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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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Kovanda A, Lovrečić L, Rudolf G, Babic Bozovic I, Jaklič H, Leonardis L, Peterlin B. Evaluation of Optical Genome Mapping in Clinical Genetic Testing of Facioscapulohumeral Muscular Dystrophy. Genes (Basel) 2023; 14:2166. [PMID: 38136988 PMCID: PMC10743191 DOI: 10.3390/genes14122166] [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: 10/18/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is the third most common hereditary muscular dystrophy, caused by the contraction of the D4Z4 repeats on the permissive 4qA haplotype on chromosome 4, resulting in the faulty expression of the DUX4 gene. Traditional diagnostics are based on Southern blotting, a time- and effort-intensive method that can be affected by single nucleotide variants (SNV) and copy number variants (CNV), as well as by the similarity of the D4Z4 repeats located on chromosome 10. We aimed to evaluate optical genome mapping (OGM) as an alternative molecular diagnostic method for the detection of FSHD. We first performed optical genome mapping with EnFocus™ FSHD analysis using DLE-1 labeling and the Saphyr instrument in patients with inconclusive diagnostic Southern blot results, negative FSHD2 results, and clinically evident FSHD. Second, we performed OGM in parallel with the classical Southern blot analysis for our prospectively collected new FSHD cases. Finally, panel exome sequencing was performed to confirm the presence of FSHD2. In two patients with diagnostically inconclusive Southern blot results, OGM was able to identify shortened D4Z4 repeats on the permissive 4qA alleles, consistent with the clinical presentation. The results of the prospectively collected patients tested in parallel using Southern blotting and OGM showed full concordance, indicating that OGM is a useful alternative to the classical Southern blotting method for detecting FSHD1. In a patient showing clinical FSHD but no shortened D4Z4 repeats in the 4qA allele using OGM or Southern blotting, a likely pathogenic variant in SMCHD1 was detected using exome sequencing, confirming FSHD2. OGM and panel exome sequencing can be used consecutively to detect FSHD2.
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Affiliation(s)
- Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Luca Lovrečić
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Gorazd Rudolf
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ivana Babic Bozovic
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
| | - Helena Jaklič
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
| | - Lea Leonardis
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Clinical Neurophysiology, University Medical Center Ljubljana, 1000 Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Center, 1000 Ljubljana, Slovenia; (A.K.)
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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Chen PS, Chao CC, Tsai LK, Huang HY, Chien YH, Huang PH, Hwu WL, Hsieh ST, Lee NC, Hsueh HW, Yang CC. Diagnostic Challenges of Neuromuscular Disorders after Whole Exome Sequencing. J Neuromuscul Dis 2023:JND230013. [PMID: 37066920 DOI: 10.3233/jnd-230013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
BACKGROUND Whole-exome sequencing (WES) facilitates the diagnosis of hereditary neuromuscular disorders. To achieve an accurate diagnosis, physicians should interpret the genetic report carefully along with clinical information and examinations. We described our experience with (1) clinical validation in patients with variants found using WES and (2) a diagnostic approach for those with negative findings from WES. METHODS WES was performed on patients with the clinical impression of hereditary neuromuscular disorders. Information on clinical manifestations, neurological examination, electrodiagnostic studies, histopathology of muscle and nerve, and laboratory tests were collected. RESULTS Forty-one patients (Male/Female: 18/23, age of onset: 34.5±15.9) accepted WES and were categorized into four scenarios: (1) patients with a positive WES result, (2) patients with an inconclusive WES result but supporting clinical data, (3) negative findings from WES, but a final diagnosis after further work-up, and (4) undetermined etiology from WES and in further work-ups. The yield rate of the initial WES was 63.4% (26/41). Among these, seventeen patients had positive WES result, while the other nine patients had inconclusive WES result but supporting clinical data. Notably, in the fifteen patients with equivocal or negative findings from WES, four patients (26.7%) achieved a diagnosis after further workup: tumor-induced osteomalacia, metabolic myopathy with pathogenic variants in mitochondrial DNA, microsatellite expansion disease, and vasculitis-related neuropathy. The etiologies remained undetermined in eleven patients (myopathy: 7, neuropathy: 4) after WES and further workup. CONCLUSIONS It is essential to design genotype-guided molecular studies to correlate the identified variants with their clinical features. For patients who had negative findings from WES, acquired diseases, mitochondrial DNA disorders and microsatellite expansion diseases should be considered.
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Affiliation(s)
- Pin-Shiuan Chen
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi-Chao Chao
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Kai Tsai
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-Yi Huang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Hsin Huang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Tsang Hsieh
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsueh-Wen Hsueh
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chih-Chao Yang
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
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Summa S, Ittiwut C, Kulsirichawaroj P, Paprad T, Likasitwattanakul S, Sanmaneechai O, Boonsimma P, Suphapeetiporn K, Shotelersuk V. Utilisation of exome sequencing for muscular disorders in Thai paediatric patients: diagnostic yield and mutational spectrum. Sci Rep 2023; 13:1376. [PMID: 36697461 PMCID: PMC9876991 DOI: 10.1038/s41598-023-28405-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
Muscular dystrophies and congenital myopathies are heterogeneous groups of inherited muscular disorders. An accurate diagnosis is challenging due to their complex clinical presentations and genetic heterogeneity. This study aimed to determine the utilisation of exome sequencing (ES) for Thai paediatric patients with muscular disorders. Of 176 paediatric patients suspected of genetic/inherited myopathies, 133 patients received a molecular diagnosis after performing conventional investigations, single gene testing, and gene panels. The remaining 43 patients from 42 families could be classified into three groups: Group 1, MLPA-negative Duchenne muscular dystrophy (DMD) with 9 patients (9/43; 21%), Group 2, other muscular dystrophies (MD) with 18 patients (18/43; 42%) and Group 3, congenital myopathies (CM) with 16 patients (16/43; 37%). All underwent exome sequencing which could identify pathogenic variants in 8/9 (89%), 14/18 (78%), and 8/16 (50%), for each Group, respectively. Overall, the diagnostic yield of ES was 70% (30/43) and 36 pathogenic/likely pathogenic variants in 14 genes were identified. 18 variants have never been previously reported. Molecular diagnoses provided by ES changed management in 22/30 (73%) of the patients. Our study demonstrates the clinical utility and implications of ES in inherited myopathies.
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Affiliation(s)
- Sarinya Summa
- Department of Paediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Department of Paediatrics, Samutprakan Hospital, Samutprakan, 10270, Thailand
| | - Chupong Ittiwut
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Paediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Pimchanok Kulsirichawaroj
- Department of Paediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Department of Paediatrics, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, 10300, Thailand
| | - Tanitnun Paprad
- Division of Neurology, Department of Paediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Surachai Likasitwattanakul
- Department of Paediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Oranee Sanmaneechai
- Department of Paediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Ponghatai Boonsimma
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Paediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand. .,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand.
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Paediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Paediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
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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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Wu MJ, Liao WA, Lin PY, Sun YT. Muscle Biopsy: A Requirement for Precision Medicine in Adult-Onset Myopathy. J Clin Med 2022; 11:jcm11061580. [PMID: 35329906 PMCID: PMC8951002 DOI: 10.3390/jcm11061580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Muscle biopsy is a fundamental procedure to assist the final diagnosis of myopathy. With the recent advances in molecular diagnosis, serology tests, and mechanism-based classification in myopathy, the précised diagnosis for myopathy required the applications of multiple tools. This study intends to reappraise the benefit of muscle biopsy in adult-onset myopathy under the setting of an optimized muscle biopsy protocol and comprehensive serology tests. A one-group pretest-posttest study design was used. The pre- and post-biopsy diagnoses and treatments in 69 adult patients were compared. Muscle biopsy yielded 85.5% of definitive diagnoses, including changes in pre-biopsy diagnoses (40.6%) and narrowing down the suspicious myopathies (49.3%). The demographic data and clinical parameters between the group “with change” and “without change” after biopsy were not different. Among those with changes in diagnosis, 39.3% also had a corresponding shift in treatment, which benefits the patients significantly. Regarding the most common adult-onset myopathy, idiopathic inflammatory myopathy (IIM), 41% of patients with pre-biopsy diagnosis as IIM had changes in their IIM subtype diagnosis, and 53% was finally not IIM after muscle biopsy. Although there have been advances in molecular diagnosis recently, muscle biopsy still undoubtedly critically guided the diagnosis and treatment of adult-onset myopathy in the era of precision medicine.
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Affiliation(s)
- Meng-Ju Wu
- Department of Neurology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (M.-J.W.); (P.-Y.L.)
| | - Wei-An Liao
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
| | - Po-Yu Lin
- Department of Neurology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (M.-J.W.); (P.-Y.L.)
| | - Yuan-Ting Sun
- Department of Neurology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; (M.-J.W.); (P.-Y.L.)
- Department of Medical Genomics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Correspondence:
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