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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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Dwianingsih EK, Iskandar K, Hapsara S, Ping Liu C, Malueka RG, Gunadi, Matsuo M, Lai PS. Mutation spectrum analysis of DMD gene in Indonesian Duchenne and Becker muscular dystrophy patients. F1000Res 2023; 11:148. [PMID: 38009102 PMCID: PMC10668572 DOI: 10.12688/f1000research.73476.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/13/2023] [Indexed: 11/28/2023] Open
Abstract
Background Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are allelic disorders caused by mutations in the DMD gene. The full mutation spectrum of the DMD gene in Indonesian patients is currently unknown. Mutation-specific therapies are currently being developed, such as exon skipping or stop codon read-through therapy. This study was conducted with the aim of identifying the mutation spectrum of the DMD gene in Indonesia to guide future development and application of feasible therapeutic strategies. Methods This study is a cross sectional study that enrolled 43 male patients with a clinical suspicion of DMD or BMD. Multiplex ligation-dependent probe amplification (MLPA) reaction was performed to screen for the common mutations in the DMD gene. Results Out of 43 subjects, deletions accounted for 69.77% (n=30) cases, while duplications were found in 11.63% (n=5) cases. One novel duplication spanning exons 2 to 62 was identified. Deletion mutations clustered around the distal (66.67%) and proximal (26.67%) hot spot regions of the DMD gene while duplication mutations were observed solely at the proximal region. Two false positive cases of single exon deletion detected through MLPA were attributed to sequence mutations affecting primer ligation sites, confirming the need to validate all single exon deletions when using this screening method. Analysis of available maternal DNA samples showed that the rate of de novo mutations (48.15%) appears higher than expected in this population. Out of 31 patients who were classified as DMD based on clinical and genotype characterizations, 60.47% (n=26) of cases were suitable for exon skipping therapy. Conclusion This is the first comprehensive study showing the feasibility of implementing the MLPA method for routine screening of DMD patients in Indonesia. This is also the first study showing the potential applicability of exon skipping therapy in the majority of DMD cases in the country.
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Affiliation(s)
- Ery Kus Dwianingsih
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Dr. Sardjito General Hospital, Yogyakarta, 55281, Indonesia
- Department of Anatomical Pathology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Kristy Iskandar
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Academic Hospital, Universitas Gadjah Mada, Yogyakarta, 55291, Indonesia
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Sunartini Hapsara
- Academic Hospital, Universitas Gadjah Mada, Yogyakarta, 55291, Indonesia
- Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Chun Ping Liu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Rusdy Ghazali Malueka
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Dr. Sardjito General Hospital, Yogyakarta, 55281, Indonesia
- Department of Neurology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Gunadi
- Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Dr. Sardjito General Hospital, Yogyakarta, 55281, Indonesia
- Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Masafumi Matsuo
- KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobegakuin University, Kobe, 651-2180, Japan
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
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Basiri K, Alizadeh M, Ansari B, Ghasemi M, Kheradmand M, Sedghi M. On genotype-phenotype relationship of dystrophinopathies among Iranian population. CURRENT JOURNAL OF NEUROLOGY 2023; 22:231-237. [PMID: 38425356 PMCID: PMC10899535 DOI: 10.18502/cjn.v22i4.14528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/12/2023] [Indexed: 03/02/2024]
Abstract
Background: Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are inherited X-linked disorders resulting from alterations in the dystrophin gene. Genotype-phenotype matching studies have revealed a link between disease severity, the amount of muscle dystrophin, and the extent of mutation/deletion on the dystrophin gene. This study aimed to assess the relationship between genetic alterations in the dystrophin gene and the clinical status of patients with dystrophinopathies among the Iranian population. Methods: This cross-sectional study examined 54 patients with muscle weakness caused by abnormalities in the dystrophin gene at a hospital affiliated to Isfahan University of Medical Sciences, Isfahan, Iran, in 2021. The participants' demographic information, including age, family history of muscle dystrophies, and family history of other medical diseases as well as the type of muscular dystrophy were recorded. Furthermore, the number and region of deleted exons based on dystrophy types were also evaluated using multiplex ligation-dependent probe amplification (MLPA). The patients' gaits were also assessed as using a wheelchair, the presence of waddling gaits, or toe gaits. The patients' clinical status and the coexistence of pulmonary, bulbar, and mental conditions were also examined and compared between the two groups of dystrophinopathies. Results: In this study, 54 patients with dystrophinopathy with the mean age of 16.63 ± 12.10 years were evaluated, of whom 22 (40.7%) and 30 (55.6%) patients were classified as BMD and DMD, respectively. The most affected regions with deleted exons were exons 45-47 (n = 5) and 45-48 (n = 4) in patients with BMD, while exons 45, 48-52, 51-55, and 53 (2 cases per exon) were the most common affected exons in patients with DMD. Further analyses revealed that deletions in exons 45-47 and 51-55 were significantly associated with older and younger ages at the onset of becoming wheelchair-bound in patients with dystrophy, respectively. The hotspot range in both BMD and DMD was within exons 45-55 (n = 15 for each group); 63% of the patients had alterations on the dystrophin gene within this range [30 patients (68.18%) in the BMD group, 15 patients (53.57%) in the DMD group]. Conclusion: Exon deletion was the most common genetic alteration in patients with dystrophinopathies. No significant difference was observed between DMD and BMD regarding the number of deleted exons. Deletions in exons 45-47 and 51-55 were linked to later and earlier onset of becoming wheelchair-bound, respectively.
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Affiliation(s)
- Keivan Basiri
- Isfahan Neuroscience Research Center, Al-Zahra Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Alizadeh
- Department of Neurology, School of Medicine, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behnaz Ansari
- Isfahan Neuroscience Research Center, Al-Zahra Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Majid Ghasemi
- Isfahan Neuroscience Research Center, Al-Zahra Research Institute, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohsen Kheradmand
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Sedghi
- Medical Genetics Laboratory, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
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Erbe LS, Hoffjan S, Janßen S, Kneifel M, Krause K, Gerding WM, Döring K, Güttsches AK, Roos A, Buena Atienza E, Gross C, Lücke T, Nguyen HHP, Vorgerd M, Köhler C. Exome Sequencing and Optical Genome Mapping in Molecularly Unsolved Cases of Duchenne Muscular Dystrophy: Identification of a Causative X-Chromosomal Inversion Disrupting the DMD Gene. Int J Mol Sci 2023; 24:14716. [PMID: 37834164 PMCID: PMC10572545 DOI: 10.3390/ijms241914716] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe progressive muscle disease that mainly affects boys due to X-linked recessive inheritance. In most affected individuals, MLPA or sequencing-based techniques detect deletions, duplications, or point mutations in the dystrophin-encoding DMD gene. However, in a small subset of patients clinically diagnosed with DMD, the molecular cause is not identified with these routine methods. Evaluation of the 60 DMD patients in our center revealed three cases without a known genetic cause. DNA samples of these patients were analyzed using whole-exome sequencing (WES) and, if unconclusive, optical genome mapping (OGM). WES led to a diagnosis in two cases: one patient was found to carry a splice mutation in the DMD gene that had not been identified during previous Sanger sequencing. In the second patient, we detected two variants in the fukutin gene (FKTN) that were presumed to be disease-causing. In the third patient, WES was unremarkable, but OGM identified an inversion disrupting the DMD gene (~1.28 Mb) that was subsequently confirmed with long-read sequencing. These results highlight the importance of reanalyzing unsolved cases using WES and demonstrate that OGM is a useful method for identifying large structural variants in cases with unremarkable exome sequencing.
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Affiliation(s)
- Leoni S. Erbe
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (L.S.E.); (W.M.G.); (K.D.); (H.H.P.N.)
| | - Sabine Hoffjan
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (L.S.E.); (W.M.G.); (K.D.); (H.H.P.N.)
- Center for Rare Diseases Ruhr (CeSER), 44791 Bochum, Germany; (C.K.); (T.L.)
| | - Sören Janßen
- Department of Neuropediatrics, University Children’s Hospital, Ruhr-University Bochum, 44801 Bochum, Germany;
| | - Moritz Kneifel
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44801 Bochum, Germany; (M.K.); (K.K.); (A.-K.G.); (A.R.); (M.V.)
| | - Karsten Krause
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44801 Bochum, Germany; (M.K.); (K.K.); (A.-K.G.); (A.R.); (M.V.)
| | - Wanda M. Gerding
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (L.S.E.); (W.M.G.); (K.D.); (H.H.P.N.)
| | - Kristina Döring
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (L.S.E.); (W.M.G.); (K.D.); (H.H.P.N.)
| | - Anne-Katrin Güttsches
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44801 Bochum, Germany; (M.K.); (K.K.); (A.-K.G.); (A.R.); (M.V.)
| | - Andreas Roos
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44801 Bochum, Germany; (M.K.); (K.K.); (A.-K.G.); (A.R.); (M.V.)
| | - Elena Buena Atienza
- Institute of Medical Genetics and Applied Genomics, University Tübingen, 72074 Tübingen, Germany; (E.B.A.); (C.G.)
- NGS Competence Center Tübingen, 72076 Tübingen, Germany
| | - Caspar Gross
- Institute of Medical Genetics and Applied Genomics, University Tübingen, 72074 Tübingen, Germany; (E.B.A.); (C.G.)
- NGS Competence Center Tübingen, 72076 Tübingen, Germany
| | - Thomas Lücke
- Center for Rare Diseases Ruhr (CeSER), 44791 Bochum, Germany; (C.K.); (T.L.)
- Department of Neuropediatrics, University Children’s Hospital, Ruhr-University Bochum, 44801 Bochum, Germany;
| | - Hoa Huu Phuc Nguyen
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany; (L.S.E.); (W.M.G.); (K.D.); (H.H.P.N.)
- Center for Rare Diseases Ruhr (CeSER), 44791 Bochum, Germany; (C.K.); (T.L.)
| | - Matthias Vorgerd
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44801 Bochum, Germany; (M.K.); (K.K.); (A.-K.G.); (A.R.); (M.V.)
| | - Cornelia Köhler
- Center for Rare Diseases Ruhr (CeSER), 44791 Bochum, Germany; (C.K.); (T.L.)
- Department of Neuropediatrics, University Children’s Hospital, Ruhr-University Bochum, 44801 Bochum, Germany;
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Kekou K, Svingou M, Vogiatzakis N, Nitsa E, Veltra D, Marinakis NM, Tilemis FN, Tzetis M, Mitrakos A, Tsaroucha C, Selenti N, Papadimas GK, Papadopoulos C, Traeger-Synodinos J, Lochmuller H, Sofocleous C. Retrospective analysis of persistent HyperCKemia with or without muscle weakness in a case series from Greece highlights vast DMD variant heterogeneity. Expert Rev Mol Diagn 2023; 23:999-1010. [PMID: 37754746 DOI: 10.1080/14737159.2023.2264181] [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: 03/27/2023] [Accepted: 09/25/2023] [Indexed: 09/28/2023]
Abstract
BACKGROUND Persistent hyperCKemia results from muscle dysfunction often attributed to genetic alterations of muscle-related genes, such as the dystrophin gene (DMD). Retrospective assessment of findings from DMD analysis, in association with persistent HyperCKemia, was conducted. PATIENTS AND METHODS Evaluation of medical records from 1354 unrelated cases referred during the period 1996-2021. Assessment of data concerning the detection of DMD gene rearrangements and nucleotide variants. RESULTS A total of 730 individuals (657 cases, 569 of Greek and 88 of Albanian origins) were identified, allowing an overall estimation of dystrophinopathy incidence at ~1:3800 live male births. The heterogeneous spectrum of 275 distinct DMD alterations comprised exon(s) deletions/duplications, nucleotide variants, and rare events, such as chromosome translocation {t(X;20)}, contiguous gene deletions, and a fused gene involving the DMD and the DOCK8 genes. Ethnic-specific findings include a common founder variant in exon 36 ('Hellenic' variant). CONCLUSIONS Some 50% of hyperCKemia cases were characterized as dystrophinopathies, highlighting that DMD variants may be considered the most common cause of hyperCKemia in Greece. Delineation of the broad genetic and clinical heterogeneity is fundamental for actionable public health decisions and theragnosis, as well as the establishment of guidelines addressing ethical considerations, especially related to the mild asymptomatic patient subgroup.
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Affiliation(s)
- Kyriaki Kekou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Svingou
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikos Vogiatzakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Nitsa
- Postgraduate Program in Biostatistics School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Danai Veltra
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- St. Sophia's Children's Hospital, Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos M Marinakis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- St. Sophia's Children's Hospital, Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, National and Kapodistrian University of Athens, Athens, Greece
| | - Faidon-Nikolaos Tilemis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Tzetis
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasios Mitrakos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- St. Sophia's Children's Hospital, Research University Institute for the Study and Prevention of Genetic and Malignant Disease of Childhood, National and Kapodistrian University of Athens, Athens, Greece
| | - Charalambia Tsaroucha
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nicoletta Selenti
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Giorgos-Konstantinos Papadimas
- Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Constantinos Papadopoulos
- Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Hanns Lochmuller
- Department of Neuropediatrics and Muscle Disorders, Medical Center - University of Freiburg, Freiburg, Germany
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Children's Hospital of Eastern Ontario Research Institute; Division of Neurology, Department of Medicine, The Ottawa Hospital, Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, St. Sophia's Children's Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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6
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Clinical, muscle imaging, and genetic characteristics of dystrophinopathies with deep-intronic DMD variants. J Neurol 2023; 270:925-937. [PMID: 36319768 DOI: 10.1007/s00415-022-11432-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Phenotypic heterogeneity within or between families with a same deep-intronic splice-altering variant in the DMD gene has never been systematically analyzed. This study aimed to determine the phenotypic and genetic characteristics of patients with deep-intronic DMD variants. METHODS Of 1338 male patients with a suspected dystrophinopathy, 38 were confirmed to have atypical pathogenic DMD variants via our comprehensive genetic testing approach. Of the 38 patients, 30 patients from 22 unrelated families with deep-intronic DMD variants underwent a detailed clinical and imaging assessment. RESULTS Nineteen different deep-intronic DMD variants were identified in the 30 patients, including 15 with Duchenne muscular dystrophy (DMD), 14 with Becker muscular dystrophy (BMD), and one with X-linked dilated cardiomyopathy. Of the 19 variants, 15 were single-nucleotide variants, 2 were structural variants (SVs), and 2 were pure-intronic large-scale SVs causing aberrant inclusion of other protein-coding genes sequences into the mature DMD transcripts. The trefoil with single fruit sign was observed in 18 patients and the concentric fatty infiltration pattern was observed in 2 patients. Remarkable phenotypic heterogeneity was observed not only in skeletal but also cardiac muscle involvement in 2 families harboring a same deep-intronic variant. Different skeletal muscle involvement between families with a same variant was observed in 4 families. High inter-individual phenotypic heterogeneity was observed within two BMD families and one DMD family. CONCLUSIONS Our study first highlights the variable phenotypic expressivity of deep-intronic DMD variants and demonstrates a new class of deep-intronic DMD variants, i.e., pure-intronic SVs involving other protein-coding genes.
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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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8
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Viggiano E, Picillo E, Passamano L, Onore ME, Piluso G, Scutifero M, Torella A, Nigro V, Politano L. Spectrum of Genetic Variants in the Dystrophin Gene: A Single Centre Retrospective Analysis of 750 Duchenne and Becker Patients from Southern Italy. Genes (Basel) 2023; 14:214. [PMID: 36672955 PMCID: PMC9859256 DOI: 10.3390/genes14010214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/29/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Dystrophinopathies are X-linked recessive muscle disorders caused by mutations in the dystrophin (DMD) gene that include deletions, duplications, and point mutations. Correct diagnosis is important for providing adequate patient care and family planning, especially at this time when mutation-specific therapies are available. We report a large single-centre study on the spectrum of DMD gene variants observed in 750 patients analyzed for suspected Duchenne (DMD) or Becker (BMD) muscular dystrophy, over the past 30 years, at the Cardiomyology and Medical Genetics of the University of Campania. We found 534 (71.21%) large deletions, 73 (9.73%) large duplications, and 112 (14.93%) point mutations, of which 44 (5.9%) were small ins/del causing frame-shifts, 57 (7.6%) nonsense mutations, 8 (1.1%) splice site and 3 (0.4%) intronic mutations, and 31 (4.13%) non mutations. Moreover, we report the prevalence of the different types of mutations in patients with DMD and BMD according to their decade of birth, from 1930 to 2020, and correlate the data to the different techniques used over the years. In the most recent decades, we observed an apparent increase in the prevalence of point mutations, probably due to the use of Next-Generation Sequencing (NGS). In conclusion, in southern Italy, deletions are the most frequent variation observed in DMD and BMD patients followed by point mutations and duplications, as elsewhere in the world. NGS was useful to identify point mutations in cases of strong suspicion of DMD/BMD negative on deletions/duplications analyses. In the era of personalized medicine and availability of new causative therapies, a collective effort is necessary to enable DMD and BMD patients to have timely genetic diagnoses and avoid late implementation of standard of care and late initiation of appropriate treatment.
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Affiliation(s)
- Emanuela Viggiano
- Department of Prevention, Hygiene and Public Health Service, ASL Roma 2, 00157 Rome, Italy
| | - Esther Picillo
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Luigia Passamano
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Maria Elena Onore
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Giulio Piluso
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Marianna Scutifero
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Annalaura Torella
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
| | - Vincenzo Nigro
- Medical Genetics and Cardiomyology, Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Luisa Politano
- Cardiomyology and Medical Genetics, Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Napoli, Italy
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SATTENAPALLI NC, ARETI AR, KOTESWARA RAO SN, ALAVALA RR, KULANDAIVELU US. Prevalence Study of Duchene Muscular Dystrophy and its Genetic Sequence in Southern India. IRANIAN JOURNAL OF CHILD NEUROLOGY 2023; 17:29-37. [PMID: 36721834 PMCID: PMC9881832 DOI: 10.22037/ijcn.v17i2.35071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 05/28/2022] [Indexed: 02/02/2023]
Abstract
Objective Duchene Muscular dystrophy (DMD) is the common X-linked heterogenous progressive muscular dystrophy characterized by mutations in the DMD gene. The frequency of dystrophin gene mutations is varied in different DMD population. A precise diagnosis can help to reduce the severity of DMD since it aids in planning of targeted medical treatment and required therapies. This study was aimed to investigate the mutation type, their rate and distribution of DMD'S in southern India. Materials & Materials An observational study was conducted on 250 genetically confirmed DMD patients from March,2019 to March,2021. The distribution pattern and rate of mutations (deletion, duplication, nonsense mutations, minor mutations) were investigated. Results Mutation spectrum was studied on 250 DMD patients, of which 63% exon deletion pattern were reported. 16% deletions were detected in proximal hot region (exons 3-28). The duplications were found 21% in the proximal hotspot largest region (exon 3-25). 16% of the patients reported single deletion (45 exon), 10.7% reported deletions of exon 44. Point mutations detected in 6%, small mutations were detected in 1.2%, non-sense mutations were detected in 2% of study population respectively. Missense Mutations were detected in 0.8% of study population. Conclusion This study estimates mutation spectrum of exon deletion pattern (63%) was predominantly identified in distal region; duplication was most frequent in proximal region. Point mutations, Nonsense mutations and small mutations have a least accountability. This study adds a real world evidence for developing research therapies in DMD.
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Affiliation(s)
| | - Anka Rao ARETI
- K L College of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram-522502, Guntur, AP, India
| | - Siva Naga KOTESWARA RAO
- K L College of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram-522502, Guntur, AP, India
| | - Rajasekhar Reddy ALAVALA
- K L College of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram-522502, Guntur, AP, India
| | - Uma Sankar KULANDAIVELU
- K L College of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram-522502, Guntur, AP, India
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RNA-seq analysis, targeted long-read sequencing and in silico prediction to unravel pathogenic intronic events and complicated splicing abnormalities in dystrophinopathy. Hum Genet 2023; 142:59-71. [PMID: 36048237 DOI: 10.1007/s00439-022-02485-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/24/2022] [Indexed: 01/18/2023]
Abstract
Dystrophinopathy is caused by alterations in DMD. Approximately 1% of patients remain genetically undiagnosed, because intronic variations are not detected by standard methods. Here, we combined laboratory and in silico analyses to identify disease-causing genomic variants in genetically undiagnosed patients and determine the regulatory mechanisms underlying abnormal DMD transcript generation. DMD transcripts from 20 genetically undiagnosed dystrophinopathy patients in whom no exon variants were identified, despite dystrophin deficiency on muscle biopsy, were analyzed by transcriptome sequencing. Genome sequencing captured intronic variants and their effects were interpreted using in silico tools. Targeted long-read sequencing was applied in cases with suspected structural genomic abnormalities. Abnormal DMD transcripts were detected in 19 of 20 cases; Exonization of intronic sequences in 15 cases, exon skipping in one case, aberrantly spliced and polyadenylated transcripts in two cases and transcription termination in one case. Intronic single nucleotide variants, chromosomal rearrangements and nucleotide repeat expansion were identified in DMD gene as pathogenic causes of transcript alteration. Our combined analysis approach successfully identified pathogenic events. Detection of diseasing-causing mechanisms in DMD transcripts could inform the therapeutic options for patients with dystrophinopathy.
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Saito Y, Takeshita E, Komaki H, Nishino I, Sasaki M. Determining neurodevelopmental manifestations in Duchenne muscular dystrophy using a battery of brief tests. J Neurol Sci 2022; 440:120340. [PMID: 35849899 DOI: 10.1016/j.jns.2022.120340] [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: 05/12/2022] [Revised: 07/07/2022] [Accepted: 07/10/2022] [Indexed: 10/17/2022]
Abstract
OBJECTIVE We report neurodevelopmental manifestations in boys with Duchenne muscular dystrophy (DMD) and evaluate the correlations between mutation location and three neurodevelopmental abnormalities: intellectual disability, autism spectrum disorder, and attentional problems. METHODS This cross-sectional study included 55 Japanese boys with genetically confirmed DMD who visited the outpatient department of the National Center for Psychiatry and Neurology of Japan from October 2017 to April 2018. Neurodevelopmental manifestations were evaluated using the Raven's Colored Progressive Matrices (RCPM), the Parent-Interview Autism Spectrum Disorder Rating Scale-Text Revision (PARS-TR), and the Attention-Deficit Hyperactivity Disorder-Rating Scale. RESULTS Among the 55 boys (mean [standard deviation, SD] age, 9.5 [1.6] years), 24 (43.6%) scored below -2.0 SD in RCPM, indicating intellectual disability. Further, 83% had DMD variants in exon 45 or downstream to it (P = 0.005). On the PARS-TR, 30 (55%) and 21 boys (38%) scored higher than the clinical cutoff score in childhood and present scores, respectively. Stereotyped behavior and restricted interests scores were found to decrease with age (P = 0.003 and P = 0.01, respectively). DISCUSSION The results show that boys with DMD who have intellectual disability commonly have DMD variants in exon 45 or downstream to it. Stereotyped behavior and restricted interests improved with age, while intellectual disability did not. CONCLUSION Understanding these characteristics of neurodevelopmental disability may reduce risky behaviors and improve the overall quality of life of patients with DMD.
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Affiliation(s)
- Yoshihiko Saito
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan.
| | - Hirofumi Komaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
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Zambon AA, Waldrop MA, Alles R, Weiss RB, Conroy S, Moore-Clingenpeel M, Previtali S, Flanigan KM. Phenotypic Spectrum of Dystrophinopathy Due to Duchenne Muscular Dystrophy Exon 2 Duplications. Neurology 2022; 98:e730-e738. [PMID: 34937785 PMCID: PMC8865888 DOI: 10.1212/wnl.0000000000013246] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/13/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES To describe the phenotypic spectrum of dystrophinopathy in a large cohort of individuals with DMD exon 2 duplications (Dup2), who may be particularly amenable to therapies directed at restoring expression of either full-length dystrophin or nearly full-length dystrophin through utilization of the DMD exon 5 internal ribosome entry site (IRES). METHODS In this retrospective observational study, we analyzed data from large genotype-phenotype databases (the United Dystrophinopathy Project [UDP] and the Italian DMD network) and classified participants into Duchenne muscular dystrophy (DMD), intermediate muscular dystrophy (IMD), or Becker muscular dystrophy (BMD) phenotypes. Log-rank tests for time-to-event variables were used to compare age at loss of ambulation (LOA) in participants with Dup2 vs controls without Dup2 in the UDP database and for comparisons between steroid-treated vs steroid-naive participants with Dup2. RESULTS Among 66 participants with Dup2 (UDP = 40, Italy = 26), 61% were classified as DMD, 9% as IMD, and 30% as BMD. Median age at last observation was 15.4 years (interquartile range 8.79-26.0) and 75% had been on corticosteroids for at least 6 months. Age at LOA differed significantly between participants with Dup2 DMD and historical controls without Dup2 DMD (p < 0.001). Valid spirometry was limited but suggested a delay in the typical age-related decline in forced vital capacity and 24 of 55 participants with adequate cardiac data had cardiomyopathy. DISCUSSION Some patients with Dup2 display a milder disease course than controls without Dup2 DMD, and prolonged ambulation with corticosteroids suggests the potential of IRES activation as a molecular mechanism. As Dup2-targeted therapies reach clinical applications, this information is critical to aid in the interpretation of the efficacy of new treatments.
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Affiliation(s)
- Alberto A Zambon
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Megan A Waldrop
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Roxane Alles
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Robert B Weiss
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Sara Conroy
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Melissa Moore-Clingenpeel
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Stefano Previtali
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City
| | - Kevin M Flanigan
- From Inspe and Division of Neuroscience (A.A.Z., S.P.), IRCCS Ospedale San Raffaele, Milan, Italy; The Center for Gene Therapy, Abigail Wexner Research Institute (M.A.W., R.A., K.M.F.), and Biostatistics Research Core (S.C., M.M.-C.), Nationwide Children's Hospital, Columbus, OH; Departments of Pediatrics and Neurology (M.A.W., K.M.F.), Ohio State University Medical Center, Columbus; and Department of Human Genetics (R.B.W.), University of Utah, Salt Lake City.
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DMD exon 2 duplication due to a complex genomic rearrangement is associated with a somatic mosaicism. Neuromuscul Disord 2021; 32:263-269. [DOI: 10.1016/j.nmd.2021.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/24/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022]
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Tong YR, Geng C, Guan YZ, Zhao YH, Ren HT, Yao FX, Ling C, Wang DC, Chen L, Cui LY, Zhang SY, Dai Y. A Comprehensive Analysis of 2013 Dystrophinopathies in China: A Report From National Rare Disease Center. Front Neurol 2020; 11:572006. [PMID: 33101180 PMCID: PMC7554367 DOI: 10.3389/fneur.2020.572006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive neuromuscular disorders caused by mutations in DMD. A high-quality database of DMD/BMD is essential not only for clinical practice but also for fundamental research. Here, we aimed to build the largest Chinese national dystrophinopathy database using the National Rare Diseases Registry System of China. Peking Union Medical College Hospital (PUMCH) was the National Rare Diseases Center of China. This research involved 2013 patients with dystrophinopathies, whose diagnoses were confirmed; they were registered and followed up at PUMCH from March 2011 to December 2018. Family history, clinical signs, and treatment data were reported for patients with DMD and BMD at different rates. All six serum biochemical indexes could accurately distinguish between DMD and BMD patients. Copy number variations were the most frequent mutation type (79.2% in DMD and 84.3% in BMD), of which large deletions accounted for 88.4 and 88.6%, large duplications accounted for 11.6 and 11.4% in DMD and BMD, respectively. An exon deletion hotspot, located in exons 45-54, was observed in DMD, and intron 44 was the most frequent deletion starting point (26.5%). Duplication and single nucleotide variations appeared to be uniformly distributed among all exons. Eleven patients were identified to have ultrarare mutation types. Eleven other patients suffered from two separate mutations simultaneously, some of which may have taken place via dependent mechanisms. Thus, we have established the largest hospital-based Chinese dystrophinopathy database via the National Rare Diseases Registry System. This study provides valuable information for further diagnostic and therapeutic studies of dystrophinopathy.
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Affiliation(s)
- Yuan-Ren Tong
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chang Geng
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu-Zhou Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yan-Huan Zhao
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hai-Tao Ren
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Feng-Xia Yao
- Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chao Ling
- Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dan-Chen Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lin Chen
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li-Ying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shu-Yang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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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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Advances in Genetic Characterization and Genotype-Phenotype Correlation of Duchenne and Becker Muscular Dystrophy in the Personalized Medicine Era. J Pers Med 2020; 10:jpm10030111. [PMID: 32899151 PMCID: PMC7565713 DOI: 10.3390/jpm10030111] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Currently, Duchenne muscular dystrophy (DMD) and the related condition Becker muscular dystrophy (BMD) can be usually diagnosed using physical examination and genetic testing. While BMD features partially functional dystrophin protein due to in-frame mutations, DMD largely features no dystrophin production because of out-of-frame mutations. However, BMD can feature a range of phenotypes from mild to borderline DMD, indicating a complex genotype–phenotype relationship. Despite two mutational hot spots in dystrophin, mutations can arise across the gene. The use of multiplex ligation amplification (MLPA) can easily assess the copy number of all exons, while next-generation sequencing (NGS) can uncover novel or confirm hard-to-detect mutations. Exon-skipping therapy, which targets specific regions of the dystrophin gene based on a patient’s mutation, is an especially prominent example of personalized medicine for DMD. To maximize the benefit of exon-skipping therapies, accurate genetic diagnosis and characterization including genotype–phenotype correlation studies are becoming increasingly important. In this article, we present the recent progress in the collection of mutational data and optimization of exon-skipping therapy for DMD/BMD.
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Torella A, Zanobio M, Zeuli R, del Vecchio Blanco F, Savarese M, Giugliano T, Garofalo A, Piluso G, Politano L, Nigro V. The position of nonsense mutations can predict the phenotype severity: A survey on the DMD gene. PLoS One 2020; 15:e0237803. [PMID: 32813700 PMCID: PMC7437896 DOI: 10.1371/journal.pone.0237803] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/03/2020] [Indexed: 12/23/2022] Open
Abstract
A nonsense mutation adds a premature stop signal that hinders any further translation of a protein-coding gene, usually resulting in a null allele. To investigate the possible exceptions, we used the DMD gene as an ideal model. First, because dystrophin absence causes Duchenne muscular dystrophy (DMD), while its reduction causes Becker muscular dystrophy (BMD). Second, the DMD gene is X-linked and there is no second allele that can interfere in males. Third, databases are accumulating reports on many mutations and phenotypic data. Finally, because DMD mutations may have important therapeutic implications. For our study, we analyzed large databases (LOVD, HGMD and ClinVar) and literature and revised critically all data, together with data from our internal patients. We totally collected 2593 patients. Positioning these mutations along the dystrophin transcript, we observed a nonrandom distribution of BMD-associated mutations within selected exons and concluded that the position can be predictive of the phenotype. Nonsense mutations always cause DMD when occurring at any point in fifty-one exons. In the remaining exons, we found milder BMD cases due to early 5’ nonsense mutations, if reinitiation can occur, or due to late 3’ nonsense when the shortened product retains functionality. In the central part of the gene, all mutations in some in-frame exons, such as in exons 25, 31, 37 and 38 cause BMD, while mutations in exons 30, 32, 34 and 36 cause DMD. This may have important implication in predicting the natural history and the efficacy of therapeutic use of drug-stimulated translational readthrough of premature termination codons, also considering the action of internal natural rescuers. More in general, our survey confirm that a nonsense mutation should be not necessarily classified as a null allele and this should be considered in genetic counselling.
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Affiliation(s)
- Annalaura Torella
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Mariateresa Zanobio
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Roberta Zeuli
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | | | - Marco Savarese
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
- Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Teresa Giugliano
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Arcomaria Garofalo
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Giulio Piluso
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Luisa Politano
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Vincenzo Nigro
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- * E-mail:
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Wonkam‐Tingang E, Nguefack S, Esterhuizen AI, Chelo D, Wonkam A. DMD-related muscular dystrophy in Cameroon: Clinical and genetic profiles. Mol Genet Genomic Med 2020; 8:e1362. [PMID: 32543101 PMCID: PMC7434738 DOI: 10.1002/mgg3.1362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Most of the previous studies on Duchenne Muscular Dystrophy (DMD) were conducted in Caucasian, Asian, and Arab populations. Therefore, little is known about the features of this disease in Africans. In this study, we aimed to determine the clinical characteristics of DMD, and the common mutations associated with this condition in a group of Cameroonian patients. METHODS We recruited DMD patients and performed a general physical examination on each of them. Multiplex ligand-dependant probe amplification was carried out to investigate exon deletions and duplications in the DMD gene (OMIM: 300377) of patients and their mothers. RESULTS A total of 17 male patients from 14 families were recruited, aged 14 ± 5.1 (8-23) years. The mean age at onset of symptoms was 4.6 ± 1.5 years, and the mean age at diagnosis was 12.1 ± 5.2 years. Proximal muscle weakness was noted in all patients and calf hypertrophy in the large majority of them (88.2%; 15/17). Flexion contractures were particularly frequent on the ankle (85.7%; 12/14). Wasting of shoulder girdle and thigh muscles was present in 50% (6/12) and 46.2% (6/13) of patients, respectively. No patient presented with hearing impairment. Deletions in DMD gene (OMIM: 300377) occurred in 45.5% of patients (5/11), while duplications were observed in 27.3% (3/11). Both mutation types were clustered between exons 45 and 50, and the proportion of de novo mutation was estimated at 18.2% (2/11). CONCLUSION Despite the first symptoms of DMD occurring in infancy, the diagnosis is frequently made later in adolescence, indicating an underestimation of the number of cases of DMD in Cameroon. Future screening of deletions and duplications in patients from Cameroon should focus on the distal part of the gene.
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Affiliation(s)
- Edmond Wonkam‐Tingang
- Division of Human GeneticsDepartment of PathologyUniversity of Cape TownCape TownSouth Africa
| | - Séraphin Nguefack
- Department of PaediatricsFaculty of Medicine and Biomedical SciencesUniversity of Yaoundé IYaoundéCameroon
- Paediatrics UnitDivision of Paediatric NeurologyGynaeco‐Obstetric and Paediatric HospitalYaoundéCameroon
| | - Alina I. Esterhuizen
- Division of Human GeneticsDepartment of PathologyUniversity of Cape TownCape TownSouth Africa
- National Health Laboratory ServiceGroote Schuur HospitalCape TownSouth Africa
| | - David Chelo
- Department of PaediatricsFaculty of Medicine and Biomedical SciencesUniversity of Yaoundé IYaoundéCameroon
- Division of Paediatric Cardiology, Mother and Child HospitalYaoundéCameroon
| | - Ambroise Wonkam
- Division of Human GeneticsDepartment of PathologyUniversity of Cape TownCape TownSouth Africa
- Department of MedicineUniversity of Cape TownCape TownSouth Africa
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Mutation Spectrum of Dystrophinopathies in India: Implications for Therapy. Indian J Pediatr 2020; 87:495-504. [PMID: 32358784 DOI: 10.1007/s12098-020-03286-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/31/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND Dystrophinopathies are common X-linked recessive neuromuscular disorders caused by pathogenic variants in the dystrophin gene (DMD). Analysis of the mutational spectrum in the Indian patients would be useful for confirming the diagnosis, provide genetic counseling, offer reproductive options, and importantly to determine the eligibility for the mutation-specific therapies currently approved/or undergoing trials, such as skipping of specific exons or read-through of stop codon. METHODS In 1660 patients diagnosed as Duchenne muscular dystrophy (DMD) /Becker muscular dystrophy (BMD) deletion- duplication analysis of all 79 exons was carried out using Multiplex ligation-dependent probe amplification (MLPA) technology. In 63 patients where no mutations were detected by MLPA, the nucleotide sequence of the DMD gene was determined by next gene sequencing. In seven cases where MLPA showed deletion of a single exon, and amplification of the specific exon was successful by polymerase chain reaction (PCR), Sanger sequencing of the concerned region was carried out to detect changes in the sequence. RESULTS The mutation spectrum of 1660 patients with DMD/BMD was determined and 1188 (71.6%) patients were identified to have deletions or duplications of one or more exons. Of these, 1090 (65.7%) had true deletions of exons and 98 (5.9%) had duplications of exons. The most frequent change was the deletion of exon 45 (66/1090, 6.1%) and duplication of exon 2 (1/98, 11.2%). Sequencing of dystrophin gene was performed in 70 cases, and variants were identified in 68 patients (97.1% of those analyzed). Stop codon variants were observed in 34 (50%) patients, missense variants in 4 (5.9%), small deletions in 19 (27.9%), small insertions in 6 (8.8%) and slice site variants in 5 (7.4%) patients. Thirty one of 68 variants (45.5%) were novel. CONCLUSIONS The authors highlight the importance of identifying the type of mutation in patients with DMD. Based on the results, it is estimated that 681 (54.2%) of 1256 patients in this cohort would benefit from the currently ongoing mutation-specific therapies.
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20
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Komaki R, Hashimoto Y, Mori-Yoshimura M, Oya Y, Takizawa H, Minami N, Nishino I, Aoki Y, Takahashi Y. Severe cardiac involvement with preserved truncated dystrophin expression in Becker muscular dystrophy by +1G>A DMD splice-site mutation: a case report. J Hum Genet 2020; 65:903-909. [PMID: 32504006 PMCID: PMC7449875 DOI: 10.1038/s10038-020-0788-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/21/2020] [Indexed: 01/16/2023]
Abstract
Becker muscular dystrophy (BMD) is caused by specific mutations in the DMD gene that causes progressive muscle weakness and primarily affects skeletal and cardiac muscle. Although cardiac involvement is a significant cause of mortality in BMD, the genetic–phenotype correlation for skeletal and cardiac muscles has not been elucidated. Here, we described a 39-year-old man with BMD, who presented with subtle skeletal muscle weakness in the right leg in his 20s and underwent left ventricular restoration for severe dilated cardiomyopathy at the age of 29. He had difficulty climbing stairs after the age of 35. Neither duplication nor deletion of exons was detected by multiplex ligation-dependent probe amplification. A hemizygous c.264 + 1G>A mutation in intron 4 of the DMD was identified by next-generation sequencing. Furthermore, exon 4 skipping of the DMD was confirmed in both skeletal and cardiac muscles evaluated by reverse transcriptase PCR. Endomyocardial and skeletal muscle biopsies revealed dystrophic pathology characterized by muscle fiber atrophy and hypertrophy with a mild degree of interstitial fibrosis. Interestingly, dystrophin immunohistochemistry demonstrated patchy and faint staining of the skeletal muscle membranes but almost normal staining of the cardiac muscle membranes. Western blot analysis revealed a decreased amount of truncated dystrophin in skeletal muscle but surprisingly almost normal amount in cardiac muscle. This case indicates that BMD patients may have severe cardiac dysfunction despite preserved cardiac truncated dystrophin expression.
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Affiliation(s)
- Ryouhei Komaki
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Yasumasa Hashimoto
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Madoka Mori-Yoshimura
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan.
| | - Yasushi Oya
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Hotake Takizawa
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan.,Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Narihiro Minami
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan.,Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan.,Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan.
| | - Yuji Takahashi
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
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21
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Dzierlega K, Yokota T. Optimization of antisense-mediated exon skipping for Duchenne muscular dystrophy. Gene Ther 2020; 27:407-416. [DOI: 10.1038/s41434-020-0156-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/28/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022]
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22
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Zamani G, Hosseini Bereshneh A, Azizi Malamiri R, Bagheri S, Moradi K, Ashrafi MR, Tavasoli AR, Mohammadi M, Badv RS, Ghahvechi Akbari M, Heidari M. The First Comprehensive Cohort of the Duchenne Muscular Dystrophy in Iranian Population: Mutation Spectrum of 314 Patients and Identifying Two Novel Nonsense Mutations. J Mol Neurosci 2020; 70:1565-1573. [DOI: 10.1007/s12031-020-01594-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/14/2020] [Indexed: 12/17/2022]
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23
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Exon skipping induced by nonsense/frameshift mutations in DMD gene results in Becker muscular dystrophy. Hum Genet 2020; 139:247-255. [PMID: 31919629 PMCID: PMC6981323 DOI: 10.1007/s00439-019-02107-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/27/2019] [Indexed: 01/13/2023]
Abstract
Duchenne muscular dystrophy (DMD) is caused by a nonsense or frameshift mutation in the DMD gene, while its milder form, Becker muscular dystrophy (BMD) is caused by an in-frame deletion/duplication or a missense mutation. Interestingly, however, some patients with a nonsense mutation exhibit BMD phenotype, which is mostly attributed to the skipping of the exon containing the nonsense mutation, resulting in in-frame deletion. This study aims to find BMD cases with nonsense/frameshift mutations in DMD and to investigate the exon skipping rate of those nonsense/frameshift mutations. We searched for BMD cases with nonsense/frameshift mutations in DMD in the Japanese Registry of Muscular Dystrophy. For each DMD mutation identified, we constructed minigene plasmids containing one exon with/without a mutation and its flanking intronic sequence. We then introduced them into HeLa cells and measured the skipping rate of transcripts of the minigene by RT-qPCR. We found 363 cases with a nonsense/frameshift mutation in DMD gene from a total of 1497 dystrophinopathy cases in the registry. Among them, 14 had BMD phenotype. Exon skipping rates were well correlated with presence or absence of dystrophin, suggesting that 5% exon skipping rate is critical for the presence of dystrophin in the sarcolemma, leading to milder phenotypes. Accurate quantification of the skipping rate is important in understanding the exact functions of the nonsense/frameshift mutations in DMD and for interpreting the phenotypes of the BMD patients.
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24
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Ling C, Dai Y, Fang L, Yao F, Liu Z, Qiu Z, Cui L, Xia F, Zhao C, Zhang S, Wang K, Zhang X. Exonic rearrangements in DMD in Chinese Han individuals affected with Duchenne and Becker muscular dystrophies. Hum Mutat 2019; 41:668-677. [PMID: 31705731 PMCID: PMC7028077 DOI: 10.1002/humu.23953] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 01/12/2023]
Abstract
Exonic deletions and duplications within DMD are the main pathogenic variants in Duchenne and Becker muscular dystrophies (DMD/BMD). However, few studies have profiled the flanking sequences of breakpoints and the potential mechanism underlying the breakpoints in different fragile regions of DMD. In this study, 896 Chinese male probands afflicted with DMD/BMD were selected from unrelated families and analyzed using multiplex ligation‐dependent probe amplification of the DMD gene, in which we identified exon deletions in 784 subjects and duplications in 112 subjects. Deletions occurred most frequently in the genomic region encompassing exons 45–55, accounting for 73% of all deletion patterns. Furthermore, to unravel the potential mechanism that induced breaks, DMD gene capture and sequencing were performed to identify the breakpoints in 37 subjects with deletions encompassing exons 45–55 of DMD; we found that DMD instability did not arise from a single cause; instead, long‐sequence motifs, nonconsensus microhomologies, low‐copy repeats, and microindels were embedded around the breakpoints, which may predispose DMD to instability. In summary, this study highlights the heterogeneous characteristics of the flanking sequences around the breakpoints and helps us to understand the mechanism underlying DMD gene instability.
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Affiliation(s)
- Chao Ling
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Fang
- Department of Pathology & Laboratory Medicine, Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Fengxia Yao
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhe Liu
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhengqing Qiu
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Chen Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Kai Wang
- Department of Pathology & Laboratory Medicine, Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xue Zhang
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, McKusick-Zhang Center for GeneticMedicine, School of Basic Medicine Peking, Union Medical College, Beijing, China
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25
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Toksoy G, Durmus H, Aghayev A, Bagirova G, Sevinc Rustemoglu B, Basaran S, Avci S, Karaman B, Parman Y, Altunoglu U, Yapici Z, Tekturk P, Deymeer F, Topaloglu H, Kayserili H, Oflazer-Serdaroglu P, Uyguner ZO. Mutation spectrum of 260 dystrophinopathy patients from Turkey and important highlights for genetic counseling. Neuromuscul Disord 2019; 29:601-613. [DOI: 10.1016/j.nmd.2019.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 03/20/2019] [Accepted: 03/25/2019] [Indexed: 12/24/2022]
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26
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Wang D, Gao M, Zhang K, Jin R, Lv Y, Liu Y, Ma J, Wan Y, Gai Z, Liu Y. Molecular Genetics Analysis of 70 Chinese Families With Muscular Dystrophy Using Multiplex Ligation-Dependent Probe Amplification and Next-Generation Sequencing. Front Pharmacol 2019; 10:814. [PMID: 31404137 PMCID: PMC6669794 DOI: 10.3389/fphar.2019.00814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/24/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Muscular dystrophy (MD) includes multiple types, of which dystrophinopathies caused by dystrophin (DMD) mutations are the most common types in children. An accurate identification of the causative mutation at the genomic level is critical for genetic counseling of the family, and analysis of genotype-phenotype correlations, as well as a reference for the development of gene therapy. Methods: Totally, 70 Chinese families with suspected MD probands were enrolled in the study. The multiplex ligation-dependent probe amplification (MLPA) was first performed to screen large deletions/duplications of DMD exons in the patients, and then, next-generation sequencing (NGS) was carried out to detect small mutations in the MLPA-negative patients. Results: Totally, 62 mutations of DMD were found in 62 probands with DMD/BMD, and two compound heterozygous mutations in LAMA2 were identified in two probands with MDC1A (a type of congenital MD), indicating that the diagnostic yield was 91.4% by MLPA plus NGS for MD diagnosis in this cohort. Out of the mutations, 51 large mutations encompassing 47 (75.8%) deletions and four duplications (6.5%) were identified by MLPA; 11 small mutations including six (9.7%) nonsense, two (3.2%) small deletions, two splice-site mutations (3.2%), and one small insertion (1.6%) were found by NGS. Large mutations were found most frequently in the hotspot region between exons 45 and 55 (70.6%). Out of the 11 patients harboring point mutations in DMD, 8 were novel mutations. Additionally, one novel mutation in LAMA2 was identified. All the novel mutations were analyzed and predicted as pathogenic according to American College of Medical Genetics and Genomics (ACMG) guideline. Finally, 34 DMD, 4 BMD, 24 BMD/DMD, and 2 MDC1A were diagnosed in the cohort. Conclusion: Our data indicated that the MLPA plus NGS can be a comprehensive and effective tool for precision diagnosis and potential treatment of MD and is particularly necessary for the patients at very young age with only two clinical indicators (persistent hyperCKemia and typical myopathy performance on electromyogram) but no definite clinical manifestations.
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Affiliation(s)
- Dong Wang
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Min Gao
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Kaihui Zhang
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Ruifeng Jin
- Neurology Department, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Yuqiang Lv
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Yong Liu
- Neurology Department, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Jian Ma
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Ya Wan
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Yi Liu
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
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27
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Polavarapu K, Preethish-Kumar V, Sekar D, Vengalil S, Nashi S, Mahajan NP, Thomas PT, Sadasivan A, Warrier M, Gupta A, Arunachal G, Debnath M, Keerthipriya MS, Pradeep-Chandra-Reddy C, Puttegowda A, John AP, Tavvala A, Gunasekaran S, Sathyaprabha TN, Chandra SR, Kramer B, Delhaas T, Nalini A. Mutation pattern in 606 Duchenne muscular dystrophy children with a comparison between familial and non-familial forms: a study in an Indian large single-center cohort. J Neurol 2019; 266:2177-2185. [PMID: 31139960 DOI: 10.1007/s00415-019-09380-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
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28
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Tomar S, Moorthy V, Sethi R, Chai J, Low PS, Hong STK, Lai PS. Mutational spectrum of dystrophinopathies in Singapore: Insights for genetic diagnosis and precision therapy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:230-244. [DOI: 10.1002/ajmg.c.31704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Swati Tomar
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Vikaesh Moorthy
- Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Raman Sethi
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Josiah Chai
- Department of Neurology, National Neuroscience Institute Singapore
| | - Poh Sim Low
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Stacey Tay Kiat Hong
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of Singapore Singapore
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29
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Multiple Exon Skipping in the Duchenne Muscular Dystrophy Hot Spots: Prospects and Challenges. J Pers Med 2018; 8:jpm8040041. [PMID: 30544634 PMCID: PMC6313462 DOI: 10.3390/jpm8040041] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/24/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
Duchenne muscular dystrophy (DMD), a fatal X-linked recessive disorder, is caused mostly by frame-disrupting, out-of-frame deletions in the dystrophin (DMD) gene. Antisense oligonucleotide-mediated exon skipping is a promising therapy for DMD. Exon skipping aims to convert out-of-frame mRNA to in-frame mRNA and induce the production of internally-deleted dystrophin as seen in the less severe Becker muscular dystrophy. Currently, multiple exon skipping has gained special interest as a new therapeutic modality for this approach. Previous retrospective database studies represented a potential therapeutic application of multiple exon skipping. Since then, public DMD databases have become more useful with an increase in patient registration and advances in molecular diagnosis. Here, we provide an update on DMD genotype-phenotype associations using a global DMD database and further provide the rationale for multiple exon skipping development, particularly for exons 45–55 skipping and an emerging therapeutic concept, exons 3–9 skipping. Importantly, this review highlights the potential of multiple exon skipping for enabling the production of functionally-corrected dystrophin and for treating symptomatic patients not only with out-of-frame deletions but also those with in-frame deletions. We will also discuss prospects and challenges in multiple exon skipping therapy, referring to recent progress in antisense chemistry and design, as well as disease models.
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30
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Kobayashi M, Hatakeyama T, Ishizaki M, Adachi K, Morita M, Yonemoto N, Matsumura T, Toyoshima I, Kimura E. Medical Attitudes Survey for Female Dystrophinopathy Carriers in Japan. Intern Med 2018; 57. [PMID: 29526935 PMCID: PMC6148176 DOI: 10.2169/internalmedicine.0163-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Objective This study attempted to clarify the current status of female dystrophinopathy carriers, including the numbers of patients, the status of genetic screening, the status of counseling, physicians' understanding, and barriers to registration. Methods We sent out questionnaires to 402 physicians registered in the Remudy dystrophinopathy registry. The total number of responses received was 130 (response rate: 32%). Result In total, 1,212 cases of Duchenne muscular dystrophy, 365 cases of Becker muscular dystrophy, and 132 cases of female dystrophinopathy with a confirmed genetic mutation were encountered, and genetic testing was performed in the mother in 137, 23, and 12 cases, respectively. With respect to the risk of the onset of health problems, 25% of physicians always explained, 29% usually explained, 29% sometimes explained, and 13% never explained the risk to the mothers and female siblings of dystrophinopathy patients. The most common reason for not explaining the risk was a lack of knowledge/information. Thirty-five percent were familiar with the guidelines for testing the heart function of carriers. Conclusion Fewer mothers of dystrophinopathy patients have undergone genetic testing in Japan than in other countries. A significant portion of doctors did not explain the risks of health problems due to a lack of knowledge. We hope this survey will lead to an increased discussion of female dystrophinopathy patients.
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Affiliation(s)
| | | | | | - Katsuhito Adachi
- Department of Internal Medicine, Tokushima National Hospital, Japan
| | - Mizuki Morita
- Department of Biorepository Research and Networking, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Japan
| | | | | | | | - En Kimura
- Translational Medical Center, National Center of Neurology and Psychiatry, Japan
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31
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Ma P, Zhang S, Zhang H, Fang S, Dong Y, Zhang Y, Hao W, Wu S, Zhao Y. Comprehensive genetic characteristics of dystrophinopathies in China. Orphanet J Rare Dis 2018; 13:109. [PMID: 29973226 PMCID: PMC6032532 DOI: 10.1186/s13023-018-0853-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/20/2018] [Indexed: 11/10/2022] Open
Abstract
Background Dystrophinopathies are a set of severe and incurable X-linked neuromuscular disorders caused by mutations in the dystrophin gene (DMD). These mutations form a complex spectrum. A national registration network is essential not only to provide more information about the prevalence and natural history of the disease, but also to collect genetic data for analyzing the mutational spectrum. This information is extremely beneficial for basic scientific research, genetic diagnosis, trial planning, clinical care, and gene therapy. Methods We collected data from 1400 patients (1042 patients with confirmed unrelated Duchenne muscular dystrophy [DMD] or Becker muscular dystrophy [BMD]) registered in the Chinese Genetic Disease Registry from March 2012 to August 2017 and analyzed the genetic mutational characteristics of these patients. Results Large deletions were the most frequent type of mutation (72.2%), followed by nonsense mutations (11.9%), exon duplications (8.8%), small deletions (3.0%), splice-site mutations (2.1%), small insertions (1.3%), missense mutations (0.6%), and a combination mutation of a deletion and a duplication (0.1%). Exon 45–50 deletion was the most frequent deletion type, while exon 2 duplication was the most common duplication type. Two deletion hotspots were calculated—one located toward the central part (exon 45–52) of the gene and the other toward the 5’end (exon 8–26). We found no significant difference between hereditary and de novo mutations on deletion hotspots. Nonsense mutations accounted for 62.9% of all small mutations (197 patients). Conclusion We built a comprehensive national dystrophinopathy mutation database in China, which is essential for basic and clinical research in this field. The mutational spectrum and characteristics of this DMD/BMD group were largely consistent with those in previous international DMD/BMD studies, with some differences. Based on our results, about 12% of DMD/BMD patients with nonsense mutations may benefit from stop codon read-through therapy. Additionally, the top three targets for exon-skipping therapy are exon 51 (141, 13.5%), exon 53 (115, 11.0%), and exon 45 (84, 8.0%). Electronic supplementary material The online version of this article (10.1186/s13023-018-0853-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peipei Ma
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Shu Zhang
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Hao Zhang
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Siying Fang
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Yuru Dong
- Department of Magnetic Resonance, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Yan Zhang
- Department of Precision Medicine Laboratory, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Weiwei Hao
- Department of Precision Medicine Laboratory, the General Hospital of Chinese People's Armed Police Force, Beijing, China
| | - Shiwen Wu
- Department of Neurology, the General Hospital of Chinese People's Armed Police Force, Beijing, China.
| | - Yuying Zhao
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, Shandong, China.
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