1
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Saad FA, Siciliano G, Angelini C. Advances in Dystrophinopathy Diagnosis and Therapy. Biomolecules 2023; 13:1319. [PMID: 37759719 PMCID: PMC10526396 DOI: 10.3390/biom13091319] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Dystrophinopathies are x-linked muscular disorders which emerge from mutations in the Dystrophin gene, including Duchenne and Becker muscular dystrophy, and dilated cardiomyopathy. However, Duchenne muscular dystrophy interconnects with bone loss and osteoporosis, which are exacerbated by glucocorticoids therapy. Procedures for diagnosing dystrophinopathies include creatine kinase assay, haplotype analysis, Southern blot analysis, immunological analysis, multiplex PCR, multiplex ligation-dependent probe amplification, Sanger DNA sequencing, and next generation DNA sequencing. Pharmacological therapy for dystrophinopathies comprises glucocorticoids (prednisone, prednisolone, and deflazacort), vamorolone, and ataluren. However, angiotensin-converting enzyme (ACE) inhibitors, angiotensin receptor blockers (ARBs), and β-blockers are the first-line to prevent dilated cardiomyopathy in dystrophinopathy patients. Duchenne muscular dystrophy gene therapy strategies involve gene transfer, exon skipping, exon reframing, and CRISPR gene editing. Eteplirsen, an antisense-oligonucleotide drug for skipping exon 51 from the Dystrophin gene, is available on the market, which may help up to 14% of Duchenne muscular dystrophy patients. There are various FDA-approved exon skipping drugs including ExonDys-51 for exon 51, VyonDys-53 and Viltolarsen for exon 53 and AmonDys-45 for exon 45 skipping. Other antisense oligonucleotide drugs in the pipeline include casimersen for exon 45, suvodirsen for exon 51, and golodirsen for exon 53 skipping. Advances in the diagnosis and therapy of dystrophinopathies offer new perspectives for their early discovery and care.
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Affiliation(s)
- Fawzy A. Saad
- Department of Gene Therapy, Saad Pharmaceuticals, Juhkentali 8, 10132 Tallinn, Estonia
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Pisa University School of Medicine, Via Paradisa 2, 56100 Pisa, Italy;
| | - Corrado Angelini
- Department of Neurosciences, Padova University School of Medicine, Via Giustiniani 5, 35128 Padova, Italy;
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2
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RNA-seq analysis, targeted long-read sequencing and in silico prediction to unravel pathogenic intronic events and complicated splicing abnormalities in dystrophinopathy. Hum Genet 2023; 142:59-71. [PMID: 36048237 DOI: 10.1007/s00439-022-02485-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/24/2022] [Indexed: 01/18/2023]
Abstract
Dystrophinopathy is caused by alterations in DMD. Approximately 1% of patients remain genetically undiagnosed, because intronic variations are not detected by standard methods. Here, we combined laboratory and in silico analyses to identify disease-causing genomic variants in genetically undiagnosed patients and determine the regulatory mechanisms underlying abnormal DMD transcript generation. DMD transcripts from 20 genetically undiagnosed dystrophinopathy patients in whom no exon variants were identified, despite dystrophin deficiency on muscle biopsy, were analyzed by transcriptome sequencing. Genome sequencing captured intronic variants and their effects were interpreted using in silico tools. Targeted long-read sequencing was applied in cases with suspected structural genomic abnormalities. Abnormal DMD transcripts were detected in 19 of 20 cases; Exonization of intronic sequences in 15 cases, exon skipping in one case, aberrantly spliced and polyadenylated transcripts in two cases and transcription termination in one case. Intronic single nucleotide variants, chromosomal rearrangements and nucleotide repeat expansion were identified in DMD gene as pathogenic causes of transcript alteration. Our combined analysis approach successfully identified pathogenic events. Detection of diseasing-causing mechanisms in DMD transcripts could inform the therapeutic options for patients with dystrophinopathy.
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3
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Ban R, Lu X, Pu C, Shi Q, Wang H, Liu H, Zhang Y. A Symptomatic Female Patient with Duchenne Muscular Dystrophy Gene Mutation Showing Rimmed Vacuole in Muscle Biopsy. Neurol India 2022; 70:2262-2264. [PMID: 36352669 DOI: 10.4103/0028-3886.359224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Rui Ban
- Department of Neurology, Chinese General PLA Hospital, Beijing; Nankai University, Nankai Qu, Tianjin, P.R. China
| | - Xianghui Lu
- Department of Neurology, Chinese General PLA Hospital, Beijing, P.R. China
| | - Chuanqiang Pu
- Department of Neurology, Chinese General PLA Hospital, Beijing, P.R. China
| | - Qiang Shi
- Department of Neurology, Chinese General PLA Hospital, Beijing, P.R. China
| | - Huifang Wang
- First Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi, P.R. China
| | - Huaxu Liu
- Department of Neurology, Chinese General PLA Hospital, Beijing, P.R. China
| | - Yutong Zhang
- Department of Neurology, Chinese General PLA Hospital, Beijing, P.R. China
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4
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Luce L, Carcione M, Mazzanti C, Buonfiglio PI, Dalamón V, Mesa L, Dubrovsky A, Corderí J, Giliberto F. Theragnosis for Duchenne Muscular Dystrophy. Front Pharmacol 2021; 12:648390. [PMID: 34149409 PMCID: PMC8209366 DOI: 10.3389/fphar.2021.648390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/17/2021] [Indexed: 12/12/2022] Open
Abstract
Dystrophinopathies cover a spectrum of rare progressive X-linked muscle diseases, arising from DMD mutations. They are among the most common pediatric muscular dystrophies, being Duchenne muscular dystrophy (DMD) the most severe form. Despite the fact that there is still no cure for these serious diseases, unprecedented advances are being made for the development of therapies for DMD. Some of which are already conditionally approved: exon skipping and premature stop codon read-through. The present work aimed to characterize the mutational spectrum of DMD in an Argentinian cohort, to identify candidates for available pharmacogenetic treatments and finally, to conduct a comparative analysis of the Latin American (LA) frequencies of mutations amenable for available DMD therapies. We studied 400 patients with clinical diagnosis of dystrophinopathy, implementing a diagnostic molecular algorithm including: MLPA/PCR/Sanger/Exome and bioinformatics. We also performed a meta-analysis of LA's metrics for DMD available therapies. The employed algorithm resulted effective for the achievement of differential diagnosis, reaching a detection rate of 97%. Because of this, corticosteroid treatment was correctly indicated and validated in 371 patients with genetic confirmation of dystrophinopathy. Also, 20 were eligible for exon skipping of exon 51, 21 for exon 53, 12 for exon 45 and another 70 for premature stop codon read-through therapy. We determined that 87.5% of DMD patients will restore the reading frame with the skipping of only one exon. Regarding nonsense variants, UGA turned out to be the most frequent premature stop codon observed (47%). According to the meta-analysis, only four LA countries (Argentina, Brazil, Colombia and Mexico) provide the complete molecular algorithm for dystrophinopathies. We observed different relations among the available targets for exon skipping in the analyzed populations, but a more even proportion of nonsense variants (∼40%). In conclusion, this manuscript describes the theragnosis carried out in Argentinian dystrophinopathy patients. The implemented molecular algorithm proved to be efficient for the achievement of differential diagnosis, which plays a crucial role in patient management, determination of the standard of care and genetic counseling. Finally, this work contributes with the international efforts to characterize the frequencies and variants in LA, pillars of drug development and theragnosis.
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Affiliation(s)
- Leonela Luce
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Micaela Carcione
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Chiara Mazzanti
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula I Buonfiglio
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) "Dr. Héctor N. Torres", CONICET, Buenos Aires, Argentina
| | - Viviana Dalamón
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) "Dr. Héctor N. Torres", CONICET, Buenos Aires, Argentina
| | - Lilia Mesa
- Instituto de Neurociencias, Fundación Favaloro, Buenos Aires, Argentina
| | - Alberto Dubrovsky
- Instituto de Neurociencias, Fundación Favaloro, Buenos Aires, Argentina
| | - José Corderí
- Instituto de Neurociencias, Fundación Favaloro, Buenos Aires, Argentina
| | - Florencia Giliberto
- Laboratorio de Distrofinopatías, Cátedra de Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
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5
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Luce L, Abelleyro MM, Carcione M, Mazzanti C, Rossetti L, Radic P, Szijan I, Menazzi S, Francipane L, Nevado J, Lapunzina P, De Brasi C, Giliberto F. Analysis of complex structural variants in the DMD gene in one family. Neuromuscul Disord 2021; 31:253-263. [PMID: 33451931 DOI: 10.1016/j.nmd.2020.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 11/24/2022]
Abstract
This work describes a family with Duchenne muscular dystrophy (DMD) with a rare case of a symptomatic pregnant woman. The main aim was to perform prenatal molecular diagnosis to provide genetic counseling. The secondary aim was to suggest the molecular mechanisms causing the complex structural variant (cxSV) identified. To accomplish this, we used a multi-technique algorithm including segregation analysis, Multiplex Ligation-dependent Probe Amplification, PCR, X-chromosome inactivation studies, microarrays, whole genome sequencing and bioinformatics. We identified a duplication of exons 38-43 in the DMD gene in all affected and obligate carrier members, proving that this was the DMD-causing mutation. We also observed a skewed X-chromosome inactivation in the symptomatic woman that explained her symptomatology. In addition, we identified a cxSV (duplication of exons 38-43 and deletion of exons 45-54) in the affected boy. The molecular characterization and bioinformatic analyses of the breakpoint junctions allowed us to identify Double Strand Breaks stimulator motifs and suggested the replication-dependent Fork Stalling and Template Switching as the most probable mechanisms leading to the duplication. In addition, the de novo deletion might have been the result of a germline inter-chromosome non-allelic recombination involving the Non-Homologous End Joining mechanism. In conclusion, the diagnostic strategy used allowed us to provide accurate molecular diagnosis and genetic counseling. In addition, the familial molecular diagnosis together with the in-depth characterization of the cxSV helped to determine the chronology of the molecular events, and propose and understand the molecular mechanisms involved in the generation of this complex rearrangement.
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Affiliation(s)
- Leonela Luce
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética, Laboratorio de Distrofinopatías, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Martín M Abelleyro
- CONICET-Academia Nacional de Medicina, Instituto de Medicina Experimental (IMEX), Buenos Aires, Argentina
| | - Micaela Carcione
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética, Laboratorio de Distrofinopatías, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Chiara Mazzanti
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética, Laboratorio de Distrofinopatías, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Liliana Rossetti
- CONICET-Academia Nacional de Medicina, Instituto de Medicina Experimental (IMEX), Buenos Aires, Argentina
| | - Pamela Radic
- CONICET-Academia Nacional de Medicina, Instituto de Medicina Experimental (IMEX), Buenos Aires, Argentina
| | - Irene Szijan
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética, Laboratorio de Distrofinopatías, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sebastián Menazzi
- Hospital de Clínicas "José de San Martín", División de Genética, Universidad de Buenos Aires, Buenos Aires Argentina
| | - Liliana Francipane
- Hospital de Clínicas "José de San Martín", División de Genética, Universidad de Buenos Aires, Buenos Aires Argentina
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, Spain; Centro de Investigaciones Biomédicas en Red para Enfermedades Raras (CIBERER), Madrid, Spain; ITHACA-ERN (European Reference Network), La Paz University Hospital, Madrid, Spain
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma, Madrid, Spain; Centro de Investigaciones Biomédicas en Red para Enfermedades Raras (CIBERER), Madrid, Spain; ITHACA-ERN (European Reference Network), La Paz University Hospital, Madrid, Spain
| | - Carlos De Brasi
- CONICET-Academia Nacional de Medicina, Instituto de Medicina Experimental (IMEX), Buenos Aires, Argentina
| | - Florencia Giliberto
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética, Laboratorio de Distrofinopatías, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Inmunología, Genética y Metabolismo (INIGEM), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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6
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Wang Y, Chen Y, Wang SM, Liu X, Gu YN, Feng Z. Prenatal diagnosis of Duchenne muscular dystrophy revealed a novel mosaic mutation in Dystrophin gene: a case report. BMC MEDICAL GENETICS 2020; 21:222. [PMID: 33176713 PMCID: PMC7661169 DOI: 10.1186/s12881-020-01157-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/25/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Duchenne muscular dystrophies (DMDs) are X-linked recessive neuromuscular disorders with malfunction or absence of the Dystrophin protein. Precise genetic diagnosis is critical for proper planning of patient care and treatment. In this study, we described a Chinese family with mosaic DMD mutations and discussed the best method for prenatal diagnosis and genetic counseling of X-linked familial disorders. METHODS We investigated all variants of the whole dystrophin gene using multiple DNA samples isolated from the affected family and identified two variants of the DMD gene in a sick boy and two female carriers by targeted next generation sequencing (TNGS), Sanger sequencing, and haplotype analysis. RESULTS We identified the hemizygous mutation c.6794delG (p.G2265Efs*6) of DMD in the sick boy, which was inherited from his mother. Unexpectedly, a novel heterozygous mutation c.6796delA (p.I2266Ffs*5) of the same gene, which was considered to be a de novo variant, was detected from his younger sister instead of his mother by Sanger sequencing. However, further NGS analysis of the mother and her amniotic fluid samples revealed that the mother carried a low-level mosaic c.6796delA mutation. CONCLUSIONS We reported two different mutations of the DMD gene in two siblings, including the novel mutation c.6796delA (p.I2266Ffs*5) inherited from the asymptomatic mosaic-carrier mother. This finding has enriched the knowledge of the pathogenesis of DMD. If no mutation is detected in obligate carriers, the administration of intricate STR/NGS/Sanger analysis will provide new ideas on the prenatal diagnosis of DMD.
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Affiliation(s)
- Yan Wang
- Department of Clinical Genetics, BaYi Children's Hospital, Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100700, China. .,National Engineering Laboratory for Birth defects prevention and control of key technology, Beijing, 100700, China. .,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China. .,Clinical Biobank Center, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Yuhan Chen
- Department of Clinical Genetics, BaYi Children's Hospital, Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100700, China.,National Engineering Laboratory for Birth defects prevention and control of key technology, Beijing, 100700, China.,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China.,Department of Pediatrics, Chinese PLA General Hospital, Beijing, 100700, China
| | - San Mei Wang
- Department of Clinical Genetics, BaYi Children's Hospital, Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100700, China.,National Engineering Laboratory for Birth defects prevention and control of key technology, Beijing, 100700, China.,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China.,Department of Pediatrics, Chinese PLA General Hospital, Beijing, 100700, China
| | - Xin Liu
- Department of Clinical Genetics, BaYi Children's Hospital, Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100700, China.,National Engineering Laboratory for Birth defects prevention and control of key technology, Beijing, 100700, China.,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China.,Department of Pediatrics, Chinese PLA General Hospital, Beijing, 100700, China
| | - Ya Nan Gu
- Department of Clinical Genetics, BaYi Children's Hospital, Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100700, China.,National Engineering Laboratory for Birth defects prevention and control of key technology, Beijing, 100700, China.,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China.,Department of Pediatrics, Chinese PLA General Hospital, Beijing, 100700, China
| | - Zhichun Feng
- Department of Clinical Genetics, BaYi Children's Hospital, Seventh Medical Center of Chinese PLA General Hospital, Beijing, 100700, China. .,National Engineering Laboratory for Birth defects prevention and control of key technology, Beijing, 100700, China. .,Beijing Key Laboratory of Pediatric Organ Failure, Beijing, 100700, China. .,Department of Pediatrics, Chinese PLA General Hospital, Beijing, 100700, China.
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7
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Ban R, Lu X, Pu C, Shi Q, Wang H, Liu H, Zhang Y, Fang F. A symptomatic female patient with duchenne muscular dystrophy gene mutation showing rimmed vacuoles in muscle biopsy. Neurol India 2020; 68:518-521. [PMID: 32415039 DOI: 10.4103/0028-3886.284351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Rui Ban
- Neurological Department of the First Medical Center, Chinese PLA General Hospital; Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, P.R. China
| | - Xianghui Lu
- Geriatric Neurological Department of the Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, P.R. China
| | - Chuanqiang Pu
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, P.R. China
| | - Qiang Shi
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, P.R. China
| | - Huifang Wang
- Neurological Department, First Affiliated Hospital of Shanxi Medical University, P.R. China
| | - Huaxu Liu
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, P.R. China
| | - Yutong Zhang
- Neurological Department of the First Medical Center, Chinese PLA General Hospital, P.R. China
| | - Fang Fang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, P.R. China
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8
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Shariati G, Shakerian S, Mohammadi Anaie M, Abdorasouli N, Nanvazadeh F, Sedaghat A, Sedighi M, Saberi A. Deletion and duplication mutations spectrum in Duchenne muscular dystrophy in the southwest of Iran. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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9
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Exon skipping induced by nonsense/frameshift mutations in DMD gene results in Becker muscular dystrophy. Hum Genet 2020; 139:247-255. [PMID: 31919629 PMCID: PMC6981323 DOI: 10.1007/s00439-019-02107-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/27/2019] [Indexed: 01/13/2023]
Abstract
Duchenne muscular dystrophy (DMD) is caused by a nonsense or frameshift mutation in the DMD gene, while its milder form, Becker muscular dystrophy (BMD) is caused by an in-frame deletion/duplication or a missense mutation. Interestingly, however, some patients with a nonsense mutation exhibit BMD phenotype, which is mostly attributed to the skipping of the exon containing the nonsense mutation, resulting in in-frame deletion. This study aims to find BMD cases with nonsense/frameshift mutations in DMD and to investigate the exon skipping rate of those nonsense/frameshift mutations. We searched for BMD cases with nonsense/frameshift mutations in DMD in the Japanese Registry of Muscular Dystrophy. For each DMD mutation identified, we constructed minigene plasmids containing one exon with/without a mutation and its flanking intronic sequence. We then introduced them into HeLa cells and measured the skipping rate of transcripts of the minigene by RT-qPCR. We found 363 cases with a nonsense/frameshift mutation in DMD gene from a total of 1497 dystrophinopathy cases in the registry. Among them, 14 had BMD phenotype. Exon skipping rates were well correlated with presence or absence of dystrophin, suggesting that 5% exon skipping rate is critical for the presence of dystrophin in the sarcolemma, leading to milder phenotypes. Accurate quantification of the skipping rate is important in understanding the exact functions of the nonsense/frameshift mutations in DMD and for interpreting the phenotypes of the BMD patients.
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10
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Wang D, Gao M, Zhang K, Jin R, Lv Y, Liu Y, Ma J, Wan Y, Gai Z, Liu Y. Molecular Genetics Analysis of 70 Chinese Families With Muscular Dystrophy Using Multiplex Ligation-Dependent Probe Amplification and Next-Generation Sequencing. Front Pharmacol 2019; 10:814. [PMID: 31404137 PMCID: PMC6669794 DOI: 10.3389/fphar.2019.00814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 06/24/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Muscular dystrophy (MD) includes multiple types, of which dystrophinopathies caused by dystrophin (DMD) mutations are the most common types in children. An accurate identification of the causative mutation at the genomic level is critical for genetic counseling of the family, and analysis of genotype-phenotype correlations, as well as a reference for the development of gene therapy. Methods: Totally, 70 Chinese families with suspected MD probands were enrolled in the study. The multiplex ligation-dependent probe amplification (MLPA) was first performed to screen large deletions/duplications of DMD exons in the patients, and then, next-generation sequencing (NGS) was carried out to detect small mutations in the MLPA-negative patients. Results: Totally, 62 mutations of DMD were found in 62 probands with DMD/BMD, and two compound heterozygous mutations in LAMA2 were identified in two probands with MDC1A (a type of congenital MD), indicating that the diagnostic yield was 91.4% by MLPA plus NGS for MD diagnosis in this cohort. Out of the mutations, 51 large mutations encompassing 47 (75.8%) deletions and four duplications (6.5%) were identified by MLPA; 11 small mutations including six (9.7%) nonsense, two (3.2%) small deletions, two splice-site mutations (3.2%), and one small insertion (1.6%) were found by NGS. Large mutations were found most frequently in the hotspot region between exons 45 and 55 (70.6%). Out of the 11 patients harboring point mutations in DMD, 8 were novel mutations. Additionally, one novel mutation in LAMA2 was identified. All the novel mutations were analyzed and predicted as pathogenic according to American College of Medical Genetics and Genomics (ACMG) guideline. Finally, 34 DMD, 4 BMD, 24 BMD/DMD, and 2 MDC1A were diagnosed in the cohort. Conclusion: Our data indicated that the MLPA plus NGS can be a comprehensive and effective tool for precision diagnosis and potential treatment of MD and is particularly necessary for the patients at very young age with only two clinical indicators (persistent hyperCKemia and typical myopathy performance on electromyogram) but no definite clinical manifestations.
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Affiliation(s)
- Dong Wang
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Min Gao
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Kaihui Zhang
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Ruifeng Jin
- Neurology Department, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Yuqiang Lv
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Yong Liu
- Neurology Department, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Jian Ma
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Ya Wan
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
| | - Yi Liu
- Pediatric Research Institute, Qilu Children’s Hospital, Shandong University, Ji’nan, China
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11
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Polavarapu K, Preethish-Kumar V, Sekar D, Vengalil S, Nashi S, Mahajan NP, Thomas PT, Sadasivan A, Warrier M, Gupta A, Arunachal G, Debnath M, Keerthipriya MS, Pradeep-Chandra-Reddy C, Puttegowda A, John AP, Tavvala A, Gunasekaran S, Sathyaprabha TN, Chandra SR, Kramer B, Delhaas T, Nalini A. Mutation pattern in 606 Duchenne muscular dystrophy children with a comparison between familial and non-familial forms: a study in an Indian large single-center cohort. J Neurol 2019; 266:2177-2185. [PMID: 31139960 DOI: 10.1007/s00415-019-09380-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
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12
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Sánchez AI, Mariño N, Araujo AF, Espinosa E. Distrofia muscular de Becker con duplicación en el exón 5del gen DMD. REPERTORIO DE MEDICINA Y CIRUGÍA 2019. [DOI: 10.31260/repertmedcir.v28.n2.2019.920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Las distrofinopatías son un grupo de enfermedades ligadas al cromosoma X que abarcan diferentes entidades, siendo las más importantes la distrofia muscular de Duchenne (DMD) y la de Becker (DMB). Están causadas por mutaciones en el gen de la distrofina (gen DMD) localizado en el cromosoma X, locus Xp21.1. En relación con el tipo de mutaciones reportadas en el gen DMD, las delecciones y las mutaciones puntuales son las más comunes, mientras que las duplicaciones corresponden a 10-12%. Aunque las duplicaciones que abarcan el exón 5 ya han sido reportadas en la literatura, a la fecha no existen informes de casos que establezcan una relación genotipo fenotipo clara. Presentamos el caso de un paciente con distrofia muscular de Becker con un fenotipo no tan severo, en quien se encontró una duplicación en el exón 5. Con este caso pretendemos profundizar en la relación genotipo-fenotipo de la DMB, reportando las características clínicas en relación con la duplicación del exón 5 encontrada.
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Dabrowska M, Czubak K, Juzwa W, Krzyzosiak WJ, Olejniczak M, Kozlowski P. qEva-CRISPR: a method for quantitative evaluation of CRISPR/Cas-mediated genome editing in target and off-target sites. Nucleic Acids Res 2018; 46:e101. [PMID: 29878242 PMCID: PMC6158505 DOI: 10.1093/nar/gky505] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
Genome editing technology based on engineered nucleases has been increasingly applied for targeted modification of genes in a variety of cell types and organisms. However, the methods currently used for evaluating the editing efficiency still suffer from many limitations, including preferential detection of some mutation types, sensitivity to polymorphisms that hamper mismatch detection, lack of multiplex capability, or sensitivity to assay conditions. Here, we describe qEva-CRISPR, a new quantitative method that overcomes these limitations and allows simultaneous (multiplex) analysis of CRISPR/Cas9-induced modifications in a target and the corresponding off-targets or in several different targets. We demonstrate all of the advantages of the qEva-CRISPR method using a number of sgRNAs targeting the TP53, VEGFA, CCR5, EMX1 and HTT genes in different cell lines and under different experimental conditions. Unlike other methods, qEva-CRISPR detects all types of mutations, including point mutations and large deletions, and its sensitivity does not depend on the mutation type. Moreover, this approach allows for successful analysis of targets located in 'difficult' genomic regions. In conclusion, qEva-CRISPR may become a method of choice for unbiased sgRNA screening to evaluate experimental conditions that affect genome editing or to distinguish homology-directed repair from non-homologous end joining.
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Affiliation(s)
- Magdalena Dabrowska
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karol Czubak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech Juzwa
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marta Olejniczak
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Zhao HH, Sun XP, Shi MC, Yi YX, Cheng H, Wang XX, Xu QC, Ma HM, Wu HQ, Jin QW, Niu Q. Molecular Analysis-Based Genetic Characterization of a Cohort of Patients with Duchenne and Becker Muscular Dystrophy in Eastern China. Chin Med J (Engl) 2018; 131:770-775. [PMID: 29578119 PMCID: PMC5887734 DOI: 10.4103/0366-6999.228237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are common X-linked recessive neuromuscular disorders caused by mutations in dystrophin gene. Multiplex polymerase chain reaction (multiplex PCR) and multiplex ligation-dependent probe amplification (MLPA) are the most common methods for detecting dystrophin gene mutations. This study aimed to contrast the two methods and discern the genetic characterization of patients with DMD/BMD in Eastern China. Methods: We collected 121 probands, 64 mothers of probands, and 15 fetuses in our study. The dystrophin gene was detected by multiplex PCR primarily in 28 probands, and MLPA was used in multiplex PCR-negative cases subsequently. The dystrophin gene of the remaining 93 probands and 62 female potential carriers was tested by MLPA directly. In fetuses, multiplex PCR and MLPA were performed on 4 fetuses and 10 fetuses, respectively. In addition, sequencing was also performed in 4 probands with negative MLPA. Results: We found that 61.98% of the subjects had genetic mutations including deletions (50.41%) and duplications (11.57%). There were 43.75% of mothers as carriers of the mutation. In 15 fetuses, 2 out of 7 male fetuses were found to be unhealthy and 2 out of 8 female fetuses were found to be carriers. Exons 3–26 and 45–52 have the maximum frequency in mutation regions. In the frequency of exons individually, exon 47 and exon 50 were the most common in deleted regions and exons 5, 6, and 7 were found most frequently in duplicated regions. Conclusions: MLPA has better productivity and sensitivity than multiplex PCR. Prenatal diagnosis should be applied in DMD high-risk fetuses to reduce the disease incidence. Furthermore, it is the responsibility of physicians to inform female carriers the importance of prenatal diagnosis.
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Affiliation(s)
- Hui-Hui Zhao
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xue-Ping Sun
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Ming-Chao Shi
- Department of Neurology, The Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yong-Xiang Yi
- Department of Neurology, The Second Hospital of Nanjing, Nanjing, Jiangsu 210003, China
| | - Hong Cheng
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xing-Xia Wang
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Qing-Cheng Xu
- Department of Neurology, Nanjing First Hospital, Nanjing, Jiangsu 210012, China
| | - Hong-Ming Ma
- Department of Biomedical Sciences, Texas Tech University Health Science Center, Texas 79430, USA
| | - Hao-Quan Wu
- Department of Biomedical Sciences, Texas Tech University Health Science Center, Texas 79430, USA
| | - Qing-Wen Jin
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029; Department of Neurology, The Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qi Niu
- Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Klonowska K, Handschuh L, Swiercz A, Figlerowicz M, Kozlowski P. MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency. Oncotarget 2018; 7:67266-67276. [PMID: 27572310 PMCID: PMC5341873 DOI: 10.18632/oncotarget.11646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 07/28/2016] [Indexed: 02/06/2023] Open
Abstract
Although currently available strategies for the preparation of exome-enriched libraries are well established, a final validation of the libraries in terms of exome enrichment efficiency prior to the sequencing step is of considerable importance. Here, we present a strategy for the evaluation of exome enrichment, i.e., the Multipoint Test for Targeted-enrichment Efficiency (MTTE), PCR-based approach utilizing multiplex ligation-dependent probe amplification with capillary electrophoresis separation. We used MTTE for the analysis of subsequent steps of the Illumina TruSeq Exome Enrichment procedure. The calculated values of enrichment-associated parameters (i.e., relative enrichment, relative clearance, overall clearance, and fold enrichment) and the comparison of MTTE results with the actual enrichment revealed the high reliability of our assay. Additionally, the MTTE assay enabled the determination of the sequence-associated features that may confer bias in the enrichment of different targets. Importantly, the MTTE is low cost method that can be easily adapted to the region of interest important for a particular project. Thus, the MTTE strategy is attractive for post-capture validation in a variety of targeted/exome enrichment NGS projects.
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Affiliation(s)
- Katarzyna Klonowska
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Luiza Handschuh
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Aleksandra Swiercz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Marek Figlerowicz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Piotr Kozlowski
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Institute of Technology and Chemical Engineering, Poznan University of Technology, 60-965 Poznan, Poland
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16
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Okubo M, Goto K, Komaki H, Nakamura H, Mori-Yoshimura M, Hayashi YK, Mitsuhashi S, Noguchi S, Kimura E, Nishino I. Comprehensive analysis for genetic diagnosis of Dystrophinopathies in Japan. Orphanet J Rare Dis 2017; 12:149. [PMID: 28859693 PMCID: PMC5580216 DOI: 10.1186/s13023-017-0703-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/23/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is the most common disease in children caused by mutations in the DMD gene, and DMD and Becker muscular dystrophy (BMD) are collectively called dystrophinopathies. Dystrophinopathies show a complex mutation spectrum. The importance of mutation databases, with clinical phenotypes and protein studies of patients, is increasingly recognized as a reference for genetic diagnosis and for the development of gene therapy. METHODS We used the data from the Japanese Registry of Muscular Dystrophy (Remudy) compiled during from July 2009 to March 2017, and reviewed 1497 patients with dystrophinopathies. RESULTS The spectrum of identified mutations contained exon deletions (61%), exon duplications (13%), nonsense mutations (13%), small deletions (5%), small insertions (3%), splice-site mutations (4%), and missense mutations (1%). Exon deletions were found most frequently in the central hot spot region between exons 45-52 (42%), and most duplications were detected in the proximal hot spot region between exons 3-25 (47%). In the 371 patients harboring a small mutation, 194 mutations were reported and 187 mutations were unreported. CONCLUSIONS We report the largest dystrophinopathies mutation dataset in Japan from a national patient registry, "Remudy". This dataset provides a useful reference to support the genetic diagnosis and treatment of dystrophinopathy.
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Affiliation(s)
- Mariko Okubo
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Pediatrics, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kanako Goto
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Genome Medicine Development, Medical Genome Center, NCNP, Tokyo, Japan
| | - Hirofumi Komaki
- Department of Child Neurology, National Center Hospital, NCNP, Tokyo, Japan
| | - Harumasa Nakamura
- Department of Neurology, National Center Hospital, NCNP, Tokyo, Japan
| | | | - Yukiko K Hayashi
- Department of Pathophysiology, Tokyo Medical University, Tokyo, Japan
| | - Satomi Mitsuhashi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Genome Medicine Development, Medical Genome Center, NCNP, Tokyo, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan
| | - En Kimura
- Department of Promoting Clinical Trial and Translational Medicine, Translational Medical Center, NCNP, Tokyo, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan. .,Department of Genome Medicine Development, Medical Genome Center, NCNP, Tokyo, Japan.
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17
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Deepha S, Vengalil S, Preethish-Kumar V, Polavarapu K, Nalini A, Gayathri N, Purushottam M. MLPA identification of dystrophin mutations and in silico evaluation of the predicted protein in dystrophinopathy cases from India. BMC MEDICAL GENETICS 2017; 18:67. [PMID: 28610567 PMCID: PMC5470271 DOI: 10.1186/s12881-017-0431-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/31/2017] [Indexed: 11/18/2022]
Abstract
Background Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are X-linked recessive disorders caused by mutations in the DMD gene. The aim of this study was to predict the effect of gene mutations on the dystrophin protein and study its impact on clinical phenotype. Methods In this study, 415 clinically diagnosed patients were tested for mutations by Multiplex ligation dependent probe amplification (MLPA). Muscle biopsy was performed in 34 patients with negative MLPA. Phenotype-genotype correlation was done using PROVEAN, hydrophobicity and eDystrophin analysis. We have utilized bioinformatics tools in order to evaluate the observed mutations both at the level of primary as well as secondary structure. Results Mutations were identified in 75.42% cases, of which there were deletions in 91.6% and duplications in 8.30%. As per the reading frame rule, 84.6% out-of frame and 15.3% in-frame mutations were noted. Exon 50 was the most frequently deleted exon and the exon 45–52 region was the hot-spot for deletions in this cohort. There was no correlation noted between age of onset or creatine kinase (CK) values with extent of gene mutation. The PROVEAN analysis showed a deleterious effect in 94.5% cases and a neutral effect in 5.09% cases. Mutations in exon 45–54 (out of frame) and exon 46–54 (in-frame) regions in the central rod domain of dystrophin showed more negative scores compared to other domains in the present study. Hydrophobicity profile analysis showed that the hydrophobic regions I & III were equally affected. Analysis of deletions in hinge III hydrophobic region by the eDystrophin programme also predicted a hybrid repeat seen to be associated with a BMD like disease progression, thus making the hinge III region relatively tolerant to mutations. Conclusions We found that, while the predictions made by the software utilized might have overall significance, the results were not convincing on a case by case basis. This reflects the inadequacy of the currently available tools and also underlines the possible inadequacy of MLPA to detect other minor mutations that might enhance or suppress the effect of the primary mutation in this large gene. Next Generation Sequencing or targeted Sanger sequencing on a case by case basis might improve phenotype- genotype correlation. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0431-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sekar Deepha
- Department of Neuropathology, Neuromuscular Laboratory, Bengaluru, Karnataka, India
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Veeramani Preethish-Kumar
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Kiran Polavarapu
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, Karnataka, India
| | - Narayanappa Gayathri
- Department of Neuropathology, Neuromuscular Laboratory, Bengaluru, Karnataka, India
| | - Meera Purushottam
- Molecular Genetics Laboratory, Neurobiology Research Centre, Department of Psychiatry, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka, India.
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18
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Suh MR, Lee KA, Kim EY, Jung J, Choi WA, Kang SW. Multiplex Ligation-Dependent Probe Amplification in X-linked Recessive Muscular Dystrophy in Korean Subjects. Yonsei Med J 2017; 58:613-618. [PMID: 28332368 PMCID: PMC5368148 DOI: 10.3349/ymj.2017.58.3.613] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 12/06/2016] [Accepted: 12/08/2016] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are similar genetic disorders whose patterns of mutation and disease phenotypes might be expected to show differences among different countries. We analyzed multiplex ligation-dependent probe amplification (MLPA) data in a large number of Korean patients with DMD/BMD. MATERIALS AND METHODS We obtained 130 positive MLPA results (86 DMD, 27 BMD, and 17 female carriers) from 272 candidates (237 clinically suspected patients and 35 possible female carriers) who took part in this study. We analyzed the mutation patterns among 113 patients diagnosed by MLPA and calculated deletion/duplication percentages from a total of 128 patients, including 15 patients who were diagnosed using methods other than MLPA. We also analyzed hot spot locations among the 130 MLPA-positive results. RESULTS Most mutations were detected in a central hot spot region between exons 44 and 55 (80 samples, 60.6%). Unlike previous reports, a second frequently observed hot spot near the 5'-end was not distinctive. MLPA detected deletions in specific exons in 92 patients with DMD/BMD (71.8%) and duplications in 21 patients (16.4%). CONCLUSION Our MLPA study of a large number of Korean patients with DMD/BMD identified the most frequent mutation hot spot, as well as a unique hot spot pattern. DMD gene mutation patterns do not appear to show significant ethnic differences.
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Affiliation(s)
- Mi Ri Suh
- Department of Rehabilitation Medicine, Gangnam Severance Hospital and Rehabilitation Institute of Neuromuscular Disease, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung A Lee
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Kim
- Department of Rehabilitation Medicine, Gangnam Severance Hospital and Rehabilitation Institute of Neuromuscular Disease, Yonsei University College of Medicine, Seoul, Korea
| | - Jiho Jung
- Department of Rehabilitation Medicine, Gangnam Severance Hospital and Rehabilitation Institute of Neuromuscular Disease, Yonsei University College of Medicine, Seoul, Korea
| | - Won Ah Choi
- Department of Rehabilitation Medicine, Gangnam Severance Hospital and Rehabilitation Institute of Neuromuscular Disease, Yonsei University College of Medicine, Seoul, Korea
| | - Seong Woong Kang
- Department of Rehabilitation Medicine, Gangnam Severance Hospital and Rehabilitation Institute of Neuromuscular Disease, Yonsei University College of Medicine, Seoul, Korea.
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Luce LN, Dalamon V, Ferrer M, Parma D, Szijan I, Giliberto F. MLPA analysis of an Argentine cohort of patients with dystrophinopathy: Association of intron breakpoints hot spots with STR abundance in DMD gene. J Neurol Sci 2016; 365:22-30. [PMID: 27206868 DOI: 10.1016/j.jns.2016.03.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/10/2016] [Accepted: 03/30/2016] [Indexed: 01/11/2023]
Abstract
Dystrophinopathies are X-linked recessive diseases caused by mutations in the DMD gene. Our objective was to identify mutations in this gene by Multiplex Ligation Probe Amplification (MLPA), to confirm the clinical diagnosis and determine the carrier status of at-risk relatives. Also, we aimed to characterize the Dystrophinopathies argentine population and the DMD gene. We analyzed a cohort of 121 individuals (70 affected boys, 11 symptomatic women, 37 at-risk women and 3 male villus samples). The MLPA technique identified 56 mutations (45 deletions, 9 duplications and 2 point mutations). These results allowed confirming the clinical diagnosis in 63% (51/81) of patients and symptomatic females. We established the carrier status of 54% (20/37) of females at-risk and 3 male villus samples. We could establish an association between the most frequent deletion intron breakpoints and the abundance of dinucleotide microsatellites loci, despite the underlying mutational molecular mechanism remains to be elucidated. The MLPA demonstrate, again, to be the appropriate first mutation screening methodology for molecular diagnosis of Dystrophinopathies. The reported results permitted to characterize the Dystrophinopathies argentine population and lead to better understanding of the genetic and molecular basis of rearrangements in the DMD gene, useful information for the gene therapies being developed.
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Affiliation(s)
- Leonela N Luce
- Laboratory of Dystrophinopathies, Department of Genetics, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina.
| | | | - Marcela Ferrer
- Molecular Neurobiology Laboratory, Neurosurgery Division, Hospital de Clínicas "José de San Martín", University of Buenos Aires, Buenos Aires, Argentina
| | - Diana Parma
- Laboratory of Dystrophinopathies, Department of Genetics, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
| | - Irene Szijan
- Laboratory of Dystrophinopathies, Department of Genetics, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
| | - Florencia Giliberto
- Laboratory of Dystrophinopathies, Department of Genetics, School of Pharmacy and Biochemistry, University of Buenos Aires, Buenos Aires, Argentina
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Next-generation sequencing discloses a nonsense mutation in the dystrophin gene from long preserved dried umbilical cord and low-level somatic mosaicism in the proband mother. J Hum Genet 2016; 61:351-5. [DOI: 10.1038/jhg.2015.157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/09/2015] [Accepted: 11/30/2015] [Indexed: 11/08/2022]
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21
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Farashi S, Garous NF, Vakili S, Ashki M, Imanian H, Azarkeivan A, Najmabadi H. Characterization of Homozygous Hb Setif (HBA2: c.283G>T) in the Iranian Population. Hemoglobin 2015; 40:53-5. [PMID: 26574177 DOI: 10.3109/03630269.2015.1091357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hemoglobin (Hb) variants are abnormalities resulting from point mutations in either of the two α-globin genes (HBA2 or HBA1) or the β-globin gene (HBB). Various reports of Hb variants have been described in Iran and other countries around the world. Hb Setif (or HBA2: c.283G>T) is one of these variants with a mutation at codon 94 of of the α2-globin gene that is characterized in clinically normal heterozygous individuals. We here report clinical and hematological findings in two homozygous cases of Iranian origin for this unstable Hb variant.
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Affiliation(s)
- Samaneh Farashi
- a Genetics Research Centre, University of Social Welfare & Rehabilitation Sciences , Tehran , Iran.,b Kariminejad-Najmabadi Pathology & Genetics Centre , Tehran , Iran
| | - Negin F Garous
- b Kariminejad-Najmabadi Pathology & Genetics Centre , Tehran , Iran
| | - Shadi Vakili
- b Kariminejad-Najmabadi Pathology & Genetics Centre , Tehran , Iran
| | - Mehri Ashki
- b Kariminejad-Najmabadi Pathology & Genetics Centre , Tehran , Iran
| | - Hashem Imanian
- b Kariminejad-Najmabadi Pathology & Genetics Centre , Tehran , Iran
| | - Azita Azarkeivan
- b Kariminejad-Najmabadi Pathology & Genetics Centre , Tehran , Iran.,c Iranian Blood Transfusion Organization, High Institute for Transfusion Research Centre , Tehran , Iran
| | - Hossein Najmabadi
- a Genetics Research Centre, University of Social Welfare & Rehabilitation Sciences , Tehran , Iran.,b Kariminejad-Najmabadi Pathology & Genetics Centre , Tehran , Iran
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Farashi S, Vakili S, Garous NF, Ashki M, Imanian H, Azarkeivan A, Najmabadi H. Mutations on theα2-Globin Gene That May Triggerα+-Thalassemia. Hemoglobin 2015; 39:398-402. [DOI: 10.3109/03630269.2015.1075890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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23
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Farashi S, Vakili S, Faramarzi Garous N, Ashki M, Imanian H, Azarkeivan A, Najmabadi H. Copy number variations of six and seven α-globin genes in a family with intermedia and major thalassemia phenotypes. Expert Rev Hematol 2015; 8:693-8. [DOI: 10.1586/17474086.2015.1075385] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Hori H, Maeda Y, Ishizaki M, Hirahara T, Watanabe M, Yamashita S, Yamashita T, Uchino M, Ando Y. A carrier with de novo
Mutation in the dystrophin gene whose myopathic symptoms became seriously progressive after pregnancy and delivery. Muscle Nerve 2015; 52:913-4. [DOI: 10.1002/mus.24744] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroko Hori
- Department of Neurology; Graduate School of Medical Sciences, Kumamoto University; Kumamoto Japan
| | - Yasushi Maeda
- Department of Neurology; Graduate School of Medical Sciences, Kumamoto University; Kumamoto Japan
| | - Masatoshi Ishizaki
- Department of Neurology; Graduate School of Medical Sciences, Kumamoto University; Kumamoto Japan
| | - Tomoo Hirahara
- Department of Neurology; Graduate School of Medical Sciences, Kumamoto University; Kumamoto Japan
| | - Masaki Watanabe
- Department of Neurology; Graduate School of Medical Sciences, Kumamoto University; Kumamoto Japan
| | - Satoshi Yamashita
- Department of Neurology; Graduate School of Medical Sciences, Kumamoto University; Kumamoto Japan
| | - Taro Yamashita
- Department of Neurology; Graduate School of Medical Sciences, Kumamoto University; Kumamoto Japan
| | - Makoto Uchino
- Department of Neurology; Graduate School of Medical Sciences, Kumamoto University; Kumamoto Japan
| | - Yukio Ando
- Department of Neurology; Graduate School of Medical Sciences, Kumamoto University; Kumamoto Japan
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Chen CA, Wang CC, Jong YJ, Wu SM. Label-Free Fluorescent Copper Nanoclusters for Genotyping of Deletion and Duplication of Duchenne Muscular Dystrophy. Anal Chem 2015; 87:6228-32. [DOI: 10.1021/acs.analchem.5b00918] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | | | - Yuh-Jyh Jong
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- College of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Shou-Mei Wu
- Department of Chemistry, College of Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
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26
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Farashi S, Faramarzi Garous N, Zeinali F, Vakili S, Ashki M, Imanian H, Najmabadi H, Azarkeivan A, Tamaddoni A. A 21 Nucleotide Duplication on theα1- andα2-Globin Genes Involves a Variety of Hypochromic Microcytic Anemias, From Mild to Hb H Disease. Hemoglobin 2015; 39:196-200. [DOI: 10.3109/03630269.2015.1030757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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27
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Aoyama Y, Yamamoto T, Sakaguchi N, Ishige M, Tanaka T, Ichihara T, Ohara K, Kouzan H, Kinosada Y, Fukao T. Application of multiplex ligation-dependent probe amplification, and identification of a heterozygous Alu-associated deletion and a uniparental disomy of chromosome 1 in two patients with 3-hydroxy-3-methylglutaryl-CoA lyase deficiency. Int J Mol Med 2015; 35:1554-60. [PMID: 25872961 PMCID: PMC4432928 DOI: 10.3892/ijmm.2015.2184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/19/2015] [Indexed: 01/28/2023] Open
Abstract
Mitochondrial 3-hydroxy-3-methylglutaryl-CoA lyase (HMGCL) deficiency is an autosomal recessive disorder affecting the leucine catabolic pathway and ketone body synthesis, and is clinically characterized by metabolic crises with hypoketotic hypoglycemia, metabolic acidosis and hyperammonemia. In the present study, we initially used PCR with genomic followed by direct sequencing to investigate the molecular genetic basis of HMGCL deficiency in two patients clinically diagnosed with the condition. Although we identified a mutation in each patient, the inheritance patterns of these mutations were not consistent with disease causation. Therefore, we investigated HMGCL using multiplex ligation-dependent probe amplification (MLPA) to determine the copy numbers of all exons. A heterozygous deletion that included exons 2–4 was identified in one of the patients. MLPA revealed that the other patient had two copies for all HMGCL exons. Paternal uniparental isodisomy of chromosome 1 was confirmed in this patient by microarray analysis. These findings indicate that MLPA is useful for the identification of genomic aberrations and mutations other than small-scale nucleotide alterations. To the best of our knowledge, this is the first study describing HMGCL deficiency caused by uniparental disomy.
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Affiliation(s)
- Yuka Aoyama
- Medical Information Sciences Division, United Graduate School of Drug Discovery and Medical information Sciences, Gifu University, Gifu 501-1194, Japan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences (TIIMS), Tokyo 162‑8666, Japan
| | - Naomi Sakaguchi
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu 501‑1194, Japan
| | - Mika Ishige
- Department of Pediatrics, Nihon University School of Medicine, Sapporo, Hokkaido 063‑0005, Japan
| | - Toju Tanaka
- Department of Pediatrics and Clinical Research, NHO Hokkaido Medical Center, Sapporo, Hokkaido 063‑0005, Japan
| | - Tomoko Ichihara
- Department of Pediatrics, Takamatsu Red Cross Hospital, Takamatsu, Kagawa 760-0017, Japan
| | - Katsuaki Ohara
- Department of Pediatrics, Takamatsu Red Cross Hospital, Takamatsu, Kagawa 760-0017, Japan
| | - Hiroko Kouzan
- Department of Pediatrics, Takamatsu Red Cross Hospital, Takamatsu, Kagawa 760-0017, Japan
| | - Yasutomi Kinosada
- Medical Information Sciences Division, United Graduate School of Drug Discovery and Medical information Sciences, Gifu University, Gifu 501-1194, Japan
| | - Toshiyuki Fukao
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu 501‑1194, Japan
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28
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Prior TW. Duchenne muscular dystrophy diagnostics: it only gets better but some of the same challenges remain. Clin Chem 2015; 61:792-3. [PMID: 25851048 DOI: 10.1373/clinchem.2015.240697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas W Prior
- Department of Pathology, The Ohio State University, Columbus, OH.
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29
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MLPA based detection of mutations in the dystrophin gene of 180 Polish families with Duchenne/Becker muscular dystrophy. Neurol Neurochir Pol 2014; 48:416-22. [DOI: 10.1016/j.pjnns.2014.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 10/03/2014] [Accepted: 10/15/2014] [Indexed: 11/17/2022]
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Park JH, Park KS, Lee K, Jang H, Park HG. Universal probe amplification: multiplex screening technologies for genetic variations. Biotechnol J 2014; 10:45-55. [PMID: 25350275 DOI: 10.1002/biot.201400219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/04/2014] [Accepted: 09/25/2014] [Indexed: 11/06/2022]
Abstract
In order to achieve multiplex screening of genetic variations, multiplex amplification of target genomic DNA is necessary. Universal amplification technology meets this requirement by simultaneously amplifying a number of different regions within the target genomic DNA using a single pair of universal primers and thus eliminating the limitations associated with the use of multiple pairs of primers. We comprehensively review universal probe amplification and its use with multiplex technologies for the identification of the most representative genetic variation, i. e. single nucleotide polymorphisms. The progress and key issues relating to universal probe amplification are discussed and the representative technologies are summarized with an emphasis on their application for the identification of susceptibility to human diseases.
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Affiliation(s)
- Jung Hun Park
- Department of Chemical and Biomolecular Engineering, KAIST, Yuseong-gu, Daejeon, Republic of Korea
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31
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Syu JR, Wang CC, Jong YJ, Wu SM. Genotyping of exons 1 to 20 in Duchenne muscular dystrophy by universal multiplex PCR and short-end capillary electrophoresis. Electrophoresis 2014; 35:3387-94. [DOI: 10.1002/elps.201400172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/25/2014] [Accepted: 08/05/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Jing-Rou Syu
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung Taiwan
| | - Chun-Chi Wang
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung Taiwan
| | - Yuh-Jyh Jong
- Graduate Institute of Medicine; Kaohsiung Medical University; Kaohsiung Taiwan
- Department of Pediatrics; Kaohsiung Medical University Hospital; Kaohsiung Taiwan
- College of Biological Science and Technology; National Chiao Tung University; Hsinchu Taiwan
| | - Shou-Mei Wu
- School of Pharmacy; College of Pharmacy; Kaohsiung Medical University; Kaohsiung Taiwan
- Department of Chemistry; College of Sciences; National Sun Yat-Sen University; Kaohsiung Taiwan
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Ta MH, Tran TH, Do NH, Pham LAT, Bui TH, Ta VT, Tran VK. Rapid method for targeted prenatal diagnosis of Duchenne muscular dystrophy in Vietnam. Taiwan J Obstet Gynecol 2014; 52:534-9. [PMID: 24411039 DOI: 10.1016/j.tjog.2013.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 08/09/2013] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE Since there is no effective curative treatment for Duchenne muscular dystrophy (DMD), prevention mostly depends on genetic counseling and prenatal diagnosis. About two-thirds of the affected patients have large deletions or duplications, which can be detected by multiplex ligation-dependent amplification (MLPA). The remaining cases include small mutations, which cannot be easily identified by routine techniques. In such cases, linkage analysis may be a useful tool for prenatal diagnosis. Here we compared results obtained from linkage using short tandem repeats (STRs) with those by MLPA and sequencing analysis. MATERIALS AND METHODS Eight Vietnamese pregnant women at risk of having a baby with DMD and requesting prenatal diagnosis were recruited in this study. MLPA and direct sequencing were applied to screen large rearrangements and point mutations in the dystrophin gene in the DMD probands and the fetal samples. STR linkage was also performed to analyze fetal mutation status. RESULTS By MLPA and sequencing analysis, five DMD patients showed deletions of the dystrophin gene, and no deletions of exons were detected in seven amniotic fluid cell samples; one patient harbored the out-of-frame small deletion of exon 43, which was also found in the fetal sample of this family. STR analysis revealed the transmission of a mutant allele inside each family. CONCLUSION Our results suggest that the combination of STR and MLPA could be a rapid, reliable, and affordable detection protocol for determination of the carrier's status and prenatal diagnosis of DMD in a developing country such as Vietnam.
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Affiliation(s)
- Minh-Hieu Ta
- Center for Gene-Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | - Thinh Huy Tran
- Center for Gene-Protein Research, Hanoi Medical University, Hanoi, Vietnam; Department of Biochemistry, Hanoi Medical University, Hanoi, Vietnam
| | - Ngoc-Hai Do
- Center for Gene-Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | - Le Anh-Tuan Pham
- Center for Gene-Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | - The-Hung Bui
- Karolinska Institutet, Department of Molecular Medicine, Clinical Genetics Unit, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Van-Thanh Ta
- Center for Gene-Protein Research, Hanoi Medical University, Hanoi, Vietnam; Department of Biochemistry, Hanoi Medical University, Hanoi, Vietnam
| | - Van-Khanh Tran
- Center for Gene-Protein Research, Hanoi Medical University, Hanoi, Vietnam.
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Garcia S, de Haro T, Zafra-Ceres M, Poyatos A, Gomez-Capilla JA, Gomez-Llorente C. Identification of de novo mutations of Duchénnè/Becker muscular dystrophies in southern Spain. Int J Med Sci 2014; 11:988-93. [PMID: 25076844 PMCID: PMC4115237 DOI: 10.7150/ijms.8391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/12/2014] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Duchénnè/Becker muscular dystrophies (DMD/BMD) are X-linked diseases, which are caused by a de novo gene mutation in one-third of affected males. The study objectives were to determine the incidence of DMD/BMD in Andalusia (Spain) and to establish the percentage of affected males in whom a de novo gene mutation was responsible. METHODS Multiplex ligation-dependent probe amplification (MLPA) technology was applied to determine the incidence of DMD/BMD in 84 males with suspicion of the disease and 106 female relatives. RESULTS Dystrophin gene exon deletion (89.5%) or duplication (10.5%) was detected in 38 of the 84 males by MLPA technology; de novo mutations account for 4 (16.7%) of the 24 mother-son pairs studied. CONCLUSIONS MLPA technology is adequate for the molecular diagnosis of DMD/BMD and establishes whether the mother carries the molecular alteration responsible for the disease, a highly relevant issue for genetic counseling.
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Affiliation(s)
- Susana Garcia
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
| | - Tomás de Haro
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
- 2. Instituto de Investigación Biosanitaria ibs. Granada, Spain
| | - Mercedes Zafra-Ceres
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
| | - Antonio Poyatos
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
| | - Jose A. Gomez-Capilla
- 1. UGC Laboratorios Clínicos. Hospital Universitario San Cecilio. Avd/Doctor Olóriz s/n 18012 Granada, Spain
- 2. Instituto de Investigación Biosanitaria ibs. Granada, Spain
- 3. Departamento de Bioquímica y Biología Molecular III e Inmunología. Facultad de Medicina. Universidad de Granada. Avd/ Madrid s/n 18071, Granada, Spain
| | - Carolina Gomez-Llorente
- 4. Departamento de Bioquímica y Biología Molecular II. Instituto de Nutrición y Tecnología de los Alimentos “José Mataix”. Centro de Investigaciones Biomédicas. Universidad de Granada. Avd/ Conocimiento s/n 18100 Armilla, Granada, Spain
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Wang Y, Yang Y, Liu J, Chen XC, Liu X, Wang CZ, He XY. Whole dystrophin gene analysis by next-generation sequencing: a comprehensive genetic diagnosis of Duchenne and Becker muscular dystrophy. Mol Genet Genomics 2014; 289:1013-21. [DOI: 10.1007/s00438-014-0847-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 03/23/2014] [Indexed: 12/23/2022]
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Uwineza A, Hitayezu J, Murorunkwere S, Ndinkabandi J, Kalala Malu CK, Caberg JH, Dideberg V, Bours V, Mutesa L. Genetic diagnosis of Duchenne and Becker muscular dystrophy using multiplex ligation-dependent probe amplification in Rwandan patients. J Trop Pediatr 2014; 60:112-7. [PMID: 24213305 DOI: 10.1093/tropej/fmt090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Duchenne and Becker muscular dystrophies are the most common clinical forms of muscular dystrophies. They are genetically X-linked diseases caused by a mutation in the dystrophin (DMD) gene. A genetic diagnosis was carried out in six Rwandan patients presenting a phenotype of Duchenne and Becker muscular dystrophies and six asymptomatic female carrier relatives using multiplex ligation-dependent probe amplification (MLPA). Our results revealed deletion of the exons 48-51 in one patient, an inherited deletion of the exons 8-21 in two brothers and a de novo deletion of the exons 46-50 in the fourth patient. No copy number variation was found in two patients. Only one female carrier presented exon deletion in the DMD gene. This is the first cohort of genetic analysis in Rwandan patients affected by Duchenne and Becker muscular dystrophies. This report confirmed that MLPA assay can be easily implemented in low-income countries.
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Affiliation(s)
- Annette Uwineza
- Center for Medical Genetics, Department of Molecular Biology & Cytogenetics, Faculty of Medicine, National University of Rwanda, PO Box 30-Butare, Rwanda
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36
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Capillary electrophoresis for analysis of deletion and duplication in exon 44-55 of Duchenne muscular dystrophy gene. Electrophoresis 2013; 34:2503-10. [DOI: 10.1002/elps.201300207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 05/28/2013] [Accepted: 05/28/2013] [Indexed: 01/30/2023]
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Fukao T, Aoyama Y, Murase K, Hori T, Harijan RK, Wierenga RK, Boneh A, Kondo N. Development of MLPA for human ACAT1 gene and identification of a heterozygous Alu-mediated deletion of exons 3 and 4 in a patient with mitochondrial acetoacetyl-CoA thiolase (T2) deficiency. Mol Genet Metab 2013; 110:184-7. [PMID: 23920042 DOI: 10.1016/j.ymgme.2013.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/08/2013] [Accepted: 07/08/2013] [Indexed: 01/15/2023]
Abstract
Mitochondrial acetoacetyl-CoA thiolase deficiency is an autosomal recessive disorder, characterized by intermittent ketoacidosis. We developed a multiplex ligation-dependent probe amplification method for mutation detection in the ACAT1 gene, which encodes this enzyme, and validated it using DNAs from two previously reported patients having partial deletion and duplication in this gene. Using this method, we identified a heterozygous deletion including exons 3-4 in a third patient, likely due to Alu-mediated non-equal homologous recombination between Alu sequences.
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Affiliation(s)
- Toshiyuki Fukao
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan.
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Gatta V, Gennaro E, Franchi S, Cecconi M, Antonucci I, Tommasi M, Palka G, Coviello D, Stuppia L, Grasso M. MS-MLPA analysis for FMR1 gene: evaluation in a routine diagnostic setting. BMC MEDICAL GENETICS 2013; 14:79. [PMID: 23914933 PMCID: PMC3751107 DOI: 10.1186/1471-2350-14-79] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 07/23/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Fragile X Syndrome (FXS), the most common cause of familiar mental retardation, is associated in over 99% of cases to an expansion over 200 repeats of a CGG sequence in the 5' UTR of the FMR1 gene (Xq27.3), leading to the hypermethylation of the promoter. Molecular diagnosis of FXS have been so far based on the use of the Southern Blot (SB) analysis, a low throughput and time consuming technique. In order to update the diagnostic approach for FXS, we evaluated the usefulness of the Methylation-Specific Multiplex-Ligation-dependent Probe Amplification assay (MS-MLPA). METHODS The study was carried out by retrospectively analysing 44 male patients, 10 Chorionic Villus Sampling (CVS) samples and 10 females previously analyzed by SB. In addition, a prospective study on 98 male subjects, 20 females and 1 CVS sample was carried out for assessing the feasibility and the impact of MS-MLPA in a routine lab work. RESULT Results provided by both the retrospective and the prospective parts of this study strongly demonstrate the robustness and reproducibility of the MS-MLPA assay, able to correctly detect the methylation status in all normal and full mutation male samples analyzed, including CVS male samples. On the other hand, MS-MLPA analysis on females samples produced unreliable results. CONCLUSION Based on our results, we suggest the necessity of a separate workflow for male and female patients with suspected FXS in the routine diagnostic setting. MS-MLPA, in combination with CGG repeat sizing using a single-tube primed FMR1 PCR, represents a reliable diagnostic protocol in the molecular diagnosis of FXS male patients.
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Affiliation(s)
- Valentina Gatta
- Laboratory of Molecular Genetics, Department of Psychological, Humanities and Territorial Sciences, School of Medicine and Health Sciences, G, d'Annunzio University, via dei Vestini 31, Chieti, 66013, Italy.
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Clinical, immunohistochemical, Western blot, and genetic analysis in dystrophinopathy. J Clin Neurosci 2013; 20:1099-105. [DOI: 10.1016/j.jocn.2012.09.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 09/10/2012] [Accepted: 09/14/2012] [Indexed: 01/09/2023]
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40
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Yang J, Li SY, Li YQ, Cao JQ, Feng SW, Wang YY, Zhan YX, Yu CS, Chen F, Li J, Sun XF, Zhang C. MLPA-based genotype-phenotype analysis in 1053 Chinese patients with DMD/BMD. BMC MEDICAL GENETICS 2013; 14:29. [PMID: 23453023 PMCID: PMC3599358 DOI: 10.1186/1471-2350-14-29] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 02/08/2013] [Indexed: 12/23/2022]
Abstract
Background Large-scale analysis of the transmission, mutation characteristics and the relationship between the reading frame and phenotype of the DMD gene has previously been performed in several countries, however, analogous studies have yet to be performed in Chinese populations. Methods Clinical data from 1053 Chinese patients with DMD/BMD were collected, and the DMD gene was tested by MLPA in all patients and 400 proband mothers. In 20 patients with negative MLPA, sequencing was also performed. Results We found that 27.50% of cases had a family medical history of DMD/BMD, and large rearrangements were identified in 70.56% of the probands, of which 59.35% and 11.21% were deletions or duplications, respectively. The carrier status of the mothers in the study was determined to be 50.75%, and it was established that the DMD mutation was inherited from the mother in 51.72% of the probands. Exons 45–54 and 3–22 were the most frequently deleted regions, and exons 3–11 and 21–37 were the most prevalently duplicated regions of the gene. Breakpoints mainly occurred in introns 43–55 for deletion mutations and in introns 2 and 7 for duplication mutations. No breakpoints were found at the 5′ or 3′ end of introns 31, 35, 36, 40, 65, 68, and 74–78 in any of the deletion or duplication mutations. The reading frame rule held true for 86.4% of the DMD patients and 74.55% of the BMD patients. Conclusion It is essential to increase physicians’ understanding of DMD/BMD, to promote scientific information, and to increase awareness in regards to genetic counseling and prenatal diagnosis in pedigrees with a family history of the disease, particularly in families with small DMD lesions in China. In addition, such a large-scale analysis will prove to be instructive for leading translational studies between basic science and clinical medicine.
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Affiliation(s)
- Juan Yang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhong Shaner Road, Guangzhou City, 510080, People's Republic of China
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Improved Detection of Deletions and Duplications in the DMD Gene Using the Multiplex Ligation-Dependent Probe Amplification (MLPA) Method. Biochem Genet 2012; 51:189-201. [DOI: 10.1007/s10528-012-9554-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 08/01/2012] [Indexed: 11/27/2022]
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The muscular dystrophies. Neurogenetics 2012. [DOI: 10.1017/cbo9781139087711.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Stuppia L, Antonucci I, Palka G, Gatta V. Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases. Int J Mol Sci 2012; 13:3245-3276. [PMID: 22489151 PMCID: PMC3317712 DOI: 10.3390/ijms13033245] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/16/2022] Open
Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA) assay is a recently developed technique able to evidence variations in the copy number of several human genes. Due to this ability, MLPA can be used in the molecular diagnosis of several genetic diseases whose pathogenesis is related to the presence of deletions or duplications of specific genes. Moreover, MLPA assay can also be used in the molecular diagnosis of genetic diseases characterized by the presence of abnormal DNA methylation. Due to the large number of genes that can be analyzed by a single technique, MLPA assay represents the gold standard for molecular analysis of all pathologies derived from the presence of gene copy number variation. In this review, the main applications of the MLPA technique for the molecular diagnosis of human diseases are described.
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Affiliation(s)
- Liborio Stuppia
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Ivana Antonucci
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Giandomenico Palka
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Valentina Gatta
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
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Lee BL, Nam SH, Lee JH, Ki CS, Lee M, Lee J. Genetic analysis of dystrophin gene for affected male and female carriers with Duchenne/Becker muscular dystrophy in Korea. J Korean Med Sci 2012; 27:274-80. [PMID: 22379338 PMCID: PMC3286774 DOI: 10.3346/jkms.2012.27.3.274] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 12/12/2011] [Indexed: 01/23/2023] Open
Abstract
Duchenne and Becker muscular dystrophy (DMD/BMD) are X-linked recessive disorders caused by mutation in dystrophin gene. We analyzed the results of a genetic test in 29 DMD/BMD patients, their six female relatives, and two myopathic female patients in Korea. As the methods developed, we applied different procedures for dystrophin gene analysis; initially, multiplex polymerase chain reaction was used, followed by multiplex ligation-dependent probe amplification (MLPA). Additionally, we used direct DNA sequencing for some patients who had negative results using the above methods. The overall mutation detection rate was 72.4% (21/29) in DMD/BMD patients, identifying deletions in 58.6% (17/29). Most of the deletions were confined to the central hot spot region between exons 44 and 55 (52.9%, 7/19). The percentage of deletions and duplications revealed by MLPA was 45.5% (5/11) and 27.2% (3/11), respectively. Using the MLPA method, we detected mutations confirming their carrier status in all female relatives and symptomatic female patients. In one patient in whom MLPA revealed a single exon deletion of the dystrophin gene, subsequent DNA sequencing analysis identified a novel nonsense mutation (c.4558G > T; Gln1520X). The MLPA assay is a useful quantitative method for detecting mutation in asymptomatic or symptomatic carriers as well as DMD/BMD patients.
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Affiliation(s)
- Bo Lyun Lee
- Department of Pediatrics, Pusan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Sook Hyun Nam
- Department of Pediatrics, Eulji General Hospital, Seoul, Korea
| | - Jun Hwa Lee
- Department of Pediatrics, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Chang Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Munhyang Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Khordadpoor-Deilamani F, Akbari MT, Nafissi S, Zamani G. Dystrophin Gene Mutation Analysis in Iranian Males and Females Using Multiplex Polymerase Chain Reaction and Multiplex Ligation-Dependent Probe Amplification Methods. Genet Test Mol Biomarkers 2011; 15:893-9. [DOI: 10.1089/gtmb.2011.0057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Mohammad Taghi Akbari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- Tehran Medical Genetics Laboratory, Tehran, Iran
| | - Shahriar Nafissi
- Department of Neurology, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Gholamreza Zamani
- Division of Child Neurology, Tehran University of Medical Sciences (TUMS), Tehran, Iran
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Yan JB, Xu M, Xiong C, Zhou DW, Ren ZR, Huang Y, Mommersteeg M, van Beuningen R, Wang YT, Liao SX, Zeng F, Wu Y, Zeng YT. Rapid screening for chromosomal aneuploidies using array-MLPA. BMC MEDICAL GENETICS 2011; 12:68. [PMID: 21575262 PMCID: PMC3111339 DOI: 10.1186/1471-2350-12-68] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/17/2011] [Indexed: 11/23/2022]
Abstract
Background Chromosome abnormalities, especially trisomy of chromosome 21, 13, or 18 as well as sex chromosome aneuploidy, are a well-established cause of pregnancy loss. Cultured cell karyotype analysis and FISH have been considered reliable detectors of fetal abnormality. However, results are usually not available for 3-4 days or more. Multiplex ligation-dependent probe amplification (MLPA) has emerged as an alternative rapid technique for detection of chromosome aneuploidies. However, conventional MLPA does not allow for relative quantification of more than 50 different target sequences in one reaction and does not detect mosaic trisomy. A multiplexed MLPA with more sensitive detection would be useful for fetal genetic screening. Methods We developed a method of array-based MLPA to rapidly screen for common aneuploidies. We designed 116 universal tag-probes covering chromosomes 13, 18, 21, X, and Y, and 8 control autosomal genes. We performed MLPA and hybridized the products on a 4-well flow-through microarray system. We determined chromosome copy numbers by analyzing the relative signals of the chromosome-specific probes. Results In a blind study of 161 peripheral blood and 12 amniotic fluid samples previously karyotyped, 169 of 173 (97.7%) including all the amniotic fluid samples were correctly identified by array-MLPA. Furthermore, we detected two chromosome X monosomy mosaic cases in which the mosaism rates estimated by array-MLPA were basically consistent with the results from karyotyping. Additionally, we identified five Y chromosome abnormalities in which G-banding could not distinguish their origins for four of the five cases. Conclusions Our study demonstrates the successful application and strong potential of array-MLPA in clinical diagnosis and prenatal testing for rapid and sensitive chromosomal aneuploidy screening. Furthermore, we have developed a simple and rapid procedure for screening copy numbers on chromosomes 13, 18, 21, X, and Y using array-MLPA.
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Affiliation(s)
- Jing-Bin Yan
- Institute of Medical Genetics, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai, P.R. China
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Yoon J, Kim SH, Ki CS, Kwon MJ, Lim MJ, Kwon SR, Joo K, Moon CG, Park W. Carrier woman of Duchenne muscular dystrophy mimicking inflammatory myositis. J Korean Med Sci 2011; 26:587-91. [PMID: 21468271 PMCID: PMC3069583 DOI: 10.3346/jkms.2011.26.4.587] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 12/06/2010] [Indexed: 11/20/2022] Open
Abstract
Carrier woman of Duchenne muscular dystrophy (DMD) can mimic the inflammatory myositis in presenting symptoms. Two diseases should be differentiated by the clinical history, muscle biopsy and genetic study. There are few reports in which both histochemical and genetic study showed the possible link of overlapping inflammatory pathophysiology with dystrophinopathy. We report a 40-yr-old woman who presented with subacute proximal muscle weakness and high serum level of creatine kinase. She had a history of Graves' disease and fluctuation of serum liver aminotransferase without definite cause. MRI, EMG and NCV were compatible with proximal muscle myopathy. Muscle biopsy on vastus lateralis showed suspicious perifascicular atrophy and infiltration of mono-macrophage lineage cells complicating the diagnosis. Dystrophin staining showed heterogeneous diverse findings from normal to interrupted mosaic pattern. Multiple ligation probe amplification and X chromosome inactivation test confirmed DMD gene deletion mutation in exon 44 and highly skewed X inactivation.
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Affiliation(s)
- Jiyeol Yoon
- Division of Rheumatology, Department of Internal Medicine, Inha University Hospital, Incheon, Korea
| | - Se Hoon Kim
- Department of Pathology, College of Medicine, Yonsei University, Seoul, Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Min-Jung Kwon
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mie-Jin Lim
- Division of Rheumatology, Department of Internal Medicine, Inha University Hospital, Incheon, Korea
| | - Seong-Ryul Kwon
- Division of Rheumatology, Department of Internal Medicine, Inha University Hospital, Incheon, Korea
| | - Kowoon Joo
- Division of Rheumatology, Department of Internal Medicine, Inha University Hospital, Incheon, Korea
| | - Chang-Gi Moon
- Division of Rheumatology, Department of Internal Medicine, Inha University Hospital, Incheon, Korea
| | - Won Park
- Division of Rheumatology, Department of Internal Medicine, Inha University Hospital, Incheon, Korea
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Alaeddini R, Ahmadi M, Walsh SJ, Abbas A. Semi-quantitative PCR Analysis of DNA Degradation. AUST J FORENSIC SCI 2011. [DOI: 10.1080/00450618.2010.498026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Song MH, Lee HK, Choi JY, Kim S, Bok J, Kim UK. Clinical evaluation of DFN3 patients with deletions in the POU3F4 locus and detection of carrier female using MLPA. Clin Genet 2011; 78:524-32. [PMID: 20412083 DOI: 10.1111/j.1399-0004.2010.01426.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
X-linked deafness type 3 (DFN3), the most prevalent X-linked form of hereditary deafness, is caused by mutations of the POU3F4 locus in the Xq21 region. We evaluated two Korean families showing typical characteristics of DFN3, such as congenital hearing loss and pathognomonic inner ear anomalies. Genetic analysis of these families did not reveal any mutations in the POU3F4 coding sequence. Instead, one family carried a genomic deletion upstream of POU3F4 gene, where the regulatory element is predicted to reside, and the other family possessed a deletion of almost the entire Xq21 region. The lack of mutation in the POU3F4 coding sequence makes the detection of carrier females using conventional sequencing methods difficult. By applying the multiplex ligation-dependent probe amplification (MLPA) method, we successfully determined the carrier status of female members in these families, demonstrating that MLPA is a rapid and accurate way to detect POU3F4 deletions in sporadic undiagnosed carriers of DNF3.
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Affiliation(s)
- M H Song
- Department of Otorhinolaryngology, Kwandong University College of Medicine, Goyang, South Korea
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Identification of the second CFTR mutation in patients with congenital bilateral absence of vas deferens undergoing ART protocols. Asian J Androl 2010; 12:819-26. [PMID: 20657600 DOI: 10.1038/aja.2010.58] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Congenital bilateral absence of vas deferens (CBAVD) is a manifestation of the mildest form of cystic fibrosis (CF) and is characterized by obstructive azoospermia in otherwise healthy patients. Owing to the availability of assisted reproductive technology, CBAVD patients can father children. These fathers are at risk of transmitting a mutated allele of the CF transmembrane conductance regulator (CFTR) gene, responsible for CF, to their offspring. The identification of mutations in both CFTR alleles in CBAVD patients is a crucial requirement for calculating the risk of producing a child with full-blown CF if the female partner is a healthy CF carrier. However, in the majority of CBAVD patients, conventional mutation screening is not able to detect mutations in both CFTR alleles, and this difficulty hampers the execution of correct genetic counselling. To obtain information about the most represented CFTR mutations in CBAVD patients, we analysed 23 CBAVD patients, 15 of whom had a single CFTR mutation after screening for 36 mutations and the 5T allele. The search for the second CFTR mutation in these cases was performed by using a triplex approach: (i) first, a reverse dot-blot analysis was performed to detect mutations with regional impact; (ii) next, multiple ligation-dependent probe amplification assays were conducted to search for large rearrangements; and (iii) finally, denaturing high-performance liquid chromatography was used to search for point mutations in the entire coding region. Using these approaches, the second CFTR mutation was detected in six patients, which increased the final detection rate to 60.8%.
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