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Sabbagh Q, Larrieux M, Schneider A, Theze C, Vincent MC, Coubes C, Puechberty J, Renard S, Koenig M, Pellestor F, Cossée M, Gatinois V. Confined placental mosaicism is a diagnostic pitfall in dystrophinopathies: a clinical report. Eur J Hum Genet 2024:10.1038/s41431-024-01665-0. [PMID: 39014012 DOI: 10.1038/s41431-024-01665-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 06/04/2024] [Accepted: 06/26/2024] [Indexed: 07/18/2024] Open
Abstract
Single-gene copy number variants (CNVs) limited to placenta although rarely identified may have clinical implications. We describe a pregnant woman referred for chorionic villus sampling due to increased fetal nuchal translucency. Incident intragenic deletion of Duchenne muscular dystrophy (DMD) gene, affecting exons 56 and 57, was identified in a male fetus in ~23-30% of placental cells by chromosomal microarray and confirmed using multiplex ligation-dependent probe amplification (MLPA). Rapid aneuploidy testing showed normal results and the deletion was not detected in the mother. Subsequent analyses on amniotic cells yielded a normal DMD gene result, corroborating the confined placental nature of the mosaicism. Hence, this report emphasizes the importance of conducting amniocentesis following detection of mosaicism for single gene CNVs on chorionic villi, in order to preclude confined placental mosaicism (CPM). As far as we know, this report marks only the second documented situation of CPM involving an intragenic DMD deletion.
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Affiliation(s)
- Quentin Sabbagh
- Montpellier University, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France.
| | - Marion Larrieux
- Montpellier University, Molecular Diagnostic Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Anouck Schneider
- Montpellier University, Laboratory of Cytogenomics, University Hospital of Montpellier, Montpellier, France
| | - Corinne Theze
- Montpellier University, Molecular Diagnostic Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Marie-Claire Vincent
- Montpellier University, Molecular Diagnostic Laboratory, University Hospital of Montpellier, Montpellier, France
- Montpellier University, INSERM, CNRS, PhyMedExp, Montpellier, France
| | - Christine Coubes
- Montpellier University, Centre de Référence « Anomalies du Développement et Syndromes Malformatifs », ERN-ITHACA, Department of Clinical Genetics, University Hospital of Montpellier, Montpellier, France
| | - Jacques Puechberty
- Montpellier University, Laboratory of Cytogenomics, University Hospital of Montpellier, Montpellier, France
| | - Sarah Renard
- Department of Obstetrics and Gynecology, Perpignan Hospital, Perpignan, France
| | - Michel Koenig
- Montpellier University, Molecular Diagnostic Laboratory, University Hospital of Montpellier, Montpellier, France
- Montpellier University, INSERM, CNRS, PhyMedExp, Montpellier, France
| | - Franck Pellestor
- Montpellier University, Laboratory of Cytogenomics, University Hospital of Montpellier, Montpellier, France
| | - Mireille Cossée
- Montpellier University, Molecular Diagnostic Laboratory, University Hospital of Montpellier, Montpellier, France
- Montpellier University, INSERM, CNRS, PhyMedExp, Montpellier, France
| | - Vincent Gatinois
- Montpellier University, Laboratory of Cytogenomics, University Hospital of Montpellier, Montpellier, France
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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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3
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Abaji M, Gorokhova S, Da Silva N, Busa T, Grelet M, Missirian C, Sigaudy S, Philip N, Leturcq F, Lévy N, Krahn M, Bartoli M. Novel Exon-Skipping Therapeutic Approach for the DMD Gene Based on Asymptomatic Deletions of Exon 49. Genes (Basel) 2022; 13:genes13071277. [PMID: 35886062 PMCID: PMC9323532 DOI: 10.3390/genes13071277] [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: 06/07/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Exon skipping is a promising therapeutic approach. One important condition for this approach is that the exon-skipped form of the gene can at least partially perform the required function and lead to improvement of the phenotype. It is therefore critical to identify the exons that can be skipped without a significant deleterious effect on the protein function. Pathogenic variants in the DMD gene are responsible for Duchenne muscular dystrophy (DMD). We report for the first time a deletion of the in-frame exon 49 associated with a strikingly normal muscular phenotype. Based on this observation, and on previously known therapeutic approaches using exon skipping in DMD for other single exons, we aimed to extend the clinical use of exon skipping for patients carrying truncating mutations in exon 49. We first determined the precise genomic position of the exon 49 deletion in our patients. We then demonstrated the feasibility of skipping exon 49 using an in vitro AON (antisense oligonucleotide) approach in human myotubes carrying a truncating pathogenic variant as well as in healthy ones. This work is a proof of concept aiming to expand exon-skipping approaches for DMD exon 49.
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Affiliation(s)
- Mario Abaji
- Medical Genetics Department, Assistance Publique Hôpitaux de Marseille, La Timone Children’s Hospital, 13005 Marseille, France; (M.A.); (S.G.); (T.B.); (C.M.); (S.S.); (N.P.); (N.L.); (M.K.)
- MMG, INSERM, Aix Marseille University, 13385 Marseille, France;
| | - Svetlana Gorokhova
- Medical Genetics Department, Assistance Publique Hôpitaux de Marseille, La Timone Children’s Hospital, 13005 Marseille, France; (M.A.); (S.G.); (T.B.); (C.M.); (S.S.); (N.P.); (N.L.); (M.K.)
- MMG, INSERM, Aix Marseille University, 13385 Marseille, France;
| | | | - Tiffany Busa
- Medical Genetics Department, Assistance Publique Hôpitaux de Marseille, La Timone Children’s Hospital, 13005 Marseille, France; (M.A.); (S.G.); (T.B.); (C.M.); (S.S.); (N.P.); (N.L.); (M.K.)
- MMG, INSERM, Aix Marseille University, 13385 Marseille, France;
| | - Maude Grelet
- Centre Hospitalier Inter-Communal Toulon-La Seyne, Medical Genetics Unit, Sainte Musse Hospital, 83100 Toulon, France;
| | - Chantal Missirian
- Medical Genetics Department, Assistance Publique Hôpitaux de Marseille, La Timone Children’s Hospital, 13005 Marseille, France; (M.A.); (S.G.); (T.B.); (C.M.); (S.S.); (N.P.); (N.L.); (M.K.)
- MMG, INSERM, Aix Marseille University, 13385 Marseille, France;
| | - Sabine Sigaudy
- Medical Genetics Department, Assistance Publique Hôpitaux de Marseille, La Timone Children’s Hospital, 13005 Marseille, France; (M.A.); (S.G.); (T.B.); (C.M.); (S.S.); (N.P.); (N.L.); (M.K.)
- MMG, INSERM, Aix Marseille University, 13385 Marseille, France;
| | - Nicole Philip
- Medical Genetics Department, Assistance Publique Hôpitaux de Marseille, La Timone Children’s Hospital, 13005 Marseille, France; (M.A.); (S.G.); (T.B.); (C.M.); (S.S.); (N.P.); (N.L.); (M.K.)
- MMG, INSERM, Aix Marseille University, 13385 Marseille, France;
| | - France Leturcq
- Department of Medical Genetics, APHP Centre Université Paris Cité Cochin Hospital, 75014 Paris, France;
| | - Nicolas Lévy
- Medical Genetics Department, Assistance Publique Hôpitaux de Marseille, La Timone Children’s Hospital, 13005 Marseille, France; (M.A.); (S.G.); (T.B.); (C.M.); (S.S.); (N.P.); (N.L.); (M.K.)
- MMG, INSERM, Aix Marseille University, 13385 Marseille, France;
| | - Martin Krahn
- Medical Genetics Department, Assistance Publique Hôpitaux de Marseille, La Timone Children’s Hospital, 13005 Marseille, France; (M.A.); (S.G.); (T.B.); (C.M.); (S.S.); (N.P.); (N.L.); (M.K.)
- MMG, INSERM, Aix Marseille University, 13385 Marseille, France;
| | - Marc Bartoli
- MMG, INSERM, Aix Marseille University, 13385 Marseille, France;
- Correspondence: ; Tel.: +33-491-32-49-06
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4
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Qi M, Stenson PD, Ball EV, Tainer JA, Bacolla A, Kehrer-Sawatzki H, Cooper DN, Zhao H. Distinct sequence features underlie microdeletions and gross deletions in the human genome. Hum Mutat 2021; 43:328-346. [PMID: 34918412 PMCID: PMC9069542 DOI: 10.1002/humu.24314] [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: 09/10/2021] [Revised: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 11/18/2022]
Abstract
Microdeletions and gross deletions are important causes (~20%) of human inherited disease and their genomic locations are strongly influenced by the local DNA sequence environment. This notwithstanding, no study has systematically examined their underlying generative mechanisms. Here, we obtained 42,098 pathogenic microdeletions and gross deletions from the Human Gene Mutation Database (HGMD) that together form a continuum of germline deletions ranging in size from 1 to 28,394,429 bp. We analyzed the DNA sequence within 1 kb of the breakpoint junctions and found that the frequencies of non‐B DNA‐forming repeats, GC‐content, and the presence of seven of 78 specific sequence motifs in the vicinity of pathogenic deletions correlated with deletion length for deletions of length ≤30 bp. Further, we found that the presence of DR, GQ, and STR repeats is important for the formation of longer deletions (>30 bp) but not for the formation of shorter deletions (≤30 bp) while significantly (χ2, p < 2E−16) more microhomologies were identified flanking short deletions than long deletions (length >30 bp). We provide evidence to support a functional distinction between microdeletions and gross deletions. Finally, we propose that a deletion length cut‐off of 25–30 bp may serve as an objective means to functionally distinguish microdeletions from gross deletions.
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Affiliation(s)
- Mengling Qi
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Huiying Zhao
- Department of Medical Research Center, Sun Yat-sen Memorial Hospital; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
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5
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Geng C, Tong Y, Zhang S, Ling C, Wu X, Wang D, Dai Y. Sequence and Structure Characteristics of 22 Deletion Breakpoints in Intron 44 of the DMD Gene Based on Long-Read Sequencing. Front Genet 2021; 12:638220. [PMID: 34211494 PMCID: PMC8240811 DOI: 10.3389/fgene.2021.638220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/29/2021] [Indexed: 12/27/2022] Open
Abstract
Purpose: Exon deletions make up to 80% of mutations in the DMD gene, which cause Duchenne and Becker muscular dystrophy. Exon 45-55 regions were reported as deletion hotspots and intron 44 harbored more than 25% of deletion start points. We aimed to investigate the fine structures of breakpoints in intron 44 to find potential mechanisms of large deletions in intron 44. Methods: Twenty-two dystrophinopathy patients whose deletion started in intron 44 were sequenced using long-read sequencing of a DMD gene capture panel. Sequence homology, palindromic sequences, and polypyrimidine sequences were searched at the breakpoint junctions. RepeatMasker was used to analyze repetitive elements and Mfold was applied to predict secondary DNA structure. Results: With a designed DMD capture panel, 22 samples achieved 2.25 gigabases and 1.28 million reads on average. Average depth was 308× and 99.98% bases were covered at least 1×. The deletion breakpoints in intron 44 were scattered and no breakpoints clustered in any region less than 500 bp. A total of 72.7% of breakpoints located in distal 100 kb of intron 44 and more repetitive elements were found in this region. Microhomologies of 0–1 bp were found in 36.4% (8/22) of patients, which corresponded with non-homologous end-joining. Microhomologies of 2–20 bp were found in 59.1% (13/22) of patients, which corresponded with microhomology-mediated end-joining. Moreover, a 7 bp insertion was found in one patient, which might be evidence of aberrant replication origin firing. Palindromic sequences, polypyrimidine sequences, and small hairpin loops were found near several breakpoint junctions. No evidence of large hairpin loop formation in deletion root sequences was observed. Conclusion: This study was the first to explore possible mechanisms underlying exon deletions starting from intron 44 of the DMD gene based on long-read sequencing. Diverse mechanisms might be associated with deletions in the DMD gene.
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Affiliation(s)
- Chang Geng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuanren Tong
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | | | - Chao Ling
- Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Wu
- GrandOmics Biosciences, Beijing, China
| | | | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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6
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Neri M, Rossi R, Trabanelli C, Mauro A, Selvatici R, Falzarano MS, Spedicato N, Margutti A, Rimessi P, Fortunato F, Fabris M, Gualandi F, Comi G, Tedeschi S, Seia M, Fiorillo C, Traverso M, Bruno C, Giardina E, Piemontese MR, Merla G, Cau M, Marica M, Scuderi C, Borgione E, Tessa A, Astrea G, Santorelli FM, Merlini L, Mora M, Bernasconi P, Gibertini S, Sansone V, Mongini T, Berardinelli A, Pini A, Liguori R, Filosto M, Messina S, Vita G, Toscano A, Vita G, Pane M, Servidei S, Pegoraro E, Bello L, Travaglini L, Bertini E, D'Amico A, Ergoli M, Politano L, Torella A, Nigro V, Mercuri E, Ferlini A. The Genetic Landscape of Dystrophin Mutations in Italy: A Nationwide Study. Front Genet 2020; 11:131. [PMID: 32194622 PMCID: PMC7063120 DOI: 10.3389/fgene.2020.00131] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/03/2020] [Indexed: 12/11/2022] Open
Abstract
Dystrophinopathies are inherited diseases caused by mutations in the dystrophin (DMD) gene for which testing is mandatory for genetic diagnosis, reproductive choices and eligibility for personalized trials. We genotyped the DMD gene in our Italian cohort of 1902 patients (BMD n = 740, 39%; DMD n =1162, 61%) within a nationwide study involving 11 diagnostic centers in a 10-year window (2008–2017). In DMD patients, we found deletions in 57%, duplications in 11% and small mutations in 32%. In BMD, we found deletions in 78%, duplications in 9% and small mutations in 13%. In BMD, there are a higher number of deletions, and small mutations are more frequent than duplications. Among small mutations that are generally frequent in both phenotypes, 44% of DMD and 36% of BMD are nonsense, thus, eligible for stop codon read-through therapy; 63% of all out-of-frame deletions are eligible for single exon skipping. Patients were also assigned to Italian regions and showed interesting regional differences in mutation distribution. The full genetic characterization in this large, nationwide cohort has allowed us to draw several correlations between DMD/BMD genotype landscapes and mutation frequency, mutation types, mutation locations along the gene, exon/intron architecture, and relevant protein domain, with effects on population genetic characteristics and new personalized therapies.
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Affiliation(s)
- Marcella Neri
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Rachele Rossi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Cecilia Trabanelli
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Antonio Mauro
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Rita Selvatici
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Maria Sofia Falzarano
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Noemi Spedicato
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alice Margutti
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Paola Rimessi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Fortunato
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Marina Fabris
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Francesca Gualandi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Giacomo Comi
- Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Silvana Tedeschi
- Laboratory of Medical Genetics, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Manuela Seia
- Laboratory of Medical Genetics, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Fiorillo
- Paediatric Neurology and Muscular Diseases Unit, University of Genoa and G. Gaslini Institute, Genoa, Italy
| | - Monica Traverso
- Paediatric Neurology and Muscular Diseases Unit, University of Genoa and G. Gaslini Institute, Genoa, Italy
| | - Claudio Bruno
- Center of Translational and Experimental Myology, IRCCS Gaslini, Genova, Italy
| | - Emiliano Giardina
- Molecular Genetics Laboratory UILDM, Santa Lucia Foundation, Rome, Italy
| | | | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, Foggia, Italy
| | - Milena Cau
- Laboratory of Genetics and Genomics, Department of Medical Science and Public Health, University of Cagliari, Cagliari, Italy
| | - Monica Marica
- Clinica Pediatrica e Malattie Rare, Brotzu, Cagliari, Italy
| | - Carmela Scuderi
- Unit of Neuromuscular Diseases, Oasi Research Institute-IRCCS, Troina, Italy
| | - Eugenia Borgione
- Unit of Neuromuscular Diseases, Oasi Research Institute-IRCCS, Troina, Italy
| | - Alessandra Tessa
- Department of Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Guia Astrea
- Department of Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | | | - Luciano Merlini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Pia Bernasconi
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Sara Gibertini
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valeria Sansone
- Neurorehabilitation Unit, Department Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Tiziana Mongini
- Neuromuscular Center, AOU Città della Salute e della Scienza, University of Turin, Turin, Italy
| | - Angela Berardinelli
- Child Neurology and Psychiatry Unit, "Casimiro Mondino" Foundation, Pavia, Italy
| | - Antonella Pini
- Child Neurology Unit, IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Rocco Liguori
- Department of Biomedical and Neuro Motor Sciences, University of Bologna, Bologna, Italy
| | - Massimiliano Filosto
- Laboratory of Medical Genetics, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sonia Messina
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Gianluca Vita
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Antonio Toscano
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Giuseppe Vita
- Department of Clinical and Experimental Medicine, University of Messina and Nemo Sud Clinical Center, Messina, Italy
| | - Marika Pane
- Centro Clinico Nemo, Policlinico A. Gemelli, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Serenella Servidei
- UOC Neurofisiopatologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Institute of Neurology, Catholic University of Sacred Heart, Rome, Italy
| | - Elena Pegoraro
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Luca Bello
- Department of Neurosciences, University of Padua, Padua, Italy
| | - Lorena Travaglini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Adele D'Amico
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesu Children's Research Hospital IRCCS, Rome, Italy
| | - Manuela Ergoli
- Cardiomiology and Medical Genetics, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Luisa Politano
- Cardiomiology and Medical Genetics, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli, Naples, Italy
| | - Eugenio Mercuri
- Centro Clinico Nemo, Policlinico A. Gemelli, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Pediatric Neurology, Catholic University, Rome, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy.,Dubowitz Neuromuscular Unit, Institute of Child Health, University College London, London, United Kingdom
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7
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Ling C, Dai Y, Fang L, Yao F, Liu Z, Qiu Z, Cui L, Xia F, Zhao C, Zhang S, Wang K, Zhang X. Exonic rearrangements in DMD in Chinese Han individuals affected with Duchenne and Becker muscular dystrophies. Hum Mutat 2019; 41:668-677. [PMID: 31705731 PMCID: PMC7028077 DOI: 10.1002/humu.23953] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 01/12/2023]
Abstract
Exonic deletions and duplications within DMD are the main pathogenic variants in Duchenne and Becker muscular dystrophies (DMD/BMD). However, few studies have profiled the flanking sequences of breakpoints and the potential mechanism underlying the breakpoints in different fragile regions of DMD. In this study, 896 Chinese male probands afflicted with DMD/BMD were selected from unrelated families and analyzed using multiplex ligation‐dependent probe amplification of the DMD gene, in which we identified exon deletions in 784 subjects and duplications in 112 subjects. Deletions occurred most frequently in the genomic region encompassing exons 45–55, accounting for 73% of all deletion patterns. Furthermore, to unravel the potential mechanism that induced breaks, DMD gene capture and sequencing were performed to identify the breakpoints in 37 subjects with deletions encompassing exons 45–55 of DMD; we found that DMD instability did not arise from a single cause; instead, long‐sequence motifs, nonconsensus microhomologies, low‐copy repeats, and microindels were embedded around the breakpoints, which may predispose DMD to instability. In summary, this study highlights the heterogeneous characteristics of the flanking sequences around the breakpoints and helps us to understand the mechanism underlying DMD gene instability.
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Affiliation(s)
- Chao Ling
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yi Dai
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Fang
- Department of Pathology & Laboratory Medicine, Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Fengxia Yao
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhe Liu
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhengqing Qiu
- Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Chen Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Kai Wang
- Department of Pathology & Laboratory Medicine, Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xue Zhang
- The Laboratory of Clinical Genetics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, McKusick-Zhang Center for GeneticMedicine, School of Basic Medicine Peking, Union Medical College, Beijing, China
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