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Zídková J, Kramářová T, Kopčilová J, Réblová K, Haberlová J, Mazanec R, Voháňka S, Gřegořová A, Langová M, Honzík T, Šoukalová J, Ošlejšková H, Solařová P, Vyhnálková E, Fajkusová L. Genetic findings in Czech patients with limb girdle muscular dystrophy. Clin Genet 2023; 104:542-553. [PMID: 37526466 DOI: 10.1111/cge.14407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/03/2023] [Accepted: 07/13/2023] [Indexed: 08/02/2023]
Abstract
Limb girdle muscular dystrophies (LGMD) are a genetically heterogeneous group of muscular dystrophies. The study presents an overview of molecular characteristics of a large cohort of LGMD patients who are representative of the Czech LGMD population. We present 226 LGMD probands in which 433 mutant alleles carrying 157 different variants with a supposed pathogenic effect were identified. Fifty-four variants have been described only in the Czech LGMD population so far. LGMD R1 caplain3-related is the most frequent subtype of LGMD involving 53.1% of patients with genetically confirmed LGMD, followed by LGMD R9 FKRP-related (11.1%), and LGMD R12 anoctamin5-related (7.1%). If we consider identified variants, then all but five were small-scale variants. One large gene deletion was identified in the LAMA2 gene and two deletions in each of CAPN3 and SGCG. We performed comparison our result with other published studies. The results obtained in the Czech LGMD population clearly differ from the outcome of other LGMD populations in two aspects-we have a more significant proportion of patients with LGMD R1 calpain3-related and a smaller proportion of LGMD R2 dysferlin-related.
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Affiliation(s)
- Jana Zídková
- Centre of Molecular Biology and Genetics, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Tereza Kramářová
- Centre of Molecular Biology and Genetics, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Johana Kopčilová
- Centre of Molecular Biology and Genetics, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Kamila Réblová
- Centre of Molecular Biology and Genetics, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Jana Haberlová
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Praha, Czech Republic
| | - Radim Mazanec
- Department of Neurology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Stanislav Voháňka
- Department of Neurology, University Hospital Brno, Brno, Czech Republic
| | - Andrea Gřegořová
- Department of Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic
| | - Martina Langová
- Department of Medical Genetics, Thomayer University Hospital, Praha, Czech Republic
| | - Tomáš Honzík
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Praha, Czech Republic
| | - Jana Šoukalová
- Institute of Medical Genetics and Genomics, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Hana Ošlejšková
- Department of Child Neurology, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Pavla Solařová
- Department of Medical Genetics, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Emílie Vyhnálková
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology and Genetics, University Hospital Brno and Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
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Plevova P, Indrakova J, Savige J, Kuhnova P, Tvrda P, Cerna D, Hilscherova S, Kudrejova M, Polendova D, Jaklova R, Langova M, Jahnova H, Lastuvkova J, Dusek J, Gut J, Vlckova M, Solarova P, Kreckova G, Kantorova E, Soukalova J, Slavkovsky R, Zapletalova J, Tichy T, Thomasova D. A founder COL4A4 pathogenic variant resulting in autosomal recessive Alport syndrome accounts for most genetic kidney failure in Romani people. Front Med (Lausanne) 2023; 10:1096869. [PMID: 36844206 PMCID: PMC9948603 DOI: 10.3389/fmed.2023.1096869] [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: 11/12/2022] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
Introduction Romani people have a high prevalence of kidney failure. This study examined a Romani cohort for pathogenic variants in the COL4A3, COL4A4, and COL4A5 genes that are affected in Alport syndrome (AS), a common cause of genetic kidney disease, characterized by hematuria, proteinuria, end-stage kidney failure, hearing loss, and eye anomalies. Materials and methods The study included 57 Romani from different families with clinical features that suggested AS who underwent next-generation sequencing (NGS) of the COL4A3, COL4A4, and COL4A5 genes, and 83 family members. Results In total, 27 Romani (19%) had autosomal recessive AS caused by a homozygous pathogenic c.1598G>A, p.Gly533Asp variant in COL4A4 (n = 20) or a homozygous c.415G>C, p.Gly139Arg variant in COL4A3 (n = 7). For p.Gly533Asp, 12 (80%) had macroscopic hematuria, 12 (63%) developed end-stage kidney failure at a median age of 22 years, and 13 (67%) had hearing loss. For p.Gly139Arg, none had macroscopic hematuria (p = 0.023), three (50%) had end-stage kidney failure by a median age of 42 years (p = 0.653), and five (83%) had hearing loss (p = 0.367). The p.Gly533Asp variant was associated with a more severe phenotype than p.Gly139Arg, with an earlier age at end-stage kidney failure and more macroscopic hematuria. Microscopic hematuria was very common in heterozygotes with both p.Gly533Asp (91%) and p.Gly139Arg (92%). Conclusion These two founder variants contribute to the high prevalence of kidney failure in Czech Romani. The estimated population frequency of autosomal recessive AS from these variants and consanguinity by descent is at least 1:11,000 in Czech Romani. This corresponds to a population frequency of autosomal dominant AS from these two variants alone of 1%. Romani with persistent hematuria should be offered genetic testing.
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Affiliation(s)
- Pavlina Plevova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia,Department of Biomedical Sciences, Faculty of Medicine, University of Ostrava, Ostrava, Czechia,*Correspondence: Pavlina Plevova,
| | - Jana Indrakova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Judy Savige
- Department of Medicine (Melbourne Health and Northern Health), The University of Melbourne, Royal Melbourne Hospital, Melbourne, Australia
| | - Petra Kuhnova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Petra Tvrda
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Dita Cerna
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Sarka Hilscherova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Monika Kudrejova
- Department of Clinical and Molecular Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czechia
| | - Daniela Polendova
- Department of Medical Genetics, Faculty of Medicine in Plzeň, Charles University and University Hospital Plzeň, Plzeň, Czechia
| | - Radka Jaklova
- Department of Medical Genetics, Faculty of Medicine in Plzeň, Charles University and University Hospital Plzeň, Plzeň, Czechia
| | - Martina Langova
- Department of Medical Genetics, Thomayer University Hospital, Prague, Czechia
| | - Helena Jahnova
- Department of Pediatrics, Third Faculty of Medicine, Charles University and University Hospital Královské Vinohrady, Prague, Czechia
| | - Jana Lastuvkova
- Department of Medical Genetics, Krajská zdravotní, a.s., Masaryk Hospital in Ústí nad Labem, Ústí nad Labem, Czechia
| | - Jiri Dusek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Josef Gut
- Department of Pediatrics, Hospital Česká Lípa, Česká Lípa, Czechia
| | - Marketa Vlckova
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
| | - Pavla Solarova
- Department of Medical Genetics, University Hospital Hradec Králové, Hradec Králové, Czechia
| | | | - Eva Kantorova
- Department of Medical Genetics, Hospital České Budějovice a.s., České Budějovice, Czechia
| | - Jana Soukalova
- Department of Medical Genetics and Genomics, University Hospital Brno, Brno, Czechia
| | - Rastislav Slavkovsky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - Jana Zapletalova
- Department of Medical Biophysics, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - Tomas Tichy
- Institute of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - Dana Thomasova
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czechia
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Clinical, genetic profile and disease progression of sarcoglycanopathies in a large cohort from India: high prevalence of SGCB c.544A > C. Neurogenetics 2022; 23:187-202. [DOI: 10.1007/s10048-022-00690-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/08/2022] [Indexed: 10/18/2022]
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Ozyilmaz B, Kirbiyik O, Ozdemir TR, Ozer OK, Kutbay YB, Erdogan KM, Guvenc MS, Arıkan Ş, Turk TS, Kale MY, Uludag IF, Baydan F, Sertpoyraz F, Gencpinar P, Diniz G. Experiences in the molecular genetic and histopathological evaluation of calpainopathies. Neurogenetics 2022; 23:103-114. [DOI: 10.1007/s10048-022-00687-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
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Siavrienė E, Petraitytė G, Burnytė B, Morkūnienė A, Mikštienė V, Rančelis T, Utkus A, Kučinskas V, Preikšaitienė E. Compound heterozygous c.598_612del and c.1746-20C > G CAPN3 genotype cause autosomal recessive limb-girdle muscular dystrophy-1: a case report. BMC Musculoskelet Disord 2021; 22:1020. [PMID: 34863162 PMCID: PMC8645139 DOI: 10.1186/s12891-021-04920-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/28/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Autosomal recessive limb-girdle muscular dystrophy-1 (LGMDR1), also known as calpainopathy, is a genetically heterogeneous disorder characterised by progression of muscle weakness. Homozygous or compound heterozygous variants in the CAPN3 gene are known genetic causes of this condition. The aim of this study was to confirm the molecular consequences of the CAPN3 variant NG_008660.1(NM_000070.3):c.1746-20C > G of an individual with suspected LGMDR1 by extensive complementary DNA (cDNA) analysis. CASE PRESENTATION In the present study, we report on a male with proximal muscular weakness in his lower limbs. Compound heterozygous NM_000070.3:c.598_612del and NG_008660.1(NM_000070.3):c.1746-20C > G genotype was detected on the CAPN3 gene by targeted next-generation sequencing (NGS). To confirm the pathogenicity of the variant c.1746-20C > G, we conducted genetic analysis based on Sanger sequencing of the proband's cDNA sample. The results revealed that this splicing variant disrupts the original 3' splice site on intron 13, thus leading to the skipping of the DNA fragment involving exon 14 and possibly exon 15. However, the lack of exon 15 in the CAPN3 isoforms present in a blood sample was explained by cell-specific alternative splicing rather than an aberrant splicing mechanism. In silico the c.1746-20C > G splicing variant consequently resulted in frameshift and formation of a premature termination codon (NP_000061.1:p.(Glu582Aspfs*62)). CONCLUSIONS Based on the results of our study and the literature we reviewed, both c.598_612del and c.1746-20C > G variants are pathogenic and together cause LGMDR1. Therefore, extensive mRNA and/or cDNA analysis of splicing variants is critical to understand the pathogenesis of the disease.
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Affiliation(s)
- Evelina Siavrienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu street 2, LT-08661, Vilnius, Lithuania.
- Biobank of Lithuanian Population and Rare Disorders, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.
| | - Gunda Petraitytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu street 2, LT-08661, Vilnius, Lithuania
| | - Birutė Burnytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu street 2, LT-08661, Vilnius, Lithuania
| | - Aušra Morkūnienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu street 2, LT-08661, Vilnius, Lithuania
| | - Violeta Mikštienė
- Biobank of Lithuanian Population and Rare Disorders, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Tautvydas Rančelis
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu street 2, LT-08661, Vilnius, Lithuania
- Biobank of Lithuanian Population and Rare Disorders, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu street 2, LT-08661, Vilnius, Lithuania
- Biobank of Lithuanian Population and Rare Disorders, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu street 2, LT-08661, Vilnius, Lithuania
| | - Eglė Preikšaitienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu street 2, LT-08661, Vilnius, Lithuania
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Macias A, Fichna JP, Topolewska M, Rȩdowicz MJ, Kaminska AM, Kostera-Pruszczyk A. Targeted Next-Generation Sequencing Reveals Mutations in Non-coding Regions and Potential Regulatory Sequences of Calpain-3 Gene in Polish Limb-Girdle Muscular Dystrophy Patients. Front Neurosci 2021; 15:692482. [PMID: 34720847 PMCID: PMC8551377 DOI: 10.3389/fnins.2021.692482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/17/2021] [Indexed: 01/22/2023] Open
Abstract
Limb–girdle muscular dystrophy type R1 (LGMDR1) is caused by mutations in CAPN3 and is the most common type of recessive LGMD. Even with the use of whole-exome sequencing (WES), only one mutant allele of CAPN3 is found in a significant number of LGMDR patients. This points to a role of non-coding, intronic or regulatory, sequence variants in the disease pathogenesis. Targeted sequencing of the whole CAPN3 gene including not only intronic, 3′ and 5′ UTRs but also potential regulatory regions was performed in 27 patients suspected with LGMDR1. This group included 13 patients with only one mutated CAPN3 allele detected previously with exome sequencing. A second rare variant in the non-coding part of CAPN3 was found in 11 of 13 patients with previously identified single mutation. Intronic mutations were found in 10 cases, with c.1746-20C>G variant present in seven patients. In addition, a large deletion of exons 2–8 was found in one patient. In the patients with no causative mutation previously found, we detected rare CAPN3 variants in 5 out of 10 patients and in two of them in a compound heterozygous state. Rare variants within putative regulatory sequences distant from the CAPN3 gene were found in 15 patients, although in 11 of these cases, other variants are deemed causative. The results indicate that intronic mutations are common in Polish LGMDR patients, and testing for non-coding mutations in CAPN3 should be performed in apparently single heterozygous patients.
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Affiliation(s)
- Anna Macias
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Jakub Piotr Fichna
- Laboratory of Neurogenetics, Department of Neurodegenerative Disorders, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Malgorzata Topolewska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Maria J Rȩdowicz
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna M Kaminska
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
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Abstract
The limb-girdle muscular dystrophies (LGMD) are a collection of genetic diseases united in their phenotypical expression of pelvic and shoulder area weakness and wasting. More than 30 subtypes have been identified, five dominant and 26 recessive. The increase in the characterization of new genotypes in the family of LGMDs further adds to the heterogeneity of the disease. Meanwhile, better understanding of the phenotype led to the reconsideration of the disease definition, which resulted in eight old subtypes to be no longer recognized officially as LGMD and five new diseases to be added to the LGMD family. The unique variabilities of LGMD stem from genetic mutations, which then lead to protein and ultimately muscle dysfunction. Herein, we review the LGMD pathway, starting with the genetic mutations that encode proteins involved in muscle maintenance and repair, and including the genotype–phenotype relationship of the disease, the epidemiology, disease progression, burden of illness, and emerging treatments.
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8
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Two Novel Mutations in the JAG1 Gene in Pediatric Patients with Alagille Syndrome: The First Case Series in Czech Republic. Diagnostics (Basel) 2021; 11:diagnostics11060983. [PMID: 34071626 PMCID: PMC8230072 DOI: 10.3390/diagnostics11060983] [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: 05/04/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 11/30/2022] Open
Abstract
Background: Alagille syndrome (ALGS) is a highly variable multisystem disorder inherited in an autosomal dominant pattern with incomplete penetration. The disorder is caused by mutations in the JAG1 gene, only rarely in the NOTCH2 gene, which gives rise to malformations in multiple organs. Bile duct paucity is the main characteristic feature of the disease. Methods: Molecular-genetic examination of genes JAG1 and NOTCH2 in four probands of Czech origin who complied with the diagnostic criteria of ALGS was performed using targeted next-generation sequencing of genes JAG1 and NOTCH2. Segregation of variants in a family was assessed by Sanger sequencing of parental DNA. Results: Mutations in the JAG1 gene were confirmed in all four probands. We identified two novel mutations: c.3189dupG and c.1913delG. Only in one case, the identified JAG1 mutation was de novo. None of the parents carrying JAG1 pathogenic mutation was diagnosed with ALGS. Conclusion: Diagnosis of the ALGS is complicated due to the absence of clear genotype-phenotype correlations and the extreme phenotypic variability in the patients even within the same family. This fact is of particular importance in connection to genetic counselling and prenatal genetic testing.
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Escobar H, Krause A, Keiper S, Kieshauer J, Müthel S, de Paredes MG, Metzler E, Kühn R, Heyd F, Spuler S. Base editing repairs an SGCA mutation in human primary muscle stem cells. JCI Insight 2021; 6:145994. [PMID: 33848270 PMCID: PMC8262330 DOI: 10.1172/jci.insight.145994] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/07/2021] [Indexed: 11/28/2022] Open
Abstract
Skeletal muscle can regenerate from muscle stem cells and their myogenic precursor cell progeny, myoblasts. However, precise gene editing in human muscle stem cells for autologous cell replacement therapies of untreatable genetic muscle diseases has not yet been reported. Loss-of-function mutations in SGCA, encoding α-sarcoglycan, cause limb-girdle muscular dystrophy 2D/R3, an early-onset, severe, and rapidly progressive form of muscular dystrophy affecting both male and female patients. Patients suffer from muscle degeneration and atrophy affecting the limbs, respiratory muscles, and heart. We isolated human muscle stem cells from 2 donors, with the common SGCA c.157G>A mutation affecting the last coding nucleotide of exon 2. We found that c.157G>A is an exonic splicing mutation that induces skipping of 2 coregulated exons. Using adenine base editing, we corrected the mutation in the cells from both donors with > 90% efficiency, thereby rescuing the splicing defect and α-sarcoglycan expression. Base-edited patient cells regenerated muscle and contributed to the Pax7+ satellite cell compartment in vivo in mouse xenografts. Here, we provide the first evidence to our knowledge that autologous gene–repaired human muscle stem cells can be harnessed for cell replacement therapies of muscular dystrophies.
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Affiliation(s)
- Helena Escobar
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Anne Krause
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Sandra Keiper
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Berlin, Germany
| | - Janine Kieshauer
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Stefanie Müthel
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Manuel García de Paredes
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany
| | - Eric Metzler
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany.,Charité Universitätsmedizin Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Berlin, Germany
| | - Simone Spuler
- Muscle Research Unit, Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité, Universitätsmedizin Berlin, Germany
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Chakravorty S, Nallamilli BRR, Khadilkar SV, Singla MB, Bhutada A, Dastur R, Gaitonde PS, Rufibach LE, Gloster L, Hegde M. Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent. Front Neurol 2020; 11:559327. [PMID: 33250842 PMCID: PMC7674836 DOI: 10.3389/fneur.2020.559327] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Objective: Inherited myopathies comprise more than 200 different individually rare disease-subtypes, but when combined together they have a high prevalence of 1 in 6,000 individuals across the world. Our goal was to determine for the first time the clinical- and gene-variant spectrum of genetic myopathies in a substantial cohort study of the Indian subcontinent. Methods: In this cohort study, we performed the first large clinical exome sequencing (ES) study with phenotype correlation on 207 clinically well-characterized inherited myopathy-suspected patients from the Indian subcontinent with diverse ethnicities. Results: Clinical-correlation driven definitive molecular diagnosis was established in 49% (101 cases; 95% CI, 42–56%) of patients with the major contributing pathogenicity in either of three genes, GNE (28%; GNE-myopathy), DYSF (25%; Dysferlinopathy), and CAPN3 (19%; Calpainopathy). We identified 65 variant alleles comprising 37 unique variants in these three major genes. Seventy-eight percent of the DYSF patients were homozygous for the detected pathogenic variant, suggesting the need for carrier-testing for autosomal-recessive disorders like Dysferlinopathy that are common in India. We describe the observed clinical spectrum of myopathies including uncommon and rare subtypes in India: Sarcoglycanopathies (SGCA/B/D/G), Collagenopathy (COL6A1/2/3), Anoctaminopathy (ANO5), telethoninopathy (TCAP), Pompe-disease (GAA), Myoadenylate-deaminase-deficiency-myopathy (AMPD1), myotilinopathy (MYOT), laminopathy (LMNA), HSP40-proteinopathy (DNAJB6), Emery-Dreifuss-muscular-dystrophy (EMD), Filaminopathy (FLNC), TRIM32-proteinopathy (TRIM32), POMT1-proteinopathy (POMT1), and Merosin-deficiency-congenital-muscular-dystrophy-type-1 (LAMA2). Thirteen patients harbored pathogenic variants in >1 gene and had unusual clinical features suggesting a possible role of synergistic-heterozygosity/digenic-contribution to disease presentation and progression. Conclusions: Application of clinically correlated ES to myopathy diagnosis has improved our understanding of the clinical and genetic spectrum of different subtypes and their overlaps in Indian patients. This, in turn, will enhance the global gene-variant-disease databases by including data from developing countries/continents for more efficient clinically driven molecular diagnostics.
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Affiliation(s)
- Samya Chakravorty
- Emory University Department of Pediatrics, Atlanta, GA, United States.,Emory University Department of Human Genetics, Atlanta, GA, United States.,Division of Neurosciences, Children's Healthcare of Atlanta, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | | | - Satish Vasant Khadilkar
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | - Madhu Bala Singla
- Department of Neurology, Bombay Hospital, Mumbai, India.,Department of Neurology, Sir J J Group of Hospitals, Grant Medical College, Mumbai, India.,Bombay Hospital Institute of Medical Sciences, Mumbai, India
| | | | - Rashna Dastur
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | - Pradnya Satish Gaitonde
- Centre for Advanced Molecular Diagnostics in Neuromuscular Disorders (CAMDND), Mumbai, India
| | | | - Logan Gloster
- Emory University Department of Pediatrics, Atlanta, GA, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Madhuri Hegde
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,PerkinElmer Genomics, Global Laboratory Services, Waltham, MA, United States
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11
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Liang WC, Jong YJ, Wang CH, Wang CH, Tian X, Chen WZ, Kan TM, Minami N, Nishino I, Wong LJC. Clinical, pathological, imaging, and genetic characterization in a Taiwanese cohort with limb-girdle muscular dystrophy. Orphanet J Rare Dis 2020; 15:160. [PMID: 32576226 PMCID: PMC7310488 DOI: 10.1186/s13023-020-01445-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Background Limb-girdle muscular dystrophy (LGMD) is a genetically heterogeneous, hereditary disease characterized by limb-girdle weakness and histologically dystrophic changes. The prevalence of each subtype of LGMD varies among different ethnic populations. This study for the first time analyzed the phenotypes and genotypes in Taiwanese patients with LGMD in a referral center for neuromuscular diseases (NMDs). Results We enrolled 102 patients clinically suspected of having LGMD who underwent muscle biopsy with subsequent genetic analysis in the previous 10 years. On the basis of different pathological categories, we performed sequencing of target genes or panel for NMDs and then identified patients with type 1B, 1E, 2A, 2B, 2D, 2I, 2G, 2 N, and 2Q. The 1B patients with LMNA mutation presented with mild limb-girdle weakness but no conduction defect at the time. All 1E patients with DES mutation exhibited predominantly proximal weakness along with distal weakness. In our cohort, 2B and 2I were the most frequent forms of LGMD; several common or founder mutations were identified, including c.1097_1099delACA (p.Asn366del) in DES, homozygous c.101G > T (p.Arg34Leu) in SGCA, homozygous c.26_33dup (p.Glu12Argfs*20) in TCAP, c.545A > G (p.Tyr182Cys), and c.948delC (p.Cys317Alafs*111) in FKRP. Clinically, the prevalence of dilated cardiomyopathy in our patients with LGMD2I aged > 18 years was 100%, much higher than that in European cohorts. The only patient with LGMD2Q with PLEC mutation did not exhibit skin lesions or gastrointestinal abnormalities but had mild facial weakness. Muscle imaging of LGMD1E and 2G revealed a more uniform involvement than did other LGMD types. Conclusion Our study revealed that detailed clinical manifestation together with muscle pathology and imaging remain critical in guiding further molecular analyses and are crucial for establishing genotype–phenotype correlations. We also determined the common mutations and prevalence for different subtypes of LGMD in our cohort, which could be useful when providing specific care and personalized therapy to patients with LGMD.
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Affiliation(s)
- Wen-Chen Liang
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Translational Research Center of Neuromuscular Diseases, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuh-Jyh Jong
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Translational Research Center of Neuromuscular Diseases, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Chien-Hua Wang
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chen-Hua Wang
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Xia Tian
- Baylor Genetics, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wan-Zi Chen
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tzu-Min Kan
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Narihiro Minami
- Department of Laboratory Medicine, 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.,Department of Genome Medicine Development, Medical Genome Center, 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.,Department of Genome Medicine Development, Medical Genome Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Lee-Jun C Wong
- Baylor Genetics, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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12
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Růžička M, Souček P, Kulhánek P, Radová L, Fajkusová L, Réblová K. Bending of DNA duplexes with mutation motifs. DNA Res 2019; 26:341-352. [PMID: 31230075 PMCID: PMC6704406 DOI: 10.1093/dnares/dsz013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/27/2019] [Indexed: 01/30/2023] Open
Abstract
Mutations can be induced by environmental factors but also arise spontaneously during DNA replication or due to deamination of methylated cytosines at CpG dinucleotides. Sites where mutations occur with higher frequency than would be expected by chance are termed hotspots while sites that contain mutations rarely are termed coldspots. Mutations are permanently scanned and repaired by repair systems. Among them, the mismatch repair targets base pair mismatches, which are discriminated from canonical base pairs by probing altered elasticity of DNA. Using biased molecular dynamics simulations, we investigated the elasticity of coldspots and hotspots motifs detected in human genes associated with inherited disorders, and also of motifs with Czech population hotspots and de novo mutations. Main attention was paid to mutations leading to G/T and A+/C pairs. We observed that hotspots without CpG/CpHpG sequences are less flexible than coldspots, which indicates that flexible sequences are more effectively repaired. In contrary, hotspots with CpG/CpHpG sequences exhibited increased flexibility as coldspots. Their mutability is more likely related to spontaneous deamination of methylated cytosines leading to C > T mutations, which are primarily targeted by base excision repair. We corroborated conclusions based on computer simulations by measuring melting curves of hotspots and coldspots containing G/T mismatch.
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Affiliation(s)
- Michal Růžička
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Přemysl Souček
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Radová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Fajkusová
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno, Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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13
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ten Dam L, Frankhuizen WS, Linssen WH, Straathof CS, Niks EH, Faber K, Fock A, Kuks JB, Brusse E, de Coo R, Voermans N, Verrips A, Hoogendijk JE, van der Pol L, Westra D, de Visser M, van der Kooi AJ, Ginjaar I. Autosomal recessive limb‐girdle and Miyoshi muscular dystrophies in the Netherlands: The clinical and molecular spectrum of 244 patients. Clin Genet 2019; 96:126-133. [DOI: 10.1111/cge.13544] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/24/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Leroy ten Dam
- Department of NeurologyAmsterdam University Medical Centre, Amsterdam Neuroscience Amsterdam The Netherlands
| | - Wendy S. Frankhuizen
- Department of Clinical GeneticsLeiden University Medical Centre Leiden The Netherlands
| | | | - Chiara S. Straathof
- Department of NeurologyLeiden University Medical Centre Leiden The Netherlands
| | - Erik H. Niks
- Department of NeurologyLeiden University Medical Centre Leiden The Netherlands
| | - Karin Faber
- Department of NeurologyMaastricht University Medical Centre Maastricht The Netherlands
| | - Annemarie Fock
- Department of NeurologyUniversity Medical Centre Groningen Groningen The Netherlands
| | - Jan B. Kuks
- Department of NeurologyUniversity Medical Centre Groningen Groningen The Netherlands
| | - Esther Brusse
- Department of NeurologyErasmus MC University Medical Centre Rotterdam The Netherlands
| | - René de Coo
- Department of NeurologyErasmus MC University Medical Centre Rotterdam The Netherlands
| | - Nicol Voermans
- Department of NeurologyRadboud University Medical Centre Nijmegen The Netherlands
| | - Aad Verrips
- Department of NeurologyCanisius Wilhelmina Hospital Nijmegen Nijmegen The Netherlands
| | - Jessica E. Hoogendijk
- Department of NeurologyRudolf Magnus Institute of Neuroscience, University Medical Center Utrecht The Netherlands
| | - Ludo van der Pol
- Department of NeurologyRudolf Magnus Institute of Neuroscience, University Medical Center Utrecht The Netherlands
| | - Dineke Westra
- Department of Human GeneticsRadboud University Medical Centre Nijmegen The Netherlands
| | - Marianne de Visser
- Department of NeurologyAmsterdam University Medical Centre, Amsterdam Neuroscience Amsterdam The Netherlands
| | - Anneke J. van der Kooi
- Department of NeurologyAmsterdam University Medical Centre, Amsterdam Neuroscience Amsterdam The Netherlands
| | - Ieke Ginjaar
- Department of Clinical GeneticsLeiden University Medical Centre Leiden The Netherlands
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14
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YİŞ ULUÇ, DİNİZ GÜLDEN, HAZAN FILIZ, DAİMAGÜLER HÜLYASEVCAN, BAYSAL BAHARTOKLU, BAYDAN FIGEN, AKINCI GÜLÇIN, ÜNALP AYCAN, AKTAN GÜL, BAYRAM ERHAN, HIZ SEMRA, PAKETÇİ CEM, OKUR DERYA, ÖZER ERDENER, DANYELİ AYÇAERSEN, POLAT MUZAFFER, UYANIK GÖKHAN, ÇIRAK SEBAHATTIN. Childhood onset limb-girdle muscular dystrophies in the Aegean part of Turkey. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2018; 37:210-220. [PMID: 30838351 PMCID: PMC6390111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The aim of this study is to analyze the epidemiology of the clinical and genetic features of childhood-onset limb-girdle muscular dystrophies (LGMD) in the Aegean part of Turkey. In total fifty-six pediatric cases with LGMD followed in four different pediatric neurology departments in the Aegean region of Turkey were evaluated. Among them, LGMD2C was the most common followed by LGMD2A, LGMD2D, and LGMD2F with equal frequencies. In twenty-eight patients (50%) the diagnosis could be confirmed by genetic analysis, where SGCG proved to be disease-causing in most of the cases. About half of the patients were diagnosed with whole exome or targeted gene sequencing. A positive correlation between muscle biopsy and genetic findings were observed in 11% of the patients. We report one novel frameshifting mutation in TTN. Knowledge on frequencies of childhood-onset limb-girdle muscular dystrophies and related genes in Turkey will lead to a prompt diagnosis of these neuromuscular disorders.
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Affiliation(s)
- ULUÇ YİŞ
- Dokuz Eylül University,
School of Medicine, Department of Pediatrics, Division of
Child Neurology, İzmir, Turkey,Address for correspondence: Uluç Yiş, Dokuz Eylül
University School of Medicine Department of Pediatrics Division of
Child Neurology, 35340/Balçova/İzmir. Tel. +90 232
4126216. E-mail:
| | - GÜLDEN DİNİZ
- Neuromuscular Disease
Center, Tepecik Research Hospital, İzmir,
Turkey
| | - FILIZ HAZAN
- Dr Behçet Uz Children’s
Research Hospital, Department of Medical Genetics,
İzmir, Turkey
| | - HÜLYA SEVCAN DAİMAGÜLER
- University Hospital
Cologne, Department of Pediatrics, Cologne,
Germany, Center for Molecular Medicine Cologne
(CMMC), University of Cologne,
Cologne, Germany
| | - BAHAR TOKLU BAYSAL
- Dr Behçet Uz Children’s
Research Hospital, Department of Pediatric Neurology,
İzmir, Turkey
| | - FIGEN BAYDAN
- Neuromuscular Disease
Center, Tepecik Research Hospital, İzmir,
Turkey
| | - GÜLÇIN AKINCI
- Dr Behçet Uz Children’s
Research Hospital, Department of Pediatric Neurology,
İzmir, Turkey
| | - AYCAN ÜNALP
- Dr Behçet Uz Children’s
Research Hospital, Department of Pediatric Neurology,
İzmir, Turkey
| | - GÜL AKTAN
- Ege University, School of
Medicine, Department of Pediatrics, Division of Child
Neurology, İzmir, Turkey
| | - ERHAN BAYRAM
- Dokuz Eylül University,
School of Medicine, Department of Pediatrics, Division of
Child Neurology, İzmir, Turkey
| | - SEMRA HIZ
- Dokuz Eylül University,
School of Medicine, Department of Pediatrics, Division of
Child Neurology, İzmir, Turkey
| | - CEM PAKETÇİ
- Dokuz Eylül University,
School of Medicine, Department of Pediatrics, Division of
Child Neurology, İzmir, Turkey
| | - DERYA OKUR
- Dokuz Eylül University,
School of Medicine, Department of Pediatrics, Division of
Child Neurology, İzmir, Turkey
| | - ERDENER ÖZER
- Dokuz Eylül University,
School of Medicine, Department of Pathology,
İzmir, Turkey
| | - AYÇA ERSEN DANYELİ
- Dokuz Eylül University,
School of Medicine, Department of Pathology,
İzmir, Turkey
| | - MUZAFFER POLAT
- Celal Bayar University,
School of Medicine, Department of Pediatrics, Division of
Child Neurology, Manisa, Turkey
| | - GÖKHAN UYANIK
- Center for Medical Genetics,
Hanusch Hospital, Vienna,
Austria, Medical Faculty, Sigmund
Freud Private University, Vienna,
Austria
| | - SEBAHATTIN ÇIRAK
- University Hospital
Cologne, Department of Pediatrics, Cologne,
Germany, Center for Molecular Medicine Cologne
(CMMC), University of Cologne,
Cologne, Germany
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15
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STRC Deletion is a Frequent Cause of Slight to Moderate Congenital Hearing Impairment in the Czech Republic. Otol Neurotol 2018; 38:e393-e400. [PMID: 28984810 DOI: 10.1097/mao.0000000000001571] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE This study aimed to clarify the molecular epidemiology of hearing loss by identifying the responsible genes in patients without GJB2 mutations. STUDY DESIGN Prospective genetic study. SETTING Tertiary referral hospital. PATIENTS Fifty one patients with bilateral sensorineural hearing loss, 20 men, and 31 women, mean age 24.9 years, range 3 to 64 years, from 49 families. GJB2 and deltaGJB6-D13S1830 mutations were excluded previously. INTERVENTION Diagnostic. Sixty-nine genes reported to be causative of hearing loss were analyzed. Sequence capture technology, next-generation sequencing, and multiplex ligation-dependent probe amplification (MLPA) were used. Coverage of STRC was screened in Integrative Genomics Viewer software. MAIN OUTCOME MEASURE Identification of causal pathogenic mutations in genes related to deafness. RESULTS Five families (10%) had recessive STRC deletions or mutations. Five unrelated patients (10%) had recessive mutations in TMPRSS3, USH2A, PCDH15, LOXHD1, and MYO15A. Three families (6%) had autosomal dominant mutations in MYO6A, KCNQ4, and SIX1. One family (2%) had an X-linked POU3F4 mutation. Thus, we identified the cause of hearing loss in 28% of the families studied. CONCLUSIONS Following GJB2, STRC was the second most frequently mutated gene in patients from the Czech Republic with hearing loss. To decrease the cost of testing, we recommend STRC deletion screening with MLPA before next-generation sequencing. The existence of a pseudogene and polymorphic STRC regions can lead to false-positive or false-negative results when copy number variation analysis is based on next-generation sequencing data.
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16
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Medrano-Soto A, Moreno-Hagelsieb G, McLaughlin D, Ye ZS, Hendargo KJ, Saier MH. Bioinformatic characterization of the Anoctamin Superfamily of Ca2+-activated ion channels and lipid scramblases. PLoS One 2018; 13:e0192851. [PMID: 29579047 PMCID: PMC5868767 DOI: 10.1371/journal.pone.0192851] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/31/2018] [Indexed: 01/01/2023] Open
Abstract
Our laboratory has developed bioinformatic strategies for identifying distant phylogenetic relationships and characterizing families and superfamilies of transport proteins. Results using these tools suggest that the Anoctamin Superfamily of cation and anion channels, as well as lipid scramblases, includes three functionally characterized families: the Anoctamin (ANO), Transmembrane Channel (TMC) and Ca2+-permeable Stress-gated Cation Channel (CSC) families; as well as four families of functionally uncharacterized proteins, which we refer to as the Anoctamin-like (ANO-L), Transmembrane Channel-like (TMC-L), and CSC-like (CSC-L1 and CSC-L2) families. We have constructed protein clusters and trees showing the relative relationships among the seven families. Topological analyses suggest that the members of these families have essentially the same topologies. Comparative examination of these homologous families provides insight into possible mechanisms of action, indicates the currently recognized organismal distributions of these proteins, and suggests drug design potential for the disease-related channel proteins.
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Affiliation(s)
- Arturo Medrano-Soto
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | | | - Daniel McLaughlin
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | - Zachary S. Ye
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | - Kevin J. Hendargo
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
- * E-mail:
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17
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Angelini C, Fanin M. Limb girdle muscular dystrophies: clinical-genetical diagnostic update and prospects for therapy. Expert Opin Orphan Drugs 2017. [DOI: 10.1080/21678707.2017.1367283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Corrado Angelini
- Department of Neurodegenerative Disorders, Neuromuscular Center, San Camillo Hospital IRCCS, Venice, Italy
| | - Marina Fanin
- Department of Neurosciences, University of Padova, Padova, Italy
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18
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Khadilkar SV, Faldu HD, Patil SB, Singh R. Limb-girdle Muscular Dystrophies in India: A Review. Ann Indian Acad Neurol 2017; 20:87-95. [PMID: 28615891 PMCID: PMC5470147 DOI: 10.4103/aian.aian_81_17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Limb-girdle muscular dystrophies (LGMDs) are common in India. Information on LGMDs has been gradually evolving in the recent years. This information is scattered in case series and case studies. The aim of this study is to collate available Indian information on LGMDs and put it in perspective. PubMed search using keywords such as limb-girdle muscular dystrophies in India, sarcoglycanopathies, dysferlinopathy, calpainopathy, and GNE myopathy was carried out. The published information on LGMDs in Indian context suggests that dysferlinopathy, calpainopathy, sarcoglycanopathies, and other myopathies such as GNE myopathy are frequently seen in India. Besides these, anecdotal reports of many other forms are available, some with genetic support and others showing immunocytochemical defects. The genotypic information on LGMDs is gradually evolving and founder mutations have been detected in selected populations. Further multicenter studies are necessary to document the incidence and prevalence of these common conditions in India.
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Affiliation(s)
| | - Hinaben Dayalal Faldu
- Department of Neurology, Grant Government Medical College and J. J. Hospital, Mumbai, Maharashtra, India
| | - Sarika Bapuso Patil
- Department of Neurology, Grant Government Medical College and J. J. Hospital, Mumbai, Maharashtra, India
| | - Rakesh Singh
- Department of Neurology, Grant Government Medical College and J. J. Hospital, Mumbai, Maharashtra, India
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19
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Ylikallio E, Auranen M, Mahjneh I, Lamminen A, Kousi M, Träskelin AL, Muurinen T, Löfberg M, Salmi T, Paetau A, Lehesjoki AE, Piirilä P, Kiuru-Enari S. Decreased Aerobic Capacity in ANO5-Muscular Dystrophy. J Neuromuscul Dis 2016; 3:475-485. [DOI: 10.3233/jnd-160186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Emil Ylikallio
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Finland
| | - Mari Auranen
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Finland
| | - Ibrahim Mahjneh
- Division of Neurology, Pietarsaari District Hospital, Pietarsaari, Finland
- Department of Neurology, MRC Oulu, Oulu University Hospital and University of Oulu, Finland
| | - Antti Lamminen
- Department of Radiology, HUS Medical Imaging Center, Helsinki, Finland
| | - Maria Kousi
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | | | - Tiina Muurinen
- Unit of Clinical Physiology, HUS Medical Imaging Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Mervi Löfberg
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Finland
| | - Tapani Salmi
- Department of Clinical Neurophysiology, Medical Imaging Center, Helsinki University Hospital, Helsinki, Finland
| | - Anders Paetau
- Department of Pathology, HUSLAB and University of Helsinki, Helsinki, Finland
| | - Anna-Elina Lehesjoki
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Neuroscience Center, University of Helsinki, Finland
| | - Päivi Piirilä
- Unit of Clinical Physiology, HUS Medical Imaging Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Sari Kiuru-Enari
- Clinical Neurosciences, Neurology, University of Helsinki and Helsinki University Hospital, Finland
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20
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Stehlíková K, Skálová D, Zídková J, Haberlová J, Voháňka S, Mazanec R, Mrázová L, Vondráček P, Ošlejšková H, Zámečník J, Honzík T, Zeman J, Magner M, Šišková D, Langová M, Gregor V, Godava M, Smolka V, Fajkusová L. Muscular dystrophies and myopathies: the spectrum of mutated genes in the Czech Republic. Clin Genet 2016; 91:463-469. [PMID: 27447704 DOI: 10.1111/cge.12839] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 01/12/2023]
Abstract
Inherited neuromuscular disorder (NMD) is a wide term covering different genetic disorders affecting muscles, nerves, and neuromuscular junctions. Genetic and clinical heterogeneity is the main drawback in a routine gene-by-gene diagnostics. We present Czech NMD patients with a genetic cause identified using targeted next-generation sequencing (NGS) and the spectrum of these causes. Overall 167 unrelated patients presenting NMD falling into categories of muscular dystrophies, congenital muscular dystrophies, congenital myopathies, distal myopathies, and other myopathies were tested by targeted NGS of 42 known NMD-related genes. Pathogenic or probably pathogenic sequence changes were identified in 79 patients (47.3%). In total, 37 novel and 51 known disease-causing variants were detected in 23 genes. In addition, variants of uncertain significance were suspected in 7 cases (4.2%), and in 81 cases (48.5%) sequence changes associated with NMD were not found. Our results strongly indicate that for molecular diagnostics of heterogeneous disorders such as NMDs, targeted panel testing has a high-clinical yield and should therefore be the preferred first-tier approach. Further, we show that in the genetic diagnostic practice of NMDs, it is necessary to take into account different types of inheritance including the occurrence of an autosomal recessive disorder in two generations of one family.
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Affiliation(s)
- K Stehlíková
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - D Skálová
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - J Zídková
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - J Haberlová
- Department of Child Neurology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - S Voháňka
- Department of Neurology, University Hospital Brno, Brno, Czech Republic
| | - R Mazanec
- Department of Neurology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - L Mrázová
- Department of Child Neurology, University Hospital Brno, Brno, Czech Republic
| | - P Vondráček
- Department of Child Neurology, University Hospital Brno, Brno, Czech Republic
| | - H Ošlejšková
- Department of Child Neurology, University Hospital Brno, Brno, Czech Republic
| | - J Zámečník
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - T Honzík
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - J Zeman
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - M Magner
- Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - D Šišková
- Child Neurology, Thomayer's Hospital, Prague, Czech Republic
| | - M Langová
- Department of Medical Genetics, Thomayer's Hospital, Prague, Czech Republic
| | - V Gregor
- Department of Medical Genetics, Thomayer's Hospital, Prague, Czech Republic
| | - M Godava
- Centre of Fetal Medicine and Genetics, Olomouc, Czech Republic
| | - V Smolka
- Department of Paediatrics, University Hospital Olomouc, Olomouc, Czech Republic
| | - L Fajkusová
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno and Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
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21
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Inashkina I, Jankevics E, Stavusis J, Vasiljeva I, Viksne K, Micule I, Strautmanis J, Naudina MS, Cimbalistiene L, Kucinskas V, Krumina A, Utkus A, Burnyte B, Matuleviciene A, Lace B. Robust genotyping tool for autosomal recessive type of limb-girdle muscular dystrophies. BMC Musculoskelet Disord 2016; 17:200. [PMID: 27142102 PMCID: PMC4855345 DOI: 10.1186/s12891-016-1058-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/28/2016] [Indexed: 11/29/2022] Open
Abstract
Background Limb-girdle muscular dystrophies are characterized by predominant involvement of the shoulder and pelvic girdle and trunk muscle groups. Currently, there are 31 genes implicated in the different forms of limb-girdle muscular dystrophies, which exhibit similar phenotypes and clinical overlap; therefore, advanced molecular techniques are required to achieve differential diagnosis. Methods We investigated 26 patients from Latvia and 34 patients from Lithuania with clinical symptoms of limb-girdle muscular dystrophies, along with 565 healthy unrelated controls from general and ethnic populations using our developed test kit based on the Illumina VeraCode GoldenGate genotyping platform, Ion AmpliSeq Inherited Disease Panel and direct sequencing of mutations in calpain 3 (CAPN3), anoctamin 5 (ANO5) and fukutin related protein (FKRP) genes. Results Analysis revealed a homozygous CAPN3 c.550delA mutation in eight patients and three heterozygous variants in controls: dysferlin (DYSF) c.5028delG, CAPN3 c.2288A > G, and FKRP c.135C > T. Additionally, three mutations within FKRP gene were found: homozygous c.826C > A, and two compound – c.826C > A/c.404_405insT and c.826C > A/c.204_206delCTC mutations, and one mutation within CLCN1 gene – c.2680C > T p.Arg894Ter. ANO5 c.191dupA was not present. Conclusions Genetic diagnosis was possible in 12 of 60 patients (20 %). The allele frequency of CAPN3 gene mutation c.550delA in Latvia is 0.0016 and in Lithuania - 0.0029. The allele frequencies of CAPN3 gene mutation c.2288A > G and DYSF gene mutation c.4872delG are 0.003. Electronic supplementary material The online version of this article (doi:10.1186/s12891-016-1058-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Inna Inashkina
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia.
| | - Eriks Jankevics
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia
| | - Janis Stavusis
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia
| | - Inta Vasiljeva
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia
| | - Kristine Viksne
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia
| | - Ieva Micule
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia
| | - Jurgis Strautmanis
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia
| | - Maruta S Naudina
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia
| | - Loreta Cimbalistiene
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,Centre for Medical Genetics, Vilnius University Hospital Santariškių Klinikos, Santariškių str. 2, LT-08661, Vilnius, Lithuania
| | - Vaidutis Kucinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Astrida Krumina
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,Centre for Medical Genetics, Vilnius University Hospital Santariškių Klinikos, Santariškių str. 2, LT-08661, Vilnius, Lithuania
| | - Birute Burnyte
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,Centre for Medical Genetics, Vilnius University Hospital Santariškių Klinikos, Santariškių str. 2, LT-08661, Vilnius, Lithuania
| | - Ausra Matuleviciene
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania.,Centre for Medical Genetics, Vilnius University Hospital Santariškių Klinikos, Santariškių str. 2, LT-08661, Vilnius, Lithuania
| | - Baiba Lace
- Biomedical Research and Study Centre, Ratsupites str. 1, k-1, LV-1067, Riga, Latvia.,Laval University, Quebec, Canada.,Centre hospitalier universitaire de Québec, 2705, boulevard Laurier, Québec, Québec, G1V 4G2, Canada
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22
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Dorobek M, Ryniewicz B, Kabzińska D, Fidziańska A, Styczyńska M, Hausmanowa-Petrusewicz I. The Frequency of c.550delA Mutation of the CANP3 Gene in the Polish LGMD2A Population. Genet Test Mol Biomarkers 2015; 19:637-40. [DOI: 10.1089/gtmb.2015.0131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Małgorzata Dorobek
- Department of Neurology, Central Clinical Hospital of the Ministry of Interior in Warsaw, Warsaw, Poland
| | | | - Dagmara Kabzińska
- Neuromuscular Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Fidziańska
- Neuromuscular Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Maria Styczyńska
- Department of Neurology, Central Clinical Hospital of the Ministry of Interior in Warsaw, Warsaw, Poland
- Department of Neurodegenerative Disorders, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
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23
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Fanin M, Angelini C. Protein and genetic diagnosis of limb girdle muscular dystrophy type 2A: The yield and the pitfalls. Muscle Nerve 2015; 52:163-73. [PMID: 25900067 DOI: 10.1002/mus.24682] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2015] [Indexed: 12/20/2022]
Abstract
Limb girdle muscular dystrophy type 2A (LGMD2A) is the most frequent form of LGMD worldwide. Comprehensive clinical assessment and laboratory testing is essential for diagnosis of LGMD2A. Muscle immunoblot analysis of calpain-3 is the most useful tool to direct genetic testing, as detection of calpain-3 deficiency has high diagnostic value. However, calpain-3 immunoblot testing lacks sensitivity in about 30% of cases due to gene mutations that inactivate the enzyme. The best diagnostic strategy should be determined on a case-by-case basis, depending on which tissues are available, and which molecular and/or genetic methods are adopted. In this work we survey the current knowledge, advantages, limitations, and pitfalls of protein testing and mutation detection in LGMD2A and provide an update of genetic epidemiology.
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Affiliation(s)
- Marina Fanin
- Department of Neurosciences, Biomedical Campus "Pietro d'Abano," via Giuseppe Orus 2B, 35129, Padova, Italy
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