (myocarditis without phenotype of DCM) and 20 patients with DCM (myocarditis with phenotype of DCM). RESULTS Myocarditis with phenotype of DCM patients (median age 1.4 years) were younger than myocarditis without phenotype of DCM patients (median age 16.1 years; P<0.001) and were corresponding to heart failure-like and coronary syndrome-like phenotypes, respectively. At least one likely pathogenic/pathogenic variant was identified in 9 out of 42 patients (22%), 8 of them were heterozygous, and 7 out of 9 were in myocarditis with phenotype of DCM. Likely pathogenic/pathogenic variants were found in genes validated for primary DCM (BAG3, DSP, LMNA, MYH7, TNNI3, TNNT2, and TTN). Rare variant enrichment analysis revealed significant accumulation of high-impact disease variants in myocarditis with phenotype of DCM versus healthy individuals (P=0.0003). Event-free survival was lower (P=0.008) in myocarditis with phenotype of DCM patients compared with myocarditis without phenotype of DCM and primary DCM. CONCLUSIONS We report heterozygous likely pathogenic/pathogenic variants in biopsy-proven pediatric myocarditis. Myocarditis patients with DCM phenotype were characterized by early-onset heart failure, significant enrichment of likely pathogenic/pathogenic variants, and poor outcome. These phenotype-specific and age group-specific findings will be useful for personalized management of these patients. Genetic evaluation in children newly diagnosed with myocarditis and DCM phenotype is warranted.
Collapse
Affiliation(s)
- Franziska Seidel
- German Heart Center Berlin, Department of Congenital Heart Disease - Pediatric Cardiology (F.S., N.A.-W.-M., F.B., S.S.).,Department of Pediatric Cardiology (F.S., B.O.-R., F.B., S.K.), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin & Berlin Institute of Health.,Institute for Imaging Science & Computational Modelling in Cardiovascular Medicine (F.S., N.A.-W.-M.), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin & Berlin Institute of Health.,Experimental & Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association & Charité - Universitätsmedizin Berlin (F.S., J.D., C.H., J.K., S.K.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin (F.S., N.A.-W.-M., F.B., S.S., J.K., S.K.)
| | - Manuel Holtgrewe
- Core Facility Bioinformatik (M.H.), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin & Berlin Institute of Health.,Berlin Institute of Health (BIH), Core Unit Bioinformatics (M.H., D.B.)
| | - Nadya Al-Wakeel-Marquard
- German Heart Center Berlin, Department of Congenital Heart Disease - Pediatric Cardiology (F.S., N.A.-W.-M., F.B., S.S.).,Institute for Imaging Science & Computational Modelling in Cardiovascular Medicine (F.S., N.A.-W.-M.), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin & Berlin Institute of Health.,DZHK (German Centre for Cardiovascular Research), partner site Berlin (F.S., N.A.-W.-M., F.B., S.S., J.K., S.K.)
| | - Bernd Opgen-Rhein
- Department of Pediatric Cardiology (F.S., B.O.-R., F.B., S.K.), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin & Berlin Institute of Health
| | - Josephine Dartsch
- Experimental & Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association & Charité - Universitätsmedizin Berlin (F.S., J.D., C.H., J.K., S.K.)
| | - Christopher Herbst
- Experimental & Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association & Charité - Universitätsmedizin Berlin (F.S., J.D., C.H., J.K., S.K.)
| | - Dieter Beule
- Berlin Institute of Health (BIH), Core Unit Bioinformatics (M.H., D.B.).,Max-Delbrück-Center for Molecular Medicine, Berlin, Germany (D.B.)
| | - Thomas Pickardt
- Competence Network for Congenital Heart Defects, Berlin (T.P.)
| | - Karin Klingel
- Cardiopathology, Institute for Pathology and Neuropathology, University Hospital Tuebingen (K.K.)
| | - Daniel Messroghli
- Department of Internal Medicine & Cardiology (D.M.), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin & Berlin Institute of Health.,German Heart Center Berlin, Department of Internal Medicine - Cardiology (D.M.)
| | - Felix Berger
- German Heart Center Berlin, Department of Congenital Heart Disease - Pediatric Cardiology (F.S., N.A.-W.-M., F.B., S.S.).,Department of Pediatric Cardiology (F.S., B.O.-R., F.B., S.K.), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin & Berlin Institute of Health.,DZHK (German Centre for Cardiovascular Research), partner site Berlin (F.S., N.A.-W.-M., F.B., S.S., J.K., S.K.)
| | - Stephan Schubert
- German Heart Center Berlin, Department of Congenital Heart Disease - Pediatric Cardiology (F.S., N.A.-W.-M., F.B., S.S.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin (F.S., N.A.-W.-M., F.B., S.S., J.K., S.K.).,Center for Congenital Heart Disease/Pediatric Cardiology, Heart- and Diabetescenter NRW & University Clinic of Ruhr-University Bochum, Bad Oeynhausen, Germany (S.S.)
| | - Jirko Kühnisch
- Experimental & Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association & Charité - Universitätsmedizin Berlin (F.S., J.D., C.H., J.K., S.K.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin (F.S., N.A.-W.-M., F.B., S.S., J.K., S.K.)
| | - Sabine Klaassen
- Department of Pediatric Cardiology (F.S., B.O.-R., F.B., S.K.), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin & Berlin Institute of Health.,Experimental & Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association & Charité - Universitätsmedizin Berlin (F.S., J.D., C.H., J.K., S.K.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin (F.S., N.A.-W.-M., F.B., S.S., J.K., S.K.)
| |
Collapse
|
32
|
Vogt G, El Choubassi N, Herczegfalvi Á, Kölbel H, Lekaj A, Schara U, Holtgrewe M, Krause S, Horvath R, Schuelke M, Hübner C, Mundlos S, Roos A, Lochmüller H, Karcagi V, Kornak U, Fischer‐Zirnsak B. Expanding the clinical and molecular spectrum of ATP6V1A related metabolic cutis laxa. J Inherit Metab Dis 2021; 44:972-986. [PMID: 33320377 PMCID: PMC8638669 DOI: 10.1002/jimd.12341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022]
Abstract
Several inborn errors of metabolism show cutis laxa as a highly recognizable feature. One group of these metabolic cutis laxa conditions is autosomal recessive cutis laxa type 2 caused by defects in v-ATPase components or the mitochondrial proline cycle. Besides cutis laxa, muscular hypotonia and cardiac abnormalities are hallmarks of autosomal recessive cutis laxa type 2D (ARCL2D) due to pathogenic variants in ATP6V1A encoding subunit A of the v-ATPase. Here, we report on three affected individuals from two families with ARCL2D in whom we performed whole exome and Sanger sequencing. We performed functional studies in fibroblasts from one individual, summarized all known probands' clinical, molecular, and biochemical features and compared them, also to other metabolic forms of cutis laxa. We identified novel missense and the first nonsense variant strongly affecting ATP6V1A expression. All six ARCL2D affected individuals show equally severe cutis laxa and dysmorphism at birth. While for one no information was available, two died in infancy and three are now adolescents with mild or absent intellectual disability. Muscular weakness, ptosis, contractures, and elevated muscle enzymes indicated a persistent myopathy. In cellular studies, a fragmented Golgi compartment, a delayed Brefeldin A-induced retrograde transport and glycosylation abnormalities were present in fibroblasts from two individuals. This is the second and confirmatory report on pathogenic variants in ATP6V1A as the cause of this extremely rare condition and the first to describe a nonsense allele. Our data highlight the tremendous clinical variability of ATP6V1A related phenotypes even within the same family.
Collapse
Affiliation(s)
- Guido Vogt
- Institut für Medizinische Genetik und Humangenetik, Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Max Planck Institute for Molecular Genetics, RG Development & DiseaseBerlinGermany
| | - Naji El Choubassi
- Institut für Medizinische Genetik und Humangenetik, Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Max Planck Institute for Molecular Genetics, RG Development & DiseaseBerlinGermany
| | - Ágnes Herczegfalvi
- Department of Pediatric NeurologySemmelweis Medical University, II. Pediatric ClinicBudapestHungary
| | - Heike Kölbel
- Department of Pediatric NeurologyUniversity Hospital Essen, University Duisburg‐EssenEssenGermany
| | - Anja Lekaj
- Institut für Medizinische Genetik und Humangenetik, Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Ulrike Schara
- Department of Pediatric NeurologyUniversity Hospital Essen, University Duisburg‐EssenEssenGermany
| | - Manuel Holtgrewe
- CUBI – Core Unit BioinformaticsBerlin Institute of HealthBerlinGermany
| | - Sabine Krause
- Friedrich‐Baur‐Institute, Department of NeurologyLudwig‐Maximilians‐University of MunichMunichGermany
| | - Rita Horvath
- Department of Clinical NeurosciencesUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
| | - Markus Schuelke
- Department of Neuropediatrics, Charité‐Universitätsmedizin Berlincorporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Christoph Hübner
- Department of Neuropediatrics, Charité‐Universitätsmedizin Berlincorporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Stefan Mundlos
- Institut für Medizinische Genetik und Humangenetik, Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Max Planck Institute for Molecular Genetics, RG Development & DiseaseBerlinGermany
| | - Andreas Roos
- Department of Pediatric NeurologyUniversity Hospital Essen, University Duisburg‐EssenEssenGermany
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaOntarioCanada
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaOntarioCanada
- Division of Neurology, Department of Medicine, The Ottawa HospitalOttawaCanada
- Brain and Mind Research InstituteUniversity of OttawaOttawaCanada
| | - Veronika Karcagi
- NIEH, Department of Molecular Genetics and DiagnosticsBudapestHungary
- Istenhegyi Genetic Diagnostic CentreBudapestHungary
| | - Uwe Kornak
- Institut für Medizinische Genetik und Humangenetik, Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Max Planck Institute for Molecular Genetics, RG Development & DiseaseBerlinGermany
- Institute of Human GeneticsUniversity Medical Center GöttingenGöttingenGermany
| | - Björn Fischer‐Zirnsak
- Institut für Medizinische Genetik und Humangenetik, Charité ‐ Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Max Planck Institute for Molecular Genetics, RG Development & DiseaseBerlinGermany
| |
Collapse
|
33
|
Genome sequencing in families with congenital limb malformations. Hum Genet 2021; 140:1229-1239. [PMID: 34159400 PMCID: PMC8263393 DOI: 10.1007/s00439-021-02295-y] [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: 03/18/2021] [Accepted: 05/10/2021] [Indexed: 12/20/2022]
Abstract
The extensive clinical and genetic heterogeneity of congenital limb malformation calls for comprehensive genome-wide analysis of genetic variation. Genome sequencing (GS) has the potential to identify all genetic variants. Here we aim to determine the diagnostic potential of GS as a comprehensive one-test-for-all strategy in a cohort of undiagnosed patients with congenital limb malformations. We collected 69 cases (64 trios, 1 duo, 5 singletons) with congenital limb malformations with no molecular diagnosis after standard clinical genetic testing and performed genome sequencing. We also developed a framework to identify potential noncoding pathogenic variants. We identified likely pathogenic/disease-associated variants in 12 cases (17.4%) including four in known disease genes, and one repeat expansion in HOXD13. In three unrelated cases with ectrodactyly, we identified likely pathogenic variants in UBA2, establishing it as a novel disease gene. In addition, we found two complex structural variants (3%). We also identified likely causative variants in three novel high confidence candidate genes. We were not able to identify any noncoding variants. GS is a powerful strategy to identify all types of genomic variants associated with congenital limb malformation, including repeat expansions and complex structural variants missed by standard diagnostic approaches. In this cohort, no causative noncoding SNVs could be identified.
Collapse
|
34
|
Vogt G, Verheyen S, Schwartzmann S, Ehmke N, Potratz C, Schwerin-Nagel A, Plecko B, Holtgrewe M, Seelow D, Blatterer J, Speicher MR, Kornak U, Horn D, Mundlos S, Fischer-Zirnsak B, Boschann F. Biallelic truncating variants in ATP9A cause a novel neurodevelopmental disorder involving postnatal microcephaly and failure to thrive. J Med Genet 2021; 59:662-668. [PMID: 34379057 PMCID: PMC9252857 DOI: 10.1136/jmedgenet-2021-107843] [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: 03/24/2021] [Accepted: 05/20/2021] [Indexed: 12/04/2022]
Abstract
Background Genes implicated in the Golgi and endosomal trafficking machinery are crucial for brain development, and mutations in them are particularly associated with postnatal microcephaly (POM). Methods Exome sequencing was performed in three affected individuals from two unrelated consanguineous families presenting with delayed neurodevelopment, intellectual disability of variable degree, POM and failure to thrive. Patient-derived fibroblasts were tested for functional effects of the variants. Results We detected homozygous truncating variants in ATP9A. While the variant in family A is predicted to result in an early premature termination codon, the variant in family B affects a canonical splice site. Both variants lead to a substantial reduction of ATP9A mRNA expression. It has been shown previously that ATP9A localises to early and recycling endosomes, whereas its depletion leads to altered gene expression of components from this compartment. Consistent with previous findings, we also observed overexpression of ARPC3 and SNX3, genes strongly interacting with ATP9A. Conclusion In aggregate, our findings show that pathogenic variants in ATP9A cause a novel autosomal recessive neurodevelopmental disorder with POM. While the physiological function of endogenous ATP9A is still largely elusive, our results underline a crucial role of this gene in endosomal transport in brain tissue.
Collapse
Affiliation(s)
- Guido Vogt
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sarah Verheyen
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Sarina Schwartzmann
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Cornelia Potratz
- Department of Pediatric Neurology, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anette Schwerin-Nagel
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Barbara Plecko
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Manuel Holtgrewe
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Bioinformatics and Translational Genetics, Berlin Institute of Health, Berlin, Germany
| | - Jasmin Blatterer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Uwe Kornak
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Institute of Human Genetics, University Medical Center Göttingen, Gottingen, Germany
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,RG Development and Disease, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Björn Fischer-Zirnsak
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,RG Development and Disease, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
35
|
Schwarz JM, Lüpken R, Seelow D, Kehr B. Novel sequencing technologies and bioinformatic tools for deciphering the non-coding genome. MED GENET-BERLIN 2021; 33:133-145. [PMID: 38836034 PMCID: PMC11006320 DOI: 10.1515/medgen-2021-2072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/24/2021] [Indexed: 06/06/2024]
Abstract
High-throughput sequencing techniques have significantly increased the molecular diagnosis rate for patients with monogenic disorders. This is primarily due to a substantially increased identification rate of disease mutations in the coding sequence, primarily SNVs and indels. Further progress is hampered by difficulties in the detection of structural variants and the interpretation of variants outside the coding sequence. In this review, we provide an overview about how novel sequencing techniques and state-of-the-art algorithms can be used to discover small and structural variants across the whole genome and introduce bioinformatic tools for the prediction of effects variants may have in the non-coding part of the genome.
Collapse
Affiliation(s)
- Jana Marie Schwarz
- Department of Neuropediatrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard Lüpken
- BIH-Junior Research Group Genome Informatics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik Seelow
- BIH-Bioinformatics and Translational Genetics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Birte Kehr
- BIH-Junior Research Group Genome Informatics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Algorithmic Bioinformatics, Regensburg Center for Interventional Immunology (RCI), Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
- University Regensburg, Regensburg, Germany
| |
Collapse
|
36
|
Stürznickel J, Jähn-Rickert K, Zustin J, Hennig F, Delsmann MM, Schoner K, Rehder H, Kreczy A, Schinke T, Amling M, Kornak U, Oheim R. Compound Heterozygous Frameshift Mutations in MESD Cause a Lethal Syndrome Suggestive of Osteogenesis Imperfecta Type XX. J Bone Miner Res 2021; 36:1077-1087. [PMID: 33596325 DOI: 10.1002/jbmr.4277] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/03/2021] [Accepted: 02/14/2021] [Indexed: 12/11/2022]
Abstract
Multiple genes are known to be associated with osteogenesis imperfecta (OI), a phenotypically and genetically heterogenous bone disorder, marked predominantly by low bone mineral density and increased risk of fractures. Recently, mutations affecting MESD, which encodes for a chaperone required for trafficking of the low-density lipoprotein receptors LRP5 and LRP6 in the endoplasmic reticulum, were described to cause autosomal-recessive OI XX in homozygous children. In the present study, whole-exome sequencing of three stillbirths in one family was performed to evaluate the presence of a hereditary disorder. To further characterize the skeletal phenotype, fetal autopsy, bone histology, and quantitative backscattered electron imaging (qBEI) were performed, and the results were compared with those from an age-matched control with regular skeletal phenotype. In each of the affected individuals, compound heterozygous mutations in MESD exon 2 and exon 3 were detected. Based on the skeletal phenotype, which was characterized by multiple intrauterine fractures and severe skeletal deformity, OI XX was diagnosed in these individuals. Histological evaluation of MESD specimens revealed an impaired osseous development with an altered osteocyte morphology and reduced canalicular connectivity. Moreover, analysis of bone mineral density distribution by qBEI indicated an impaired and more heterogeneous matrix mineralization in individuals with MESD mutations than in controls. In contrast to the previously reported phenotypes of individuals with OI XX, the more severe phenotype in the present study is likely explained by a mutation in exon 2, located within the chaperone domain of MESD, that leads to a complete loss of function, which indicates the relevance of MESD in early skeletal development. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR)..
Collapse
Affiliation(s)
- Julian Stürznickel
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Jähn-Rickert
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jozef Zustin
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Floriane Hennig
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maximilian M Delsmann
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Schoner
- Institute of Pathology, Fetal Pathology, Philipps-University Marburg, Marburg, Germany
| | - Helga Rehder
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Alfons Kreczy
- Department of Pathology, REGIOMED Klinikum Coburg, Coburg, Germany
| | - Thorsten Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Amling
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,BIH Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ralf Oheim
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
37
|
Kaur H, Kumar R, Lathwal A, Raghava GPS. Computational resources for identification of cancer biomarkers from omics data. Brief Funct Genomics 2021; 20:213-222. [PMID: 33788922 DOI: 10.1093/bfgp/elab021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/11/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
Cancer is one of the most prevailing, deadly and challenging diseases worldwide. The advancement in technology led to the generation of different types of omics data at each genome level that may potentially improve the current status of cancer patients. These data have tremendous applications in managing cancer effectively with improved outcome in patients. This review summarizes the various computational resources and tools housing several types of omics data related to cancer. Major categorization of resources includes-cancer-associated multiomics data repositories, visualization/analysis tools for omics data, machine learning-based diagnostic, prognostic, and predictive biomarker tools, and data analysis algorithms employing the multiomics data. The review primarily focuses on providing comprehensive information on the open-source multiomics tools and data repositories, owing to their broader applicability, economic-benefit and usability. Sections including the comparative analysis, tools applicability and possible future directions have also been discussed in detail. We hope that this information will significantly benefit the researchers and clinicians, especially those with no sound background in bioinformatics and who lack sufficient data analysis skills to interpret something from the plethora of cancer-specific data generated nowadays.
Collapse
|
38
|
Cerebellar atrophy on top of motor neuron compromise as indicator of late-onset GM2 gangliosidosis. J Neurol 2021; 268:2259-2262. [PMID: 33751187 PMCID: PMC8179894 DOI: 10.1007/s00415-021-10492-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/05/2022]
|
39
|
Horn D, Fernández-Núñez E, Gomez-Carmona R, Rivera-Barahona A, Nevado J, Schwartzmann S, Ehmke N, Lapunzina P, Otaify GA, Temtamy S, Aglan M, Boschann F, Ruiz-Perez VL. Biallelic truncating variants in MAPKAPK5 cause a new developmental disorder involving neurological, cardiac, and facial anomalies combined with synpolydactyly. Genet Med 2021; 23:679-688. [PMID: 33442026 DOI: 10.1038/s41436-020-01052-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE This study aimed to identify the genetic cause of a new multiple congenital anomalies syndrome observed in three individuals from two unrelated families. METHODS Clinical assessment was conducted prenatally and at different postnatal stages. Genetic studies included exome sequencing (ES) combined with single-nucleotide polymorphism (SNP) array based homozygosity mapping and trio ES. Dermal fibroblasts were used for functional assays. RESULTS A clinically recognizable syndrome characterized by severe developmental delay, variable brain anomalies, congenital heart defects, dysmorphic facial features, and a distinctive type of synpolydactyly with an additional hypoplastic digit between the fourth and fifth digits of hands and/or feet was identified. Additional features included eye abnormalities, hearing impairment, and electroencephalogram anomalies. ES detected different homozygous truncating variants in MAPKAPK5 in both families. Patient-derived cells showed no expression of MAPKAPK5 protein isoforms and reduced levels of the MAPKAPK5-interacting protein ERK3. F-actin recovery after latrunculin B treatment was found to be less efficient in patient-derived fibroblasts than in control cells, supporting a role of MAPKAPK5 in F-actin polymerization. CONCLUSION Our data indicate that loss-of-function variants in MAPKAPK5 result in a severe developmental disorder and reveal a major role of this gene in human brain, heart, and limb development.
Collapse
Affiliation(s)
- Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Elisa Fernández-Núñez
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Ricardo Gomez-Carmona
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Ana Rivera-Barahona
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Julian Nevado
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Paris, France
| | - Sarina Schwartzmann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Pablo Lapunzina
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Paris, France
| | - Ghada A Otaify
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, Egypt
| | - Samia Temtamy
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, Egypt
| | - Mona Aglan
- Department of Clinical Genetics, Division of Human Genetics and Genome Research, Center of Excellence for Human Genetics, National Research Centre, Cairo, Egypt
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Victor L Ruiz-Perez
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain. .,Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Paris, France.
| |
Collapse
|