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Bouhamdani N, McConkey H, Leblanc A, Sadikovic B, Amor MB. Diagnostic utility of DNA methylation episignature analysis for early diagnosis of KMT2B-related disorders: case report. Front Genet 2024; 15:1346044. [PMID: 38425714 PMCID: PMC10902455 DOI: 10.3389/fgene.2024.1346044] [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: 11/28/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
The lysine methyltransferase 2B (KMT2B) gene product is important for epigenetic modifications associated with active gene transcription in normal development and in maintaining proper neural function. Pathogenic variants in KMT2B have been associated with childhood-onset Dystonia-28 and Intellectual developmental disorder, autosomal dominant 68 (MRD 68) for cases of neurodevelopmental impairment without dystonia (DYT28; OMIM 617284 and MRD68; OMIM 619934, respectively). Since its first description in 2016, approximately one hundred KMT2B genetic variants have been reported with heterogeneous phenotypes, including atypical patterns of dystonia evolution and non-dystonic neurodevelopmental phenotypes. KMT2B-related disorders share many overlapping phenotypic characteristics with other neurodevelopmental disorders and delayed dystonia, that can appear later in childhood, often delaying clinical diagnosis. Furthermore, conventional genetic testing may not always provide actionable information (e.g., gene panel selection based on early clinical presentation or variants of uncertain significance), which prevents patients and families from obtaining early access to treatments and support. Herein, we describe the early diagnosis of KMT2B-related neurodevelopmental disorder by DNA methylation episignature testing in a 4-year-old patient without features of dystonia at diagnosis, which is reported to develop in more than 80% of KMT2B-related disorder cases. The proband, a 4-year-old female of Jewish-Israeli descent, presented with speech delay, microcephaly, poor weight gain, attention-deficit and hyperactivity disorder, dysmorphism, intellectual disabilities and joint hyperlaxity, but presented no signs of dystonia at initial evaluation. Episignature screening in this pre-symptomatic patient enabled accurate genetic diagnosis and timely and actionable intervention earlier in the natural history of Childhood-onset Dystonia-28.
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Affiliation(s)
- Nadia Bouhamdani
- Vitalité Health Network, Moncton, NB, Canada
- Faculty of medicine and health sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Formation Médicale du Nouveau-Brunswick, Université de Moncton, Moncton, NB, Canada
- Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry Western University, London, ON, Canada
| | - Amélie Leblanc
- Vitalité Health Network, Moncton, NB, Canada
- Faculty of medicine and health sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Formation Médicale du Nouveau-Brunswick, Université de Moncton, Moncton, NB, Canada
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry Western University, London, ON, Canada
| | - Mouna Ben Amor
- Vitalité Health Network, Moncton, NB, Canada
- Faculty of medicine and health sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Formation Médicale du Nouveau-Brunswick, Université de Moncton, Moncton, NB, Canada
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Thomsen M, Lange LM, Zech M, Lohmann K. Genetics and Pathogenesis of Dystonia. ANNUAL REVIEW OF PATHOLOGY 2024; 19:99-131. [PMID: 37738511 DOI: 10.1146/annurev-pathmechdis-051122-110756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Dystonia is a clinically and genetically highly heterogeneous neurological disorder characterized by abnormal movements and postures caused by involuntary sustained or intermittent muscle contractions. A number of groundbreaking genetic and molecular insights have recently been gained. While they enable genetic testing and counseling, their translation into new therapies is still limited. However, we are beginning to understand shared pathophysiological pathways and molecular mechanisms. It has become clear that dystonia results from a dysfunctional network involving the basal ganglia, cerebellum, thalamus, and cortex. On the molecular level, more than a handful of, often intertwined, pathways have been linked to pathogenic variants in dystonia genes, including gene transcription during neurodevelopment (e.g., KMT2B, THAP1), calcium homeostasis (e.g., ANO3, HPCA), striatal dopamine signaling (e.g., GNAL), endoplasmic reticulum stress response (e.g., EIF2AK2, PRKRA, TOR1A), autophagy (e.g., VPS16), and others. Thus, different forms of dystonia can be molecularly grouped, which may facilitate treatment development in the future.
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Affiliation(s)
- Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Lara M Lange
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
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Sugeno N, Hasegawa T, Haginoya K, Kubota T, Ikeda K, Nakamura T, Ishiyama S, Sato K, Yoshida S, Koshimizu E, Uematsu M, Miyatake S, Matsumoto N, Aoki M. Detection of Modified Histones from Oral Mucosa of a Patient with DYT- KMT2B Dystonia. Mol Syndromol 2023; 14:461-468. [PMID: 38108041 PMCID: PMC10722472 DOI: 10.1159/000530625] [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: 03/16/2023] [Accepted: 04/07/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction DYT-KMT2B is a rare childhood-onset, hereditary movement disorder typically characterized by lower-limb dystonia and subsequently spreads into the craniocervical and laryngeal muscles. Recently, KMT2B-encoding lysine (K)-specific histone methyltransferase 2B was identified as the causative gene for DYT-KMT2B, also known as DYT28. In addition to the fact that many physicians do not have sufficient experience or knowledge of hereditary dystonia, the clinical features of DYT-KMT2B overlap with those of other hereditary dystonia, and limited clinical biomarkers make the diagnosis difficult. Methods Histone proteins were purified from the oral mucosa of patients with de novo KMT2B mutation causing premature stop codon, and then trimethylated fourth lysine residue of histone H3 (H3K4me3) which was catalyzed by KMT2B was analyzed by immunoblotting with specific antibody. We further analyzed the significance of H3K4me3 in patients with DYT-KMT2B using publicly available datasets. Results H3K4me3 histone mark was markedly lower in the patient than in the control group. Additionally, a reanalysis of publicly available datasets concerning DNA methylation also demonstrated that KMT2B remained inactive in DYT-KMT2B. Discussion Although only one case was studied due to the rarity of the disease, the reduction of H3K4me3 in the patient's biological sample supports the dysfunction of KMT2B in DYT-KMT2B. Together with informatics approaches, our results suggest that KMT2B haploinsufficiency contributes to the DYT-KMT2B pathogenic process.
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Affiliation(s)
- Naoto Sugeno
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takafumi Hasegawa
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuhiro Haginoya
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
- Department of Pediatric Neurology, Miyagi Children’s Hospital, Sendai, Japan
| | - Takafumi Kubota
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kensuke Ikeda
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takaaki Nakamura
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shun Ishiyama
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kazuki Sato
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shun Yoshida
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Mitsugu Uematsu
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Masashi Aoki
- Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan
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Lee S, Menzies L, Hay E, Ochoa E, Docquier F, Rodger F, Deshpande C, Foulds NC, Jacquemont S, Jizi K, Kiep H, Kraus A, Löhner K, Morrison PJ, Popp B, Richardson R, van Haeringen A, Martin E, Toribio A, Li F, Jones WD, Sansbury FH, Maher ER. Epigenotype-genotype-phenotype correlations in SETD1A and SETD2 chromatin disorders. Hum Mol Genet 2023; 32:3123-3134. [PMID: 37166351 PMCID: PMC10630252 DOI: 10.1093/hmg/ddad079] [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: 02/16/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/12/2023] Open
Abstract
Germline pathogenic variants in two genes encoding the lysine-specific histone methyltransferase genes SETD1A and SETD2 are associated with neurodevelopmental disorders (NDDs) characterized by developmental delay and congenital anomalies. The SETD1A and SETD2 gene products play a critical role in chromatin-mediated regulation of gene expression. Specific methylation episignatures have been detected for a range of chromatin gene-related NDDs and have impacted clinical practice by improving the interpretation of variant pathogenicity. To investigate if SETD1A and/or SETD2-related NDDs are associated with a detectable episignature, we undertook targeted genome-wide methylation profiling of > 2 M CpGs using a next-generation sequencing-based assay. A comparison of methylation profiles in patients with SETD1A variants (n = 6) did not reveal evidence of a strong methylation episignature. A review of the clinical and genetic features of the SETD2 patient group revealed that, as reported previously, there were phenotypic differences between patients with truncating mutations (n = 4, Luscan-Lumish syndrome; MIM:616831) and those with missense codon 1740 variants [p.Arg1740Trp (n = 4) and p.Arg1740Gln (n = 2)]. Both SETD2 subgroups demonstrated a methylation episignature, which was characterized by hypomethylation and hypermethylation events, respectively. Within the codon 1740 subgroup, both the methylation changes and clinical phenotype were more severe in those with p.Arg1740Trp variants. We also noted that two of 10 cases with a SETD2-NDD had developed a neoplasm. These findings reveal novel epigenotype-genotype-phenotype correlations in SETD2-NDDs and predict a gain-of-function mechanism for SETD2 codon 1740 pathogenic variants.
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Affiliation(s)
- Sunwoo Lee
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Lara Menzies
- Department of Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Eleanor Hay
- Department of Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Eguzkine Ochoa
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - France Docquier
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Fay Rodger
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Charu Deshpande
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Saint Mary’s Hospital, Manchester, UK
| | - Nicola C Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Sébastien Jacquemont
- CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Khadije Jizi
- CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada
| | - Henriette Kiep
- Department of Neuropediatrics, University Hospital for Children and Adolescents, Leipzig, Germany
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Katharina Löhner
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrick J Morrison
- Patrick G Johnston Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, UK
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center of Functional Genomics, Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Ruth Richardson
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Hospital, Leiden, The Netherlands
| | - Ezequiel Martin
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Ana Toribio
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Fudong Li
- MOE Key Laboratory for Cellular Dynamics, The School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wendy D Jones
- Department of Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Francis H Sansbury
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board and Institute of Medical Genetics, University Hospital of Wales, Heath Park, Cardiff, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
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5
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Lee S, Ochoa E, Badura-Stronka M, Donnelly D, Lederer D, Lynch SA, Gardham A, Morton J, Stewart H, Docquier F, Rodger F, Martin E, Toribio A, Maher ER, Balasubramanian M. Germline pathogenic variants in HNRNPU are associated with alterations in blood methylome. Eur J Hum Genet 2023; 31:1040-1047. [PMID: 37407733 PMCID: PMC10474128 DOI: 10.1038/s41431-023-01422-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/24/2023] [Accepted: 06/22/2023] [Indexed: 07/07/2023] Open
Abstract
HNRNPU encodes a multifunctional RNA-binding protein that plays critical roles in regulating pre-mRNA splicing, mRNA stability, and translation. Aberrant expression and dysregulation of HNRNPU have been implicated in various human diseases, including cancers and neurological disorders. We applied a next generation sequencing based assay (EPIC-NGS) to investigate genome-wide methylation profiling for >2 M CpGs for 7 individuals with a neurodevelopmental disorder associated with HNRNPU germline pathogenic loss-of-function variants. Compared to healthy individuals, 227 HNRNPU-associated differentially methylated positions were detected. Both hyper- and hypomethylation alterations were identified but the former predominated. The identification of a methylation episignature for HNRNPU-associated neurodevelopmental disorder (NDD) implicates HNPRNPU-related chromatin alterations in the aetiopathogenesis of this disorder and suggests that episignature profiling should have clinical utility as a predictor for the pathogenicity of HNRNPU variants of uncertain significance. The detection of a methylation episignaure for HNRNPU-associated NDD is consistent with a recent report of a methylation episignature for HNRNPK-associated NDD.
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Affiliation(s)
- Sunwoo Lee
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Eguzkine Ochoa
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | | | - Deirdre Donnelly
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust/City Hospital, Belfast, Northern Ireland, UK
| | | | - Sally A Lynch
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin, Republic of Ireland
| | - Alice Gardham
- London North West University Healthcare NHS Trust Genetics Service, Middlesex, UK
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - France Docquier
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge, UK
| | - Fay Rodger
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge, UK
| | - Ezequiel Martin
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge, UK
| | - Ana Toribio
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Meena Balasubramanian
- Department of Oncology & Metabolism, University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK.
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6
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Oexle K, Zech M, Stühn LG, Siegert S, Brunet T, Schmidt WM, Wagner M, Schmidt A, Engels H, Tilch E, Monestier O, Destrėe A, Hanker B, Boesch S, Jech R, Berutti R, Kaiser F, Haslinger B, Haack TB, Garavaglia B, Krawitz P, Winkelmann J, Mirza-Schreiber N. Episignature analysis of moderate effects and mosaics. Eur J Hum Genet 2023; 31:1032-1039. [PMID: 37365401 PMCID: PMC10474287 DOI: 10.1038/s41431-023-01406-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/14/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
DNA methylation classifiers ("episignatures") help to determine the pathogenicity of variants of uncertain significance (VUS). However, their sensitivity is limited due to their training on unambiguous cases with strong-effect variants so that the classification of variants with reduced effect size or in mosaic state may fail. Moreover, episignature evaluation of mosaics as a function of their degree of mosaicism has not been developed so far. We improved episignatures with respect to three categories. Applying (i) minimum-redundancy-maximum-relevance feature selection we reduced their length by up to one order of magnitude without loss of accuracy. Performing (ii) repeated re-training of a support vector machine classifier by step-wise inclusion of cases in the training set that reached probability scores larger than 0.5, we increased the sensitivity of the episignature-classifiers by 30%. In the newly diagnosed patients we confirmed the association between DNA methylation aberration and age at onset of KMT2B-deficient dystonia. Moreover, we found evidence for allelic series, including KMT2B-variants with moderate effects and comparatively mild phenotypes such as late-onset focal dystonia. Retrained classifiers also can detect mosaics that previously remained below the 0.5-threshold, as we showed for KMT2D-associated Kabuki syndrome. Conversely, episignature-classifiers are able to revoke erroneous exome calls of mosaicism, as we demonstrated by (iii) comparing presumed mosaic cases with a distribution of artificial in silico-mosaics that represented all the possible variation in degree of mosaicism, variant read sampling and methylation analysis.
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Affiliation(s)
- Konrad Oexle
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz Munich, 85764, Neuherberg, Germany.
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany.
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany.
| | - Michael Zech
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Lara G Stühn
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076, Tübingen, Germany
- Centre for Rare Diseases, University of Tuebingen, 72076, Tuebingen, Germany
| | - Sandy Siegert
- Department of Pediatric and Adolescent Medicine, Medical University of Vienna, 1090, Wien, Austria
| | - Theresa Brunet
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Wolfgang M Schmidt
- Neuromuscular Research Department, Center for Anatomy and Cell Biology, Medical University of Vienna, 1090, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Axel Schmidt
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Erik Tilch
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
| | - Olivier Monestier
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique ASBL, 6041, Gosselies, Belgium
| | - Anne Destrėe
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique ASBL, 6041, Gosselies, Belgium
| | - Britta Hanker
- Institute of Human Genetics, Universitätsklinikum Schleswig-Holstein, 23538, Lübeck, Germany
| | - Sylvia Boesch
- Department of Neurology, Medizinische Universität, 6020, Insbruck, Austria
| | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, 12108, Prague, Czech Republic
| | - Riccardo Berutti
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Frank Kaiser
- Institute of Human Genetics, Universitätsklinikum Essen, 45122, Essen, Germany
| | - Bernhard Haslinger
- Department of Neurology, Technical University of Munich, School of Medicine, 81675, Munich, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076, Tübingen, Germany
- Centre for Rare Diseases, University of Tuebingen, 72076, Tuebingen, Germany
| | - Barbara Garavaglia
- Fondazione IRCCS, Istituto Neurologico Carlo Besta, 20133, Milano, Italy
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, Universität Bonn, 53127, Bonn, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Human Genetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
- Chair of Neurogenetics, Technical University of Munich, School of Medicine, 81675, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany
| | - Nazanin Mirza-Schreiber
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz Munich, 85764, Neuherberg, Germany
- Institute of Neurogenomics,Helmholtz Munich, 85764, Neuherberg, Germany
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7
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Barili V, Ambrosini E, Uliana V, Bellini M, Vitetta G, Martorana D, Cannizzaro IR, Taiani A, De Sensi E, Caggiati P, Hilton S, Banka S, Percesepe A. Success and Pitfalls of Genetic Testing in Undiagnosed Diseases: Whole Exome Sequencing and Beyond. Genes (Basel) 2023; 14:1241. [PMID: 37372421 DOI: 10.3390/genes14061241] [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: 04/30/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Novel approaches to uncover the molecular etiology of neurodevelopmental disorders (NDD) are highly needed. Even using a powerful tool such as whole exome sequencing (WES), the diagnostic process may still prove long and arduous due to the high clinical and genetic heterogeneity of these conditions. The main strategies to improve the diagnostic rate are based on family segregation, re-evaluation of the clinical features by reverse-phenotyping, re-analysis of unsolved NGS-based cases and epigenetic functional studies. In this article, we described three selected cases from a cohort of patients with NDD in which trio WES was applied, in order to underline the typical challenges encountered during the diagnostic process: (1) an ultra-rare condition caused by a missense variant in MEIS2, identified through the updated Solve-RD re-analysis; (2) a patient with Noonan-like features in which the NGS analysis revealed a novel variant in NIPBL causing Cornelia de Lange syndrome; and (3) a case with de novo variants in genes involved in the chromatin-remodeling complex, for which the study of the epigenetic signature excluded a pathogenic role. In this perspective, we aimed to (i) provide an example of the relevance of the genetic re-analysis of all unsolved cases through network projects on rare diseases; (ii) point out the role and the uncertainties of the reverse phenotyping in the interpretation of the genetic results; and (iii) describe the use of methylation signatures in neurodevelopmental syndromes for the validation of the variants of uncertain significance.
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Affiliation(s)
- Valeria Barili
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Melissa Bellini
- Department of Pediatrics and Neonatology, Guglielmo da Saliceto Hospital, 29121 Piacenza, Italy
| | - Giulia Vitetta
- Medical Genetics, University of Bologna, 40138 Bologna, Italy
| | - Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Ilenia Rita Cannizzaro
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Antonietta Taiani
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Erika De Sensi
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Sarah Hilton
- Division of Evolution, Infection & Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Antonio Percesepe
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
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