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Kamiya Y, Aihara N, Shiga T, Horiuchi N, Kamiie J. Diversity of mutations in the dystrophin gene and details of muscular lesions in porcine dystrophinopathies. Vet Pathol 2024; 61:432-441. [PMID: 38006213 DOI: 10.1177/03009858231214028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
Abstract
During meat inspections in pigs, dystrophinopathies are among the muscle lesions targeted for disposal. In this study, the authors examined the lesions and the distribution of dystrophin expression in 25 pigs with dystrophinopathy. In addition, complementary deoxyribonucleic acid (cDNA) sequencing and western blotting were performed in 6 of the 25 cases, all of which were characterized by degeneration, necrosis, and fat replacement of muscle fibers. Comparing the results of immunohistochemistry with anti-dystrophin antibodies that recognized at different sites in the protein, the authors noted that the loss of dystrophin expression was most pronounced in the C-terminus-recognizing antibody (19/25 cases). The authors detected 5 missense mutations and 3 types of shortened transcripts generated by the skipping of exons in the cDNA, which were associated with the pathogenesis. One missense mutation had been reported previously, whereas the remaining mutations identified had not been previously documented in pigs. In the cases with shortened transcripts, normal-sized transcripts were detected together with the defective transcripts, suggesting that these mutations were caused by splicing abnormalities. In addition, they were in-frame mutations, all of which have similar pathogeneses of Becker muscular dystrophy in humans. These cases were 6 months of age and exhibited macroscopic discoloration, fatty replacement, and muscle degeneration, suggesting that the effect of these mutations on skeletal muscle was significant.
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Nagabushana D, Polavarapu K, Bardhan M, Arunachal G, Gunasekaran S, Preethish-Kumar V, Anjanappa RM, Thomas P, Sadasivan A, Vengalil S, Nashi S, Chawla T, Warrier M, Keerthipriya M, Raju S, Mohan D, Nalini A. Comparison of The Carrier Frequency of Pathogenic Variants of DMD Gene in an Indian Cohort. J Neuromuscul Dis 2021; 8:525-535. [PMID: 33843695 DOI: 10.3233/jnd-210658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is an X-linked disorder caused due to large deletions, duplications,and small pathogenic variants. This article compares the carrier frequency of different pathogenic variants in the DMD gene for the first time in an Indian cohort. METHODS Ninety-one mothers of genetically confirmed DMD probands are included in this study. Pathogenic variants in the DMD gene in probands were detected by multiplex ligation-dependent probe amplification (MLPA) or next-generation sequencing (NGS). Maternal blood samples were evaluated either by MLPA or Sanger sequencing. The demographic and clinical details for screening of muscle weakness and cardiomyopathy were collected from the confirmed carriers. RESULTS Out of 91 probands, large deletions and duplications were identified in 46 and 6 respectively, while 39 had small variants. Among the small variants, substitutions predicted to cause nonsense mutations were the most common (61.5%), followed by frameshift causing small insertion/deletions (25.6%) and splice affecting intronic variants (12.8%). Notably, 19 novel small variants predicted to be disease-causing were identified. Of the 91 mothers, 53 (58.7%) were confirmed to be carriers. Exonic deletions had a significantly lower carrier frequency of 47.8% as compared to small variants (64.1%). The mean age of the carriers at evaluation was 30 years. Among the carriers, two were symptomatic with onset in the 4th decade, manifesting with progressive proximal muscle weakness and dilated cardiomyopathy. CONCLUSION Carrier frequency of small pathogenic variants differs significantly from large deletions. Small pathogenic variants are more commonly inherited, whereas large deletions arise de novo.
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Affiliation(s)
- Divya Nagabushana
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Kiran Polavarapu
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India.,Children's Hospital of Eastern Ontario Research Institute, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada.,Brain and Mind Research Institute, University of Ottawa, ON, Canada
| | - Mainak Bardhan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Gautham Arunachal
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Swetha Gunasekaran
- Department of Human Genetics, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | | | - Ram Murthy Anjanappa
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - PriyaTreesa Thomas
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Arun Sadasivan
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Saraswati Nashi
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Tanushree Chawla
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Manjusha Warrier
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Muddasu Keerthipriya
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Sanita Raju
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Dhaarini Mohan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru, India
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Tortajada-Genaro LA, Niñoles R, Mena S, Maquieira Á. Digital versatile discs as platforms for multiplexed genotyping based on selective ligation and universal microarray detection. Analyst 2019; 144:707-715. [DOI: 10.1039/c8an01830h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The development of a high-performance assay readout using integrated detectors is a current challenge in the implementation of DNA tests in diagnostic laboratories, particularly for supporting pharmacogenetic tests.
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Affiliation(s)
- Luis A. Tortajada-Genaro
- Departamento de Química
- Universitat Politècnica de València
- Valencia
- Spain
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
| | - Regina Niñoles
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universitat Politècnica de València-Universitat de València
- Valencia
- Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)
| | - Salvador Mena
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Universitat Politècnica de València-Universitat de València
- Valencia
- Spain
| | - Ángel Maquieira
- Departamento de Química
- Universitat Politècnica de València
- Valencia
- Spain
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
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4
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Atehortúa SC, Lugo LH, Ceballos M, Orozco E, Castro PA, Arango JC, Mateus HE. Cost-Effectiveness Analysis of Diagnosis of Duchenne/Becker Muscular Dystrophy in Colombia. Value Health Reg Issues 2018. [PMID: 29529586 DOI: 10.1016/j.vhri.2017.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVES To determine the cost-effectiveness ratio of different courses of action for the diagnosis of Duchenne or Becker muscular dystrophy in Colombia. METHODS The cost-effectiveness analysis was performed from the Colombian health system perspective. Decision trees were constructed, and different courses of action were compared considering the following tests: immunohistochemistry (IHC), Western blot (WB), multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification (MLPA), and the complete sequencing of the dystrophin gene. The time horizon matched the duration of sample extraction and analysis. Transition probabilities were obtained from a systematic review. Costs were constructed with a type-case methodology using the consensus of experts and the valuation of resources from consulting laboratories and the 2001 Social Security Institute cost manual. Deterministic sensitivity and scenario analyses were performed with one or more unavailable alternatives. Costs were converted from Colombian pesos to US dollars using the 2014 exchange rate. RESULTS In the base case, WB was the dominant strategy, with a cost of US $419.07 and a sensitivity of 100%. This approach remains the dominant strategy down to a 98.2% sensitivity and while costs do not exceed US $837.38. If WB was not available, IHC had the best cost-effectiveness ratio, followed by MLPA and sequencing. CONCLUSIONS WB is a cost-effective alternative for the diagnosis of patients suspected of having Duchenne or Becker muscular dystrophy in the Colombian health system. The IHC test is rated as the second-best detection method. If these tests are not available, MLPA followed by sequencing would be the most cost-effective alternative.
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Affiliation(s)
- Sara C Atehortúa
- Departamento de Economía, Facultad de Ciencias Económicas, Universidad de Antioquia, Medellín, Colombia; Grupo de Economía de la Salud, Facultad de Ciencias Económicas, Universidad de Antioquia, Medellín, Colombia.
| | - Luz H Lugo
- Grupo de Rehabilitation en Salud, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia; Clínica Las Américas, Medellín, Colombia
| | - Mateo Ceballos
- Grupo de Economía de la Salud, Facultad de Ciencias Económicas, Universidad de Antioquia, Medellín, Colombia
| | - Esteban Orozco
- Grupo de Economía de la Salud, Facultad de Ciencias Económicas, Universidad de Antioquia, Medellín, Colombia
| | - Paula A Castro
- Grupo de Epidemiología Clínica, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan C Arango
- Grupo de Biología y Clínica, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Heidi E Mateus
- Grupo GENIUROS, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá, Colombia
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Nozoe KT, Akamine RT, Mazzotti DR, Polesel DN, Grossklauss LF, Tufik S, Andersen ML, Moreira GA. Phenotypic contrasts of Duchenne Muscular Dystrophy in women: Two case reports. ACTA ACUST UNITED AC 2016; 9:129-133. [PMID: 28123647 PMCID: PMC5241604 DOI: 10.1016/j.slsci.2016.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 03/30/2016] [Accepted: 07/20/2016] [Indexed: 12/23/2022]
Abstract
We discussed two cases of symptomatic female carriers to Duchenne Muscular Dystrophy. The first case is a 20 year-old girl with classical phenotypic manifestation of the disease, similar to the condition in boys. The case 2 is a 62 year-old woman with progressive muscular weakness. The disease is much less common in woman than men so both cases described here are considered rare forms of the disease, with several clinical implications. In both cases, a progressive muscle weakness, impairment in walking and sleeping was observed, in addition to obstructive sleep apnea syndrome and alveolar hypoventilation, that required noninvasive ventilatory support.
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Affiliation(s)
- Karen T. Nozoe
- Department of Psychobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Ricardo T. Akamine
- Department of Psychobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Diego R. Mazzotti
- Department of Psychobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Daniel N. Polesel
- Department of Psychobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Luís F. Grossklauss
- Department of Neurology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Sergio Tufik
- Department of Psychobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Monica L. Andersen
- Department of Psychobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Gustavo A. Moreira
- Department of Psychobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Corresponding author.
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Sánchez JA, Henry O, Joda H, Solnestam B, Kvastad L, Johansson E, Akan P, Lundeberg J, Lladach N, Ramakrishnan D, Riley I, O'Sullivan C. Multiplex PCB-based electrochemical detection of cancer biomarkers using MLPA-barcode approach. Biosens Bioelectron 2016; 82:224-32. [DOI: 10.1016/j.bios.2016.04.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 03/15/2016] [Accepted: 04/06/2016] [Indexed: 11/15/2022]
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7
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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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8
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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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9
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Shin GW, Chung B, Jung GY, Jung GY. Multiplex ligase-based genotyping methods combined with CE. Electrophoresis 2013; 35:1004-16. [PMID: 24123070 DOI: 10.1002/elps.201300361] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 12/30/2022]
Abstract
In this genomic era, the ability to assay multiple genomic hot spots that have strong clinical implications is greatly desired. Conventional PCR-based methods suffer from frequent false-positive detections, particularly when a multiplex analysis is desirable. As an alternative to the error-prone conventional methods, multiplex ligase-based genotyping methods combined with CE have a strong potential. In this review, both previously developed methods and emerging methods are described to reveal the specificity, sensitivity, and simplicity of the ligase-based methods. For each step (ligation, amplification, and separation), the principles of several alternative methods are discussed along with their applications to explore the future development of ligase-based diagnostic methods.
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Affiliation(s)
- Gi Won Shin
- Institute of Environmental and Energy Technology, Pohang University of Sciences and Technology, Pohang, Gyeongbuk, Korea
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10
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Shin GW, Na J, Seo M, Chung B, Nam HG, Lee SJ, Jung GY. Precise Expression Profiling by Stuffer-Free Multiplex Ligation-Dependent Probe Amplification. Anal Chem 2013; 85:9383-9. [DOI: 10.1021/ac402314h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gi Won Shin
- Institute of Environmental
and Energy Technology, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Jeongkyeong Na
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Mihwa Seo
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Boram Chung
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
| | - Hong Gil Nam
- Department
of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 711-873, Korea
| | - Seung-Jae Lee
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
- Department of
Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
- World Class University
Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang,Gyeongbuk 790-784, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary
Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
- Department
of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Korea
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11
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Martin EA, Barresi R, Byrne BJ, Tsimerinov EI, Scott BL, Walker AE, Gurudevan SV, Anene F, Elashoff RM, Thomas GD, Victor RG. Tadalafil alleviates muscle ischemia in patients with Becker muscular dystrophy. Sci Transl Med 2013. [PMID: 23197572 DOI: 10.1126/scitranslmed.3004327] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Becker muscular dystrophy (BMD) is a progressive X-linked muscle wasting disease for which there is no treatment. Like Duchenne muscular dystrophy (DMD), BMD is caused by mutations in the gene encoding dystrophin, a structural cytoskeletal protein that also targets other proteins to the muscle sarcolemma. Among these is neuronal nitric oxide synthase (nNOSμ), which requires certain spectrin-like repeats in dystrophin's rod domain and the adaptor protein α-syntrophin to be targeted to the sarcolemma. When healthy skeletal muscle is subjected to exercise, sarcolemmal nNOSμ-derived NO attenuates local α-adrenergic vasoconstriction, thereby optimizing perfusion of muscle. We found previously that this protective mechanism is defective-causing functional muscle ischemia-in dystrophin-deficient muscles of the mdx mouse (a model of DMD) and of children with DMD, in whom nNOSμ is mislocalized to the cytosol instead of the sarcolemma. We report that this protective mechanism also is defective in men with BMD in whom the most common dystrophin mutations disrupt sarcolemmal targeting of nNOSμ. In these men, the vasoconstrictor response, measured as a decrease in muscle oxygenation, to reflex sympathetic activation is not appropriately attenuated during exercise of the dystrophic muscles. In a randomized placebo-controlled crossover trial, we show that functional muscle ischemia is alleviated and normal blood flow regulation is fully restored in the muscles of men with BMD by boosting NO-cGMP (guanosine 3',5'-monophosphate) signaling with a single dose of the drug tadalafil, a phosphodiesterase 5A inhibitor. These results further support an essential role for sarcolemmal nNOSμ in the normal modulation of sympathetic vasoconstriction in exercising human skeletal muscle and implicate the NO-cGMP pathway as a putative new target for treating BMD.
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Affiliation(s)
- Elizabeth A Martin
- The Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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12
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Mendell JR, Lloyd-Puryear M. Report of MDA muscle disease symposium on newborn screening for Duchenne muscular dystrophy. Muscle Nerve 2013; 48:21-6. [PMID: 23716304 DOI: 10.1002/mus.23810] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2013] [Indexed: 11/11/2022]
Abstract
This report summarizes the progress made in newborn screening for Duchenne muscular dystrophy (DMD). This subject was discussed fully at a symposium held on September 11-12, 2012, in Bethesda, Maryland, by a group of experts from multiple disciplines. The meeting was triggered by the simultaneous combination of improvements in methods for newborn screening for DMD and greater potential for treatment. On the screening side, a two-tier system of newborn screening was introduced that enabled creatine kinase levels and DMD gene analysis to be done on the same dried blood spots obtained at birth. Treatment improvements included promising results from exon skipping as well as multiple studies showing long-term benefits of glucocorticoids and data indicating that early intervention of both forms of therapy was the most beneficial. Conclusions from this symposium with supportive data could have a significant impact on propelling efforts for approval of newborn screening for DMD.
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Affiliation(s)
- Jerry R Mendell
- Nationwide Children's Hospital, Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and Department of Pediatrics, Ohio State University, 700 Childrens Drive, Columbus, Ohio, 43205, USA.
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Mercier S, Toutain A, Toussaint A, Raynaud M, de Barace C, Marcorelles P, Pasquier L, Blayau M, Espil C, Parent P, Journel H, Lazaro L, Andoni Urtizberea J, Moerman A, Faivre L, Eymard B, Maincent K, Gherardi R, Chaigne D, Ben Yaou R, Leturcq F, Chelly J, Desguerre I. Genetic and clinical specificity of 26 symptomatic carriers for dystrophinopathies at pediatric age. Eur J Hum Genet 2013; 21:855-63. [PMID: 23299919 DOI: 10.1038/ejhg.2012.269] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 08/30/2012] [Accepted: 09/25/2012] [Indexed: 01/30/2023] Open
Abstract
The molecular basis underlying the clinical variability in symptomatic Duchenne muscular dystrophy (DMD) carriers are still to be precised. We report 26 cases of early symptomatic DMD carriers followed in the French neuromuscular network. Clinical presentation, muscular histological analysis and type of gene mutation, as well as X-chromosome inactivation (XCI) patterns using DNA extracted from peripheral blood or muscle are detailed. The initial symptoms were significant weakness (88%) or exercise intolerance (27%). Clinical severity varied from a Duchenne-like progression to a very mild Becker-like phenotype. Cardiac dysfunction was present in 19% of the cases. Cognitive impairment was worthy of notice, as 27% of the carriers are concerned. The muscular analysis was always contributive, revealing muscular dystrophy (83%), mosaic in immunostaining (81%) and dystrophin abnormalities in western blot analysis (84%). In all, 73% had exonic deletions or duplications and 27% had point mutations. XCI pattern was biased in 62% of the cases. In conclusion, we report the largest series of manifesting DMD carriers at pediatric age and show that exercise intolerance and cognitive impairment may reveal symptomatic DMD carriers. The complete histological and immunohistological study of the muscle is the key of the diagnosis leading to the dystrophin gene analysis. Our study shows also that cognitive impairment in symptomatic DMD carriers is associated with mutations in the distal part of the DMD gene. XCI study does not fully explain the mechanisms as well as the wide spectrum of clinical phenotype, though a clear correlation between the severity of the phenotype and inactivation bias was observed.
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15
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Shin GW, Kim YT, Heo HY, Chung B, Seo TS, Jung GY. Triblock copolymer-based microchip device for rapid analysis of stuffer-free multiplex ligation-dependent probe amplification products. Electrophoresis 2012; 33:3574-8. [PMID: 23135832 DOI: 10.1002/elps.201200436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/01/2012] [Accepted: 09/08/2012] [Indexed: 11/06/2022]
Abstract
Recent improvements in the multiplex ligation-dependent probe amplification (MLPA) method promise successful multiplex analysis of various genetic markers. In particular, it has been demonstrated that elimination of the stuffer sequence included in MLPA probes for length-dependent analysis substantially simplifies the probe design process and improves the accuracy of the analysis. As is the case for other CE-based methods, MLPA could be further developed on a microchip platform. However, high-resolution analysis of short MLPA probes requires careful microchip operation. In this study, we developed a microchip device for the multiplex analysis of five food-borne pathogens using a stuffer-free probe set. Microchip channel design and electrophoresis operating conditions were first optimized for reproducible analysis, after which two sieving matrices were tested. Finally, the method was validated using DNA samples isolated from intentionally infected milk.
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Affiliation(s)
- Gi Won Shin
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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16
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Shin GW, Jung SH, Yim SH, Chung B, Yeol Jung G, Chung YJ. Stuffer-free multiplex ligation-dependent probe amplification based on conformation-sensitive capillary electrophoresis: a novel technology for robust multiplex determination of copy number variation. Electrophoresis 2012; 33:3052-61. [PMID: 22965760 DOI: 10.1002/elps.201200334] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 07/18/2012] [Accepted: 07/23/2012] [Indexed: 01/12/2023]
Abstract
Developing diagnostic tools based on the application of known disease/phenotype-associated copy number variations (CNVs) requires the capacity to measure CNVs in a multiplex format with sufficient reliability and methodological simplicity. In this study, we developed a reliable and user-friendly multiplex CNV detection method, termed stuffer-free MLPA-CE-SSCP, that combines a variation of multiplex ligation-dependent probe amplification (MLPA) with CE-SSCP. In this variation, MLPA probes were designed without the conventionally required stuffer sequences. To separate the similar-sized stuffer-free MLPA products, we adopted CE-SSCP rather than length-dependent conventional CE analysis. An examination of the genomic DNA from five cell lines known to vary in X-chromosome copy number (1-5) revealed that copy number determinations using stuffer-free MLPA-CE-SSCP were more accurate than those of conventional MLPA, and the CV of the measured copy numbers was significantly lower. Applying our system to measure the CNVs on autosomes between two HapMap individuals, we found that all peaks for CNV targets showed the expected copy number changes. Taken together, our results indicate that this new strategy can overcome the limitations of conventional MLPA, which are mainly related to long probe length and difficulties of probe preparation.
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Affiliation(s)
- Gi Won Shin
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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17
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Zhou WJ, Liu WY, Liu D, Jiang JH, Zhou DM, Zhong ZY, Xu XM. A quantitative assay to detect α-thalassemia deletions and triplications using multiplex nested real-time quantitative polymerase chain reaction. Anal Biochem 2012; 427:144-50. [DOI: 10.1016/j.ab.2012.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/09/2012] [Accepted: 05/13/2012] [Indexed: 01/10/2023]
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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: 149] [Impact Index Per Article: 12.4] [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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19
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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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20
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Abstract
DNaseI-hypersensitive sites within chromatin are indicative of genomic loci with regulatory function. Several techniques have been described for analyzing these regions, but are either laborious, offer low-throughput possibilities, or are expensive. We have developed a new approach based on a modified version of multiplex ligation-dependent probe amplification (MLPA). Using this method, it is possible to analyse up to 50 defined genomic regions for DNaseI-hypersensitivity in a single PCR-based reaction. This chapter outlines the approach and discusses the critical features of each step of the procedure.
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Affiliation(s)
- Thomas Ohnesorg
- Molecular Development Laboratory, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
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21
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Chung B, Shin GW, Hwang HS, Chung YJ, Jung SW, Jung GY. Precise H1N1 swine influenza detection using stuffer-free multiplex ligation-dependent probe amplification in conformation-sensitive capillary electrophoresis. Anal Biochem 2012; 424:54-6. [PMID: 22342882 DOI: 10.1016/j.ab.2012.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/05/2012] [Accepted: 02/06/2012] [Indexed: 11/19/2022]
Abstract
The H1N1 influenza virus has spread worldwide to become pandemic. Here, we developed a new method to discriminate various types of influenza A, including H1N1, using stuffer-free multiplex ligation-dependent probe amplification based on a conformation-sensitive separation method, namely capillary electrophoresis-single-strand conformation polymorphism. Unlike conventional methods, our approach precisely detects five relevant gene markers permitting confirmation of infection.
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Affiliation(s)
- Boram Chung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
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22
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Hasib L, Dilcher M, Hufert F, Meyer-König U, Weidmann M. Development of a flow-through [corrected] microarray based reverse transcriptase multiplex ligation-dependent probe amplification assay for the detection of European Bunyaviruses. [corrected]. Mol Biotechnol 2012; 49:176-86. [PMID: 21390485 PMCID: PMC3172416 DOI: 10.1007/s12033-011-9389-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is suspected that apart from tick-borne encephalitis virus several additional European Arboviruses such as the sandfly borne Toscana virus, sandfly fever Sicilian virus and sandfly fever Naples virus, mosquito-borne Tahyna virus, Inkoo virus, Batai virus and tick-borne Uukuniemi virus cause aseptic meningo-encephalitis or febrile disease in Europe. Currently, the microarray technology is developing rapidly and there are many efforts to apply it to infectious diseases diagnostics. In order to arrive at an assay system useful for high throughput analysis of samples from aseptic meningo-encephalitis cases the authors developed a combined multiplex ligation-dependent probe amplification and flow-through microarray assay for the detection of European Bunyaviruses. These results show that this combined assay indeed is highly sensitive, and specific for the accurate detection of multiple viruses.
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Affiliation(s)
- Lekbira Hasib
- Department of Virology, University Medical Center Göttingen, Kreuzbergring 57 37075, Göttingen, Germany.
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23
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Ceulemans S, van der Ven K, Del-Favero J. Targeted screening and validation of copy number variations. Methods Mol Biol 2012; 838:311-28. [PMID: 22228019 DOI: 10.1007/978-1-61779-507-7_15] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The accessibility of genome-wide screening technologies considerably facilitated the identification and characterization of copy number variations (CNVs). The increasing amount of available data describing these variants, clearly demonstrates their abundance in the human genome. This observation shows that not only SNPs, but also CNVs and other structural variants strongly contribute to genetic variation. Even though not all structural variants have an obvious phenotypic effect, there is evidence that CNVs influence gene dosage and hence can have profound effects on human disease susceptibility, disease manifestation, and disease severity. Therefore, CNV screening and analysis methodologies, specifically focusing on disease-related CNVs are actively progressing. This chapter specifically describes different techniques currently available for the targeted screening and validation of CNVs. We not only provide an overview of all these CNV analysis methods, but also address their strong and weak points. Methods covered include fluorescence in situ hybridization (FISH), quantitative real-time PCR (qPCR), paralogue ratio test (PRT), molecular copy-number counting (MCC), and multiplex PCR-based approaches, such as multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), multiplex PCR-based real-time invader assay (mPCR-RETINA), quantitative multiplex PCR of short fluorescent fragments (QMPSF), and multiplex amplicon quantification (MAQ). We end with some general remarks and conclusions, furthermore briefly addressing the future perspectives.
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Affiliation(s)
- Shana Ceulemans
- Applied Molecular Genomics Unit, VIB, Department of Molecular Genetics, Flanders, Belgium
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24
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Abstract
Our knowledge about human genes and the consequences of mutations leading to human genetic diseases has drastically improved over the last few years. It has been recognized that many mutations are indeed pathogenic because they impact the mRNA rather than the protein itself. With our better understanding of the very complex mechanism of splicing, various bioinformatics tools have been developed. They are now frequently used not only to search for sequence motifs corresponding to splicing signals (splice sites, branch points, ESE, and ESS) but also to predict the impact of mutations on these signals. We now need to address the impact of mutations that affect the splicing process, as their consequences could vary from the activation of cryptic signals to the skipping of one or multiple exons. Despite the major developments of the bioinformatics field coupled to experimental data generated on splicing, it is today still not possible to efficiently predict the consequences of mutations impacting splicing signals, especially to predict if they will lead to exon skipping or to cryptic splice site activation.
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25
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Li Y, Guo SJ, Shao N, Tu S, Xu M, Ren ZR, Ling X, Wang GQ, Lin ZX, Tao SC. A universal multiplex PCR strategy for 100-plex amplification using a hydrophobically patterned microarray. LAB ON A CHIP 2011; 11:3609-3618. [PMID: 21909519 DOI: 10.1039/c1lc20526a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Both basic research and clinical medicine have urgent demands for highly efficient strategies to simultaneously identify many different DNA sequences within a single tube. Effective and simultaneous amplification of multiple target sequences is a prerequisite for any successful multiple nucleic acid detection method. Multiplex PCR is one of the best choices for this purpose. However, due to the intrinsic interference and competition among primer pairs in the same tube, multiple rounds of highly empirical optimization procedures are usually required to establish a successful multiplex PCR reaction. To address this challenge, we report here a universal multiplex PCR strategy that is capable of over 100-plex amplification using a specially designed microarray in which hydrophilic microwells are patterned on a hydrophobic chip. On such an array, primer pairs tagged with a universal sequence are physically separated in individual hydrophilic microwells on an otherwise hydrophobic chip, enabling many unique PCR reactions to be proceeded simultaneously during the first step of the procedure. The PCR products are then isolated and further amplified from the universal sequences, producing a sufficient amount of material for analysis by conventional gel electrophoresis or DNA microarray technology. This strategy is abbreviated as "MPH&HPM" for "Multiplex PCR on a Hydrophobically and Hydrophilically Patterned Microarray". The feasibility of this method is first demonstrated by a multiplex PCR reaction for the simultaneous detection of eleven pneumonia-causing pathogens. Further, we demonstrate the power of this strategy with a highly successful 116-plex PCR reaction that required only little prior optimization. The effectiveness of the MPH&HPM strategy with clinical samples is then illustrated with the detection of deleted exons of the Duchenne Muscular Dystrophy (DMD) gene, the results are in excellent agreement with the clinical records. Because of its generality, simplicity, flexibility, specificity and capacity of more than 100-plex amplification, the MPH&HPM strategy should have broad applications in both laboratory research and clinical applications when multiplex nucleic acid analysis is required.
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Affiliation(s)
- Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
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26
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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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27
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Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA) is a PCR-based technique that was developed for identifying deletions and duplications in genomic DNA. The simplicity and sensitivity of this approach has led to it being implemented in many laboratories around the world. Since the original publication, there have been several variants of MLPA described, allowing the quantitative analysis of mRNA transcript levels, CpG methylation, complex genomic regions, and DNaseI hypersensitive sites. This chapter outlines the basic MLPA protocol, describes the different modifications and applications that have been published, and discusses the critical points during each of the steps.
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Affiliation(s)
- Thomas Ohnesorg
- Molecular Development, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
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28
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Goodeve AC. Another step towards understanding hemophilia A molecular pathogenesis. J Thromb Haemost 2010; 8:2693-5. [PMID: 21188793 DOI: 10.1111/j.1538-7836.2010.04071.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A C Goodeve
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK.
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29
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Marcinkowska M, Wong KK, Kwiatkowski DJ, Kozlowski P. Design and generation of MLPA probe sets for combined copy number and small-mutation analysis of human genes: EGFR as an example. ScientificWorldJournal 2010; 10:2003-18. [PMID: 20953551 PMCID: PMC4004796 DOI: 10.1100/tsw.2010.195] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Multiplex ligation-dependent probe amplification (MLPA) is a multiplex copy number analysis method that is routinely used to identify large mutations in many clinical and research labs. One of the most important drawbacks of the standard MLPA setup is a complicated, and therefore expensive, procedure of generating long MLPA probes. This drawback substantially limits the applicability of MLPA to those genomic regions for which ready-to-use commercial kits are available. Here we present a simple protocol for designing MLPA probe sets that are composed entirely of short oligonucleotide half-probes generated through chemical synthesis. As an example, we present the design and generation of an MLPA assay for parallel copy number and small-mutation analysis of the EGFR gene.
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Affiliation(s)
- Malgorzata Marcinkowska
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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30
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Ren ZR. [ZENG Yi-Tao]. YI CHUAN = HEREDITAS 2010; 32:869-873. [PMID: 20870606 DOI: 10.3724/sp.j.1005.2010.00869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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31
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Bian XM, Guo Q, Qi QW. Current situation and development of prenatal diagnosis in China. ACTA ACUST UNITED AC 2010; 4:271-4. [DOI: 10.1007/s11684-010-0100-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 05/17/2010] [Indexed: 11/30/2022]
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32
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Cali F, Ruggeri G, Vinci M, Meli C, Carducci C, Leuzzi V, Pozzessere S, Schinocca P, Ragalmuto A, Chiavetta V, Micciche S, Romano V. Exon deletions of the phenylalanine hydroxylase gene in Italian hyperphenylalaninemics. Exp Mol Med 2010; 42:81-6. [PMID: 19946181 DOI: 10.3858/emm.2010.42.2.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
A consistent finding of many studies describing the spectrum of mutant phenylalanine hydroxylase (PAH) alleles underlying hyperphenylalaninemia is the impossibility of achieving a 100% mutation ascertainment rate using conventional gene-scanning methods. These methods include denaturing gradient gel electrophoresis (DGGE), denaturing high performance liquid chromatography (DHPLC), and direct sequencing. In recent years, it has been shown that a significant proportion of undetermined alleles consist of large deletions overlapping one or more exons. These deletions have been difficult to detect in compound heterozygotes using gene-scanning methods due to a masking effect of the non-deleted allele. To date, no systematic search has been carried out for such exon deletions in Italian patients with phenylketonuria or mild hyperphenylalaninemia. We used multiplex ligation-dependent probe amplification (MLPA), comparative multiplex dosage analysis (CMDA), and real-time PCR to search for both large deletions and duplications of the phenylalanine hydroxylase gene in Italian hyperphenylalaninemia patients. Four deletions removing different phenylalanine hydroxylase (PAH) gene exons were identified in 12 patients. Two of these deletions involving exons 4-5-6-7-8 (systematic name c.353-?_912+?del) and exon 6 (systematic name c.510-?_706+?del) have not been reported previously. In this study, we show that exon deletion of the PAH gene accounts for 1.7% of all mutant PAH alleles in Italian hyperphenylalaninemics.
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Affiliation(s)
- Francesco Cali
- Laboratorio di Genetica Molecolare, Associazione Oasi Maria SS. (I.R.C.C.S.), Troina (EN), Italy
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Takeshima Y, Yagi M, Okizuka Y, Awano H, Zhang Z, Yamauchi Y, Nishio H, Matsuo M. Mutation spectrum of the dystrophin gene in 442 Duchenne/Becker muscular dystrophy cases from one Japanese referral center. J Hum Genet 2010; 55:379-88. [PMID: 20485447 DOI: 10.1038/jhg.2010.49] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Recent developments in molecular therapies for Duchenne muscular dystrophy (DMD) demand accurate genetic diagnosis, because therapies are mutation specific. The KUCG (Kobe University Clinical Genetics) database for DMD and Becker muscular dystrophy is a hospital-based database comprising 442 cases. Using a combination of complementary DNA (cDNA) and chromosome analysis in addition to conventional genomic DNA-based method, mutation detection was successfully accomplished in all cases, and the largest mutation database of Japanese dystrophinopathy was established. Among 442 cases, deletions and duplications encompassing one or more exons were identified in 270 (61%) and 38 (9%) cases, respectively. Nucleotide changes leading to nonsense mutations or disrupting a splice site were identified in 69 (16%) or 24 (5%) cases, respectively. Small deletion/insertion mutations were identified in 34 (8%) cases. Remarkably, two retrotransposon insertion events were also identified. Dystrophin cDNA analysis successfully revealed novel transcripts with a pseudoexon created by a single-nucleotide change deep within an intron in four cases. X-chromosome abnormalities were identified in two cases. The reading frame rule was upheld for 93% of deletion and 66% of duplication mutation cases. For the application of molecular therapies, induction of exon skipping was deemed the first priority for dystrophinopathy treatment. At one Japanese referral center, the hospital-based mutation database of the dystrophin gene was for the first time established with the highest levels of quality and patient's number.
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Affiliation(s)
- Yasuhiro Takeshima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
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Ritari J, Paulin L, Hultman J, Auvinen P. Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays. BMC Res Notes 2009; 2:249. [PMID: 20003444 PMCID: PMC2799435 DOI: 10.1186/1756-0500-2-249] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 12/14/2009] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Nucleic acid detection based on ligation reaction or single nucleotide extension of ssDNA probes followed by tag microarray hybridization provides an accurate and sensitive detection tool for various diagnostic purposes. Since microarray quality is crucial for reliable detection, these methods can benefit from correcting for microarray artefacts using specifically adapted techniques. FINDINGS Here we demonstrate the application of a per-spot hybridization control oligonucleotide probe and a novel way of computing normalization for tag array data. The method takes into account the absolute value of the detection probe signal and the variability in the control probe signal to significantly alleviate problems caused by artefacts and noise on low quality microarrays. CONCLUSIONS Diagnostic microarray platforms require experimental and computational tools to enable efficient correction of array artefacts. The techniques presented here improve the signal to noise ratio and help in determining true positives with better statistical significance and in allowing the use of arrays with poor quality that would otherwise be discarded.
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Affiliation(s)
- Jarmo Ritari
- DNA sequencing and genomics laboratory, Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland.
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35
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Abstract
Muscular dystrophies are individually rare genetic disorders that cause much chronic disability, affecting young children and adults. In the past 20 years, more than 30 genetic types of muscular dystrophy have been defined. During this time, precise diagnosis, genetic counselling, and medical management have improved. These advances in medical practice have occurred while definitive therapies based on an improved knowledge of disease pathogenesis are awaited. A wide range of therapeutic options have been tested in animal models, and some are being tested in clinical trials. Various therapeutic targets are being investigated, from personalised medicines targeting specific mutations and drugs targeting cellular pathways to gene-based and cell-based therapies.
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Affiliation(s)
- Kate Bushby
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, UK.
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36
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Wang Q, Li-Ling J, Lin C, Wu Y, Sun K, Ma H, Jin C. Characteristics of dystrophin gene mutations among Chinese patients as revealed by multiplex ligation-dependent probe amplification. Genet Test Mol Biomarkers 2009; 13:23-30. [PMID: 19309270 DOI: 10.1089/gtmb.2008.0059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS To verify whether dystrophin gene mutations among Chinese patients feature different types and frequencies from other populations. METHODS Multiplex ligation-dependent probe amplification (MLPA) in combination with multiplex PCR (mPCR) and/or short tandem repeat (STR)-based linkage analysis were applied in a large series of Chinese families affected with Duchenne muscular dystrophy (DMD) or Becker muscular dystrophy (BMD). There were a total of 19 cases seeking prenatal diagnosis during their second pregnancies. RESULTS Of the 59 family trios (51 with DMD and 8 with BMD), 40 were found to have carried various mutations of the dystrophin gene. In addition to deletions and duplications within the mutational hotspots identified by both methods, 10 mutations missed by mPCR were detected by MLPA, among which at least 3 were of rare types. Combined MLPA and linkage analysis also achieved prenatal diagnoses in all of the 19 amniocentesis samples. CONCLUSIONS Mutations of dystrophin gene among Chinese patients showed a diverse spectrum, with similarity to as well as discrepancies from other populations. For the comprehensive coverage of all exons of the dystrophin gene, MLPA should be the method of choice for initial screening of DMD/BMD patients. When combined with STR-based analysis, it can achieve diagnosis in as much as 70-80% of all referred cases.
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Affiliation(s)
- Qian Wang
- Department of Medical Genetics, China Medical University, Shenyang, China
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37
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Shen Y, Wu BL. Designing a simple multiplex ligation-dependent probe amplification (MLPA) assay for rapid detection of copy number variants in the genome. J Genet Genomics 2009; 36:257-65. [DOI: 10.1016/s1673-8527(08)60113-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2008] [Revised: 10/14/2008] [Accepted: 10/18/2008] [Indexed: 11/26/2022]
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38
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Peptide microarrays for detailed, high-throughput substrate identification, kinetic characterization, and inhibition studies on protein kinase A. Anal Biochem 2009; 387:150-61. [DOI: 10.1016/j.ab.2009.01.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 01/09/2009] [Accepted: 01/14/2009] [Indexed: 11/22/2022]
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39
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Ruszczak C, Mirza A, Menhart N. Differential stabilities of alternative exon-skipped rod motifs of dystrophin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:921-8. [PMID: 19286484 DOI: 10.1016/j.bbapap.2009.02.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 02/16/2009] [Accepted: 02/27/2009] [Indexed: 11/26/2022]
Abstract
Exon skipping repair is a strategy being investigated in early stage clinical trials to treat Duchenne muscular dystrophy. This is most applicable to the majority of cases which arise when genetic defects cause frame shift mutations, and induced exon skipping of out-of-phase exons restores the reading frame. However, the consequences to the edited protein so produced have not been considered. In many cases alternative routes to restoring the reading frame are possible, and we show in a test case involving exon 44 that the resulting differently edited proteins greatly vary in stability, with one of them very similar to normal unskipped dystrophin, and the other much less stable as assessed by the thermodynamics of folding as well as resistance to proteolysis. This has implications for the design of optimal therapeutic exon skipping strategies, which presumably wish to result repairs with as much fidelity to normal dystrophin as possible.
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Affiliation(s)
- Chris Ruszczak
- Division of Biology, Illinois Institute of Technology, Chicago IL 60616, USA
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Kozlowski P, Jasinska AJ, Kwiatkowski DJ. New applications and developments in the use of multiplex ligation-dependent probe amplification. Electrophoresis 2009; 29:4627-36. [PMID: 19053154 DOI: 10.1002/elps.200800126] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Multiplex ligation-dependent probe amplification (MLPA) is a commonly used technique for determining relative DNA sequence dosage (or copy number) in a complex DNA sample. Originally MLPA was designed as a copy number analysis tool for detecting disease-causing genomic mutations and has been successfully applied in the testing and identification of hundreds of genomic mutations in numerous genes including DMD, BRCA1, NF1, and TSC2. More recently, several modifications of the original technique have been implemented. Arguably the most important enhancement of MLPA has been probe generation by chemical synthesis, enabling the facile creation of novel probe sets for any desired application. Other newer applications of MLPA include methylation status determination, copy number analysis in segmentally duplicated regions, expression profiling, and transgene genotyping. MLPA has a potential major role in the analysis of common copy number variation in genome-wide association analyses, which may be enhanced by future improvements to increase throughput and lower costs, such as array-MLPA.
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Affiliation(s)
- Piotr Kozlowski
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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Abstract
Paediatric neurological disorders encompass a large group of clinically heterogeneous diseases, of which some are known to have a genetic cause. Over the past few years, advances in nosological classifications and in strategies for molecular testing have substantially improved the diagnosis, genetic counselling, and clinical management of many patients, and have facilitated the possibility of prenatal diagnoses for future pregnancies. However, the increasing availability of genetic tests for paediatric neurological disorders is raising important questions with regard to the appropriateness, choice of protocols, interpretation of results, and ethical and social concerns of these services. In this Review, we discuss these topics and how these concerns affect genetic counselling.
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[Preliminary application of MLPA-based array in detecting Y chromosome abnormalities]. YI CHUAN = HEREDITAS 2008; 30:1629-34. [PMID: 19073581 DOI: 10.3724/sp.j.1005.2008.01629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To explore the feasibility and accuracy of MLPA-based array (Array-MLPA) in detecting sex chromosome abnormalities, MLPA probes were designed to target against three gene loci, TSPY (p11.2), PRY (q11), and RBMY (q11.2) in human Y chromosome. Array-MLPA approach was applied to test abnormalities of Y chromosome in 15 patient samples with known karyotypes. The data were compared with karyotyping and PCR analyses. The results showed that the copy number of each site detected by Array-MLPA was basically consistent with karyotyping analysis. Moreover, small deletions of chromosomes that were not found by routine karyotyping analysis were identified by the approach described, which fully agreed with PCR analysis, indicating that Array-MLPA was able to detect small abnormalities of chromosomes that cannot be found by karyotyping analysis. Compared to the routine karyotyping method, Array-MLPA has the advantages of high efficiency and reliability in chromosomal analysis, which has great potential in clinical application of diagnosis of chromosome abnormalities.
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Trimarco A, Torella A, Piluso G, Maria Ventriglia V, Politano L, Nigro V. Log-PCR: A New Tool for Immediate and Cost-Effective Diagnosis of up to 85% of Dystrophin Gene Mutations. Clin Chem 2008; 54:973-81. [DOI: 10.1373/clinchem.2007.097881] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: Duchenne (DMD) and Becker (BMD) muscular dystrophies are caused by mutations in the dystrophin gene. Despite the progress in the technologies of mutation detection, the disease of one third of patients escapes molecular definition because the labor and expense involved has precluded analyzing the entire gene. Novel techniques with higher detection rates, such as multiplex ligation-dependent probe amplification and multiplex amplifiable probe hybridization, have been introduced.
Methods: We approached the challenge of multiplexing by modifying the PCR chemistry. We set up a rapid protocol that analyzes all dystrophin exons and flanking introns (57.5 kb). We grouped exons according to their effect on the reading frame and ran 2 PCR reactions for DMD mutations and 2 reactions for BMD mutations under the same conditions. The PCR products are evenly spaced logarithmically on the gel (Log-PCR) in an order that reproduces their chromosomal locations. This strategy enables both simultaneous mapping of all the mutation borders and distinguishing between DMD and BMD. As a proof of principle, we reexamined samples from 506 patients who had received a DMD or BMD diagnosis.
Results: We observed gross rearrangements in 428 of the patients (84.6%; 74.5% deletions and 10.1% duplications). We also recognized a much broader spectrum of mutations and identified 14.6% additional cases.
Conclusions: This study is the first exhaustive investigation of this subject and has made possible the development of a cost-effective test for diagnosing a larger proportion of cases. The benefit of this approach may allow more focused efforts for discovering small or deep-intronic mutations among the few remaining undiagnosed cases. The same protocol can be extended to set up Log-PCRs for other high-throughput applications.
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Affiliation(s)
- Amelia Trimarco
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Naples
- Telethon Institute of Genetics and Medicine (TIGEM), Naples
| | - Annalaura Torella
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Naples
| | - Giulio Piluso
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Naples
| | - Vega Maria Ventriglia
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Naples
| | - Luisa Politano
- Dipartimento di Medicina Sperimentale, Servizio di Cardiomiologia e Genetica Medica, Seconda Università degli Studi di Napoli, Naples
- Centro di Eccellenza per le Malattie Cardiovascolari, Seconda Università degli Studi di Napoli, Naples, Italy
| | - Vincenzo Nigro
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Naples
- Telethon Institute of Genetics and Medicine (TIGEM), Naples
- Centro di Eccellenza per le Malattie Cardiovascolari, Seconda Università degli Studi di Napoli, Naples, Italy
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Array-MAPH: a methodology for the detection of locus copy-number changes in complex genomes. Nat Protoc 2008; 3:849-65. [DOI: 10.1038/nprot.2008.49] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ozalp VC, Nygren AOH, O’Sullivan CK. Fluorescent resonance energy transfer (FRET) based detection of a multiplex ligation-dependent probe amplification assay (MLPA) product. MOLECULAR BIOSYSTEMS 2008; 4:950-4. [DOI: 10.1039/b802382d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tandem duplications of two separate fragments of the dystrophin gene in a patient with Duchenne muscular dystrophy. J Hum Genet 2007; 53:215-219. [PMID: 18160999 DOI: 10.1007/s10038-007-0235-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 12/03/2007] [Indexed: 01/26/2023]
Abstract
Mutations in the dystrophin gene result in the most common inherited muscle disease, Duchenne muscular dystrophy (DMD). Duplications spanning one or more exons have been found to be the second most common disease-causing mutation in the dystrophin gene. Although the duplicated exons are commonly thought to be arranged in tandem, rare noncontiguous exon duplications have been disclosed without clarifying their location or orientation. Here we present the first report that details the exact locations and orientations of noncontiguous duplications in the dystrophin gene. Multiplex ligation-dependent probe amplification analysis of the dystrophin gene of a Japanese boy with DMD revealed that his genomic DNA contained duplications of exons from two separate fragments of the gene: one from exon 45 to exon 48 and the other from exon 55 to exon 63. To clarify the locations and orientations of the duplicated exons, reverse transcription-nested PCR analysis of dystrophin mRNA was conducted. Interestingly, the extra copies of exons 45-48 and exons 55-63 were found to be properly oriented between exons 48 and 49 and exons 63 and 64, respectively. These results indicated that two tandem duplication events occurred in the dystrophin gene of this patient and should contribute to the understanding of the duplication mechanisms that contribute to the development of DMD.
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