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Ozkalayci H, Bora E, Cankaya T, Kocabey M, Zubari NC, Yis U, Giray Bozkaya O, Turan S, Pekcanlar Akay A, Caglayan AO, Ulgenalp A. Investigation of genotype-phenotype and familial features of Turkish dystrophinopathy patients. Neurogenetics 2024; 25:201-213. [PMID: 38850354 DOI: 10.1007/s10048-024-00765-9] [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: 11/20/2023] [Accepted: 05/31/2024] [Indexed: 06/10/2024]
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive allelic muscle diseases caused by dystrophin gene mutations. Eight hundred thirty-seven patients admitted between 1997 and 2022 were included in the study. Two hundred twenty patients were analyzed by multiplex PCR (mPCR) alone. Five hundred ninety-five patients were investigated by multiplex ligation-dependent probe amplification (MLPA), and 54 patients were examined by sequencing. Deletion was detected in 60% (132/220) of the cases in the mPCR group only and in 58.3% (347/595) of the cases with MLPA analysis. The rates of deletion and duplication were 87.7% and 12.3%, respectively, in the MLPA analysis. Single exon deletions were the most common mutation type. The introns 43-55 (81.8%) and exons 2-21 (13.1%) regions were detected as hot spots in deletions. It was determined that 89% of the mutations were suitable for exon skipping therapy. The reading frame rule did not hold in 7.6% of D/BMD cases (17/224). We detected twenty-five pathogenic/likely pathogenic variants in sequencing, five of which were novel variants. Nonsense mutation was the most common small mutation (44%). 21% of DMD patients were familial. We detected germline mosaicism in four families (4.3%) in the large rearrangement group and one gonosomal mosaicism in a family with a nonsense mutation. This is the largest study examining genotype and phenotype data in Turkish D/BMD families investigated by MLPA analysis. The reading frame hypothesis is not valid in all cases. Sharing the genotype and phenotype characteristics of these cases in the literature will shed light on the molecular structure of DMD and guide gene therapy research. In genetic counseling, carrier screening in the family and possible gonadal mosaicism should be emphasized.
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Affiliation(s)
- Hande Ozkalayci
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey.
- Department of Medical Genetics, Istanbul Training and Research Hospital, Istanbul, 34146, Turkey.
| | - Elcin Bora
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Tufan Cankaya
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Mehmet Kocabey
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Nadide Cemre Zubari
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Uluc Yis
- Department of Pediatric Neurology, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Ozlem Giray Bozkaya
- Department of Pediatric Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Serkan Turan
- Department of Child And Adolescent Psychiatry, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Aynur Pekcanlar Akay
- Department of Child And Adolescent Psychiatry, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Ahmet Okay Caglayan
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Ayfer Ulgenalp
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
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2
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Fortunato F, Tonelli L, Farnè M, Selvatici R, Ferlini A. DMD deletions underlining mild dystrophinopathies: literature review highlights phenotype-related mutation clusters and provides insights about genetic mechanisms and prognosis. Front Neurol 2024; 14:1288721. [PMID: 38288333 PMCID: PMC10823016 DOI: 10.3389/fneur.2023.1288721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/27/2023] [Indexed: 01/31/2024] Open
Abstract
DMD gene pathogenic variations cause a spectrum of phenotypes, ranging from severe Duchenne muscular dystrophy, the Becker milder cases, the intermediate or very mild muscle phenotypes invariably characterized by high CK, and the ultrarare fully-asymptomatic cases. Besides these phenotypes, X-linked dilated cardiomyopathy is also caused by DMD mutations. Males carrying DMD deletions with absent or very mild phenotypes have been sparsely described. We performed a horizon scan on public datasets to enroll males with the above phenotypes and carrying DMD deletions to delineate myopathic genotype-phenotype relationships. We inventoried 81 males, who were divided into the following clinical categorization: fully-asymptomatic males aged >43 years (A, N = 22); isolated hyperCKemia (CK, N = 35); and mild weakness (any age) with or without high CK (WCK, N = 24). In all cases, deleted intervals were exons 2 to 55, and no downstream exons were ever involved, apart from an exon 78 deletion in a WCK patient. All deletions were in-frame apart from the known exception to the rule of exon 2 and exon 78. We correlated the mild phenotypes (A and CK) to deleted exons, intronic breakpoints, exon-exon junctions, 3' isoforms rule, and protein epitopes, and we found that some genetic profiles are exclusively/mainly occurring in A/CK phenotypes, suggesting they are compatible with a quasi-normal muscular performance. We discussed diverse pathogenic mechanisms that may contribute to mild dystrophinopathic phenotypes, and we tried to address some "critical" genetic configurations or exon content needed to preserve a semi-functional DMD gene.
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Affiliation(s)
| | | | | | | | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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Wijekoon N, Gonawala L, Ratnayake P, Liyanage R, Amaratunga D, Hathout Y, Steinbusch HWM, Dalal A, Hoffman EP, de Silva KRD. Title-molecular diagnostics of dystrophinopathies in Sri Lanka towards phenotype predictions: an insight from a South Asian resource limited setting. Eur J Med Res 2024; 29:37. [PMID: 38195599 PMCID: PMC10775540 DOI: 10.1186/s40001-023-01600-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND The phenotype of Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) patients is determined by the type of DMD gene variation, its location, effect on reading frame, and its size. The primary objective of this investigation was to determine the frequency and distribution of DMD gene variants (deletions/duplications) in Sri Lanka through the utilization of a combined approach involving multiplex polymerase chain reaction (mPCR) followed by Multiplex Ligation Dependent Probe Amplification (MLPA) and compare to the international literature. The current consensus is that MLPA is a labor efficient yet expensive technique for identifying deletions and duplications in the DMD gene. METHODOLOGY Genetic analysis was performed in a cohort of 236 clinically suspected pediatric and adult myopathy patients in Sri Lanka, using mPCR and MLPA. A comparative analysis was conducted between our findings and literature data. RESULTS In the entire patient cohort (n = 236), mPCR solely was able to identify deletions in the DMD gene in 131/236 patients (DMD-120, BMD-11). In the same cohort, MLPA confirmed deletions in 149/236 patients [DMD-138, BMD -11]. These findings suggest that mPCR has a detection rate of 95% (131/138) among all patients who received a diagnosis. The distal and proximal deletion hotspots for DMD were exons 45-55 and 6-15. Exon 45-60 identified as a novel in-frame variation hotspot. Exon 45-59 was a hotspot for BMD deletions. Comparisons with the international literature show significant variations observed in deletion and duplication frequencies in DMD gene across different populations. CONCLUSION DMD gene deletions and duplications are concentrated in exons 45-55 and 2-20 respectively, which match global variation hotspots. Disparities in deletion and duplication frequencies were observed when comparing our data to other Asian and Western populations. Identified a 95% deletion detection rate for mPCR, making it a viable initial molecular diagnostic approach for low-resource countries where MLPA could be used to evaluate negative mPCR cases and cases with ambiguous mutation borders. Our findings may have important implications in the early identification of DMD with limited resources in Sri Lanka and to develop tailored molecular diagnostic algorithms that are regional and population specific and easily implemented in resource limited settings.
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Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | | | - Roshan Liyanage
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | | | - Yetrib Hathout
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - Harry W M Steinbusch
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500039, India
| | - Eric P Hoffman
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, 13902, USA
| | - K Ranil D de Silva
- Interdisciplinary Center for Innovation in Biotechnology and Neuroscience, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka.
- Department of Cellular and Translational Neuroscience, School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, 6200, Maastricht, The Netherlands.
- Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, 10390, Sri Lanka.
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Bakhshandeh M, Behroozi S, Ghorbani A. Next-generation sequencing approach to molecular diagnosis of Iranian patients with Duchenne/Becker muscular dystrophy: Several novel variants identified. eNeurologicalSci 2023; 30:100446. [PMID: 36845278 PMCID: PMC9945705 DOI: 10.1016/j.ensci.2023.100446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/11/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) constitute the second most prevalent muscular dystrophy, with large deletions or duplications accounting for 66% of cases. No effective treatment exists for DMD/BMD. At present, genetic diagnosis serves as the foundation for gene therapy treatments. In this study, a comprehensive molecular investigation was conducted. The subjects diagnosed with DMD/BMD were initially examined using multiplex ligation-dependent probe amplification (MLPA) technology. The negative MLPA results were analyzed further using next-generation sequencing (NGS) technology. The MLPA detected 201 deletions (65.9%) and 20 duplications (6.6%) along the dystrophin gene among the 305 Iranian patients examined. The deletion of exon 52 in the amenable skipping subgroup was associated with an earlier onset age and a more severe phenotype. Twenty-one of the small mutations found in 58 MLPA-negative patients were novel. The most prevalent variants were nonsense variants (46.5%), frameshift variants (31%), splicing variants (6.9%), missense variants (10.4%), and synonymous mutations (5.1%). Our results demonstrate that MLPA and NGS can be effective diagnostic tools for very young patients with a single exon deletion.
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Affiliation(s)
- MohammadKazem Bakhshandeh
- Hakim Children Hospital, Department of Pediatrics, Tehran University of Medical Sciences, Tehran, Iran,Corresponding author.
| | - Samira Behroozi
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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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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Szűcs Z, Pinti É, Haltrich I, Szén OP, Nagy T, Barta E, Méhes G, Bidiga L, Török O, Ujfalusi A, Koczok K, Balogh I. An Ultra-Rare Manifestation of an X-Linked Recessive Disorder: Duchenne Muscular Dystrophy in a Female Patient. Int J Mol Sci 2022; 23:ijms232113076. [PMID: 36361862 PMCID: PMC9655586 DOI: 10.3390/ijms232113076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/30/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is the most common inherited muscle dystrophy. Patients are characterized by muscle weakness, gross motor delay, and elevated serum creatinine kinase (CK) levels. The disease is caused by mutations in the DMD gene located on the X chromosome. Due to the X-linked recessive inheritance pattern, DMD most commonly affects males, who are generally diagnosed between the age of 3–5 years. Here we present an ultra-rare manifestation of DMD in a female patient. Cytogenetic examination showed that she has a t(X;10)(p21.1;p12.1) translocation, which turned out to affect the DMD gene with one of the breakpoints located in exon 54 (detected by genome sequencing). The X-inactivation test revealed skewed X-inactivation (ratio 99:1). Muscle histology and dystrophin immunohistochemistry showed severe dystrophic changes and highly reduced dystrophin expression, respectively. These results, in accordance with the clinical picture and a highly elevated serum CK, led to the diagnosis of DMD. In conclusion, although in very rare cases, DMD can manifest in female patients as well. In this case, a balanced X-autosome reciprocal translocation disrupts the DMD gene and skewed X-inactivation leads to the manifestation of the DMD phenotype.
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Affiliation(s)
- Zsuzsanna Szűcs
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Éva Pinti
- 2nd Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
| | - Irén Haltrich
- 2nd Department of Pediatrics, Semmelweis University, 1094 Budapest, Hungary
| | - Orsolya Pálné Szén
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Tibor Nagy
- Bioinformatics and Functional Genome Analysis Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Endre Barta
- Bioinformatics and Functional Genome Analysis Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - László Bidiga
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Olga Török
- Medical and Health Science Centre, Department of Obstetrics and Gynaecology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Anikó Ujfalusi
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Katalin Koczok
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (K.K.); (I.B.)
| | - István Balogh
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (K.K.); (I.B.)
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Functional analysis of variants in DMD exon/intron 10 predicted to affect splicing. J Hum Genet 2022; 67:495-501. [DOI: 10.1038/s10038-022-01035-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/08/2022] [Accepted: 03/31/2022] [Indexed: 11/08/2022]
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Zehravi M, Wahid M, Ashraf J, Fatima T. Whole-Exome Sequencing Identifies Small Mutations in Pakistani Muscular Dystrophy Patients. Genet Test Mol Biomarkers 2021; 25:218-226. [PMID: 33734897 DOI: 10.1089/gtmb.2020.0246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Muscular dystrophies are a heterogeneous group of inherited disorders that cannot be diagnosed clinically due to overlapping clinical phenotypes. Whole-exome sequencing is considered as the diagnostic strategy of choice in these cases. In this study we aimed to determine the mutational spectrum of multiplex ligation-dependent probe amplification (MLPA)-negative muscular dystrophy patients in Pakistan using whole-exome sequencing. Subsequently the mutations identified via WES were used to screen additional dystrophinopathy patients by Sanger sequencing. Materials and Methods: DNA extracted from the peripheral blood of three MLPA-negative muscular dystrophy patients was sent for whole-exome sequencing. The identified variants in these 3 patients were then checked in 18 dystrophinopathy patients using Sanger sequencing. Results: Four missense variants and one nonsense variant in the Duchenne muscular dystrophy (DMD) gene were detected. WES diagnosed a DMD patient carrying a nonsense variant c.4375C>T (rs398123953) who can benefit from Ataluren therapy. The other two patients carried missense variant (c.572G>T) in the YARS2 gene (rs11539445) labeling them as patients of MLASA (myopathy, lactic acidosis, and sideroblastic anemia). The identified missense and nonsense variants in the DMD gene were detected in 18 clinically diagnosed dystrophinopathy patients using Sanger sequencing. Three missense variants were detected in our cohort of 18 dystrophinopathy patients. One missense variant c.3406A>T (rs3827462) and a nonsense variant c.4375C>T (rs398123953) were not detected in our cohort of 18 dystrophinopathy patients. Conclusions: Whole-exome sequencing identified a nonsense variant in Pakistani muscular dystrophy patients, which is amenable to treatment by Ataluren and a missense variant in YARS2 gene responsible for causing MLASA.
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Affiliation(s)
- Mehwish Zehravi
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan
| | - Mohsin Wahid
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan.,Department of Pathology, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Junaid Ashraf
- Department of Neurosurgery, Dow University of Health Sciences, Karachi, Pakistan
| | - Tehseen Fatima
- Dow Research Institute of Biotechnology and Biomedical Sciences, Dow University of Health Sciences, Karachi, Pakistan.,Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
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Lin J, Li H, Liao Z, Wang L, Zhang C. Comparison of Carrier and de novo Pathogenic Variants in a Chinese DMD/BMD Cohort. Front Neurol 2021; 12:714677. [PMID: 34421809 PMCID: PMC8375267 DOI: 10.3389/fneur.2021.714677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/14/2021] [Indexed: 01/14/2023] Open
Abstract
Background: Duchenne and Becker muscular dystrophy (DMD/BMD) are X-linked recessively inherited neuromuscular disorders caused by deletions, duplications, or small mutations in the DMD gene. With advances in prenatal diagnosis decreasing the number of affected offspring from carrier mothers, the frequency of de novo variants could increase. Therefore, determining the differences between the carrier and de novo variants of the DMD gene, which are rarely explored, is important for trial planning and genetic diagnosis in the future. Methods: A total of 440 patients, 349 of whom had DMD and 91 had BMD, diagnosed in our department between 2012 and 2019, along with their respective mothers, were included in this study. Multiplex ligation-dependent probe amplification was used to detected deletions and duplications in patients and their mothers. Small mutations were detected using next-generation sequencing in the patients, followed by Sanger sequencing in the mothers. Results: Deletions, duplications, and small mutations were identified in 204, 46, and 99 of the 349 patients with DMD and in 50, 10, and 31 of the 91 patients with BMD, respectively. De novo deletions were more concentrated in hotspot regions than carrier deletions of DMD/BMD. No clear bias was observed in the variant distribution between carriers, de novo duplications, and small mutations in DMD/BMD. The carrier frequency of DMD (61.6%) was lower than that of BMD (69.2%), but the difference was not statistically significant. The carrier frequency of deletions of the DMD gene (51.2%) was significantly lower than those of duplications (75%) and small mutations (81.5%). Conclusion: Compared to de novo deletions, deletions from carrier mothers had a wider distribution. Moreover, there was no significant difference between the carrier frequencies of DMD and BMD. Duplications and small mutations were more commonly inherited, while deletions were present de novo.
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Affiliation(s)
- Jinfu Lin
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Huan Li
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Ziyu Liao
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Liang Wang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Cheng Zhang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
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10
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Nagabushana D, Polavarapu K, Bardhan M, Arunachal G, Gunasekaran S, Preethish-Kumar V, Anjanappa RM, Thomas P, Sadasivan A, Vengalil S, Nashi S, Chawla T, Warrier M, Keerthipriya M, Raju S, Mohan D, Nalini A. Comparison of The Carrier Frequency of Pathogenic Variants of DMD Gene in an Indian Cohort. J Neuromuscul Dis 2021; 8:525-535. [PMID: 33843695 DOI: 10.3233/jnd-210658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is an X-linked disorder caused due to large deletions, duplications,and small pathogenic variants. This article compares the carrier frequency of different pathogenic variants in the DMD gene for the first time in an Indian cohort. METHODS Ninety-one mothers of genetically confirmed DMD probands are included in this study. Pathogenic variants in the DMD gene in probands were detected by multiplex ligation-dependent probe amplification (MLPA) or next-generation sequencing (NGS). Maternal blood samples were evaluated either by MLPA or Sanger sequencing. The demographic and clinical details for screening of muscle weakness and cardiomyopathy were collected from the confirmed carriers. RESULTS Out of 91 probands, large deletions and duplications were identified in 46 and 6 respectively, while 39 had small variants. Among the small variants, substitutions predicted to cause nonsense mutations were the most common (61.5%), followed by frameshift causing small insertion/deletions (25.6%) and splice affecting intronic variants (12.8%). Notably, 19 novel small variants predicted to be disease-causing were identified. Of the 91 mothers, 53 (58.7%) were confirmed to be carriers. Exonic deletions had a significantly lower carrier frequency of 47.8% as compared to small variants (64.1%). The mean age of the carriers at evaluation was 30 years. Among the carriers, two were symptomatic with onset in the 4th decade, manifesting with progressive proximal muscle weakness and dilated cardiomyopathy. CONCLUSION Carrier frequency of small pathogenic variants differs significantly from large deletions. Small pathogenic variants are more commonly inherited, whereas large deletions arise de novo.
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Affiliation(s)
- Divya Nagabushana
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Kiran Polavarapu
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India.,Children's Hospital of Eastern Ontario Research Institute, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada.,Brain and Mind Research Institute, University of Ottawa, ON, Canada
| | - Mainak Bardhan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Gautham Arunachal
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Swetha Gunasekaran
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | | | - Ram Murthy Anjanappa
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - PriyaTreesa Thomas
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Arun Sadasivan
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Saraswati Nashi
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Tanushree Chawla
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Manjusha Warrier
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Muddasu Keerthipriya
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Sanita Raju
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Dhaarini Mohan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
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11
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Guevara-Fujita ML, Huaman-Dianderas F, Obispo D, Sánchez R, Barrenechea V, Rojas-Málaga D, Estrada-Cuzcano A, Trubnykova M, Cornejo-Olivas M, Marca V, Gallardo B, Dueñas-Roque M, Protzel A, Castañeda C, Abarca H, Celis L, La Serna-Infantes J, Fujita R. MLPA followed by target-NGS to detect mutations in the dystrophin gene of Peruvian patients suspected of DMD/DMB. Mol Genet Genomic Med 2021; 9:e1759. [PMID: 34327855 PMCID: PMC8457708 DOI: 10.1002/mgg3.1759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/09/2021] [Accepted: 07/08/2021] [Indexed: 11/11/2022] Open
Abstract
Background We report the molecular analysis of the DMD gene in a group of Peruvian patients with Duchenne/Becker dystrophinopathy. This is the first study to thoroughly characterize mutations in this population. Methods We used the combination of multiplex ligation‐dependent probe amplification (MLPA) and sequencing analysis of the DMD gene. We recruited Peruvian patients in 2 years from reference national hospitals. We performed DNA tests in 152 patients, checking first exon deletion/duplication by MLPA, and subsequently, if negative, samples were sequenced to detect point mutations. Results The average age for diagnosis was 9.8 years, suggesting a delay for timely diagnosis and care. We found causal DMD mutations in 125 patients: 72 (57.6%) exon deletions/duplications (41.6% deletions, 16.0% duplications), and 53 (42.4%) point mutations (27.2% nonsense, 9.6% small indels, and 5.6% splice site). Conclusion Due to our genetic background, we expected a higher number of novel and recurrent causal mutations in our sample. Results showed 16% of novel mutations, similar to other well‐studied populations.
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Affiliation(s)
- María Luisa Guevara-Fujita
- Centro de Genética y Biología Molecular, Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Peru
| | - Francia Huaman-Dianderas
- Centro de Genética y Biología Molecular, Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Peru
| | - Daisy Obispo
- Centro de Genética y Biología Molecular, Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Peru
| | - Rodrigo Sánchez
- Centro de Genética y Biología Molecular, Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Peru
| | - Victor Barrenechea
- Centro de Genética y Biología Molecular, Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Peru
| | - Diana Rojas-Málaga
- Centro de Genética y Biología Molecular, Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Peru.,Laboratório de Genética Molecular, Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Rio Grande do Sul, Brazil
| | - Alejandro Estrada-Cuzcano
- Centro de Genética y Biología Molecular, Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Peru.,Paris-Saclay Institute of Neuroscience, CERTO-Retina France, CNRS, Université Paris-Saclay, Orsay, 91405, France
| | - Milana Trubnykova
- Servicio de Genética y Errores Innatos del Metabolismo del Instituto Nacional de Salud del Niño, Lima, Peru
| | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima, Peru.,Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Victoria Marca
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
| | - Bertha Gallardo
- Servicio de Genética y Errores Innatos del Metabolismo del Instituto Nacional de Salud del Niño, Lima, Peru
| | | | - Ana Protzel
- Hospital Nacional Edgardo Rebagliati Martins, EsSalud, Lima, Peru
| | | | - Hugo Abarca
- Servicio de Genética y Errores Innatos del Metabolismo del Instituto Nacional de Salud del Niño, Lima, Peru
| | - Luis Celis
- Servicio de Genética, Instituto de Salud del Niño San Borja, Lima, Peru
| | | | - Ricardo Fujita
- Centro de Genética y Biología Molecular, Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Peru
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12
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Santin R, Vieira IA, Nunes JC, Benevides ML, Quadros F, Brusius-Facchin AC, Macedo G, Bertoni APS. A novel DMD intronic alteration: a potentially disease-causing variant of an intermediate muscular dystrophy phenotype. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2021; 40:93-100. [PMID: 34355126 PMCID: PMC8290513 DOI: 10.36185/2532-1900-048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Pathogenic germline variants in DMD gene, which encodes the well-known cytoskeletal protein named dystrophin, are associated with a wide range of dystrophinopathies disorders, such as Duchenne muscular dystrophy (DMD, severe form), Becker muscular dystrophy (BMD, mild form) and intermediate muscular dystrophy (IMD). Muscle biopsy, immunohistochemistry, molecular (multiplex ligation-dependent probe amplification (MLPA)/next-generation sequencing (NGS) and Sanger methods) and in silico analyses were performed in order to identify alterations in DMD gene and protein in a patient with a clinical manifestation and with high creatine kinase levels. Herein, we described a previously unreported intronic variant in DMD and reduced dystrophin staining in the muscle biopsy. This novel DMD variant allele, c.9649+4A>T that was located in a splice donor site within intron 66. Sanger sequencing analysis from maternal DNA showed the presence of both variant c.9649+4A>T and wild-type (WT) DMD alleles. Different computational tools suggested that this nucleotide change might affect splicing through a WT donor site disruption, occurring in an evolutionarily conserved region. Indeed, we observed that this novel variant, could explain the reduced dystrophin protein levels and discontinuous sarcolemmal staining in muscle biopsy, which suggests that c.9649+4A>T allele may be re-classified as pathogenic in the future. Our data show that the c.9649+4A>T intronic sequence variant in the DMD gene may be associated with an IMD phenotype and our findings reinforce the importance of a more precise diagnosis combining muscle biopsy, molecular techniques and comprehensive in silico approaches in the clinical cases with negative results for conventional genetic analysis.
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Affiliation(s)
- Ricardo Santin
- Santa Casa de Misericórdia de Porto Alegre, (ISCMPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Igor Araujo Vieira
- Programa de Pós Graduação em Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Jean Costa Nunes
- Neurodiagnostic Brazil - Floranópolis, Santa Catarina (SC), Brazil
- Departmento de Patologia, Universidade Federal de Santa Catarina (UFSC), Hospital Polydoro Ernani de São Thiago, SC, Brazil
| | - Maria Luiza Benevides
- Departmento de Neurologia, Hospital Governador Celso Ramos, Santa Catarina (SC), Brazil
| | - Fernanda Quadros
- Santa Casa de Misericórdia de Porto Alegre, (ISCMPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Carolina Brusius-Facchin
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriel Macedo
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Paula Santin Bertoni
- Departamento de Ciências Básicas da Saúde and Laboratório de Biologia Celular, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
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13
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[A predictive analysis of the association between clinical phenotypes and genotypes in children with Becker muscular dystrophy/Duchenne muscular dystrophy]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2020; 22. [PMID: 32571459 PMCID: PMC7390220 DOI: 10.7499/j.issn.1008-8830.1912133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To study the association between clinical phenotypes and genotypes in children with Becker muscular dystrophy (BMD)/Duchenne muscular dystrophy (DMD) so as to provide a theoretical basis for disease management, gene therapy, and prenatal diagnosis. METHODS A retrospective analysis was performed for the clinical data and gene detection results of 52 children with BMD/DMD. Multiplex ligation-dependent probe amplification (MLPA) was used to detect the DMD gene. The children with negative results of MLPA were further screened by exon chip capture combined with next-generation sequencing (NGS). The mothers of 20 probands were validated by sequencing. RESULTS The pathogenic genes for BMD/DMD were detected in 50 children by MLPA and NGS, with a detection rate of 96%. Among the 52 children, 36 (69%) had gene deletion, 7 (13%) had duplication, and 7 (13%) had micromutation. Among the 43 children with deletion/duplication, 32 had DMD and 11 had BMD; 37 children (86%) met the reading frame rule, among whom 27 (96%) had DMD and 10 (67%) had BMD. All 7 children with micromutation had DMD. CONCLUSIONS The reading frame rule has an extremely high predictive value for DMD but a limited predictive value for BMD.
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14
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Wayhelova M, Ryzí M, Oppelt J, Hladilkova E, Vallova V, Krskova L, Vilemova M, Polackova H, Gaillyova R, Kuglik P. Novel familial IQSEC2 pathogenic sequence variant associated with neurodevelopmental disorders and epilepsy. Neurogenetics 2020; 21:269-278. [PMID: 32564198 DOI: 10.1007/s10048-020-00616-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023]
Abstract
Pathogenic sequence variants in the IQ motif- and Sec7 domain-containing protein 2 (IQSEC2) gene have been confirmed as causative in the aetiopathogenesis of neurodevelopmental disorders (intellectual disability, autism) and epilepsy. We report on a case of a family with three sons; two of them manifest delayed psychomotor development and epilepsy. Initially proband A was examined using a multistep molecular diagnostics algorithm, including karyotype and array-comparative genomic hybridization analysis, both with negative results. Therefore, probands A and B and their unaffected parents were enrolled for an analysis using targeted "next-generation" sequencing (NGS) with a gene panel ClearSeq Inherited DiseaseXT (Agilent Technologies) and verification analysis by Sanger sequencing. A novel frameshift variant in the X-linked IQSEC2 gene NM_001111125.2:c.1813_1814del, p.(Asp605Profs*3) on protein level, was identified in both affected probands and their asymptomatic mother, having skewed X chromosome inactivation (XCI) (100:0). As the IQSEC2 gene is a known gene escaping from XCI in humans, we expect the existence of mechanisms maintaining the normal or enough level of the IQSEC2 protein in the asymptomatic mother. Further analyses may help to the characterization of the presented novel frameshift variant in the IQSEC2 gene as well as to elucidate the mechanisms leading to the rare asymptomatic phenotypes in females.
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Affiliation(s)
- Marketa Wayhelova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic
| | - Michal Ryzí
- Clinic of Children's Neurology, University Hospital Brno, Brno, Czech Republic
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Eva Hladilkova
- Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic
| | - Vladimira Vallova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic
| | - Lenka Krskova
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Marcela Vilemova
- Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic
| | - Hana Polackova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Renata Gaillyova
- Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic
| | - Petr Kuglik
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic. .,Department of Medical Genetics, University Hospital Brno, Brno, Czech Republic.
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