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Gaina G, Vossen RHAM, Manole E, Plesca DA, Ionica E. Combining Protein Expression and Molecular Data Improves Mutation Characterization of Dystrophinopathies. Front Neurol 2021; 12:718396. [PMID: 34950096 PMCID: PMC8689184 DOI: 10.3389/fneur.2021.718396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Duchenne and Becker muscular dystrophy are X-linked recessive inherited disorders characterized by progressive weakness due to skeletal muscle degeneration. Different mutations in the DMD gene, which encodes for dystrophin protein, are responsible for these disorders. The aim of our study was to investigate the relationship between type, size, and location of the mutation that occurs in the DMD gene and their effect on dystrophin protein expression in a cohort of 40 male dystrophinopathy patients and nine females, possible carriers. We evaluated the expression of dystrophin by immunofluorescence and immunoblotting. The mutational spectrum of the DMD gene was established by MLPA for large copy number variants, followed by HRM analysis for point mutations and sequencing of samples with an abnormal melting profile. MLPA revealed 30 deletions (75%) and three duplications (7.5%). HRM analysis accounted for seven-point mutations (17.5%). We also report four novel small mutations (c. 8507G>T, c.3021delG, c.9563_9563+1insAGCATGTTTATGATACAGCA, c.7661-60T>A) in DMD gene. Our work shows that the DNA translational open reading frame and the location of the mutation both influence the expression of dystrophin and disease severity phenotype. The proposed algorithm used in this study demonstrates its accuracy for the characterization of dystrophinopathy patients.
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Affiliation(s)
- Gisela Gaina
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, Bucharest, Romania
- *Correspondence: Gisela Gaina ;
| | - Rolf H. A. M. Vossen
- Center for Human and Clinical Genetics, Leiden Genome Technology Center, Leiden, Netherlands
| | - Emilia Manole
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, Bucharest, Romania
- Colentina Clinical Hospital, Bucharest, Romania
| | - Doina Anca Plesca
- Department of Pediatrics, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- Department of Clinical Pediatrics, Victor Gomoiu Children Clinical Hospital, Bucharest, Romania
| | - Elena Ionica
- Department of Biochemistry and Molecular Biology, University of Bucharest, Bucharest, Romania
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2
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Gazali FM, Nuhamunada M, Nabilla R, Supriyati E, Hakim MS, Arguni E, Daniwijaya EW, Nuryastuti T, Haryana SM, Wibawa T, Wijayanti N. Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Heliyon 2021; 7:e07936. [PMID: 34514180 PMCID: PMC8420086 DOI: 10.1016/j.heliyon.2021.e07936] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Monitoring the spread of the G614 in specific locations is critical as this variant is highly transmissible and can trigger the emergence of other mutations. Therefore, a rapid and accurate method that can reliably detect the D614G mutation will be beneficial. This study aims to analyze the potential use of the two-step Reverse Transcriptase quantitative polymerase chain reaction - high resolution melting analysis (RT-qPCR-HRM) to detect a specific mutation in the SARS-CoV-2 genome. METHODS Six SARS-CoV-2 RNA samples were synthesized into cDNA and analyzed with the qPCR-HRM method in order to detect the D614G mutation in Spike protein of SARS-CoV-2. The primers are designed to target the specific Spike region containing the D614G mutation. The qPCR-HRM analysis was conducted simultaneously, and the identification of the SARS-CoV-2 variant was confirmed by conventional PCR and Sanger sequencing methods. RESULTS The results showed that the melting temperature (Tm) of the D614 variant was 79.39 ± 0.03 °C, which was slightly lower than the Tm of the G614 variant (79.62 ± 0.015 °C). The results of the HRM analysis, visualized by the normalized melting curve and the difference curve were able to discriminate the D614 and G614 variant samples. All samples were identified as G614 variants by qPCR-HRM assay, which was subsequently confirmed by Sanger sequencing. CONCLUSIONS This study demonstrated a sensitive method that can identify the D614G mutation by a simple two-step RT-qPCR-HRM assay procedure analysis, which can be useful for active surveillance of the transmission of a specific mutation.
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Affiliation(s)
- Faris Muhammad Gazali
- Master Program in Biotechnology Study Program, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Matin Nuhamunada
- Biotechnology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rahma Nabilla
- Graduate Program in Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Diagnostic Laboratory of World Mosquito Program (WMP), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nastiti Wijayanti
- Animal Physiology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
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The sensitivity of exome sequencing in identifying pathogenic mutations for LGMD in the United States. J Hum Genet 2016; 62:243-252. [PMID: 27708273 PMCID: PMC5266644 DOI: 10.1038/jhg.2016.116] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 01/12/2023]
Abstract
The current study characterizes a cohort of limb-girdle muscular dystrophy (LGMD) in the United States using whole exome sequencing. Fifty-five families affected by LGMD were recruited using an institutionally-approved protocol. Exome sequencing was performed on probands and selected parental samples. Pathogenic mutations and co-segregation patterns were confirmed by Sanger sequencing. Twenty-two families (40%) had novel and previously reported pathogenic mutations, primarily in LGMD genes, but also in genes for Duchenne muscular dystrophy, facioscapulohumeral muscular dystrophy, congenital myopathy, myofibrillar myopathy, inclusion body myopathy, and Pompe disease. One family was diagnosed via clinical testing. Dominant mutations were identified in COL6A1, COL6A3, FLNC, LMNA, RYR1, SMCHD1, and VCP, recessive mutations in ANO5, CAPN3, GAA, LAMA2, SGCA, and SGCG, and X-linked mutations in DMD. A previously reported variant in DMD was confirmed to be benign. Exome sequencing is a powerful diagnostic tool for LGMD. Despite careful phenotypic screening, pathogenic mutations were found in other muscle disease genes, largely accounting for the increased sensitivity of exome sequencing. Our experience suggests that broad sequencing panels are useful for these analyses due to the phenotypic overlap of many neuromuscular conditions. The confirmation of a benign DMD variant illustrates the potential of exome sequencing to help determine pathogenicity.
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Meregalli M, Maciotta S, Angeloni V, Torrente Y. Duchenne muscular dystrophy caused by a frame-shift mutation in the acceptor splice site of intron 26. BMC MEDICAL GENETICS 2016; 17:55. [PMID: 27515321 PMCID: PMC4982232 DOI: 10.1186/s12881-016-0318-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 07/28/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND The dystrophin gene is the one of the largest described in human beings and mutations associated to this gene are responsible for Duchenne or Becker muscular dystrophies. CASE PRESENTATION Here we describe a nucleotide substitution in the acceptor splice site of intron 26 (c.3604-1G > C) carried by a 6-year-old boy who presented with a history of progressive proximal muscle weakness and elevated serum creatine kinase levels. RNA analysis showed that the first two nucleotides of the mutated intron 26 (AC) were not recognized by the splicing machinery and a new splicing site was created within exon 27, generating a premature stop codon and avoiding protein translation. CONCLUSIONS The evaluation of the pathogenic effect of the mutation by mRNA analysis will be useful in the optics of an antisense oligonucleotides (AON)-based therapy.
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Affiliation(s)
- Mirella Meregalli
- Department of Phatophysiology and Transplantation, Stem Cell Laboratory, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Centro Dino Ferrari, via F. Sforza 35, 20122, Milan, Italy
| | - Simona Maciotta
- Department of Phatophysiology and Transplantation, Stem Cell Laboratory, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Centro Dino Ferrari, via F. Sforza 35, 20122, Milan, Italy
| | - Valentina Angeloni
- Department of Phatophysiology and Transplantation, Stem Cell Laboratory, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Centro Dino Ferrari, via F. Sforza 35, 20122, Milan, Italy
| | - Yvan Torrente
- Department of Phatophysiology and Transplantation, Stem Cell Laboratory, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Centro Dino Ferrari, via F. Sforza 35, 20122, Milan, Italy.
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Haghshenas M, Akbari MT, Karizi SZ, Deilamani FK, Nafissi S, Salehi Z. Evaluation of point mutations in dystrophin gene in Iranian Duchenne and Becker muscular dystrophy patients: introducing three novel variants. J Genet 2016; 95:325-9. [PMID: 27350676 DOI: 10.1007/s12041-016-0641-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Duchenne and Becker muscular dystrophies (DMD and BMD) are X-linked neuromuscular diseases characterized by progressive muscular weakness and degeneration of skeletal muscles. Approximately two-thirds of the patients have large deletions or duplications in the dystrophin gene and the remaining one-third have point mutations. This study was performed to evaluate point mutations in Iranian DMD/BMD male patients. A total of 29 DNA samples from patients who did not show any large deletion/duplication mutations following multiplex polymerase chain reaction (PCR) and multiplex ligation-dependent probe amplification (MLPA) screening were sequenced for detection of point mutations in exons 50-79. Also exon 44 was sequenced in one sample in which a false positive deletion was detected by MLPA method. Cycle sequencing revealed four nonsense, one frameshift and two splice site mutations as well as two missense variants.
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Affiliation(s)
- Maryam Haghshenas
- Faculty of Sciences, Department of Biology, University of Guilan, Rasht 4199613776,
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High-resolution melting (HRM) re-analysis of a polyposis patients cohort reveals previously undetected heterozygous and mosaic APC gene mutations. Fam Cancer 2016; 14:247-57. [PMID: 25604157 PMCID: PMC4430602 DOI: 10.1007/s10689-015-9780-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Familial adenomatous polyposis is most frequently caused by pathogenic variants in either the APC gene or the MUTYH gene. The detection rate of pathogenic variants depends on the severity of the phenotype and sensitivity of the screening method, including sensitivity for mosaic variants. For 171 patients with multiple colorectal polyps without previously detectable pathogenic variant, APC was reanalyzed in leukocyte DNA by one uniform technique: high-resolution melting (HRM) analysis. Serial dilution of heterozygous DNA resulted in a lowest detectable allelic fraction of 6 % for the majority of variants. HRM analysis and subsequent sequencing detected pathogenic fully heterozygous APC variants in 10 (6 %) of the patients and pathogenic mosaic variants in 2 (1 %). All these variants were previously missed by various conventional scanning methods. In parallel, HRM APC scanning was applied to DNA isolated from polyp tissue of two additional patients with apparently sporadic polyposis and without detectable pathogenic APC variant in leukocyte DNA. In both patients a pathogenic mosaic APC variant was present in multiple polyps. The detection of pathogenic APC variants in 7 % of the patients, including mosaics, illustrates the usefulness of a complete APC gene reanalysis of previously tested patients, by a supplementary scanning method. HRM is a sensitive and fast pre-screening method for reliable detection of heterozygous and mosaic variants, which can be applied to leukocyte and polyp derived DNA.
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van den Oever JM, van Minderhout IJ, Harteveld CL, den Hollander NS, Bakker E, van der Stoep N, Boon EM. A Novel Targeted Approach for Noninvasive Detection of Paternally Inherited Mutations in Maternal Plasma. J Mol Diagn 2015; 17:590-6. [DOI: 10.1016/j.jmoldx.2015.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/21/2015] [Accepted: 05/11/2015] [Indexed: 12/12/2022] Open
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Straathof CSM, Van Heusden D, Ippel PF, Post JG, Voermans NC, De Visser M, Brusse E, Van Den Bergen JC, Van Der Kooi AJ, Verschuuren JJGM, Ginjaar HB. Diagnosis of becker muscular dystrophy: Results of Re-analysis of DNA samples. Muscle Nerve 2015; 53:44-8. [PMID: 25900853 DOI: 10.1002/mus.24691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2015] [Indexed: 11/08/2022]
Abstract
INTRODUCTION The phenotype of Becker muscular dystrophy (BMD) is highly variable, and the disease may be underdiagnosed. We searched for new mutations in the DMD gene in a cohort of previously undiagnosed patients who had been referred in the period 1985-1995. METHODS All requests for DNA analysis of the DMD gene in probands with suspected BMD were re-evaluated. If the phenotype was compatible with BMD, and no deletions or duplications were detected, DNA samples were screened for small mutations. RESULTS In 79 of 185 referrals, no mutation was found. Analysis could be performed on 31 DNA samples. Seven different mutations, including 3 novel ones, were found. Long-term clinical follow-up is described. CONCLUSIONS Refining DNA analysis in previously undiagnosed cases can identify mutations in the DMD gene and provide genetic diagnosis of BMD. A delayed diagnosis can still be valuable for the proband or the relatives of BMD patients.
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Affiliation(s)
- Chiara S M Straathof
- Department of Neurology, Leiden University Medical Center, P.O. Box 9600, 2300RC, Leiden, The Netherlands
| | - Dave Van Heusden
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pieternella F Ippel
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan G Post
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nicol C Voermans
- Department of Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marianne De Visser
- Department of Neurology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Esther Brusse
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Janneke C Van Den Bergen
- Department of Neurology, Leiden University Medical Center, P.O. Box 9600, 2300RC, Leiden, The Netherlands
| | - Anneke J Van Der Kooi
- Department of Neurology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan J G M Verschuuren
- Department of Neurology, Leiden University Medical Center, P.O. Box 9600, 2300RC, Leiden, The Netherlands
| | - Hendrika B Ginjaar
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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9
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Comparison of mutation profiles in the Duchenne muscular dystrophy gene among populations: implications for potential molecular therapies. Int J Mol Sci 2015; 16:5334-46. [PMID: 25761239 PMCID: PMC4394478 DOI: 10.3390/ijms16035334] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/17/2015] [Accepted: 02/27/2015] [Indexed: 11/16/2022] Open
Abstract
Novel therapeutic approaches are emerging to restore dystrophin function in Duchenne Muscular Dystrophy (DMD), a severe neuromuscular disease characterized by progressive muscle wasting and weakness. Some of the molecular therapies, such as exon skipping, stop codon read-through and internal ribosome entry site-mediated translation rely on the type and location of mutations. Hence, their potential applicability worldwide depends on mutation frequencies within populations. In view of this, we compared the mutation profiles of the populations represented in the DMD Leiden Open-source Variation Database with original data from Mexican patients (n = 162) with clinical diagnosis of the disease. Our data confirm that applicability of exon 51 is high in most populations, but also show that differences in theoretical applicability of exon skipping may exist among populations; Mexico has the highest frequency of potential candidates for the skipping of exons 44 and 46, which is different from other populations (p < 0.001). To our knowledge, this is the first comprehensive comparison of theoretical applicability of exon skipping targets among specific populations.
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Ji X, Zhang J, Xu Y, Long F, Sun W, Liu X, Chen Y, Jiang W. MLPA Application in Clinical Diagnosis of DMD/BMD in Shanghai. J Clin Lab Anal 2014; 29:405-11. [PMID: 25131993 DOI: 10.1002/jcla.21787] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/21/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Duchenne and Becker muscular dystrophy (DMD/BMD) are X-linked recessive disorders caused by mutation in dystrophin gene. We reported 3-year clinic experience from a single hospital in Shanghai using multiplex ligation dependent probe amplification (MLPA) assay to detect DMD mutations. METHODS Four hundred and fifty-one males and 184 females, who were clinically diagnosed as DMD/BMD patients or carriers at our hospital's outpatient clinic, were collected and performed with MLPA to detect DMD gene mutations. RESULTS Seventeen novel mutation points not reported in the Leiden Muscular Dystrophy pages were identified in this study. We found that the most frequent deletion spots ranged from exon45 to exon52, and exon2, exon19 were the two most frequently detected duplication spots. CONCLUSION The results of our study confirmed MLPA as an efficient clinical method for detecting DMD gene mutations in DMD/BMD patients. Single exon mutation detected by MLPA should be verified by other methods, and we should emphasize that only precise clinical molecular diagnosis can lead to the feasibility of prenatal diagnosis.
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Affiliation(s)
- Xing Ji
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jingmin Zhang
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yan Xu
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Fei Long
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wei Sun
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xiaoqin Liu
- Shanghai Institute for Pediatric Research, Shanghai, China.,Department of Neurology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingwei Chen
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wenting Jiang
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
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Doorenweerd N, Straathof CS, Dumas EM, Spitali P, Ginjaar IB, Wokke BH, Schrans DG, van den Bergen JC, van Zwet EW, Webb A, van Buchem MA, Verschuuren JJ, Hendriksen JG, Niks EH, Kan HE. Reduced cerebral gray matter and altered white matter in boys with Duchenne muscular dystrophy. Ann Neurol 2014; 76:403-11. [DOI: 10.1002/ana.24222] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/08/2014] [Accepted: 07/08/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Nathalie Doorenweerd
- Department of Radiology; C. J. Gorter Center for High Field MRI, Leiden University Medical Center; Leiden
- Leiden Institute for Brain and Cognition; Leiden
- Department of Neurology; Leiden University Medical Center; Leiden
| | | | - Eve M. Dumas
- Department of Neurology; Leiden University Medical Center; Leiden
| | - Pietro Spitali
- Department of Human Genetics; Leiden University Medical Center; Leiden
| | - Ieke B. Ginjaar
- Department of Clinical Genetics; Leiden University Medical Center; Leiden
| | | | - Debby G. Schrans
- Department of Neurological Learning Disabilities; Kempenhaeghe Epilepsy Center; Heeze
| | | | - Erik W. van Zwet
- Department of Medical Statistics; Leiden University Medical Center; Leiden
| | - Andrew Webb
- Department of Radiology; C. J. Gorter Center for High Field MRI, Leiden University Medical Center; Leiden
| | - Mark A. van Buchem
- Department of Radiology; C. J. Gorter Center for High Field MRI, Leiden University Medical Center; Leiden
| | | | - Jos G. Hendriksen
- Department of Neurological Learning Disabilities; Kempenhaeghe Epilepsy Center; Heeze
- Department of Neurology; Maastricht University Medical Center; Maastricht the Netherlands
| | - Erik H. Niks
- Department of Neurology; Leiden University Medical Center; Leiden
| | - Hermien E. Kan
- Department of Radiology; C. J. Gorter Center for High Field MRI, Leiden University Medical Center; Leiden
- Leiden Institute for Brain and Cognition; Leiden
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van Spaendonck-Zwarts KY, van Rijsingen IA, van den Berg MP, Lekanne Deprez RH, Post JG, van Mil AM, Asselbergs FW, Christiaans I, van Langen IM, Wilde AA, de Boer RA, Jongbloed JD, Pinto YM, van Tintelen JP. Genetic analysis in 418 index patients with idiopathic dilated cardiomyopathy: overview of 10 years' experience. Eur J Heart Fail 2014; 15:628-36. [DOI: 10.1093/eurjhf/hft013] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Karin Y. van Spaendonck-Zwarts
- Department of Genetics, University of Groningen; University Medical Centre Groningen; PO Box 30001 9700 RB Groningen The Netherlands
- Department of Genetics, Academic Medical Centre; University of Amsterdam; The Netherlands
| | | | - Maarten P. van den Berg
- Department of Cardiology, University of Groningen; University Medical Centre Groningen; The Netherlands
| | | | - Jan G. Post
- Department of Medical Genetics, University Medical Centre Utrecht; University of Utrecht; The Netherlands
| | - Anneke M. van Mil
- Department of Genetics, University Medical Centre Leiden; University of Leiden; The Netherlands
| | - Folkert W. Asselbergs
- Department of Cardiology, Heart and Lungs Division; University Medical Centre Utrecht, University of Utrecht; The Netherlands
| | - Imke Christiaans
- Department of Genetics, Academic Medical Centre; University of Amsterdam; The Netherlands
| | - Irene M. van Langen
- Department of Genetics, University of Groningen; University Medical Centre Groningen; PO Box 30001 9700 RB Groningen The Netherlands
| | - Arthur A.M. Wilde
- Department of Cardiology, Academic Medical Centre; University of Amsterdam; The Netherlands
| | - Rudolf A. de Boer
- Department of Cardiology, University of Groningen; University Medical Centre Groningen; The Netherlands
| | - Jan D.H. Jongbloed
- Department of Genetics, University of Groningen; University Medical Centre Groningen; PO Box 30001 9700 RB Groningen The Netherlands
| | - Yigal M. Pinto
- Department of Cardiology, Academic Medical Centre; University of Amsterdam; The Netherlands
| | - J. Peter van Tintelen
- Department of Genetics, University of Groningen; University Medical Centre Groningen; PO Box 30001 9700 RB Groningen The Netherlands
- Durrer Centre for Cardiogenetic Research; Utrecht The Netherlands
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13
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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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A Streamlined Protocol for Molecular Testing of the DMD Gene within a Diagnostic Laboratory: A Combination of Array Comparative Genomic Hybridization and Bidirectional Sequence Analysis. ISRN NEUROLOGY 2013; 2013:908317. [PMID: 23476807 PMCID: PMC3583148 DOI: 10.1155/2013/908317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 12/30/2012] [Indexed: 12/27/2022]
Abstract
Purpose. The aim of this study was to develop a streamlined mutation screening protocol for the DMD gene in order to confirm a clinical diagnosis of Duchenne or Becker muscular dystrophy in affected males and to clarify the carrier status of female family members. Methods. Sequence analysis and array comparative genomic hybridization (aCGH) were used to identify mutations in the dystrophin DMD gene. We analysed genomic DNA from six individuals with a range of previously characterised mutations and from eight individuals who had not previously undergone any form of molecular analysis. Results. We successfully identified the known mutations in all six patients. A molecular diagnosis was also made in three of the four patients with a clinical diagnosis who had not undergone prior genetic screening, and testing for familial mutations was successfully completed for the remaining four patients. Conclusion. The mutation screening protocol described here meets best practice guidelines for molecular testing of the DMD gene in a diagnostic laboratory. The aCGH method is a superior alternative to more conventional assays such as multiplex ligation-dependent probe amplification (MLPA). The combination of aCGH and sequence analysis will detect mutations in 98% of patients with the Duchenne or Becker muscular dystrophy.
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Helderman-van den Enden ATJM, Madan K, Breuning MH, van der Hout AH, Bakker E, de Die-Smulders CEM, Ginjaar HB. An urgent need for a change in policy revealed by a study on prenatal testing for Duchenne muscular dystrophy. Eur J Hum Genet 2013; 21:21-6. [PMID: 22669413 PMCID: PMC3522203 DOI: 10.1038/ejhg.2012.101] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 04/03/2012] [Accepted: 04/26/2012] [Indexed: 11/22/2022] Open
Abstract
Prenatal diagnosis for Duchenne muscular dystrophy (DMD) was introduced in the Netherlands in 1984. We have investigated the impact of 26 years (1984-2009) of prenatal testing. Of the 635 prenatal diagnoses, 51% were males; nearly half (46%) of these were affected or had an increased risk of DMD. As a result 145 male fetuses were aborted and 174 unaffected boys were born. The vast majority (78%) of females, now 16 years or older, who were identified prenatally have not been tested for carrier status. Their average risk of being a carrier is 28%. We compared the incidences of DMD in the periods 1961-1974 and 1993-2002. The incidence of DMD did not decline but the percentage of first affected boys increased from 62 to 88%. We conclude that a high proportion of families with de novo mutations in the DMD gene cannot make use of prenatal diagnosis, partly because the older affected boys are not diagnosed before the age of five. Current policy, widely accepted in the genetic community, dictates that female fetuses are not tested for carrier status. These females remain untested as adults and risk having affected offspring as well as progressive cardiac disease. We see an urgent need for a change in policy to improve the chances of prevention of DMD. The first step would be to introduce neonatal screening of males. The next is to test females for carrier status if requested, prenatally if fetal DNA is available or postnatally even before adulthood.
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Er TK, Chang JG. High-resolution melting: applications in genetic disorders. Clin Chim Acta 2012; 414:197-201. [PMID: 22995429 DOI: 10.1016/j.cca.2012.09.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 09/08/2012] [Accepted: 09/08/2012] [Indexed: 12/16/2022]
Abstract
High-resolution melting (HRM) analysis is a feasible and powerful method for mutation scanning of sequence variants. Denatured doubled-stranded DNA can be detected in fluorescence changes by increasing the melting temperature and wild-type and heterozygous samples can be easily differentiated in the melting plots. HRM analysis represents the next generation of mutation-scanning technology and offers considerable time and cost savings compared to other screening methods. HRM analysis is a closed-tube method, indicating that polymerase chain reaction amplification and subsequent analysis are sequentially performed in the well, making HRM analysis more convenient than other scanning methodologies. Taken together, HRM analysis can be used for high-throughput mutation screening for research, as well as for molecular diagnostic and clinical purposes. This review summarizes the effectiveness of HRM analysis in the diagnosis of autosomal recessive, dominant, and X-linked genetic disorders. Notably, we will also discuss the limitations of HRM analysis and how to overcome them.
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Affiliation(s)
- Tze-Kiong Er
- Division of Molecular Diagnostics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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Gómez-Díaz B, Rosas-Vargas H, Roque-Ramírez B, Meza-Espinoza P, Ruano-Calderón LA, Fernández-Valverde F, Escalante-Bautista D, Escobar-Cedillo RE, Sánchez-Chapul L, Vargas-Cañas S, López-Hernández LB, Bahena-Martínez E, Luna-Angulo AB, Canto P, Coral-Vázquez RM. Immunodetection analysis of muscular dystrophies in Mexico. Muscle Nerve 2012; 45:338-45. [DOI: 10.1002/mus.22314] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Benej M, Bendlova B, Vaclavikova E, Poturnajova M. Establishing high resolution melting analysis: method validation and evaluation for c-RET proto-oncogene mutation screening. Clin Chem Lab Med 2012; 50:51-60. [DOI: 10.1515/cclm.2011.730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 09/05/2011] [Indexed: 11/15/2022]
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Broman M, Heinecke K, Islander G, Schuster F, Glahn K, Bodelsson M, Treves S, Müller C. Screening of the ryanodine 1 gene for malignant hyperthermia causative mutations by high resolution melt curve analysis. Anesth Analg 2011; 113:1120-8. [PMID: 21965348 DOI: 10.1213/ane.0b013e318228293e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND A diagnosis of malignant hyperthermia (MH) can be determined by performing an in vitro (muscle) contracture test (IVCT) or by identifying a known MH causative mutation in the ryanodine receptor 1 gene (RYR1). Genetic diagnosis has an advantage over IVCT because it is less invasive. Direct sequencing of the very large RYR1 coding region (15.117 bases) is a laborious and expensive task. In this study, we applied the High Resolution Melting (HRM) curve analysis as a tool to screen the entire coding region of the gene. METHODS Genomic DNA was extracted from peripheral blood samples in a cohort of 16 MH-susceptible patients diagnosed by the IVCT. The total coding region of RYR1 was divided and amplified by polymerase chain reaction in 131 DNA fragments and the melting profiles were compared with those of control samples. HRM curves were evaluated by Rotor-Gene Q software and visual inspection. Fragments showing aberrant melting profiles were sequenced to identify the underlying sequence variation. RESULTS A subset of 520 of 2520 DNA fragments (21%) showed significantly aberrant melting profiles. Upon sequencing, 131 known polymorphisms and 17 known or suspected mutations were found in 13 of 16 MH-susceptible patients (81%). Thus, the workload of sequencing was reduced by 79%. CONCLUSION HRM curve analysis is a sensitive and cost-effective tool for the identification of nucleotide sequence variants in complex genes such as the RYR1 gene.
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Affiliation(s)
- Marcus Broman
- Department of Anaesthesiology and Intensive Care, VO Perioperativ och Intensivvård, Skåne University Hospital Lund, 205 02 Malmö, Sweden.
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Naing BT, Watanabe A, Shimada T. A novel mutation screening system for Ehlers-Danlos Syndrome, vascular type by high-resolution melting curve analysis in combination with small amplicon genotyping using genomic DNA. Biochem Biophys Res Commun 2011; 405:368-72. [PMID: 21219851 DOI: 10.1016/j.bbrc.2011.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 01/04/2011] [Indexed: 11/27/2022]
Abstract
Ehlers-Danlos syndrome, vascular type (vEDS) (MIM #130050) is an autosomal dominant disorder caused by type III procollagen gene (COL3A1) mutations. Most COL3A1 mutations are detected by using total RNA from patient-derived fibroblasts, which requires an invasive skin biopsy. High-resolution melting curve analysis (hrMCA) has recently been developed as a post-PCR mutation scanning method which enables simple, rapid, cost-effective, and highly sensitive mutation screening of large genes. We established a hrMCA method to screen for COL3A1 mutations using genomic DNA. PCR primers pairs for COL3A1 (52 amplicons) were designed to cover all coding regions of the 52 exons, including the splicing sites. We used 15 DNA samples (8 validation samples and 7 samples of clinically suspected vEDS patients) in this study. The eight known COL3A1 mutations in validation samples were all successfully detected by the hrMCA. In addition, we identified five novel COL3A1 mutations, including one deletion (c.2187delA) and one nonsense mutation (c.2992C>T) that could not be determined by the conventional total RNA method. Furthermore, we established a small amplicon genotyping (SAG) method for detecting three high frequency coding-region SNPs (rs1800255:G>A, rs1801184:T>C, and rs2271683:A>G) in COL3A1 to differentiate mutations before sequencing. The use of hrMCA in combination with SAG from genomic DNA enables rapid detection of COL3A1 mutations with high efficiency and specificity. A better understanding of the genotype-phenotype correlation in COL3A1 using this method will lead to improve in diagnosis and treatment.
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Affiliation(s)
- Banyar Than Naing
- Department of Biochemistry and Molecular Biology, Nippon Medical School, and Division of Clinical Genetics, Nippon Medical School Hospital, Tokyo, Japan
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Cheng J, Yim OS, Low PS, Tay SKH, Yap EPH, Lai PS. Detection of hemi/homozygotes through heteroduplex formation in high-resolution melting analysis. Anal Biochem 2010; 410:158-60. [PMID: 21111703 DOI: 10.1016/j.ab.2010.11.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 11/07/2010] [Accepted: 11/17/2010] [Indexed: 01/06/2023]
Abstract
Heteroduplex formation, required for the complete detection of hemi/homozygotes using high-resolution melting analysis, can be induced either by pre-PCR mixing of genomic DNAs or by post-PCR mixing of PCR products from unknown and reference samples. This study investigates the effects of both methods using two single nucleotide polymorphisms in X-linked DMD gene. The results show that both methods resulted in the same effect when mixing samples with the same gene copy number. Mixing samples with different gene copy numbers has not been previously explored and we show that post-PCR mixing is insensitive to gene copy number differences as compared to pre-PCR mixing.
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Affiliation(s)
- Jinting Cheng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
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22
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Montgomery JL, Sanford LN, Wittwer CT. High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 2010; 10:219-40. [PMID: 20214540 DOI: 10.1586/erm.09.84] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Among nucleic acid analytical methods, high-resolution melting analysis is gaining more and more attention. High-resolution melting provides simple, homogeneous solutions for variant scanning and genotyping, addressing the needs of today's overburdened laboratories with rapid turnaround times and minimal cost. The flexibility of the technique has allowed it to be adopted by a wide range of disciplines for a variety of applications. In this review we examine the broad use of high-resolution melting analysis, including gene scanning, genotyping (including small amplicon, unlabeled probe and snapback primers), sequence matching and methylation analysis. Four major application arenas are examined to demonstrate the methods and approaches commonly used in particular fields. The appropriate usage of high-resolution melting analysis is discussed in the context of known constraints, such as sample quality and quantity, with a particular focus placed on proper experimental design in order to produce successful results.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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Abbs S, Tuffery-Giraud S, Bakker E, Ferlini A, Sejersen T, Mueller CR. Best practice guidelines on molecular diagnostics in Duchenne/Becker muscular dystrophies. Neuromuscul Disord 2010; 20:422-7. [PMID: 20466545 DOI: 10.1016/j.nmd.2010.04.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stephen Abbs
- GSTS Pathology, Guy's Hospital, London SE1 9RT, UK
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Nettuwakul C, Sawasdee N, Yenchitsomanus PT. Rapid detection of solute carrier family 4, member 1 (SLC4A1) mutations and polymorphisms by high-resolution melting analysis. Clin Biochem 2010; 43:497-504. [DOI: 10.1016/j.clinbiochem.2009.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 12/07/2009] [Accepted: 12/09/2009] [Indexed: 11/28/2022]
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Vossen RHAM, Aten E, Roos A, den Dunnen JT. High-Resolution Melting Analysis (HRMA)-More than just sequence variant screening. Hum Mutat 2009; 30:860-6. [PMID: 19418555 DOI: 10.1002/humu.21019] [Citation(s) in RCA: 357] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rolf H A M Vossen
- Leiden Genome Technology Center (LGTC), Human and Clincal Genetics, Leiden University Medical Center, Leiden, The Netherlands
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