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Lee CL, Chuang CK, Chiu HC, Chang YH, Tu YR, Lo YT, Lin HY, Lin SP. Application of whole exome sequencing in the diagnosis of muscular disorders: a study of Taiwanese pediatric patients. Front Genet 2024; 15:1365729. [PMID: 38818036 PMCID: PMC11137626 DOI: 10.3389/fgene.2024.1365729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Background Muscular dystrophies and congenital myopathies encompass various inherited muscular disorders that present diagnostic challenges due to clinical complexity and genetic heterogeneity. Methods This study aimed to investigate the use of whole exome sequencing (WES) in diagnosing muscular disorders in pediatric patients in Taiwan. Out of 161 pediatric patients suspected to have genetic/inherited myopathies, 115 received a molecular diagnosis through conventional tests, single gene testing, and gene panels. The remaining 46 patients were divided into three groups: Group 1 (multiplex ligation-dependent probe amplification-negative Duchenne muscular dystrophy) with three patients (6.5%), Group 2 (various forms of muscular dystrophies) with 21 patients (45.7%), and Group 3 (congenital myopathies) with 22 patients (47.8%). Results WES analysis of these groups found pathogenic variants in 100.0% (3/3), 57.1% (12/21), and 68.2% (15/22) of patients in Groups 1 to 3, respectively. WES had a diagnostic yield of 65.2% (30 patients out of 46), detecting 30 pathogenic or potentially pathogenic variants across 28 genes. Conclusion WES enables the diagnosis of rare diseases with symptoms and characteristics similar to congenital myopathies and muscular dystrophies, such as muscle weakness. Consequently, this approach facilitates targeted therapy implementation and appropriate genetic counseling.
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Affiliation(s)
- Chung-Lin Lee
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, Taipei, Taiwan
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
| | - Chih-Kuang Chuang
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- College of Medicine, Fu-Jen Catholic University, Taipei, Taiwan
| | - Huei-Ching Chiu
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ya-Hui Chang
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yuan-Rong Tu
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yun-Ting Lo
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
| | - Hsiang-Yu Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, Taipei, Taiwan
- Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Shuan-Pei Lin
- Department of Pediatrics, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, Mackay Medical College, Taipei, Taiwan
- Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
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van Niekerk M, Moosa S, van Toorn R, Solomons R. Utility of next generation sequencing in paediatric neurological disorders: experience from South Africa. Eur J Hum Genet 2024:10.1038/s41431-024-01582-2. [PMID: 38702429 DOI: 10.1038/s41431-024-01582-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 05/06/2024] Open
Abstract
Next generation sequencing (NGS)-based tests have become routine first-line investigative modalities in paediatric neurology clinics in many high-income countries (HICs). Studies from these countries show that these tests are both cost-effective and reliable in diagnosing many complex childhood neurological diseases. However, NGS-based testing in low-and middle-income countries (LMICs) is limited due to affordability constraints. The primary objective of this study was to evaluate the diagnostic yield and impact of targeted gene panel sequencing in a selected paediatric cohort attending a tertiary paediatric neurology clinic in the Western Cape Province of South Africa. This retrospective study included 124 consecutive paediatric patients with neurological disease, aged 6 weeks to 17 years, referred for NGS-based multi-gene panel testing over a 41-month period. Twenty-four different disease group-specific panels were utilized. A caregiver experience questionnaire was administered when a pathogenic variant was identified. The overall study diagnostic yield (DY) was 45% (56/124 patients). The diagnostic yield in this study is similar to previously reported paediatric cohorts in HICs. The high yields for neuromuscular disorders (52%) and early epileptic encephalopathies (41%) suggest that NGS-based panels may be more cost-effective as first-line testing in well-defined phenotypes. The latter finding argues for early inclusion of all children with developmental epileptic encephalopathies (DEE), as early diagnosis leads to better treatment and avoidance of unnecessary investigations.
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Affiliation(s)
- Magriet van Niekerk
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Shahida Moosa
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
- Medical Genetics, Tygerberg Hospital, Cape Town, South Africa.
| | - Ronald van Toorn
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Regan Solomons
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Mansfield C, Boeri M, Coulter J, Baranowski E, Sparks S, An Haack K, Hamed A. The value of knowing: preferences for genetic testing to diagnose rare muscle diseases. Orphanet J Rare Dis 2024; 19:173. [PMID: 38649872 PMCID: PMC11036564 DOI: 10.1186/s13023-024-03160-7] [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: 05/03/2023] [Accepted: 03/30/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Genetic testing can offer early diagnosis and subsequent treatment of rare neuromuscular diseases. Options for these tests could be improved by understanding the preferences of patients for the features of different genetic tests, especially features that increase information available to patients. METHODS We developed an online discrete-choice experiment using key attributes of currently available tests for Pompe disease with six test attributes: number of rare muscle diseases tested for with corresponding probability of diagnosis, treatment availability, time from testing to results, inclusion of secondary findings, necessity of a muscle biopsy, and average time until final diagnosis if the first test is negative. Respondents were presented a choice between two tests with different costs, with respondents randomly assigned to one of two costs. Data were analyzed using random-parameters logit. RESULTS A total of 600 online respondents, aged 18 to 50 years, were recruited from the U.S. general population and included in the final analysis. Tests that targeted more diseases, required less time from testing to results, included information about unrelated health risks, and were linked to shorter time to the final diagnosis were preferred and associated with diseases with available treatment. Men placed relatively more importance than women on tests for diseases with available treatments. Most of the respondents would be more willing to get a genetic test that might return unrelated health information, with women exhibiting a statistically significant preference. While respondents were sensitive to cost, 30% of the sample assigned to the highest cost was willing to pay $500 for a test that could offer a diagnosis almost 2 years earlier. CONCLUSION The results highlight the value people place on the information genetic tests can provide about their health, including faster diagnosis of rare, unexplained muscle weakness, but also the value of tests for multiple diseases, diseases without treatments, and incidental findings. An earlier time to diagnosis can provide faster access to treatment and an end to the diagnostic journey, which patients highly prefer.
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Affiliation(s)
- Carol Mansfield
- Health Preference Assessment, RTI Health Solutions, Research Triangle Park, NC, USA
| | - Marco Boeri
- Health Preference Assessment, RTI Health Solutions, Research Triangle Park, NC, USA
| | - Josh Coulter
- Health Preference Assessment, RTI Health Solutions, Research Triangle Park, NC, USA
| | | | | | | | - Alaa Hamed
- Medical Affairs, Sanofi, Cambridge, MA, USA
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Krenn M, Wagner M, Zulehner G, Weng R, Jäger F, Keritam O, Sener M, Brücke C, Milenkovic I, Langer A, Buchinger D, Habersam R, Mayerhanser K, Brugger M, Brunet T, Jacob M, Graf E, Berutti R, Cetin H, Hoefele J, Winkelmann J, Zimprich F, Rath J. Next-generation sequencing and comprehensive data reassessment in 263 adult patients with neuromuscular disorders: insights into the gray zone of molecular diagnoses. J Neurol 2024; 271:1937-1946. [PMID: 38127101 PMCID: PMC10972933 DOI: 10.1007/s00415-023-12101-6] [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: 09/20/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Neuromuscular disorders (NMDs) are heterogeneous conditions with a considerable fraction attributed to monogenic defects. Despite the advancements in genomic medicine, many patients remain without a diagnosis. Here, we investigate whether a comprehensive reassessment strategy improves the diagnostic outcomes. METHODS We analyzed 263 patients with NMD phenotypes that underwent diagnostic exome or genome sequencing at our tertiary referral center between 2015 and 2023. We applied a comprehensive reassessment encompassing variant reclassification, re-phenotyping and NGS data reanalysis. Multivariable logistic regression was performed to identify predictive factors associated with a molecular diagnosis. RESULTS Initially, a molecular diagnosis was identified in 53 cases (20%), while an additional 23 (9%) had findings of uncertain significance. Following comprehensive reassessment, the diagnostic yield increased to 23%, revealing 44 distinct monogenic etiologies. Reasons for newly obtained molecular diagnoses were variant reclassifications in 7 and NGS data reanalysis in 3 cases including one recently described disease-gene association (DNAJB4). Male sex reduced the odds of receiving a molecular diagnosis (OR 0.42; 95%CI 0.21-0.82), while a positive family history (OR 5.46; 95%CI 2.60-11.76) and a myopathy phenotype (OR 2.72; 95%CI 1.11-7.14) increased the likelihood. 7% were resolved through targeted genetic testing or classified as acquired etiologies. CONCLUSION Our findings reinforce the use of NGS in NMDs of suspected monogenic origin. We show that a comprehensive reassessment enhances diagnostic accuracy. However, one needs to be aware that genetic diagnoses are often made with uncertainty and can even be downgraded based on new evidence.
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Affiliation(s)
- Martin Krenn
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Gudrun Zulehner
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Rosa Weng
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Fiona Jäger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Omar Keritam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Merve Sener
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Christof Brücke
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Ivan Milenkovic
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Agnes Langer
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Dominic Buchinger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Richard Habersam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Dr. Von Hauner's Children's Hospital, University of Munich, Munich, Germany
| | - Maureen Jacob
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Hakan Cetin
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Jakob Rath
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria.
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Piñeros-Fernández MC, Morte B, García-Giménez JL. Utility of exome sequencing for the diagnosis of pediatric-onset neuromuscular diseases beyond diagnostic yield: a narrative review. Neurol Sci 2024; 45:1455-1464. [PMID: 37989827 PMCID: PMC10942921 DOI: 10.1007/s10072-023-07210-z] [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: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 11/23/2023]
Abstract
Diagnosis of neuromuscular diseases (NMD) can be challenging because of the heterogeneity of this group of diseases. This review aimed to describe the diagnostic yield of whole exome sequencing (WES) for pediatric-onset neuromuscular disease diagnosis, as well as other benefits of this approach in patient management since WES can contribute to appropriate treatment selection in NMD patients. WES increases the possibility of reaching a conclusive genetic diagnosis when other technologies have failed and even exploring new genes not previously associated with a specific NMD. Moreover, this strategy can be useful when a dual diagnosis is suspected in complex congenital anomalies and undiagnosed cases.
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Affiliation(s)
- Martha Cecilia Piñeros-Fernández
- Servicio de Neurología Pediátrica, Hospital Pediátrico, Fundación Cardio Infantil-LaCardio, Bogotá, Colombia
- Unidad Pediátrica, Los Cobos Medical Center, Bogotá, Colombia
- Consulta Externa Especializada, Virrey Solís IPS, Bogotá, Colombia
| | - Beatriz Morte
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - José Luis García-Giménez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.
- Departamento de Fisiología, Facultad de Medicina y Odontología, Universitat de València, València, Spain.
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Sarıkaya Uzan G, Yılmaz Uzman C, Çinleti T, Günay Ç, Ülgenalp A, Hız Kurul S, Yiş U. Molecular Diagnosis of Limb-Girdle Muscular Dystrophy Using Next-Generation Sequencing Panels. Mol Syndromol 2024; 15:14-21. [PMID: 38357257 PMCID: PMC10862319 DOI: 10.1159/000533976] [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: 06/24/2023] [Accepted: 09/01/2023] [Indexed: 02/16/2024] Open
Abstract
Introduction Limb-girdle muscular dystrophies (LGMDs) are clinically and genetically heterogeneous muscle disorders. We aimed to share the diagnostic yield of an NGS gene panel containing LGMD-related genes and our experience with LGMD. Methods Between February 2019 and October 2022, patients with a suspicion of LGMD and their relatives were reviewed in terms of demographic, clinical, and individual genetic data, age of symptom onset, sex, clinical features, LGMD types, cardiac involvement, muscle biopsy results, family history, and consanguinity. Our NGS gene panel consisted of ANO5, CAPN3, CAV3, DAG1, DES, DNAJB6, DYSF, FKTN, FLNC, FRKP, GAA, GMPPB, HNRNPDL, ISPD, LIMS2, LMNA, MYOT, PLEC, POMGNT1, POMK, POMT1, POMT2, SGCA, SGCB, SGCD, SGCG, TCAP, TNPO3, TRAPPC11, TRIM32, and TTN genes. Results The diagnosis rate was 61.1% (11/18). Twelve (80%) patients with LGMD were male and three (20%) were female. The median age was 15.9 (range, 1.5-39) years. Our patient collective was drawn up out of patients with the following variants: LGMDR1 (n = 6; 40%), LGMDR2 (n = 4; 26.6%), LGMDR3 (n = 4; 26.6%), and LGMDR12 (n = 1; 6.7%). Conclusion The present study showed that the NGS panel has a high success rate in the diagnosis of LGMD and contributes to early diagnosis.
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Affiliation(s)
- Gamze Sarıkaya Uzan
- Division of Child Neurology, Department of Pediatrics, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Ceren Yılmaz Uzman
- Division of Pediatric Genetics, Department of Pediatrics, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Tayfun Çinleti
- Division of Pediatric Genetics, Department of Pediatrics, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Çağatay Günay
- Division of Child Neurology, Department of Pediatrics, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Ayfer Ülgenalp
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, İzmir, Turkey
| | - Semra Hız Kurul
- Division of Child Neurology, Department of Pediatrics, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
| | - Uluç Yiş
- Division of Child Neurology, Department of Pediatrics, Dokuz Eylül University Faculty of Medicine, İzmir, Turkey
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Jo YH, Choi SH, Yoo HW, Kwak MJ, Park KH, Kong J, Lee YJ, Nam SO, Lee BL, Chung WY, Oh SH, Kim YM. Clinical use of whole exome sequencing in children with developmental delay/intellectual disability. Pediatr Neonatol 2024:S1875-9572(24)00004-4. [PMID: 38281861 DOI: 10.1016/j.pedneo.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/14/2023] [Accepted: 05/19/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Identifying the underlying etiology of developmental delay/intellectual disability (DD/ID) is challenging but important. The genetic diagnosis of unexplained DD/ID helps in the treatment and prognosis of the disability in patients. In this study, we reported our experience of using whole exome sequencing (WES) of children with unexplained DD/ID. METHODS We conducted a retrospective analysis of WES results of children under 19 years of age with unexplained DD/ID between January 2020 and December 2021. The demographic data of all patients and variants identified through WES were evaluated. Furthermore, we evaluated the clinical characteristics that influenced the identification of genetic causes. RESULTS Forty-one patients with DD/ID were included, of whom 21 (51.2 %) were male. The average age at symptom onset was 1.6 ± 1.3 years, and the duration from symptom onset to diagnosis was 3.1 ± 3.7 years. Hypotonia was the most common symptom (17 patients, 41.5 %), and epilepsy was confirmed in 10 patients (24.4 %). Twenty-two pathogenic/likely pathogenic variants were identified in 20 patients, and three variants of uncertain significance were identified in three patients. Family-based trio Sanger sequencing for candidate variants of 12 families was conducted; 10 variants were de novo, one variant paternally inherited, and two variants compound heterozygous. The diagnostic yield of WES for DD/ID was 48.8 % and was significantly high in patients with an early onset of DD/ID and facial dysmorphism. In contrast, patients with autism spectrum disorder (ASD) were more likely to have negative WES results compared with others without ASD. CONCLUSION The diagnostic yield of WES was 48.8 %. We conclude that patients' characteristics, such as dysmorphic features and the age of symptom onset, can predict the likelihood that WES will identify a causal variant of a phenotype.
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Affiliation(s)
- Yoon Hee Jo
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Soo Han Choi
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Hye Won Yoo
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Min Jung Kwak
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Kyung Hee Park
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea
| | - Juhyun Kong
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Yun-Jin Lee
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Sang Ook Nam
- Department of Pediatrics, Pusan National University Children's Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Bo Lyun Lee
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Woo Yeong Chung
- Department of Pediatrics, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Seung Hwan Oh
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Young Mi Kim
- Department of Pediatrics, Pusan National University Hospital, Biomedical Research Institute, School of Medicine, Pusan National University, Busan, Republic of Korea.
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8
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Nallamilli BRR, Pan Y, Sniderman King L, Jagannathan L, Ramachander V, Lucas A, Markind J, Colzani R, Hegde M. Combined sequence and copy number analysis improves diagnosis of limb girdle and other myopathies. Ann Clin Transl Neurol 2023; 10:2092-2104. [PMID: 37688281 PMCID: PMC10647006 DOI: 10.1002/acn3.51896] [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: 05/17/2023] [Revised: 07/31/2023] [Accepted: 08/20/2023] [Indexed: 09/10/2023] Open
Abstract
OBJECTIVE Clinical and genetic heterogeneities make diagnosis of limb-girdle muscular dystrophy (LGMD) and other overlapping disorders of muscle weakness complicated and expensive. We aimed to develop a comprehensive next generation sequence-based multi-gene panel ("The Lantern Focused Neuromuscular Panel") to detect both sequence variants and copy number variants in one assay. METHODS Patients with clinical diagnosis of LGMD or other overlapping muscular dystrophies in the United States were tested by PerkinElmer Genomics in 2018-2021 via "The Lantern Project," a sponsored diagnostic testing program. Sixty-six genes related to LGMD subtypes- and other myopathies were investigated. Main outcomes were diagnostic yield, gene-variant spectrum, and LGMD subtypes' prevalence. RESULTS Molecular diagnosis was established in 19.6% (1266) of 6473 cases. Major genes contributing to LGMD were identified including CAPN3 (5.4%, 68), DYSF (4.0%, 51), GAA (3.7%, 47), ANO5 (3.6%, 45), and FKRP (2.7%, 34). Genes of other overlapping MD subtypes identified included PABPN1 (10.5%, 133), VCP (2.2%, 28), MYOT (1.2% 15), LDB3 (1.0%, 13), COL6A1 (1.5%, 19), FLNC (1.1%, 14), and DNAJB6 (0.8%, 10). Different sizes of copy number variants including single exon, multi-exon, and whole genes were identified in 7.5% (95) cases in genes including DMD, EMD, CAPN3, ANO5, SGCG, COL6A2, DOK7, and LAMA2. INTERPRETATION "The Lantern Focused Neuromuscular Panel" enables identification of LGMD subtypes and other myopathies with overlapping clinical features. Prevalence of some MD subtypes was higher than previously reported. Widespread deployment of this comprehensive NGS panel has the potential to ensure early, accurate diagnosis as well as re-define MD epidemiology.
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Rosenberg A, Tian C, He H, Ulm E, Collins Ruff K, B Nagaraj C. An evaluation of clinical presentation and genetic testing approaches for patients with neuromuscular disorders. Am J Med Genet A 2023; 191:2679-2692. [PMID: 37503964 DOI: 10.1002/ajmg.a.63356] [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: 02/12/2023] [Revised: 04/20/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
Inherited neuromuscular disorders (NMDs) are a large group of genetic conditions characterized by impaired peripheral nerve, motor neuron, neuromuscular junction, or skeletal muscle function. These conditions are also known to have clinical and genetic heterogeneity and variable ages of onset. Clinical evaluation for NMDs has increasingly incorporated molecular genetics. However, genetic testing is complicated by the variety of testing options and the ambiguity of NMD phenotypes. Examining test selection and yield may elucidate testing recommendations and improve the diagnostic journey for these patients. This retrospective chart review evaluated the clinical presentations, genetic testing approaches, and diagnostic outcomes of 155 patients with suspected NMDs at Cincinnati Children's Hospital Medical Center. A total of 262 individual tests were ordered, averaging 1.7 tests per patient. The clinic utilized 26 separate genetic tests, with test yields ranging from 0% to 66%. Overall, 21% of patients received a genetic diagnosis. Of all the clinical findings evaluated, elevated CPK levels with or without muscle weakness were the most informative symptoms correlated with a diagnostic result. This study highlights several genetic testing considerations for NMDs, including the variability of diagnostic outcomes. This knowledge is relevant to clinicians and patients, especially during the pretest counseling and consenting process.
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Affiliation(s)
- Amanda Rosenberg
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Cuixia Tian
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Hua He
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Elizabeth Ulm
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Chinmayee B Nagaraj
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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10
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Kurosawa R, Iida K, Ajiro M, Awaya T, Yamada M, Kosaki K, Hagiwara M. PDIVAS: Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing. BMC Genomics 2023; 24:601. [PMID: 37817060 PMCID: PMC10563346 DOI: 10.1186/s12864-023-09645-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Deep-intronic variants that alter RNA splicing were ineffectively evaluated in the search for the cause of genetic diseases. Determination of such pathogenic variants from a vast number of deep-intronic variants (approximately 1,500,000 variants per individual) represents a technical challenge to researchers. Thus, we developed a Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing (PDIVAS) to easily detect pathogenic deep-intronic variants. RESULTS PDIVAS was trained on an ensemble machine-learning algorithm to classify pathogenic and benign variants in a curated dataset. The dataset consists of manually curated pathogenic splice-altering variants (SAVs) and commonly observed benign variants within deep introns. Splicing features and a splicing constraint metric were used to maximize the predictive sensitivity and specificity, respectively. PDIVAS showed an average precision of 0.92 and a maximum MCC of 0.88 in classifying these variants, which were the best of the previous predictors. When PDIVAS was applied to genome sequencing analysis on a threshold with 95% sensitivity for reported pathogenic SAVs, an average of 27 pathogenic candidates were extracted per individual. Furthermore, the causative variants in simulated patient genomes were more efficiently prioritized than the previous predictors. CONCLUSION Incorporating PDIVAS into variant interpretation pipelines will enable efficient detection of disease-causing deep-intronic SAVs and contribute to improving the diagnostic yield. PDIVAS is publicly available at https://github.com/shiro-kur/PDIVAS .
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Affiliation(s)
- Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Kei Iida
- Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshida- Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Masahiko Ajiro
- Division of Cancer RNA Research, National Cancer Center Research Institute, Tokyo, 104- 0045, Japan
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Laboratory of Tumor Microenvironment and Immunity, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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11
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Ortiz-Vitali JL, Wu J, Xu N, Shieh AW, Niknejad N, Takeuchi M, Paradas C, Lin C, Jafar-Nejad H, Haltiwanger RS, Wang SH, Darabi R. Disease modeling and gene correction of LGMDR21 iPSCs elucidates the role of POGLUT1 in skeletal muscle maintenance, regeneration, and the satellite cell niche. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:683-697. [PMID: 37650119 PMCID: PMC10462830 DOI: 10.1016/j.omtn.2023.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Autosomal recessive limb-girdle muscular dystrophy 21 (LGMDR21) is caused by pathogenic variants in protein O-glucosyltransferase 1 (POGLUT1), which is responsible for O-glucosylation of specific epidermal growth factor (EGF) repeats found in ∼50 mammalian proteins, including Notch receptors. Previous data from patient biopsies indicated that impaired Notch signaling, reduction of muscle stem cells, and accelerated differentiation are probably involved in disease etiopathology. Using patient induced pluripotent stem cells (iPSCs), their corrected isotypes, and control iPSCs, gene expression profiling indicated dysregulation of POGLUT1, NOTCH, muscle development, extracellular matrix (ECM), cell adhesion, and migration as involved pathways. They also exhibited reduced in vitro POGLUT1 enzymatic activity and NOTCH signaling as well as defective myogenesis, proliferation, migration and differentiation. Furthermore, in vivo studies demonstrated significant reductions in engraftment, muscle stem cell formation, PAX7 expression, and maintenance, along with an increased percentage of mislocalized PAX7+ cells in the interstitial space. Gene correction in patient iPSCs using CRISPR-Cas9 nickase led to the rescue of the main in vitro and in vivo phenotypes. These results demonstrate the efficacy of iPSCs and gene correction in disease modeling and rescue of the phenotypes and provide evidence of the involvement of muscle stem cell niche localization, PAX7 expression, and cell migration as possible mechanisms in LGMDR21.
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Affiliation(s)
- Jose L. Ortiz-Vitali
- Center for Stem Cell and Regenerative Medicine (CSCRM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jianbo Wu
- Center for Stem Cell and Regenerative Medicine (CSCRM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nasa Xu
- Center for Stem Cell and Regenerative Medicine (CSCRM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Annie W. Shieh
- Center for Human Genetics, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nima Niknejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Megumi Takeuchi
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Carmen Paradas
- Neurology Department, Neuromuscular Disorders Unit, Instituto de Biomedicina de Sevilla, Hospital U. Virgen Del Rocío, CSIC, Universidad de Sevilla, Avd. Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert S. Haltiwanger
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sidney H. Wang
- Center for Human Genetics, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine (CSCRM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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12
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Fishler KP, Steber HS, Brunelli L, Shope RJ. Exploring collaboration models between geneticists and intensivists for implementing rapid genome sequencing in critical care settings. Am J Med Genet A 2023; 191:2290-2299. [PMID: 37318250 DOI: 10.1002/ajmg.a.63318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/13/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023]
Abstract
The availability of rapid genome sequencing (rGS) for children in a critical-care setting is increasing. This study explored the perspectives of geneticists and intensivists on optimal collaboration and division of roles when implementing rGS in neonatal and pediatric intensive care units (ICUs). We conducted an explanatory mixed methods study involving a survey embedded within an interview with 13 genetics and intensive care providers. Interviews were recorded, transcribed, and coded. Geneticists endorsed higher confidence in performing a physical exam and interpreting/communicating positive results. Intensivists endorsed highest confidence in determining whether genetic testing was appropriate, communicating negative results, and consenting. Major qualitative themes that emerged were: (1) concerns with both "genetics-led" and "intensivist-led" models with workflows and sustainability (2) shift the role of determining rGS eligibility to ICU medical professionals, (3) continued role of geneticists to assess phenotype, and (4) include genetic counselors (GCs) and neonatal nurse practitioners to enhance workflow and care. All geneticists supported shifting decisions regarding eligibility for rGS to the ICU team to minimize time cost for the genetics workforce. Exploring models of geneticist-led phenotyping, intensivist-led phenotyping for some indications, and/or inclusion of a dedicated inpatient GC may help offset the time burden of consenting and other tasks associated with rGS.
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Affiliation(s)
- Kristen P Fishler
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Hannah S Steber
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Luca Brunelli
- Division of Neonatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Ronald J Shope
- College of Allied Health Professions, University of Nebraska Medical Center, Omaha, Nebraska, USA
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13
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Ng KWP, Chin HL, Chin AXY, Goh DLM. Using gene panels in the diagnosis of neuromuscular disorders: A mini-review. Front Neurol 2022; 13:997551. [PMID: 36313509 PMCID: PMC9602396 DOI: 10.3389/fneur.2022.997551] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/21/2022] [Indexed: 09/26/2023] Open
Abstract
The diagnosis of inherited neuromuscular disorders is challenging due to their genetic and phenotypic variability. Traditionally, neurophysiology and histopathology were primarily used in the initial diagnostic approach to these conditions. Sanger sequencing for molecular diagnosis was less frequently utilized as its application was a time-consuming and cost-intensive process. The advent and accessibility of next-generation sequencing (NGS) has revolutionized the evaluation process of genetically heterogenous neuromuscular disorders. Current NGS diagnostic testing approaches include gene panels, whole exome sequencing (WES), and whole genome sequencing (WGS). Gene panels are often the most widely used, being more accessible due to availability and affordability. In this mini-review, we describe the benefits and risks of clinical genetic testing. We also discuss the utility, benefits, challenges, and limitations of using gene panels in the evaluation of neuromuscular disorders.
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Affiliation(s)
- Kay W. P. Ng
- Division of Neurology, Department of Medicine, National University Hospital, Singapore, Singapore
| | - Hui-Lin Chin
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amanda X. Y. Chin
- Division of Neurology, Department of Medicine, National University Hospital, Singapore, Singapore
| | - Denise Li-Meng Goh
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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14
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Hsueh HW, Weng WC, Fan PC, Chien YH, Yang FJ, Lee WT, Lin RJ, Hwu WL, Yang CC, Lee NC. The diversity of hereditary neuromuscular diseases: Experiences from molecular diagnosis. J Formos Med Assoc 2022; 121:2574-2583. [PMID: 35821219 DOI: 10.1016/j.jfma.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 03/02/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Hereditary neuromuscular diseases (NMDs) are a group of rare disorders, and the diagnosis of these diseases is a substantial burden for referral centers. Although next-generation sequencing (NGS) has identified a large number of genes associated with hereditary NMDs, the diagnostic rates still vary across centers. METHODS Patients with a suspected hereditary NMD were referred to neuromuscular specialists at the National Taiwan University Hospital. Molecular diagnoses were performed by employing a capture panel containing 194 genes associated with NMDs. RESULTS Among the 50 patients referred, 43 had a suspicion of myopathy, and seven had polyneuropathy. The overall diagnostic rate was 58%. Pathogenic variants in 19 genes were observed; the most frequent pathogenic variant found in this cohort (DYSF) was observed in only four patients, and 10 pathogenic variants were observed in one patient each. One case of motor neuron disease was clinically mistaken for myopathy. A positive family history increased the diagnostic rate (positive: 72.7% vs. negative: 56.3%). Fourteen patients with elevated plasma creatine kinase levels remained without a diagnosis. CONCLUSION The application of NGS in this single-center study proves the great diversity of hereditary NMDs. A capture panel is essential, but high-quality clinical and laboratory evaluations of patients are also indispensable.
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Affiliation(s)
- Hsueh-Wen Hsueh
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Chin Weng
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pi-Chuan Fan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Feng-Jung Yang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Wang-Tso Lee
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ru-Jen Lin
- Department of Neurology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Chao Yang
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Ni-Chung Lee
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
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15
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Nimer RM, Sumaily KM, Almuslat A, Jabar MA, Sabi EM, Al-Muhaizea MA, Rahman AMA. Dystrophin Protein Quantification as a Duchenne Muscular Dystrophy Diagnostic Biomarker in Dried Blood Spots Using Multiple Reaction Monitoring Tandem Mass Spectrometry: A Preliminary Study. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123662. [PMID: 35744792 PMCID: PMC9231037 DOI: 10.3390/molecules27123662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/23/2022] [Accepted: 05/28/2022] [Indexed: 11/16/2022]
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder characterized by progressive muscle loss, leading to difficulties in movement. Mutations in the DMD gene that code for the protein dystrophin are responsible for the development of DMD disorder, where the synthesis of this protein is completely halted. Therefore, circulating dystrophin protein could be a promising biomarker of DMD disease. Current methods for diagnosing DMD have sensitivity, specificity, and reproducibility limitations. Herein, a quantitative liquid chromatography-tandem spectrometry (LC-MS/MS) technique in multiple reaction monitoring (MRM) mode was designed and validated for accurate dystrophin protein measurement in a dried blood spot (DBS). The method was successfully validated on the basis of international guidelines regarding calibration curves, precision, and accuracy. In addition, patients and healthy controls were used to test the amount of dystrophin protein circulating in DBS samples as a potential biomarker for DMD disorders. DMD patients were found to have considerably lower levels than controls. To the best of our knowledge, this is the first study to report dystrophin levels in DBS through LC-MS/MS as a diagnostic marker for DMD to the proposed MRM method, providing a highly specific and sensitive approach to dystrophin quantification in a DBS that can be applied in DMD screening.
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Affiliation(s)
- Refat M. Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
- Correspondence: (R.M.N.); (A.M.A.R.)
| | - Khalid M. Sumaily
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (K.M.S.); (E.M.S.)
- Clinical Biochemistry Unit, Laboratory Medicine, King Saud University Medical City, King Saud University, Riyadh 11461, Saudi Arabia
| | - Arwa Almuslat
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia; (A.A.); (M.A.J.)
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Mai Abdel Jabar
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia; (A.A.); (M.A.J.)
| | - Essa M. Sabi
- Clinical Biochemistry Unit, Pathology Department, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia; (K.M.S.); (E.M.S.)
- Clinical Biochemistry Unit, Laboratory Medicine, King Saud University Medical City, King Saud University, Riyadh 11461, Saudi Arabia
| | - Mohammad A. Al-Muhaizea
- Department of Neurosciences, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia;
| | - Anas M. Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSH-RC), Zahrawi Street, Al Maather, Riyadh 11211, Saudi Arabia; (A.A.); (M.A.J.)
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Correspondence: (R.M.N.); (A.M.A.R.)
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16
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Targeted RNAseq Improves Clinical Diagnosis of Very Early-Onset Pediatric Immune Dysregulation. J Pers Med 2022; 12:jpm12060919. [PMID: 35743704 PMCID: PMC9224647 DOI: 10.3390/jpm12060919] [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: 04/28/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
Despite increased use of whole exome sequencing (WES) for the clinical analysis of rare disease, overall diagnostic yield for most disorders hovers around 30%. Previous studies of mRNA have succeeded in increasing diagnoses for clearly defined disorders of monogenic inheritance. We asked if targeted RNA sequencing could provide similar benefits for primary immunodeficiencies (PIDs) and very early-onset inflammatory bowel disease (VEOIBD), both of which are difficult to diagnose due to high heterogeneity and variable severity. We performed targeted RNA sequencing of a panel of 260 immune-related genes for a cohort of 13 patients (seven suspected PID cases and six VEOIBD) and analyzed variants, splicing, and exon usage. Exonic variants were identified in seven cases, some of which had been previously prioritized by exome sequencing. For four cases, allele specific expression or lack thereof provided additional insights into possible disease mechanisms. In addition, we identified five instances of aberrant splicing associated with four variants. Three of these variants had been previously classified as benign in ClinVar based on population frequency. Digenic or oligogenic inheritance is suggested for at least two patients. In addition to validating the use of targeted RNA sequencing, our results show that rare disease research will benefit from incorporating contributing genetic factors into the diagnostic approach.
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Barbosa-Gouveia S, Vázquez-Mosquera ME, González-Vioque E, Hermida-Ameijeiras Á, Sánchez-Pintos P, de Castro MJ, León SR, Gil-Fournier B, Domínguez-González C, Camacho Salas A, Negrão L, Fineza I, Laranjeira F, Couce ML. Rapid Molecular Diagnosis of Genetically Inherited Neuromuscular Disorders Using Next-Generation Sequencing Technologies. J Clin Med 2022; 11:jcm11102750. [PMID: 35628876 PMCID: PMC9143479 DOI: 10.3390/jcm11102750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/13/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023] Open
Abstract
Neuromuscular diseases are genetically highly heterogeneous, and differential diagnosis can be challenging. Over a 3-year period, we prospectively analyzed 268 pediatric and adult patients with a suspected diagnosis of inherited neuromuscular disorder (INMD) using comprehensive gene-panel analysis and next-generation sequencing. The rate of diagnosis increased exponentially with the addition of genes to successive versions of the INMD panel, from 31% for the first iteration (278 genes) to 40% for the last (324 genes). The global mean diagnostic rate was 36% (97/268 patients), with a diagnostic turnaround time of 4–6 weeks. Most diagnoses corresponded to muscular dystrophies/myopathies (68.37%) and peripheral nerve diseases (22.45%). The most common causative genes, TTN, RYR1, and ANO5, accounted for almost 30% of the diagnosed cases. Finally, we evaluated the utility of the differential diagnosis tool Phenomizer, which established a correlation between the phenotype and molecular findings in 21% of the diagnosed patients. In summary, comprehensive gene-panel analysis of all genes implicated in neuromuscular diseases facilitates a rapid diagnosis and provides a high diagnostic yield.
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Affiliation(s)
- Sofia Barbosa-Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
- Correspondence: (S.B.-G.); (M.L.C.); Tel.: +34-981-950-151 (M.L.C.)
| | - Maria Eugenia Vázquez-Mosquera
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Emiliano González-Vioque
- Department of Clinical Biochemistry, Puerta de Hierro-Majadahonda University Hospital, 28222 Majadahonda, Spain;
| | - Álvaro Hermida-Ameijeiras
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Paula Sánchez-Pintos
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Maria José de Castro
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Soraya Ramiro León
- Genetics Department, Hospital Universitario de Getafe, 28905 Madrid, Spain; (S.R.L.); (B.G.-F.)
| | - Belén Gil-Fournier
- Genetics Department, Hospital Universitario de Getafe, 28905 Madrid, Spain; (S.R.L.); (B.G.-F.)
| | - Cristina Domínguez-González
- Neuromuscular Unit, Imas12 Research Institute, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain;
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Camacho Salas
- Pediatric Neurology Unit, Hospital Universitario 12 de Octubre, Complutense University of Madrid, 28041 Madrid, Spain;
| | - Luis Negrão
- Neuromuscular Diseases Unit, Neurology Service, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal;
| | - Isabel Fineza
- Pediatric Neurology Department, Child Developmental Center, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra Coimbra Portugal, 3000-075 Coimbra, Portugal;
| | - Francisco Laranjeira
- Biochemical Genetics Unit, Centro de Genética Médica Doutor Jacinto Magalhães, 4050-466 Porto, Portugal;
| | - Maria Luz Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
- Correspondence: (S.B.-G.); (M.L.C.); Tel.: +34-981-950-151 (M.L.C.)
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18
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Hong SE, Kneissl J, Cho A, Kim MJ, Park S, Lee J, Woo S, Kim S, Kim JS, Kim SY, Jung S, Kim J, Shin JY, Chae JH, Choi M. Transcriptome-based variant calling and aberrant mRNA discovery enhance diagnostic efficiency for neuromuscular diseases. J Med Genet 2022; 59:1075-1081. [PMID: 35387801 PMCID: PMC9613860 DOI: 10.1136/jmedgenet-2021-108307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/08/2022] [Indexed: 12/15/2022]
Abstract
Background Whole-exome sequencing-based diagnosis of rare diseases typically yields 40%–50% of success rate. Precise diagnosis of the patients with neuromuscular disorders (NMDs) has been hampered by locus heterogeneity or phenotypic heterogeneity. We evaluated the utility of transcriptome sequencing as an independent approach in diagnosing NMDs. Methods The RNA sequencing (RNA-Seq) of muscle tissues from 117 Korean patients with suspected Mendelian NMD was performed to evaluate the ability to detect pathogenic variants. Aberrant splicing and CNVs were inspected to identify additional causal genetic factors for NMD. Aberrant splicing events in Dystrophin (DMD) were investigated by using antisense oligonucleotides (ASOs). A non-negative matrix factorisation analysis of the transcriptome data followed by cell type deconvolution was performed to cluster samples by expression-based signatures and identify cluster-specific gene ontologies. Results Our pipeline called 38.1% of pathogenic variants exclusively from the muscle transcriptomes, demonstrating a higher diagnostic rate than that achieved via exome analysis (34.9%). The discovery of variants causing aberrant splicing allowed the application of ASOs to the patient-derived cells, providing a therapeutic approach tailored to individual patients. RNA-Seq data further enabled sample clustering by distinct gene expression profiles that corresponded to clinical parameters, conferring additional advantages over exome sequencing. Conclusion The RNA-Seq-based diagnosis of NMDs achieves an increased diagnostic rate and provided pathogenic status information, which is not easily accessible through exome analysis.
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Affiliation(s)
- Sung Eun Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Jana Kneissl
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Anna Cho
- Department of Pediatrics, Rare Disease Center, Seoul National University Bundang Hospital, Gyeonggi-do, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
| | - Soojin Park
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul, Korea
| | - Jeongeun Lee
- Interdisciplinary Program in Bioengineering, Graduate School, Seoul National University, Seoul, Korea
| | - Sijae Woo
- Graduate School of Medical Science and Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Sora Kim
- Department of Genome Medicine and Science, Gachon University College of Medicine, Incheon, Korea
| | - Jun-Soon Kim
- Department of Neurology, Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Bundang Hospital, Geyonggi-do, Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea.,Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul, Korea
| | - Sungwon Jung
- Department of Genome Medicine and Science, Gachon University College of Medicine, Incheon, Korea.,Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon, Korea
| | - Jinkuk Kim
- Graduate School of Medical Science and Engineering and KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Je-Young Shin
- Department of Neurology, Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Hospital, Seoul, Korea
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea .,Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul, Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea .,Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
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19
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Krenn M, Tomschik M, Wagner M, Zulehner G, Weng R, Rath J, Klotz S, Gelpi E, Bsteh G, Keritam O, Colonna I, Paternostro C, Jäger F, Lindeck-Pozza E, Iglseder S, Grinzinger S, Schönfelder M, Hohenwarter C, Freimüller M, Embacher N, Wanschitz J, Topakian R, Töpf A, Straub V, Quasthoff S, Zimprich F, Löscher WN, Cetin H. Clinico-genetic spectrum of limb-girdle muscular weakness in Austria: a multi-centre cohort study. Eur J Neurol 2022; 29:1815-1824. [PMID: 35239206 PMCID: PMC9314602 DOI: 10.1111/ene.15306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 11/26/2022]
Abstract
Background and purpose Hereditary myopathies with limb‐girdle muscular weakness (LGW) are a genetically heterogeneous group of disorders, in which molecular diagnosis remains challenging. Our aim was to present a detailed clinical and genetic characterization of a large cohort of patients with LGW. Methods This nationwide cohort study included patients with LGW suspected to be associated with hereditary myopathies. Parameters associated with specific genetic aetiologies were evaluated, and we further assessed how they predicted the detection of causative variants by conducting genetic analyses. Results Molecular diagnoses were identified in 62.0% (75/121) of the cohort, with a higher proportion of patients diagnosed by next‐generation sequencing (NGS) than by single‐gene testing (77.3% vs. 22.7% of solved cases). The median (interquartile range) time from onset to genetic diagnosis was 8.9 (3.7–19.9) and 17.8 (7.9–27.8) years for single‐gene testing and NGS, respectively. The most common diagnoses were myopathies associated with variants in CAPN3 (n = 9), FKRP (n = 9), ANO5 (n = 8), DYSF (n = 8) and SGCA (n = 5), which together accounted for 32.2% of the cohort. Younger age at disease onset (p = 0.043), >10× elevated creatine kinase activity levels (p = 0.024) and myopathic electromyography findings (p = 0.007) were significantly associated with the detection of causative variants. Conclusions Our findings suggest that an earlier use of NGS in patients with LGW is needed to avoid long diagnostic delays. We further present parameters predictive of a molecular diagnosis that may help to select patients for genetic analyses, especially in centres with limited access to sequencing.
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Affiliation(s)
- Martin Krenn
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Matthias Tomschik
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute for Neurogenomics, Helmholtz Center Munich, Neuherberg, Germany.,LMU University Hospital, Department of Pediatrics, Dr. von Hauner Children's Hospital, Division of Pediatric Neurology, LMU Center for Development and Children with Medical Complexity, Ludwig-Maximilians-University, Munich, Germany
| | - Gudrun Zulehner
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Rosa Weng
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Jakob Rath
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Sigrid Klotz
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Ellen Gelpi
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Gabriel Bsteh
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Omar Keritam
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Isabella Colonna
- Department of Neurology, Medical University of Graz, Graz, Austria
| | | | - Fiona Jäger
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | | | - Stephan Iglseder
- Department of Neurology, KH der Barmherzigen Brüder, Linz, Austria
| | - Susanne Grinzinger
- Department of Neurology, Paracelsus Medical University of Salzburg, Salzburg, Austria
| | - Martina Schönfelder
- Department of Neurology, Klinikum Klagenfurt am Wörthersee, Klagenfurt, Austria
| | | | | | - Norbert Embacher
- Department of Neurology, University Hospital St, Pölten, St. Pölten, Austria
| | - Julia Wanschitz
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Raffi Topakian
- Department of Neurology, Klinikum Wels-Grieskirchen, Wels, Austria
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Stefan Quasthoff
- Department of Neurology, Medical University of Graz, Graz, Austria
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang N Löscher
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hakan Cetin
- Department of Neurology, Medical University of Vienna, Vienna, Austria
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20
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Narayanaswami P, Živković S. Molecular and Genetic Therapies. Neuromuscul Disord 2022. [DOI: 10.1016/b978-0-323-71317-7.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Clinical profile and multidisciplinary needs of patients with neuromuscular disorders transitioning from paediatric to adult care. Neuromuscul Disord 2021; 32:206-212. [DOI: 10.1016/j.nmd.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 09/19/2021] [Accepted: 12/08/2021] [Indexed: 11/15/2022]
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22
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Gemelli C, Traverso M, Trevisan L, Fabbri S, Scarsi E, Carlini B, Prada V, Mongini T, Ruggiero L, Patrone S, Gallone S, Iodice R, Pisciotta L, Zara F, Origone P, Rota E, Minetti C, Bruno C, Schenone A, Mandich P, Fiorillo C, Grandis M. An integrated approach to the evaluation of patients with asymptomatic or minimally symptomatic hyperCKemia. Muscle Nerve 2021; 65:96-104. [PMID: 34687219 PMCID: PMC9298868 DOI: 10.1002/mus.27448] [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: 11/11/2020] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 02/01/2023]
Abstract
Introduction/Aims Currently, there are no straightforward guidelines for the clinical and diagnostic management of hyperCKemia, a frequent and nonspecific presentation in muscle diseases. Therefore, we aimed to describe our diagnostic workflow for evaluating patients with this condition. Methods We selected 83 asymptomatic or minimally symptomatic patients with persistent hyperCKemia for participation in this Italian multicenter study. Patients with facial involvement and distal or congenital myopathies were excluded, as were patients with suspected inflammatory myopathies or predominant respiratory or cardiac involvement. All patients underwent a neurological examination and nerve conduction and electromyography studies. The first step of the investigation included a screening for Pompe disease. We then evaluated the patients for myotonic dystrophy type II–related CCTG expansion and excluded patients with copy number variations in the DMD gene. Subsequently, the undiagnosed patients were investigated using a target gene panel that included 20 genes associated with isolated hyperCKemia. Results Using this approach, we established a definitive diagnosis in one third of the patients. The detection rate was higher in patients with severe hyperCKemia and abnormal electromyographic findings. Discussion We have described our diagnostic workflow for isolated hyperCKemia, which is based on electrodiagnostic data, biochemical screening, and first‐line genetic investigations, followed by successive targeted sequencing panels. Both clinical signs and electromyographic abnormalities are associated with increased diagnostic yields.
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Affiliation(s)
- Chiara Gemelli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Genoa, Italy
| | - Monica Traverso
- Paediatric Neurology and Muscular Diseases Unit, IRCCS G. Gaslini Institute, Genoa, Italy
| | - Lucia Trevisan
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Genoa, Italy
| | - Sabrina Fabbri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Genoa, Italy
| | - Elena Scarsi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Genoa, Italy
| | - Barbara Carlini
- Unit of Medical Genetics, IRCCS G. Gaslini Institute, Genoa, Italy
| | - Valeria Prada
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Genoa, Italy
| | - Tiziana Mongini
- Neuromuscular Unit, Department of Neurosciences Rita Levi Montalcini, University of Torino, Torino, Italy
| | - Lucia Ruggiero
- Dipartimento di Neuroscienze e Scienze Riproduttive ed Odontostomatologiche, Università degli Studi di Napoli "Federico II,", Naples, Italy
| | - Serena Patrone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Genoa, Italy
| | - Salvatore Gallone
- Neurogenetic Service, Department of Neurosciences, AOU Città della salute e della scienza, Torino, Italy
| | - Rosa Iodice
- Dipartimento di Neuroscienze e Scienze Riproduttive ed Odontostomatologiche, Università degli Studi di Napoli "Federico II,", Naples, Italy
| | - Livia Pisciotta
- Department of Internal Medicine, University of Genoa, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Unit of Medical Genetics IRCCS G. Gaslini Institute, Genoa, Italy
| | - Paola Origone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Unit of Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Eugenia Rota
- Neurology Unit, ASL Alessandria, Novi Ligure, Italy
| | - Carlo Minetti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Pediatric Neurology and Muscular Diseases Unit, IRCCS G. Gaslini Institute, Genoa, Italy
| | - Claudio Bruno
- Centre of Experimental and Translational Myology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Angelo Schenone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Unit of Neurology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Paola Mandich
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Unit of Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Chiara Fiorillo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Pediatric Neurology and Muscular Diseases Unit, IRCCS G. Gaslini Institute, Genoa, Italy
| | - Marina Grandis
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genova, Unit of Neurology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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23
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Gangfuß A, Schara-Schmidt U, Roos A. [Genomics and proteomics in the research of neuromuscular diseases]. DER NERVENARZT 2021; 93:114-121. [PMID: 34622318 DOI: 10.1007/s00115-021-01201-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/04/2021] [Indexed: 11/30/2022]
Abstract
Neurological diseases affect 3-5% of children and, apart from cardiovascular diseases and cancer, represent the most prominent cause of morbidity and mortality in adults and particularly in the aged population of western Europe. Neuromuscular disorders are a subgroup of neurological diseases and often have a genetic origin, which leads to familial clustering. Despite the enormous progress in the analysis of the genome, such as by sequence analysis of coding regions of deoxyribonucleic acid or even the entire deoxyribonucleic acid sequence, in approximately 50% of the patients suffering from rare forms of neurological diseases the genetic cause remains unsolved. The reasons for this limited detection rate are presented in this article. If a treatment concept is available, under certain conditions this can have an impact on the adequate and early treatment of these patients. Considering neuromuscular disorders as a paradigm, this article reports on the advantages of the inclusion of next generation sequencing analysis-based DNA investigations as an omics technology (genomics) and the advantage of the integration with protein analyses (proteomics). A special focus is on the combination of genomics and proteomics in the sense of a proteogenomic approach in the diagnostics and research of these diseases. Along this line, this article presents a proteogenomic approach in the context of a multidisciplinary project aiming towards improved diagnostic work-up and future treatment of patients with neuromuscular diseases; "NMD-GPS: gene and protein signatures as a global positioning system in patients suffering from neuromuscular diseases".
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Affiliation(s)
- Andrea Gangfuß
- Abteilung für Neuropädiatrie, Universitätsmedizin Essen, Hufelandstrasse 55, 45147, Essen, Deutschland
| | - Ulrike Schara-Schmidt
- Abteilung für Neuropädiatrie, Universitätsmedizin Essen, Hufelandstrasse 55, 45147, Essen, Deutschland
| | - Andreas Roos
- Abteilung für Neuropädiatrie, Universitätsmedizin Essen, Hufelandstrasse 55, 45147, Essen, Deutschland. .,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Kanada.
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24
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Diagnostik von Myopathien bei Kindern und Jugendlichen. Monatsschr Kinderheilkd 2021. [DOI: 10.1007/s00112-021-01319-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Felice KJ, Whitaker CH, Khorasanizadeh S. Diagnostic yield of advanced genetic testing in patients with hereditary neuropathies: A retrospective single-site study. Muscle Nerve 2021; 64:454-461. [PMID: 34232518 DOI: 10.1002/mus.27368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 11/09/2022]
Abstract
INTRODUCTION/AIMS Advanced genetic testing including next-generation sequencing (AGT/NGS) has facilitated DNA testing in the clinical setting and greatly expanded new gene discovery for the Charcot-Marie-Tooth neuropathies and other hereditary neuropathies (CMT/HN). Herein, we report AGT/NGS results, clinical findings, and diagnostic yield in a cohort of CMT/HN patients evaluated at our neuropathy care center. METHODS We reviewed the medical records of all patients with suspected CMT/HN who underwent AGT/NGS at the Hospital for Special Care from January 2017 through January 2020. Patients with variants reported as pathogenic or likely pathogenic were included for further clinical review. RESULTS We ordered AGT/NGS on 108 patients with suspected CMT/HN. Of these, pathogenic or likely pathogenic variants were identified in 17 patients (diagnostic yield, 15.7%), including 6 (35%) with PMP22 duplications; 3 (18%) with MPZ variants; 2 (12%) with MFN2 variants; and 1 each with NEFL, IGHMBP2, GJB1, BSCL2, DNM2, and TTR variants. Diagnostic yield increased to 31.0% for patients with a positive family history. DISCUSSION AGT/NGS panels can provide specific genetic diagnoses for a subset of patients with CMT/HN disorders, which improves disease and genetic counseling and prepares patients for disease-focused therapies. Despite these advancements, many patients with known or suspected CMT/HN disorders remain without a specific genetic diagnosis. Continued advancements in genetic testing, such as multiomic technology and better understanding of genotype-phenotype correlation, will further improve detection rates for patients with suspected CMT/HN disorders.
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Affiliation(s)
- Kevin J Felice
- Department of Neuromuscular Medicine, Hospital for Special Care, New Britain, Connecticut, USA
| | - Charles H Whitaker
- Department of Neuromuscular Medicine, Hospital for Special Care, New Britain, Connecticut, USA
| | - Sadaf Khorasanizadeh
- Department of Neuromuscular Medicine, Hospital for Special Care, New Britain, Connecticut, USA
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26
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Wang W, Han R, Yang Z, Zheng S, Li H, Wan Z, Qi Y, Sun S, Ye L, Ning G. Targeted gene panel sequencing for molecular diagnosis of congenital adrenal hyperplasia. J Steroid Biochem Mol Biol 2021; 211:105899. [PMID: 33864926 DOI: 10.1016/j.jsbmb.2021.105899] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
CONTEXT Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive genetic diseases caused by genetic deficiency in nine genes encoding steroidogenesis enzymes and cofactors. OBJECTIVE To establish a targeted next-generation sequencing (NGS) assay for all nine CAH candidate genes. METHODS We developed a customized targeted NGS assay of CAH candidate genes (CYP21A2, CYP17A1, CYP11B1, StAR, CYP11A1, POR, HSD3B2, H6PD, CYP11B2) and apply this assay plus MLPA of CYP21A2 in a total of 469 patients with CAH like signs and symptoms. RESULTS We totally identified 125 variants with seven variant types in eight genes. Variant types included missense variant (46.8 %), splicing variant (21.5 %), small indel (12.5 %), large structure variation (11.8 %), nonsense variant (4.1 %), UTR variant (2.9 %), synonymous variant (0.3 %). Successful genotyping, defined as biallelic pathogenic or likely pathogenic variants, was achieved in 98.5 % (336/341) of cases, including biallelic variants in CYP21A2 (n = 254), CYP17A1 (n = 45), CYP11B1 (n = 23), StAR (n = 7), HSD3B2 (n = 4), POR (n = 1), CYP11A1 (n = 1) and CYP11B2 (n = 1) gene. Importantly, the assay found one patient with CYP11B1 deficiency, one patient with non-classic POR deficiency and two patients with non-classic CYP17A1 deficiency while clinically diagnosed differently. CONCLUSIONS Our NGS-based assay plus MLPA of CYP21A2 is a useful tool to genotype all subtypes of CAH. The test successfully achieved genotype in 98.5 % of patients with clinically determined CAH. It also efficiently facilitated the diagnosis of CAH in patients with rare subtypes as well as non-classic phenotypes.
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Affiliation(s)
- Wencui Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai National Clinical Center for Endocrine and Metabolic Diseases, Shanghai, 200025, PR China
| | - Rulai Han
- Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai, 200025, PR China
| | - Zuwei Yang
- Department of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai National Clinical Center for Endocrine and Metabolic Diseases, Shanghai, 200025, PR China
| | - Sichang Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai National Clinical Center for Endocrine and Metabolic Diseases, Shanghai, 200025, PR China
| | - Haorong Li
- Department of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai National Clinical Center for Endocrine and Metabolic Diseases, Shanghai, 200025, PR China
| | - Zhihan Wan
- Department of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai National Clinical Center for Endocrine and Metabolic Diseases, Shanghai, 200025, PR China
| | - Yan Qi
- Department of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai National Clinical Center for Endocrine and Metabolic Diseases, Shanghai, 200025, PR China
| | - Shouyue Sun
- Department of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai National Clinical Center for Endocrine and Metabolic Diseases, Shanghai, 200025, PR China.
| | - Lei Ye
- Department of Endocrine and Metabolic Diseases, Shanghai Jiao Tong University School of Medicine, Ruijin Hospital, Shanghai National Clinical Center for Endocrine and Metabolic Diseases, Shanghai, 200025, PR China.
| | - Guang Ning
- Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai, 200025, PR China.
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27
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Nicolau S, Milone M, Liewluck T. Guidelines for genetic testing of muscle and neuromuscular junction disorders. Muscle Nerve 2021; 64:255-269. [PMID: 34133031 DOI: 10.1002/mus.27337] [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: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022]
Abstract
Despite recent advances in the understanding of inherited muscle and neuromuscular junction diseases, as well as the advent of a wide range of genetic tests, patients continue to face delays in diagnosis of sometimes treatable disorders. These guidelines outline an approach to genetic testing in such disorders. Initially, a patient's phenotype is evaluated to identify myopathies requiring directed testing, including myotonic dystrophies, facioscapulohumeral muscular dystrophy, oculopharyngeal muscular dystrophy, mitochondrial myopathies, dystrophinopathies, and oculopharyngodistal myopathy. Initial investigation in the remaining patients is generally a comprehensive gene panel by next-generation sequencing. Broad panels have a higher diagnostic yield and can be cost-effective. Due to extensive phenotypic overlap and treatment implications, genes responsible for congenital myasthenic syndromes should be included when evaluating myopathy patients. For patients whose initial genetic testing is negative or inconclusive, phenotypic re-evaluation is warranted, along with consideration of genes and variants not included initially, as well as their acquired mimickers.
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Affiliation(s)
- Stefan Nicolau
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Teerin Liewluck
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
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28
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Babić Božović I, Maver A, Leonardis L, Meznaric M, Osredkar D, Peterlin B. Diagnostic yield of exome sequencing in myopathies: Experience of a Slovenian tertiary centre. PLoS One 2021; 16:e0252953. [PMID: 34106991 PMCID: PMC8189452 DOI: 10.1371/journal.pone.0252953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Our aim was to present the experience of systematic, routine use of next generation sequencing (NGS) in clinical diagnostics of myopathies. METHODS Exome sequencing was performed on patients with high risk for inherited myopathy, which were selected based on the history of the disease, family history, clinical presentation, and diagnostic workup. Exome target capture was performed, followed by sequencing on HiSeq 2500 or MiSeq platforms. Data analysis was performed using internally developed bioinformatic pipeline. RESULTS The study comprised 86 patients, including 22 paediatric cases (26%). The largest group were patients referred with an unspecified myopathy (47%), due to non-specific or incomplete clinical and laboratory findings, followed by congenital myopathies (22%) and muscular dystrophies (22%), congenital myotonias (6%), and mitochondrial myopathies (3%). Altogether, a diagnostic yield was 52%; a high diagnostic rate was present in paediatric patients (64%), while in patients with unspecified myopathies the rate was 35%. We found 51 pathogenic/likely pathogenic variants in 23 genes and two pathogenic copy number variations. CONCLUSION Our results provide evidence that phenotype driven exome analysis diagnostic approach facilitates the diagnostic rate of complex, heterogeneous disorders, such as myopathies, particularly in paediatric patients and patients with unspecified myopathies.
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Affiliation(s)
- Ivana Babić Božović
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Lea Leonardis
- Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Department of Neurology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marija Meznaric
- Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjan Osredkar
- Department of Paediatric Neurology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Péladeau C, Sandhu JK. Aberrant NLRP3 Inflammasome Activation Ignites the Fire of Inflammation in Neuromuscular Diseases. Int J Mol Sci 2021; 22:ijms22116068. [PMID: 34199845 PMCID: PMC8200055 DOI: 10.3390/ijms22116068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/24/2022] Open
Abstract
Inflammasomes are molecular hubs that are assembled and activated by a host in response to various microbial and non-microbial stimuli and play a pivotal role in maintaining tissue homeostasis. The NLRP3 is a highly promiscuous inflammasome that is activated by a wide variety of sterile triggers, including misfolded protein aggregates, and drives chronic inflammation via caspase-1-mediated proteolytic cleavage and secretion of proinflammatory cytokines, interleukin-1β and interleukin-18. These cytokines further amplify inflammatory responses by activating various signaling cascades, leading to the recruitment of immune cells and overproduction of proinflammatory cytokines and chemokines, resulting in a vicious cycle of chronic inflammation and tissue damage. Neuromuscular diseases are a heterogeneous group of muscle disorders that involve injury or dysfunction of peripheral nerves, neuromuscular junctions and muscles. A growing body of evidence suggests that dysregulation, impairment or aberrant NLRP3 inflammasome signaling leads to the initiation and exacerbation of pathological processes associated with neuromuscular diseases. In this review, we summarize the available knowledge about the NLRP3 inflammasome in neuromuscular diseases that affect the peripheral nervous system and amyotrophic lateral sclerosis, which affects the central nervous system. In addition, we also examine whether therapeutic targeting of the NLRP3 inflammasome components is a viable approach to alleviating the detrimental phenotype of neuromuscular diseases and improving clinical outcomes.
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Affiliation(s)
- Christine Péladeau
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada;
| | - Jagdeep K. Sandhu
- Human Health Therapeutics Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON K1A 0R6, Canada;
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
- Correspondence: ; Tel.: +1-613-993-5304
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30
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Barp A, Mosca L, Sansone VA. Facilitations and Hurdles of Genetic Testing in Neuromuscular Disorders. Diagnostics (Basel) 2021; 11:diagnostics11040701. [PMID: 33919863 PMCID: PMC8070835 DOI: 10.3390/diagnostics11040701] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of “unknown significance” can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain “not genetically defined”. In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss “facilitations and hurdles” of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of “therapeutic offer”.
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Affiliation(s)
- Andrea Barp
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
- Correspondence:
| | - Lorena Mosca
- Medical Genetics Unit, ASST Grande Ospedale Metropolitano Niguarda, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
| | - Valeria Ada Sansone
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
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31
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Abstract
Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of "unknown significance" can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain "not genetically defined". In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss "facilitations and hurdles" of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of "therapeutic offer".
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Affiliation(s)
- Andrea Barp
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
| | - Lorena Mosca
- Medical Genetics Unit, ASST Grande Ospedale Metropolitano Niguarda, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
| | - Valeria Ada Sansone
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
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32
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Fridman H, Bormans C, Einhorn M, Au D, Bormans A, Porat Y, Sanchez LF, Manning B, Levy-Lahad E, Behar DM. Performance comparison: exome sequencing as a single test replacing Sanger sequencing. Mol Genet Genomics 2021; 296:653-663. [PMID: 33694043 DOI: 10.1007/s00438-021-01772-3] [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: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 01/23/2023]
Abstract
Next generation sequencing tests are used routinely as first-choice tests in the clinic. However, systematic performance comparing the results of exome sequencing as a single test replacing Sanger sequencing of targeted gene(s) is still lacking. Performance comparison data are critically important for clinical case management. In this study, we compared Sanger-sequencing results of 258 genes to those obtained from next generation sequencing (NGS) using two exome-sequencing enrichment kits: Agilent-SureSelectQXT and Illumina-Nextera. Sequencing was performed on leukocytes and buccal-derived DNA from a single individual, and all 258 genes were sequenced a total of 11 times (using different sequencing methods and DNA sources). Sanger sequencing was completed for all exons, including flanking ± 8 bp regions. For the 258 genes, NGS mean coverage was > 20 × for > 98 and > 91% of the regions targeted by SureSelect and Nextera, respectively. Overall, 449 variants were identified in at least one experiment, and 407/449 (90.6%) were detected by all. Of the 42 discordant variants, 23 were determined as true calls, summing-up to a truth set of 430 variants. Sensitivity of true-variant detection was 99% for Sanger sequencing and 97-100% for the NGS experiments. Mean false-positive rates were 3.7E-6 for Sanger sequencing, 2.5E-6 for SureSelect-NGS and 5.2E-6 for Nextera-NGS. Our findings suggest a high overall concordance between Sanger sequencing and NGS performances. Both methods demonstrated false-positive and false-negative calls. High clinical suspicion for a specific diagnosis should, therefore, override negative results of either Sanger sequencing or NGS.
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Affiliation(s)
- Hila Fridman
- Medical Genetics Institute, Shaare Zedek Medical Center, 91031, Jerusalem, Israel. .,Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel.
| | | | - Moshe Einhorn
- Data Analysis Group, 6688218, Genoox, Tel Aviv, Israel
| | - Daniel Au
- Genomic Research Center, Gene By Gene, Houston, TX, 77008, USA
| | - Arjan Bormans
- Genomic Research Center, Gene By Gene, Houston, TX, 77008, USA
| | - Yuval Porat
- Data Analysis Group, 6688218, Genoox, Tel Aviv, Israel
| | | | - Brent Manning
- Genomic Research Center, Gene By Gene, Houston, TX, 77008, USA
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, 91031, Jerusalem, Israel.,Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Doron M Behar
- Genomic Research Center, Gene By Gene, Houston, TX, 77008, USA
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33
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François-Heude MC, Walther-Louvier U, Espil-Taris C, Beze-Beyrie P, Rivier F, Baudou E, Uro-Coste E, Rigau V, Martin Negrier ML, Rendu J, Morales RJ, Pégeot H, Thèze C, Lacourt D, Coville AC, Cossée M, Cances C. Evaluating next-generation sequencing in neuromuscular diseases with neonatal respiratory distress. Eur J Paediatr Neurol 2021; 31:78-87. [PMID: 33667896 DOI: 10.1016/j.ejpn.2021.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 01/19/2021] [Indexed: 02/09/2023]
Abstract
With the exception of infantile spinal muscular atrophy (SMA) and congenital myotonic dystrophy 1 (DM1), congenital myopathies and muscular dystrophies with neonatal respiratory distress pose diagnostic challenges. Next-generation sequencing (NGS) provides hope for the diagnosis of these rare diseases. We evaluated the efficiency of next-generation sequencing (NGS) in ventilated newborns with peripheral hypotonia. We compared the results of our previous study in a cohort of 19 patients analysed by Sanger sequencing from 2007 to 2012, with a diagnostic yield of 26% (5/19), and those of a new retrospective study in 28 patients from 2007 to 2018 diagnosed using MyoPanel, a neuromuscular disease panel, with a diagnostic yield of 43% (12/28 patients). Pathogenic variants were found in five genes: ACTA1 (n = 4 patients), RYR1 (n = 2), CACNA1S (n = 1), NEB (n = 3), and MTM1 (n = 2). Myopanel increased the diagnosis of congenital neuromuscular diseases, but more than half the patients remained undiagnosed. Whole exome sequencing did not seem to fully respond to this diagnostic limitation. Therefore, explorations with whole genome sequencing will be the next step.
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Affiliation(s)
- Marie-Céline François-Heude
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France
| | - Ulrike Walther-Louvier
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Montpellier University Hospital, Montpellier, France
| | - Caroline Espil-Taris
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Bordeaux University Hospital, Aquitaine, France
| | | | - François Rivier
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Montpellier University Hospital, Montpellier, France
| | - Eloise Baudou
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France
| | - Emmanuelle Uro-Coste
- Department of Pathology, Toulouse University Hospital, Toulouse, France; INSERM U1037, Cancer Research Centre of Toulouse (CRCT), Toulouse, France
| | - Valérie Rigau
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Aquitaine, France; Department of Pathology, Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | | | - John Rendu
- INSERM U1216, Grenoble Alpes University Hospital, University of Grenoble Alpes, Grenoble, France
| | - Raul Juntas Morales
- Laboratory of Rare Genetic Diseases (LGMR), University of Montpellier, Montpellier, France
| | - Henri Pégeot
- Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Corinne Thèze
- Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Delphine Lacourt
- Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Anne Cécile Coville
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France
| | - Mireille Cossée
- Laboratory of Rare Genetic Diseases (LGMR), University of Montpellier, Montpellier, France; Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Claude Cances
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France.
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34
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Zhang Y, Wang R, Liu Z, Jiang S, Du L, Qiu K, Li F, Wang Q, Jin J, Chen X, Li Z, Wu J, Zhang N. Distinct genetic patterns of shared and unique genes across four neurodevelopmental disorders. Am J Med Genet B Neuropsychiatr Genet 2021; 186:3-15. [PMID: 32929885 DOI: 10.1002/ajmg.b.32821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/04/2020] [Accepted: 08/15/2020] [Indexed: 01/09/2023]
Abstract
Neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual disability (ID), developmental disorders (DD) and epileptic encephalopathy (EE), have a strong clinical comorbidity, which indicates a common genetic etiology across various disorders. However, the underlying genetic mechanisms of comorbidity and specificity remain unknown across neurodevelopmental disorders. Based on de novo mutations, we compared systematically the functional characteristics between shared and unique genes under these disorders, as well as the spatiotemporal trajectory of development in brain and common molecular pathways of all shared genes. We observed that shared genes present more constrained against functional rare genetic variation, and harbor more pathogenic rare variants than do unique genes in each disorder. Furthermore, 71 shared genes formed two clusters related to synaptic transmission, transcription regulation and chromatin regulator. Particularly, we also found that two core genes STXBP1 and SCN2A, that were shared by the four neurodevelopmental disorders showed prominent pleiotropy. Our findings shed light on the shared and specific patterns across neurodevelopmental disorders and will enable us to further comprehend the etiology and provide valuable information for the diagnosis of neurodevelopmental disorders.
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Affiliation(s)
- Yijia Zhang
- Reproductive Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruochen Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Lifeng Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kairui Qiu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Fengxia Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qiongdan Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jing Jin
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China.,Medicine & Technology School of Zunyi Medical University, Zunyi, China
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35
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Estrella EA, Kang PB. Hunting for the perfect test: Neuromuscular diagnosis in the age of genomic bounty. Muscle Nerve 2021; 63:282-284. [PMID: 33382457 DOI: 10.1002/mus.27160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/26/2020] [Accepted: 12/28/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Elicia A Estrella
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Peter B Kang
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida.,Department of Neurology, University of Florida College of Medicine, Gainesville, Florida
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36
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Savarese M, Sarparanta J, Vihola A, Jonson PH, Johari M, Rusanen S, Hackman P, Udd B. Panorama of the distal myopathies. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2020; 39:245-265. [PMID: 33458580 PMCID: PMC7783427 DOI: 10.36185/2532-1900-028] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]
Abstract
Distal myopathies are genetic primary muscle disorders with a prominent weakness at onset in hands and/or feet. The age of onset (from early childhood to adulthood), the distribution of muscle weakness (upper versus lower limbs) and the histological findings (ranging from nonspecific myopathic changes to myofibrillar disarrays and rimmed vacuoles) are extremely variable. However, despite being characterized by a wide clinical and genetic heterogeneity, the distal myopathies are a category of muscular dystrophies: genetic diseases with progressive loss of muscle fibers. Myopathic congenital arthrogryposis is also a form of distal myopathy usually caused by focal amyoplasia. Massive parallel sequencing has further expanded the long list of genes associated with a distal myopathy, and contributed identifying as distal myopathy-causative rare variants in genes more often related with other skeletal or cardiac muscle diseases. Currently, almost 20 genes (ACTN2, CAV3, CRYAB, DNAJB6, DNM2, FLNC, HNRNPA1, HSPB8, KHLH9, LDB3, MATR3, MB, MYOT, PLIN4, TIA1, VCP, NOTCH2NLC, LRP12, GIPS1) have been associated with an autosomal dominant form of distal myopathy. Pathogenic changes in four genes (ADSSL, ANO5, DYSF, GNE) cause an autosomal recessive form; and disease-causing variants in five genes (DES, MYH7, NEB, RYR1 and TTN) result either in a dominant or in a recessive distal myopathy. Finally, a digenic mechanism, underlying a Welander-like form of distal myopathy, has been recently elucidated. Rare pathogenic mutations in SQSTM1, previously identified with a bone disease (Paget disease), unexpectedly cause a distal myopathy when combined with a common polymorphism in TIA1. The present review aims at describing the genetic basis of distal myopathy and at summarizing the clinical features of the different forms described so far.
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Affiliation(s)
- Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Jaakko Sarparanta
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Anna Vihola
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Neuromuscular Research Center, Department of Genetics, Fimlab Laboratories, Tampere, Finland
| | - Per Harald Jonson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Mridul Johari
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Salla Rusanen
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Peter Hackman
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Department of Neurology, Vaasa Central Hospital, Vaasa, Finland
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37
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Péladeau C, Jasmin BJ. Targeting IRES-dependent translation as a novel approach for treating Duchenne muscular dystrophy. RNA Biol 2020; 18:1238-1251. [PMID: 33164678 DOI: 10.1080/15476286.2020.1847894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Internal-ribosomal entry sites (IRES) are translational elements that allow the initiation machinery to start protein synthesis via internal initiation. IRESs promote tissue-specific translation in stress conditions when conventional cap-dependent translation is inhibited. Since many IRES-containing mRNAs are relevant to diseases, this cellular mechanism is emerging as an attractive therapeutic target for pharmacological and genetic modulations. Indeed, there has been growing interest over the past years in determining the therapeutic potential of IRESs for several disease conditions such as cancer, neurodegeneration and neuromuscular diseases including Duchenne muscular dystrophy (DMD). IRESs relevant for DMD have been identified in several transcripts whose protein product results in functional improvements in dystrophic muscles. Together, these converging lines of evidence indicate that activation of IRES-mediated translation of relevant transcripts in DMD muscle represents a novel and appropriate therapeutic strategy for DMD that warrants further investigation, particularly to identify agents that can modulate their activity.
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Affiliation(s)
- Christine Péladeau
- Department of Cellular and Molecular Medicine, and the Eric Poulin Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Bernard J Jasmin
- Department of Cellular and Molecular Medicine, and the Eric Poulin Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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38
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Iftikhar M, Frey J, Shohan MJ, Malek S, Mousa SA. Current and emerging therapies for Duchenne muscular dystrophy and spinal muscular atrophy. Pharmacol Ther 2020; 220:107719. [PMID: 33130193 DOI: 10.1016/j.pharmthera.2020.107719] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023]
Abstract
Many neuromuscular diseases are genetically inherited or caused by mutations in motor function proteins. Two of the most prevalent neuromuscular diseases are Duchenne Muscular Dystrophy (DMD) and Spinal Muscular Atrophy (SMA), which are often diagnosed during the early years of life, contributing to life-long debilitation and shorter longevity. DMD is caused by mutations in the dystrophin gene resulting in critical muscle wasting, with cardiac or respiratory failure by age 30. Lack of dystrophin protein is the leading cause of degeneration of skeletal and cardiac muscle. Corticosteroids and artificial respirators remain as the gold-standard management of complications and have significantly extended the life span of these patients. Additionally, drug therapies including eteplirsen (EXONDYS 51®), golodirsen (VYONDYS 53™), and viltolarsen (VILTEPSO®) have been approved by the FDA to treat specific types of DMD. SMA is defined by the degeneration of the anterior horn cells in the spinal cord and destruction of motor neuron nuclei in the lower brain-stem caused by SMN1 gene deletion. Loss of SMN1 protein is partly compensated by SMN2 protein synthesis with disease severity being affected by the success of SMN2 gene synthesis. Evidence-based recommendations for SMA are directed towards supportive therapy and providing adequate nutrition and respiratory assistance as needed. Treatment and prevention of complications of muscle weakness are crucial for reducing the phenotype expression of SMA. Furthermore, drug therapies including injectables such as onasemnogene abeparvovec-xioi (ZOLGENSMA®), nusinersen (SPINRAZA®), and an oral-solution, risdiplam (EVRYSDI™), are medications that have been FDA-approved for the treatment of SMA. This review discusses the current and emerging therapeutic options for patients with DMD and SMA.
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Affiliation(s)
- Mohsan Iftikhar
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY 12144, United States of America
| | - Justin Frey
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY 12144, United States of America
| | - Md Jasimuddin Shohan
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY 12144, United States of America
| | - Sohail Malek
- Department of Pediatric Neurology, Albany Medical Center, Albany, NY 12208, United States of America
| | - Shaker A Mousa
- The Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY 12144, United States of America.
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39
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Genotype and age at diagnosis in Thai boys with Duchenne muscular dystrophy (DMD). Neuromuscul Disord 2020; 30:839-844. [PMID: 32962870 DOI: 10.1016/j.nmd.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/04/2020] [Accepted: 09/02/2020] [Indexed: 11/24/2022]
Abstract
Gene-based therapy is a treatment for Duchenne muscular dystrophy (DMD) has become lately available; limited use for specific of mutation and percentages of the patients. Diagnosis in Thailand is made by muscle biopsy or multiplex ligation-dependent probe amplification (MLPA). Appropriate treatment in developing countries is difficult because gene sequencing is expensive and has limited availability. We aimed to identify the clinical and genetic characteristics of Thai DMD. Patients aged 0-22 years were recruited from the pediatric neuromuscular clinic of Siriraj Hospital during 2017-2019. Ninety-four charts were reviewed for clinical and laboratory data. Patients with negative MLPA who underwent next generation sequencing were consented. The mean age at onset and diagnosis was 4 and 7 years, respectively. Approximately 70% of patients had loss of ambulation by the mean age of 9.6 ± 1.8 years. Eighty percent were treated with glucocorticoids. Genetic testing was performed in 70 patients. Molecular analysis revealed mutations in 90% of cases, including exon deletions in 48.57%, nonsense mutations in 20%, frameshift mutations in 12.86%, splice site in 7.14%, exon duplications in 5.71%, and in-frame deletion in 2.86%. Gene sequencing should be performed because baseline genetic mutation data is essential for gene-based therapies that will become available in the future.
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Peterlin B, Gualandi F, Maver A, Servidei S, van der Maarel SM, Lamy F, Mejat A, Evangelista T, Ferlini A. Genetic testing offer for inherited neuromuscular diseases within the EURO-NMD reference network: A European survey study. PLoS One 2020; 15:e0239329. [PMID: 32946487 PMCID: PMC7500674 DOI: 10.1371/journal.pone.0239329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/03/2020] [Indexed: 11/19/2022] Open
Abstract
The genetic diagnostics of inherited neuromuscular diseases (NMDs) is challenging due to their clinical and genetic heterogeneity. We launched an online survey within the EURO-NMD European Reference Network (ERN) to collect information about the availability/distribution of genetic testing across 61 ERN health care providers (HCPs). A 17 items questionnaire was designed to address methods used, the number of genetic tests available, the clinical pathway to access genetic testing, the use of next-generation sequencing (NGS) and participation to quality assessment schemes (QAs). A remarkable number of HCPs (49%) offers ≥ 500 genetic tests per year, 43,6% offers 100–500 genetic tests per year, and 7,2% ≤ 100 per year. NGS is used by 94% of centres, Sanger sequencing by 84%, MLPA by 66% and Southern blotting by 36%. The majority of centres (60%) offer NGS for all patients that fulfil criteria for NMD of genetic origin. Pipelines for NGS vary amongst centres, even within the same national system. Referral of patients to genetic laboratories by specialists was frequently reported (58%), and 65% of centres participates in genetic testing QAs. We specifically evaluated how many centres cover SMA, DMD, Pompe, LGMDs, and TTR genes/diseases genetic diagnosis, since these rare diseases benefit from personalised therapies. We used the Orphanet EUGT numbers, provided by 82% of HCPs. SMA, DMD, LGMD, TTR and GAA genes are covered by EUGTs although with different numbers and modalities. The number of genetic tests for NMDs offered across HCPs National Health systems is quite high, including routine techniques and NGS. The number and type of tests offered and the clinical practices differ among centres. We provided evidence that survey tools might be useful to learn about the state-of-the-art of ERN health-related activities and to foster harmonisation and standardisation of the complex care for the rare disease patients in the EU.
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Affiliation(s)
- Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Serenella Servidei
- Neurophysiopathology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | | | | | - Teresinha Evangelista
- Neuromuscular Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, Sorbonne Université, Paris, France
- * E-mail: (AF); (TE)
| | - Alessandra Ferlini
- Unit of Medical Genetics, University Hospital Ferrara, Ferrara, Italy
- * E-mail: (AF); (TE)
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Srinivasan R, Yun P, Neuhaus S, Mohassel P, Dastgir J, Donkervoort S, Schindler A, Mankodi A, Foley AR, Arai AE, Bönnemann CG. Cardiac MRI identifies valvular and myocardial disease in a subset of ANO5-related muscular dystrophy patients. Neuromuscul Disord 2020; 30:742-749. [PMID: 32819793 DOI: 10.1016/j.nmd.2020.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 05/19/2020] [Accepted: 07/02/2020] [Indexed: 11/17/2022]
Abstract
Patients with bi-allelic loss-of-function mutations in the gene ANO5 most commonly present with muscular dystrophy. In some studies, patients with ANO5-related dystrophy (ANO5-RD) had evidence of mild cardiac abnormalities; however, cardiac magnetic resonance imaging (MRI) has not been used for myocardial characterization. Ten patients with genetically confirmed ANO5-RD were enrolled in a phenotyping study to better characterize cardiac involvement. Evaluations included medical history, neurological examination and cardiac evaluations (electrocardiogram, echocardiogram and cardiac MRI). All patients were clinically asymptomatic from a cardiac perspective. Muscle MRI was consistent with previous studies of ANO5-RD with increased T1 signal in the posterior and medial compartments of the upper leg and the posterior compartment of the lower leg. Cardiac studies using echocardiography and cardiac MRI revealed dilation of the aortic root and thickening of the aortic valve without significant stenosis in 3/10 patients. There was evidence of abnormal late gadolinium enhancement (LGE) on cardiac MRI in 2/10 patients. In ANO5-RD, the development of cardiac fibrosis, edema or inflammation as demonstrated by LGE has not yet been reported. Cardiac MRI can characterize cardiac tissue and may detect subtle changes before they appear on echocardiography, with potential prognostic implications.
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Affiliation(s)
- Ranjini Srinivasan
- Advanced Cardiovascular Imaging Laboratory, NHLBI, NIH, Bethesda, MD, United States
| | - Pomi Yun
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | - Sarah Neuhaus
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | | | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | - Alice Schindler
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | - Ami Mankodi
- Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States
| | - Andrew E Arai
- Advanced Cardiovascular Imaging Laboratory, NHLBI, NIH, Bethesda, MD, United States
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, NINDS, NIH, Bethesda, MD, United States.
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Gieron-Korthals M, Fernandez R. New Developments in Diagnosis, Treatment, and Management of Duchenne Muscular Dystrophy. Adv Pediatr 2020; 67:183-196. [PMID: 32591061 DOI: 10.1016/j.yapd.2020.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Maria Gieron-Korthals
- Department of Pediatrics, Division of Child Neurology, University of South Florida, Morsani College of Medicine, 17 Davis Boulevard, Suite 200, Tampa, FL 33606, USA.
| | - Raymond Fernandez
- Pediatric Neurology Associates, 4150 North Armenia Avenue, Suite 103, Tampa, FL 33607, USA; Muscular Dystrophy Association Care Center, Shriners Hospital for Children, Tampa, FL, USA
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The ties that bind: functional clusters in limb-girdle muscular dystrophy. Skelet Muscle 2020; 10:22. [PMID: 32727611 PMCID: PMC7389686 DOI: 10.1186/s13395-020-00240-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
The limb-girdle muscular dystrophies (LGMDs) are a genetically pleiomorphic class of inherited muscle diseases that are known to share phenotypic features. Selected LGMD genetic subtypes have been studied extensively in affected humans and various animal models. In some cases, these investigations have led to human clinical trials of potential disease-modifying therapies, including gene replacement strategies for individual subtypes using adeno-associated virus (AAV) vectors. The cellular localizations of most proteins associated with LGMD have been determined. However, the functions of these proteins are less uniformly characterized, thus limiting our knowledge of potential common disease mechanisms across subtype boundaries. Correspondingly, broad therapeutic strategies that could each target multiple LGMD subtypes remain less developed. We believe that three major "functional clusters" of subcellular activities relevant to LGMD merit further investigation. The best known of these is the glycosylation modifications associated with the dystroglycan complex. The other two, mechanical signaling and mitochondrial dysfunction, have been studied less systematically but are just as promising with respect to the identification of significant mechanistic subgroups of LGMD. A deeper understanding of these disease pathways could yield a new generation of precision therapies that would each be expected to treat a broader range of LGMD patients than a single subtype, thus expanding the scope of the molecular medicines that may be developed for this complex array of muscular dystrophies.
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Gao G, Smith DI. Clinical Massively Parallel Sequencing. Clin Chem 2020; 66:77-88. [PMID: 31811004 DOI: 10.1373/clinchem.2019.303305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/24/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND The newest advances in DNA sequencing are based on technologies that perform massively parallel sequencing (MPS). Since 2006, the output from MPS platforms has increased from 20 Mb to >7 Tb. First-generation MPS platforms amplify individual DNA molecules to multiple copies and then interrogate the sequence of those molecules. Second-generation MPS analyzes single unamplified molecules to generate much longer sequence reads but with less output than first-generation MPS and lower first-pass accuracy. With MPS technologies, it is now possible to analyze genomes, exomes, a defined subset of genes, transcriptomes, and even methylation across the genome. These technologies have and will continue to completely transform the clinical practice. CONTENT The major first- and second-generation MPS platforms and how they are used in clinical practice are discussed. SUMMARY The ability to sequence terabases of DNA per run on an MPS platform will dramatically change how DNA sequencing is used in clinical practice. Currently, MPS of targeted gene panels is the most common use of this technology clinically, but as the cost for genome sequencing inches downward to $100, this may soon become the method of choice (with the caveat that, at least in the near term, clinical-grade genome sequencing with interpretation may cost much more than $100). Other uses of this technology include sequencing of a mixture of bacterial and viral species (metagenomics), as well as the characterization of methylation across the genome.
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Affiliation(s)
- Ge Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - David I Smith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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Srivastava P, Malhotra KP, Husain N, Malhotra HS, Kulshreshtha D, Anand A. Diagnosing Muscular Dystrophies: Comparison of Techniques and Their Cost Effectiveness: A Multi-institutional Study. J Neurosci Rural Pract 2020; 11:420-429. [PMID: 32753807 PMCID: PMC7394627 DOI: 10.1055/s-0040-1713301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background
The diagnosis of muscular dystrophies involves clinical discretion substantiated by dystrophic changes on muscle biopsy. The different subtypes of muscular dystrophy can be diagnosed using techniques to identify the loss of protein or molecular alterations.
Materials and Methods
Clinically suspicious cases confirmed to have muscular dystrophy on muscle biopsy seen at two tertiary care centers in North India were enrolled for the study. Immunohistochemistry (IHC) for dystrophin, merosin, sarcoglycan, emerin, and dysferlin proteins was performed. The spectrum of muscular dystrophies diagnosed was analyzed. Cost of diagnosing the cases using IHC was estimated and compared with that of standard molecular tests available for the diagnosis of muscular dystrophies.
Statistics
Descriptive statistics were used for data analysis. Mean and standard deviations were used for continuous variables, whereas categorical variables were analyzed using frequency percentage.
Results
A total of 47 cases of muscular dystrophies were studied. This included nine cases of Duchenne, three cases of Becker’s dystrophy, and one dystrophinopathy carrier. One case of α, seven cases of β, and two cases of δ sarcoglycanopathy, along with two cases of facioscapulohumeral dystrophy and a single case of dysferlinopathy were detected. Genetic studies were required for a subset of 16 cases. The cost of using muscle biopsy and IHC was substantially lower than that of molecular methods for the identification of muscular dystrophy subtypes.
Conclusion
We detailed an algorithmic approach for diagnosing muscular dystrophies using muscle biopsy. The prevalence of biopsy proven muscular dystrophies from two tertiary care centers in North India is compared with that from other centers. Genetic studies are currently of limited availability in India and are more expensive as compared with biopsy and IHC. Using these methodologies sequentially with a “biopsy first approach” may be the prudent approach for low-income countries.
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Affiliation(s)
- Pallavi Srivastava
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Kiran Preet Malhotra
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Nuzhat Husain
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | | | - Dinkar Kulshreshtha
- Department of Neurology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Akanksha Anand
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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Thiffault I, Atherton A, Heese BA, T Abdelmoity A, Pawar K, Farrow E, Zellmer L, Miller N, Soden S, Saunders C. Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a003970. [PMID: 32358097 PMCID: PMC7304362 DOI: 10.1101/mcs.a003970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/16/2020] [Indexed: 11/24/2022] Open
Abstract
Status epilepticus is not rare in critically ill intensive care unit patients, but its diagnosis is often delayed or missed. The mortality for convulsive status epilepticus is dependent on the underlying aetiologies and the age of the patients and thus varies from study to study. In this context, effective molecular diagnosis in a pediatric patient with a genetically heterogeneous phenotype is essential. Homozygous or compound heterozygous variants in KPTN have been recently associated with a syndrome typified by macrocephaly, neurodevelopmental delay, and seizures. We describe a comprehensive investigation of a 9-yr-old male patient who was admitted to the intensive care unit, with focal epilepsy, static encephalopathy, autism spectrum disorder, and macrocephaly of unknown etiology, who died of status epilepticus. Clinical whole-genome sequencing revealed compound heterozygous variants in the KPTN gene. The first variant is a previously characterized 18-bp in-frame duplication (c.714_731dup) in exon 8, resulting in the protein change p.Met241_Gln246dup. The second variant, c.394 + 1G > A, affects the splice junction of exon 3. These results are consistent with a diagnosis of autosomal recessive KPTN-related disease. This is the fourth clinical report for KPTN deficiency, providing further evidence of a wider range of severity.
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Affiliation(s)
- Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri 64108, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri 64108, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri 64108, USA
| | - Andrea Atherton
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, Missouri 64108, USA
| | - Bryce A Heese
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, Missouri 64108, USA
| | - Ahmed T Abdelmoity
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, Missouri 64108, USA
| | - Kailash Pawar
- Department of Pediatrics, Children's Mercy Hospitals, Kansas City, Missouri 64108, USA
| | - Emily Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri 64108, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri 64108, USA.,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, Missouri 64108, USA
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri 64108, USA
| | - Neil Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri 64108, USA
| | - Sarah Soden
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri 64108, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri 64108, USA.,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, Missouri 64108, USA
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri 64108, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri 64108, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri 64108, USA
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Han JY, Lee IG. Genetic tests by next-generation sequencing in children with developmental delay and/or intellectual disability. Clin Exp Pediatr 2020; 63:195-202. [PMID: 32024334 PMCID: PMC7303420 DOI: 10.3345/kjp.2019.00808] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/24/2019] [Indexed: 02/07/2023] Open
Abstract
Developments in next-generation sequencing (NGS) techogies have assisted in clarifying the diagnosis and treatment of developmental delay/intellectual disability (DD/ID) via molecular genetic testing. Advances in DNA sequencing technology have not only allowed the evolution of targeted panels but also, and more currently enabled genome-wide analyses to progress from research era to clinical practice. Broad acceptance of accuracy- guided targeted gene panel, whole-exome sequencing (WES), and whole-genome sequencing (WGS) for DD/ID need prospective analyses of the increasing cost-effectiveness versus conventional genetic testing. Choosing the appropriate sequencing method requires individual planning. Data are required to guide best-practice recommendations for genomic testing, regarding various clinical phenotypes in an etiologic approach. Targeted panel testing may be recommended as a first-tier testing approach for children with DD/ID. Family-based trio testing by WES/WGS can be used as a second test for DD/ ID in undiagnosed children who previously tested negative on a targeted panel. The role of NGS in molecular diagnostics, treatment, prediction of prognosis will continue to increase further in the coming years. Given the rapid pace of changes in the past 10 years, all medical providers should be aware of the changes in the transformative genetics field.
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Affiliation(s)
- Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Goo Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Advances in the diagnosis of inherited neuromuscular diseases and implications for therapy development. Lancet Neurol 2020; 19:522-532. [PMID: 32470424 DOI: 10.1016/s1474-4422(20)30028-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/19/2022]
Abstract
Advances in DNA sequencing technologies have resulted in a near doubling, in under 10 years, of the number of causal genes identified for inherited neuromuscular disorders. However, around half of patients, whether children or adults, do not receive a molecular diagnosis after initial diagnostic workup. Massively parallel technologies targeting RNA, proteins, and metabolites are being increasingly used to diagnose these unsolved cases. The use of these technologies to delineate pathways, biomarkers, and therapeutic targets has led to new approaches entering the drug development pipeline. However, these technologies might give rise to misleading conclusions if used in isolation, and traditional techniques including comprehensive neurological evaluation, histopathology, and biochemistry continue to have a crucial role in diagnostics. For optimal diagnosis, prognosis, and precision medicine, no single ruling technology exists. Instead, an interdisciplinary approach combining novel and traditional neurological techniques with computer-aided analysis and international data sharing is needed to advance the diagnosis and treatment of neuromuscular disorders.
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The Clinical Application of RNA Sequencing in Genetic Diagnosis of Mendelian Disorders. Clin Lab Med 2020; 40:121-133. [PMID: 32439064 DOI: 10.1016/j.cll.2020.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Shademan B, Biray Avci C, Nikanfar M, Nourazarian A. Application of Next-Generation Sequencing in Neurodegenerative Diseases: Opportunities and Challenges. Neuromolecular Med 2020; 23:225-235. [PMID: 32399804 DOI: 10.1007/s12017-020-08601-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 12/28/2022]
Abstract
Genetic factors (gene mutations) lead to various rare and prevalent neurological diseases. Identification of underlying mutations in neurodegenerative diseases is of paramount importance due to the heterogeneous nature of the genome and different clinical manifestations. An early and accurate molecular diagnosis are cardinal for neurodegenerative patients to undergo proper therapeutic regimens. The next-generation sequencing (NGS) method examines up to millions of sequences at a time. As a result, the rare molecular diagnoses, previously presented with "unknown causes", are now possible in a short time. This method generates a large amount of data that can be utilized in patient management. Since each person has a unique genome, the NGS has transformed diagnostic and therapeutic strategies into sequencing and individual genomic mapping. However, this method has disadvantages like other diagnostic methods. Therefore, in this review, we aimed to briefly summarize the NGS method and correlated studies to unravel the genetic causes of neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, epilepsy, and MS. Finally, we discuss the NGS challenges and opportunities in neurodegenerative diseases.
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Affiliation(s)
- Behrouz Shademan
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey
| | - Cigir Biray Avci
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey.
| | - Masoud Nikanfar
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Nourazarian
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Golgasht St., 51666-16471, Tabriz, Iran. .,Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran.
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