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Wijekoon N, Gonawala L, Ratnayake P, Liyanage R, Amaratunga D, Hathout Y, Steinbusch HWM, Dalal A, Hoffman EP, de Silva KRD. Title-molecular diagnostics of dystrophinopathies in Sri Lanka towards phenotype predictions: an insight from a South Asian resource limited setting. Eur J Med Res 2024; 29:37. [PMID: 38195599 PMCID: PMC10775540 DOI: 10.1186/s40001-023-01600-x] [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: 06/23/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND The phenotype of Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) patients is determined by the type of DMD gene variation, its location, effect on reading frame, and its size. The primary objective of this investigation was to determine the frequency and distribution of DMD gene variants (deletions/duplications) in Sri Lanka through the utilization of a combined approach involving multiplex polymerase chain reaction (mPCR) followed by Multiplex Ligation Dependent Probe Amplification (MLPA) and compare to the international literature. The current consensus is that MLPA is a labor efficient yet expensive technique for identifying deletions and duplications in the DMD gene. METHODOLOGY Genetic analysis was performed in a cohort of 236 clinically suspected pediatric and adult myopathy patients in Sri Lanka, using mPCR and MLPA. A comparative analysis was conducted between our findings and literature data. RESULTS In the entire patient cohort (n = 236), mPCR solely was able to identify deletions in the DMD gene in 131/236 patients (DMD-120, BMD-11). In the same cohort, MLPA confirmed deletions in 149/236 patients [DMD-138, BMD -11]. These findings suggest that mPCR has a detection rate of 95% (131/138) among all patients who received a diagnosis. The distal and proximal deletion hotspots for DMD were exons 45-55 and 6-15. Exon 45-60 identified as a novel in-frame variation hotspot. Exon 45-59 was a hotspot for BMD deletions. Comparisons with the international literature show significant variations observed in deletion and duplication frequencies in DMD gene across different populations. CONCLUSION DMD gene deletions and duplications are concentrated in exons 45-55 and 2-20 respectively, which match global variation hotspots. Disparities in deletion and duplication frequencies were observed when comparing our data to other Asian and Western populations. Identified a 95% deletion detection rate for mPCR, making it a viable initial molecular diagnostic approach for low-resource countries where MLPA could be used to evaluate negative mPCR cases and cases with ambiguous mutation borders. Our findings may have important implications in the early identification of DMD with limited resources in Sri Lanka and to develop tailored molecular diagnostic algorithms that are regional and population specific and easily implemented in resource limited settings.
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Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | | | - Roshan Liyanage
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - Harry W M Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Eric P Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - K Ranil D de Silva
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka.
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands.
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, 10390, Sri Lanka.
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Bakhshandeh M, Behroozi S, Ghorbani A. Next-generation sequencing approach to molecular diagnosis of Iranian patients with Duchenne/Becker muscular dystrophy: Several novel variants identified. eNeurologicalSci 2023; 30:100446. [PMID: 36845278 PMCID: PMC9945705 DOI: 10.1016/j.ensci.2023.100446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/11/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) constitute the second most prevalent muscular dystrophy, with large deletions or duplications accounting for 66% of cases. No effective treatment exists for DMD/BMD. At present, genetic diagnosis serves as the foundation for gene therapy treatments. In this study, a comprehensive molecular investigation was conducted. The subjects diagnosed with DMD/BMD were initially examined using multiplex ligation-dependent probe amplification (MLPA) technology. The negative MLPA results were analyzed further using next-generation sequencing (NGS) technology. The MLPA detected 201 deletions (65.9%) and 20 duplications (6.6%) along the dystrophin gene among the 305 Iranian patients examined. The deletion of exon 52 in the amenable skipping subgroup was associated with an earlier onset age and a more severe phenotype. Twenty-one of the small mutations found in 58 MLPA-negative patients were novel. The most prevalent variants were nonsense variants (46.5%), frameshift variants (31%), splicing variants (6.9%), missense variants (10.4%), and synonymous mutations (5.1%). Our results demonstrate that MLPA and NGS can be effective diagnostic tools for very young patients with a single exon deletion.
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Affiliation(s)
- MohammadKazem Bakhshandeh
- Hakim Children Hospital, Department of Pediatrics, Tehran University of Medical Sciences, Tehran, Iran,Corresponding author.
| | - Samira Behroozi
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Zamani G, Hosseinpour S, Ashrafi MR, Mohammadi M, Badv RS, Tavasoli AR, Akbari MG, Bereshneh AH, Malamiri RA, Heidari M. Characteristics of disease progression and genetic correlation in ambulatory Iranian boys with Duchenne muscular dystrophy. BMC Neurol 2022; 22:162. [PMID: 35501714 PMCID: PMC9059913 DOI: 10.1186/s12883-022-02687-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is the most common muscular dystrophy in the pediatric population. The manifestations of this disease include progressive muscle weakness, gait dysfunction, and motor impairment, leading to a loss of ambulation by the age of 13 years. Molecular diagnosis is the standard diagnostic tool for DMD. This study aimed to investigate disease progression and genetic patterns in Iranian ambulant boys and to find the correlation between genotypes and motor function phenotypes. METHODS This study was performed on 152 DMD patients. Clinical history, including the disease phenotype, steroid therapy, and the North Star Ambulatory Assessment (NSAA) score, was taken for all the patients. Molecular diagnoses were confirmed by multiplex ligation-dependent probe amplification and next-generation sequencing tests. RESULTS A total of 152 Iranian DMD patients were examined in this study. The mean age at the time of disease onset was 4.04 ± 2.00 years, and the mean age at diagnosis was 5.05 ± 2.08 years. The mean age of ambulation loss was 10.9 years. Contracture was reported in 38.9% of cases. In terms of age, the mean total NSAA score showed a peak at 4 years of age, with a mean NSAA score of 24. Annual changes in the NSAA score were determined for all cases, based on the mutation type and exon site. Deletion mutation was found in 79.1% of cases, duplication in 6.8%, nonsense in 12.8%, and splice site in 1.4%. The most common single exon deletion was exon 44 (5.3%), and the most common multiexon deletions were attributed to exons 45-50 and exons 45-52 (4.6%). The results did not indicate any correlation between the mutation type and age at the time of disease onset, loss of ambulation age, and wheelchair dependence; however, a significant association was found between contracture and mutation type. The results showed a significant difference in the NSAA score between the deletion and nonsense groups at the age of 3 years (P = 0.04). No significant correlation was found between the phenotype and exon site. Overall, 91.1% of the study population had a history of corticosteroid use, and 54.1% showed compliance with rehabilitation therapy. CONCLUSION This study demonstrated the phenotypes and mutational features of Iranian DMD boys and provided information regarding the natural motor history of the disease, disease progression, diagnosis, and status of DMD management in Iran. The present findings can promote the development of clinical trials and future advanced molecular therapies in Iran.
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Affiliation(s)
- Gholamreza Zamani
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sareh Hosseinpour
- Department of Pediatric Neurology, Vali-e-Asr Hospital, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Reza Ashrafi
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Mohammadi
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shervin Badv
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Reza Tavasoli
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Masood Ghahvechi Akbari
- Physical Medicine and Rehabilitation Department, Children's Medical Center , Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Hosseini Bereshneh
- Prenatal Diagnosis and Genetic Research Center, Dastgheib Hospital, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Reza Azizi Malamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Morteza Heidari
- Pediatrics Center of Excellence, Department of Pediatric Neurology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
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Genetic Analysis of Forty MLPA-Negative Duchenne Muscular Dystrophy Patients by Whole-Exome Sequencing. J Mol Neurosci 2022; 72:1098-1107. [PMID: 35218518 DOI: 10.1007/s12031-022-01980-5] [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: 12/18/2021] [Accepted: 01/26/2022] [Indexed: 10/19/2022]
Abstract
This manuscript aimed to determine the underlying point mutations causing Duchenne muscular dystrophy (DMD) in a heterogeneous group of Iranian patients, who are clinically suspected. Whole-exome sequencing was utilized to detect disease-causing variants in 40 MLPA-negative DMD patients. Disease-causing variants were detected in the DMD gene in 36/40 of the patients (90%), and 4/40 of them (10%) remained undiagnosed. WES analysis revealed that nonsense variant was the most common type in our study (23/36 of the cases). Besides, 12/36 of the cases had frameshift variant, and one of the patients had a likely pathogenic splice variant in the DMD gene. Carrier testing revealed that 21/40 of the mothers had the identified variant. Therefore, most variants were inherited (58.3%), while 19/40 were de novo (41. 7%). The present study has demonstrated the importance of performing WES to detect disease-causing point mutations in MLPA-negative DMD patients and to identify carrier females. Due to regulatory challenges, the clinical development of therapeutic approaches is time-consuming and may not be available to all patients shortly. Therefore, it appears that the techniques used to accurately detect disease-causing variants in carrier mothers are a more efficient solution to prevent the increased prevalence of DMD.
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Xie Z, Sun C, Liu Y, Yu M, Zheng Y, Meng L, Wang G, Cornejo-Sanchez DM, Bharadwaj T, Yan J, Zhang L, Pineda-Trujillo N, Zhang W, Leal SM, Schrauwen I, Wang Z, Yuan Y. Practical approach to the genetic diagnosis of unsolved dystrophinopathies: a stepwise strategy in the genomic era. J Med Genet 2020; 58:743-751. [PMID: 32978268 DOI: 10.1136/jmedgenet-2020-107113] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/02/2020] [Accepted: 08/08/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To investigate the diagnostic value of implementing a stepwise genetic testing strategy (SGTS) in genetically unsolved cases with dystrophinopathies. METHODS After routine genetic testing in 872 male patients with highly suspected dystrophinopathies, we identified 715 patients with a pathogenic DMD variant. Of the 157 patients who had no pathogenic DMD variants and underwent a muscle biopsy, 142 patients were confirmed to have other myopathies, and 15 suspected dystrophinopathies remained genetically undiagnosed. These 15 patients underwent a more comprehensive evaluation as part of the SGTS pipeline, which included the stepwise analysis of dystrophin mRNA, short-read whole-gene DMD sequencing, long-read whole-gene DMD sequencing and in silico bioinformatic analyses. RESULTS SGTS successfully yielded a molecular diagnosis of dystrophinopathy in 11 of the 15 genetically unsolved cases. We identified 8 intronic and 2 complex structural variants (SVs) leading to aberrant splicing in 10 of 11 patients, of which 9 variants were novel. In one case, a molecular defect was detected on mRNA and protein level only. Aberrant splicing mechanisms included 6 pseudoexon inclusions and 4 alterations of splice sites and splicing regulatory elements. We showed for the first time the exonisation of a MER48 element as a novel pathogenic mechanism in dystrophinopathies. CONCLUSION Our study highlights the high diagnostic utility of implementing a SGTS pipeline in dystrophinopathies with intronic variants and complex SVs.
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Affiliation(s)
- Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Chengyue Sun
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yilin Liu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yiming Zheng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Gao Wang
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Diana M Cornejo-Sanchez
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Jin Yan
- Science and Technology, Beijing Epigen Medical Technology Inc, Beijing, China
| | - Lingxiang Zhang
- Science and Technology, Beijing Epigen Medical Technology Inc, Beijing, China
| | - Nicolas Pineda-Trujillo
- Grupo Mapeo Genetico, Departamento de Pediatría, Facultad de Medicina, Universidad de Antioquia, Medellin, Colombia
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Suzanne M Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, China
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