1
|
Zhang Y, Du Q, Gao H, Pan Y, Liu N, Qiu C, Liu X. Prenatal risk assessment of Xp21.1 duplication involving the DMD gene by optical genome mapping. Life Sci Alliance 2024; 7:e202402780. [PMID: 39117454 PMCID: PMC11310561 DOI: 10.26508/lsa.202402780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
Structural variants (SVs) of unknown significance are great challenges for prenatal risk assessment, especially when involving dose-sensitive genes such as DMD The pathogenicities of 5'-terminal DMD duplications in the database remain controversial. Four prenatal cases with Xp21.1 duplications were identified by routine prenatal genomic testing, encompassing the 5'-UTR to exons 1-2 in family 1 and family 2, and to exons 1-9 in family 3. The duplication in family 4 was non-contiguous covering the 5'-UTR to exon 1 and exons 3-7. All were traced to unaffected males in the family pedigrees. A new genome-wide approach of optical genome mapping was performed in families 1, 2, and 3 to delineate the breakpoints and orientation of the duplicated fragments. The extra copies were tandemly inserted into the upstream of DMD, preserving the integrity of ORF from the second copy. The pathogenicities were thus reclassified as likely benign. Our data highlight the importance of structural delineation by optical genome mapping in prenatal risk assessment of incidentally identified SVs involving DMD and other similar large dose-sensitive genes.
Collapse
Affiliation(s)
- Yuanyuan Zhang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qiang Du
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Haiming Gao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yujie Pan
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ningyang Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chuang Qiu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoliang Liu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Reproductive Health, Liaoning Research Institute of Reproductive Health and Development, Reproductive Hospital of China Medical University, Shenyang, China
| |
Collapse
|
2
|
Nallamilli BRR, Guruju N, Jump V, Liu R, Hegde M. Molecular Diagnosis of Duchenne Muscular Dystrophy Using Single NGS-Based Assay. Curr Protoc 2023; 3:e669. [PMID: 36748823 DOI: 10.1002/cpz1.669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Duchenne Muscular Dystrophy (DMD) is an X-linked inherited neuromuscular disorder caused by pathogenic variants in the dystrophin gene (DMD; locus Xp21.2). The variant spectrum of DMD is unique in that 65% of causative mutations are intragenic deletions, with intragenic duplications and point mutations (along with other sequence variants) accounting for 6% to 10% and 30% to 35%, respectively. The traditional strategy for molecular diagnostic testing for DMD involves initial screening for deletions/duplications using microarray-based comparative genomic hybridization followed by a full-sequence analysis of DMD for sequence variants. This traditional strategy is expensive and time-consuming due to the involvement of two separate tests to detect all types of variants in the DMD gene. Recent advancements in next-generation sequencing (NGS) technology and improvements in analysis algorithms related to copy number variant detection ultimately resulted in the development of a single NGS-based assay to detect all variant types, including deletions/duplications and sequence variants. This article initially discusses the strategic algorithm for establishing a molecular diagnosis of DMD and later provides detailed molecular diagnostic protocols for DMD, including an NGS-based sequencing assay with sequence and copy number variant analysis. © 2023 Wiley Periodicals LLC. Basic Protocol: Next-generation sequencing of the entire genomic sequence of the DMD gene using IDT xGen Lockdown Probes.
Collapse
Affiliation(s)
| | - Naga Guruju
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts
| | - Vanessa Jump
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts
| | - Ruby Liu
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts
| | - Madhuri Hegde
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts
| |
Collapse
|
3
|
Prenatal Diagnosis of Dystrophinopathy and Cytogenetic Analysis in 303 Chinese Families. MATERNAL-FETAL MEDICINE 2021. [DOI: 10.1097/fm9.0000000000000089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
4
|
Nallamilli BRR, Chaubey A, Valencia CA, Stansberry L, Behlmann AM, Ma Z, Mathur A, Shenoy S, Ganapathy V, Jagannathan L, Ramachander V, Ferlini A, Bean L, Hegde M. A single NGS-based assay covering the entire genomic sequence of the DMD gene facilitates diagnostic and newborn screening confirmatory testing. Hum Mutat 2021; 42:626-638. [PMID: 33644936 DOI: 10.1002/humu.24191] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/08/2021] [Accepted: 02/09/2021] [Indexed: 01/14/2023]
Abstract
Molecular diagnosis for Duchenne and Becker muscular dystrophies (DMD/BMD) involves a two-tiered approach for detection of deletions/duplications using MLPA or array CGH, followed by sequencing of coding and flanking intronic regions to detect sequence variants, which is time-consuming and expensive. We have developed a comprehensive next-generation sequencing (NGS)-based single-step assay to sequence the entire 2.2 Mb of the DMD gene to detect all copy number and sequence variants in both index males and carrier females. Assay validation was 100% concordant with other methodologies. A total of 772 samples have been tested, of which 62% (N = 480) were index cases with a clinical suspicion of DMD. Carrier testing females account for 38% (N = 292). Molecular diagnosis was confirmed in 86% (N = 413) of the index cases. Intragenic deletions and duplications (single-exon or multi-exon) were detected in 60% (N = 247) and 14% (N = 58) of the index cases, respectively. Full-sequence analysis of the entire gene allows for detection of deep intronic pathogenic variants and accurate breakpoint detection of CNVs involving similar exons, which could have an impact on the outcome of clinical trials. This comprehensive assay is highly sensitive for diagnostic testing for DMD and is also suitable for confirmatory testing for newborn screening for DMD.
Collapse
Affiliation(s)
| | - Alka Chaubey
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts, USA
| | - C A Valencia
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts, USA
| | - Leah Stansberry
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts, USA
| | | | - Zeqiang Ma
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts, USA
| | - Abhinav Mathur
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts, USA
| | - Suresh Shenoy
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts, USA
| | | | | | | | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Lora Bean
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts, USA
| | - Madhuri Hegde
- PerkinElmer Genomics, PerkinElmer Inc, Waltham, Massachusetts, USA
| |
Collapse
|
5
|
Cardiac Phenotype-Genotype Associations in DMD/BMD: A Meta-Analysis and Systematic Review. Pediatr Cardiol 2021; 42:189-198. [PMID: 33037470 DOI: 10.1007/s00246-020-02470-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 09/18/2020] [Indexed: 01/16/2023]
Abstract
Cardiac involvement of Duchenne and Becker muscular dystrophies (DMD/BMD) is the most common cause of fatal outcomes. It is still unclear whether some DMD/BMD gene mutations might be predictive of cardiac involvement. In this study, we provide a comprehensive overview on genotypes of cardiac disease in DMD/BMD. We systematically searched the PubMed/Medline, EMBASE and Cochrane electronic databases. Search results were filtered to include only human studies, English language and all dates up to August 2019. We summarized and extensively reviewed all studies that passed the selection criteria and performed a meta-analysis on key genotype parameters of cardiac disease in DMD/BMD. Of 3450 articles scanned, we included 18 studies from 9 regions in the meta-analysis. The pooled studies included 2661 DMD/BMD patients and 1324 DMD/BMD patients with cardiac disease. The most common mutation type was exon deletion, with a pooled frequency of 90% (P < 0.01). In DMD/BMD patients with cardiac dysfunction, a higher frequency of involvement of exons 45 and 46 was found in DMD/BMD patients with cardiac dysfunction. This might be predictive of cardiac involvement in patients with DMD/BMD.
Collapse
|
6
|
Population-Wide Duchenne Muscular Dystrophy Carrier Detection by CK and Molecular Testing. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8396429. [PMID: 33029525 PMCID: PMC7537677 DOI: 10.1155/2020/8396429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 01/28/2023]
Abstract
Carrier screening of Duchenne muscular dystrophy (DMD) has not been widely evaluated. To identify definite DMD female carriers prior to or in early pregnancy, we studied a large population of reproductive age females and provided informed reproductive options to DMD carriers. 37268 females were recruited from the Hangzhou Family Planning Publicity and Technology Guidance Station/Hangzhou Health Service Center for Children and Women, Hangzhou, China, between October 10, 2017, and December 16, 2018. CK activity was measured with follow-up serum DMD genetic testing in subjects with hyperCKemia, defined as CK > 200 U/L. The calculated upper reference limit (97.5th percentile) of serum creatine kinase (CK) for females aged 20-50 years in this study was near the reference limit recommended by the manufacturer (200 U/L), above which was defined as hyperCKemia. 427 females (1.2%) harbored initially elevated CK, among which 281 females (response rate of 65.8%) accepted CK retesting. DMD genetic testing was conducted on 62 subjects with sustained serum CK > 200 U/L and 16 females with a family history of DMD. Finally, 6 subjects were confirmed to be DMD definite carriers. The estimated DMD female carrier rate in this study was 1 : 4088 (adjusting for response rate), an underestimated rate, since only 50% to 70% of DMD female carriers manifest elevated serum CK, and carriers in this study may have been missed due to lack of follow-up or inability to detect all DMD pathogenic variants by current genetic testing.
Collapse
|
7
|
Sheikh O, Yokota T. Advances in Genetic Characterization and Genotype-Phenotype Correlation of Duchenne and Becker Muscular Dystrophy in the Personalized Medicine Era. J Pers Med 2020; 10:E111. [PMID: 32899151 PMCID: PMC7565713 DOI: 10.3390/jpm10030111] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Currently, Duchenne muscular dystrophy (DMD) and the related condition Becker muscular dystrophy (BMD) can be usually diagnosed using physical examination and genetic testing. While BMD features partially functional dystrophin protein due to in-frame mutations, DMD largely features no dystrophin production because of out-of-frame mutations. However, BMD can feature a range of phenotypes from mild to borderline DMD, indicating a complex genotype-phenotype relationship. Despite two mutational hot spots in dystrophin, mutations can arise across the gene. The use of multiplex ligation amplification (MLPA) can easily assess the copy number of all exons, while next-generation sequencing (NGS) can uncover novel or confirm hard-to-detect mutations. Exon-skipping therapy, which targets specific regions of the dystrophin gene based on a patient's mutation, is an especially prominent example of personalized medicine for DMD. To maximize the benefit of exon-skipping therapies, accurate genetic diagnosis and characterization including genotype-phenotype correlation studies are becoming increasingly important. In this article, we present the recent progress in the collection of mutational data and optimization of exon-skipping therapy for DMD/BMD.
Collapse
Affiliation(s)
- Omar Sheikh
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, Edmonton, AB T6G 2H7, Canada;
| | - Toshifumi Yokota
- Department of Medical Genetics, University of Alberta Faculty of Medicine and Dentistry, Edmonton, AB T6G 2H7, Canada;
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada HM Toupin Neurological Science Research Chair, Edmonton, AB T6G 2H7, Canada
| |
Collapse
|
8
|
EMQN best practice guidelines for genetic testing in dystrophinopathies. Eur J Hum Genet 2020; 28:1141-1159. [PMID: 32424326 PMCID: PMC7608854 DOI: 10.1038/s41431-020-0643-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 02/04/2023] Open
Abstract
Dystrophinopathies are X-linked diseases, including Duchenne muscular dystrophy and Becker muscular dystrophy, due to DMD gene variants. In recent years, the application of new genetic technologies and the availability of new personalised drugs have influenced diagnostic genetic testing for dystrophinopathies. Therefore, these European best practice guidelines for genetic testing in dystrophinopathies have been produced to update previous guidelines published in 2010.These guidelines summarise current recommended technologies and methodologies for analysis of the DMD gene, including testing for deletions and duplications of one or more exons, small variant detection and RNA analysis. Genetic testing strategies for diagnosis, carrier testing and prenatal diagnosis (including non-invasive prenatal diagnosis) are then outlined. Guidelines for sequence variant annotation and interpretation are provided, followed by recommendations for reporting results of all categories of testing. Finally, atypical findings (such as non-contiguous deletions and dual DMD variants), implications for personalised medicine and clinical trials and incidental findings (identification of DMD gene variants in patients where a clinical diagnosis of dystrophinopathy has not been considered or suspected) are discussed.
Collapse
|
9
|
Srivastava P, Malhotra KP, Husain N, Malhotra HS, Kulshreshtha D, Anand A. Diagnosing Muscular Dystrophies: Comparison of Techniques and Their Cost Effectiveness: A Multi-institutional Study. J Neurosci Rural Pract 2020; 11:420-429. [PMID: 32753807 PMCID: PMC7394627 DOI: 10.1055/s-0040-1713301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background
The diagnosis of muscular dystrophies involves clinical discretion substantiated by dystrophic changes on muscle biopsy. The different subtypes of muscular dystrophy can be diagnosed using techniques to identify the loss of protein or molecular alterations.
Materials and Methods
Clinically suspicious cases confirmed to have muscular dystrophy on muscle biopsy seen at two tertiary care centers in North India were enrolled for the study. Immunohistochemistry (IHC) for dystrophin, merosin, sarcoglycan, emerin, and dysferlin proteins was performed. The spectrum of muscular dystrophies diagnosed was analyzed. Cost of diagnosing the cases using IHC was estimated and compared with that of standard molecular tests available for the diagnosis of muscular dystrophies.
Statistics
Descriptive statistics were used for data analysis. Mean and standard deviations were used for continuous variables, whereas categorical variables were analyzed using frequency percentage.
Results
A total of 47 cases of muscular dystrophies were studied. This included nine cases of Duchenne, three cases of Becker’s dystrophy, and one dystrophinopathy carrier. One case of α, seven cases of β, and two cases of δ sarcoglycanopathy, along with two cases of facioscapulohumeral dystrophy and a single case of dysferlinopathy were detected. Genetic studies were required for a subset of 16 cases. The cost of using muscle biopsy and IHC was substantially lower than that of molecular methods for the identification of muscular dystrophy subtypes.
Conclusion
We detailed an algorithmic approach for diagnosing muscular dystrophies using muscle biopsy. The prevalence of biopsy proven muscular dystrophies from two tertiary care centers in North India is compared with that from other centers. Genetic studies are currently of limited availability in India and are more expensive as compared with biopsy and IHC. Using these methodologies sequentially with a “biopsy first approach” may be the prudent approach for low-income countries.
Collapse
Affiliation(s)
- Pallavi Srivastava
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Kiran Preet Malhotra
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Nuzhat Husain
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | | | - Dinkar Kulshreshtha
- Department of Neurology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Akanksha Anand
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| |
Collapse
|
10
|
O. Mousa N, Osman A, Fahmy N, Abdellatif A, Zada S, El-Fawal H. Duchenne Muscular Dystrophy (DMD) Diagnosis: Past and Present Perspectives. Rare Dis 2020. [DOI: 10.5772/intechopen.90862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
|
11
|
Aravind S, Ashley B, Mannan A, Ganapathy A, Ramesh K, Ramachandran A, Nongthomba U, Shastry A. Targeted sequencing of the DMD locus: A comprehensive diagnostic tool for all mutations. Indian J Med Res 2019; 150:282-289. [PMID: 31719299 PMCID: PMC6886143 DOI: 10.4103/ijmr.ijmr_290_18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background & objectives: Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder and is caused mainly by deletion, duplication and point mutations in the DMD gene. Diagnosis of DMD has been a challenge as the mutations in the DMD gene are heterogeneous and require more than one diagnostic strategy for the validation of the mutation. This study was planned to evaluate the targeted next-generation sequencing (NGS) as a single platform to detect all types of mutations in the DMD gene, thereby reducing the time and costs compared to conventional sequential testing and also provide precise genetic information for emerging gene therapies. Methods: The study included 20 unrelated families and 22 patients from an Indian population who were screened for DMD based on phenotypes such as scoliosis, toe walking and loss of ambulation. Peripheral blood DNA was isolated and subjected to multiplex ligation-dependent probe amplification (MLPA) and targeted NGS of the DMD gene to identify the nature of the mutation. Results: In the study patients, 77 per cent of large deletion mutations and 23 per cent single-nucleotide variations (SNVs) were identified. Novel mutations were also identified along with reported deletions, point mutations and partial deletions within the exon of the DMD gene. Interpretation & conclusions: Our findings showed the importance of NGS in the routine diagnostic practice in the identification of DMD mutations over sequential testing. It may be used as a single-point diagnostic strategy irrespective of the mutation type, thereby reducing the turnaround time and cost for multiple diagnostic tests such as MLPA and Sanger sequencing. Though MLPA is a sensitive technique and is the first line of a diagnostic test, the targeted NGS of the DMD gene may have an advantage of having a single diagnostic test. A study on a larger number of patients is needed to highlight NGS as a single, comprehensive platform for the diagnosis of DMD.
Collapse
Affiliation(s)
- Sankaramoorthy Aravind
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science; Dystrophy Annihilation Research Trust, Bengaluru, Karnataka, India
| | - Berty Ashley
- Dystrophy Annihilation Research Trust, Bengaluru, Karnataka, India
| | - Ashraf Mannan
- Strand Life Sciences Private Limited, Bengaluru, Karnataka, India
| | - Aparna Ganapathy
- Strand Life Sciences Private Limited, Bengaluru, Karnataka, India
| | - Keerthi Ramesh
- Dystrophy Annihilation Research Trust, Bengaluru, Karnataka, India
| | | | - Upendra Nongthomba
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Arun Shastry
- Dystrophy Annihilation Research Trust, Bengaluru, Karnataka, India
| |
Collapse
|
12
|
Elhawary NA, Jiffri EH, Jambi S, Mufti AH, Dannoun A, Kordi H, Khogeer A, Jiffri OH, Elhawary AN, Tayeb MT. Molecular characterization of exonic rearrangements and frame shifts in the dystrophin gene in Duchenne muscular dystrophy patients in a Saudi community. Hum Genomics 2018; 12:18. [PMID: 29631625 PMCID: PMC5891934 DOI: 10.1186/s40246-018-0152-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/02/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND In individuals with Duchenne muscular dystrophy (DMD), exon skipping treatment to restore a wild-type phenotype or correct the frame shift of the mRNA transcript of the dystrophin (DMD) gene are mutation-specific. To explore the molecular characterization of DMD rearrangements and predict the reading frame, we simultaneously screened all 79 DMD gene exons of 45 unrelated male DMD patients using a multiplex ligation-dependent probe amplification (MLPA) assay for deletion/duplication patterns. Multiplex PCR was used to confirm single deletions detected by the MLPA. RESULTS There was an obvious diagnostic delay, with an extremely statistically significant difference between the age at initial symptoms and the age of clinical evaluation of DMD cases (t value, 10.3; 95% confidence interval 5.95-8.80, P < 0.0001); the mean difference between the two groups was 7.4 years. Overall, we identified 147 intragenic rearrangements: 46.3% deletions and 53.7% duplications. Most of the deletions (92.5%) were between exons 44 and 56, with exon 50 being the most frequently involved (19.1%). Eight new rearrangements, including a mixed deletion/duplication and double duplications, were linked to seven cases with DMD. Of all the cases, 17.8% had duplications with no hot spots. In addition, confirmation of the reading frame hypothesis helped account for new DMD rearrangements in this study. We found that 81% of our Saudi patients would potentially benefit from exon skipping, of which 42.9% had a mutation amenable to skipping of exon 51. CONCLUSIONS Our study could generate considerable data on mutational rearrangements that may promote future experimental therapies in Saudi Arabia.
Collapse
Affiliation(s)
- Nasser A Elhawary
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia.
- Department of Molecular Genetics, Faculty of Medicine, Ain Shams University, Cairo, 11566, Egypt.
| | - Essam H Jiffri
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Samira Jambi
- Department of Pediatrics, Al Hada Military Hospital, Al Hada, Saudi Arabia
| | - Ahmad H Mufti
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia
| | - Anas Dannoun
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia
| | - Hassan Kordi
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia
| | - Asim Khogeer
- Department of Plan and Research, General Directorate of Health Affairs, Mecca Region, Ministry of Health, Mecca, Saudi Arabia
| | - Osama H Jiffri
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | | | - Mohammed T Tayeb
- Department of Medical Genetics, Medicine College, Umm Al-Qura University, P.O. Box 57543, Mecca, 21955, Saudi Arabia
| |
Collapse
|
13
|
Molecular characterization of exonic rearrangements and frame shifts in the dystrophin gene in Duchenne muscular dystrophy patients in a Saudi community. Hum Genomics 2018. [PMID: 29631625 DOI: 10.1186/s40246-018-0152-8]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In individuals with Duchenne muscular dystrophy (DMD), exon skipping treatment to restore a wild-type phenotype or correct the frame shift of the mRNA transcript of the dystrophin (DMD) gene are mutation-specific. To explore the molecular characterization of DMD rearrangements and predict the reading frame, we simultaneously screened all 79 DMD gene exons of 45 unrelated male DMD patients using a multiplex ligation-dependent probe amplification (MLPA) assay for deletion/duplication patterns. Multiplex PCR was used to confirm single deletions detected by the MLPA. RESULTS There was an obvious diagnostic delay, with an extremely statistically significant difference between the age at initial symptoms and the age of clinical evaluation of DMD cases (t value, 10.3; 95% confidence interval 5.95-8.80, P < 0.0001); the mean difference between the two groups was 7.4 years. Overall, we identified 147 intragenic rearrangements: 46.3% deletions and 53.7% duplications. Most of the deletions (92.5%) were between exons 44 and 56, with exon 50 being the most frequently involved (19.1%). Eight new rearrangements, including a mixed deletion/duplication and double duplications, were linked to seven cases with DMD. Of all the cases, 17.8% had duplications with no hot spots. In addition, confirmation of the reading frame hypothesis helped account for new DMD rearrangements in this study. We found that 81% of our Saudi patients would potentially benefit from exon skipping, of which 42.9% had a mutation amenable to skipping of exon 51. CONCLUSIONS Our study could generate considerable data on mutational rearrangements that may promote future experimental therapies in Saudi Arabia.
Collapse
|
14
|
Clinical Utility Gene Card for: Becker muscular dystrophy. Eur J Hum Genet 2018; 26:1065-1071. [PMID: 29467387 DOI: 10.1038/s41431-017-0064-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 09/10/2017] [Accepted: 11/23/2017] [Indexed: 12/28/2022] Open
|
15
|
CUGC for Duchenne muscular dystrophy (DMD). Eur J Hum Genet 2018; 26:749-757. [PMID: 29330543 DOI: 10.1038/s41431-017-0013-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/08/2017] [Accepted: 09/09/2017] [Indexed: 11/08/2022] Open
|
16
|
Blanco-Kelly F, Palomares M, Vallespín E, Villaverde C, Martín-Arenas R, Vélez-Monsalve C, Lorda-Sánchez I, Nevado J, Trujillo-Tiebas MJ, Lapunzina P, Ayuso C, Corton M. Improving molecular diagnosis of aniridia and WAGR syndrome using customized targeted array-based CGH. PLoS One 2017; 12:e0172363. [PMID: 28231309 PMCID: PMC5322952 DOI: 10.1371/journal.pone.0172363] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/04/2017] [Indexed: 11/18/2022] Open
Abstract
Chromosomal deletions at 11p13 are a frequent cause of congenital Aniridia, a rare pan-ocular genetic disease, and of WAGR syndrome, accounting up to 30% of cases. First-tier genetic testing for newborn with aniridia, to detect 11p13 rearrangements, includes Multiplex Ligation-dependent Probe Amplification (MLPA) and karyotyping. However, neither of these approaches allow obtaining a complete picture of the high complexity of chromosomal deletions and breakpoints in aniridia. Here, we report the development and validation of a customized targeted array-based comparative genomic hybridization, so called WAGR-array, for comprehensive high-resolution analysis of CNV in the WAGR locus. Our approach increased the detection rate in a Spanish cohort of 38 patients with aniridia, WAGR syndrome and other related ocular malformations, allowing to characterize four undiagnosed aniridia cases, and to confirm MLPA findings in four additional patients. For all patients, breakpoints were accurately established and a contiguous deletion syndrome, involving a large number of genes, was identified in three patients. Moreover, we identified novel microdeletions affecting 3' PAX6 regulatory regions in three families with isolated aniridia. This tool represents a good strategy for the genetic diagnosis of aniridia and associated syndromes, allowing for a more accurate CNVs detection, as well as a better delineation of breakpoints. Our results underline the clinical importance of performing exhaustive and accurate analysis of chromosomal rearrangements for patients with aniridia, especially newborns and those without defects in PAX6 after diagnostic screening.
Collapse
Affiliation(s)
- Fiona Blanco-Kelly
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - María Palomares
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - Elena Vallespín
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - Cristina Villaverde
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Rubén Martín-Arenas
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - Camilo Vélez-Monsalve
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Isabel Lorda-Sánchez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Julián Nevado
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - María José Trujillo-Tiebas
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- Institute of Medical & Molecular Genetics (INGEMM), Hospital Universitario La Paz, Universidad Autónoma de Madrid, IdiPAZ, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- * E-mail: (CA); (MC)
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital- Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
- * E-mail: (CA); (MC)
| |
Collapse
|
17
|
Correction of the Exon 2 Duplication in DMD Myoblasts by a Single CRISPR/Cas9 System. MOLECULAR THERAPY. NUCLEIC ACIDS 2017. [PMID: 28624187 PMCID: PMC5363679 DOI: 10.1016/j.omtn.2017.02.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Exonic duplications account for 10%-15% of all mutations in Duchenne muscular dystrophy (DMD), a severe hereditary neuromuscular disorder. We report a CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-based strategy to correct the most frequent (exon 2) duplication in the DMD gene by targeted deletion, and tested the efficacy of such an approach in patient-derived myogenic cells. We demonstrate restoration of wild-type dystrophin expression at transcriptional and protein level in myotubes derived from genome-edited myoblasts in the absence of selection. Removal of the duplicated exon was achieved by the use of only one guide RNA (gRNA) directed against an intronic duplicated region, thereby increasing editing efficiency and reducing the risk of off-target effects. This study opens a novel therapeutic perspective for patients carrying disease-causing duplications.
Collapse
|
18
|
Abildinova G, Abdrakhmanova Z, Tuchinsky H, Nesher E, Pinhasov A, Raskin L. Fast detection of deletion breakpoints using quantitative PCR. Genet Mol Biol 2016; 39:365-9. [PMID: 27560363 PMCID: PMC5004823 DOI: 10.1590/1678-4685-gmb-2015-0159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/29/2015] [Indexed: 11/22/2022] Open
Abstract
The routine detection of large and medium copy number variants (CNVs) is well
established. Hemizygotic deletions or duplications in the large Duchenne muscular
dystrophy DMD gene responsible for Duchenne and Becker muscular
dystrophies are routinely identified using multiple ligation probe amplification and
array-based comparative genomic hybridization. These methods only map deleted or
duplicated exons, without providing the exact location of breakpoints. Commonly used
methods for the detection of CNV breakpoints include long-range PCR and primer
walking, their success being limited by the deletion size, GC content and presence of
DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and
large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the
DMD gene and the large autosomal heterozygous
PARK2 deletion were used to demonstrate the workflow that relies
on real-time quantitative PCR to narrow down the deletion region and Sanger
sequencing for breakpoint confirmation. The strategy is fast, reliable and
cost-efficient, making it amenable to widespread use in genetic laboratories.
Collapse
Affiliation(s)
| | | | - Helena Tuchinsky
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Elimelech Nesher
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Albert Pinhasov
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Leon Raskin
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| |
Collapse
|
19
|
Pitfalls of Multiple Ligation-Dependent Probe Amplifications in Detecting DMD Exon Deletions or Duplications. J Mol Diagn 2015; 18:253-9. [PMID: 26743743 DOI: 10.1016/j.jmoldx.2015.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 10/22/2015] [Accepted: 11/02/2015] [Indexed: 12/26/2022] Open
Abstract
Multiple ligation-dependent probe amplifications (MLPAs) are a key technology for the molecular diagnosis of Duchenne/Becker muscular dystrophy, which is mainly caused by large gene arrangements. However, little is known about the false-positive rates of MLPA for this disease. Here, we review MLPA analysis results from 398 patients suspected to have Duchenne/Becker muscular dystrophy. MLPA assay was used for screening the entire coding region. If these amplifications produced normal results, direct sequencing was performed to search for sequence variations and to determine single-exon deletions, duplications, or indeterminate results. Using MLPA, 290 cases (72.9%) showed exon deletion or duplication results. Among those, 75 cases (25.9%) resulted in a deletion or duplication of a single exon. Direct sequencing revealed that 11 single-exon deletion cases resulted in false-positives due to sequence variations within the patient population interfering with probe binding at the probe-hybridization sites. Abnormal MLPA results were closely related to the type of sequence change and the position within the probe-hybridization locus. The most common type was C-T transition (n = 19, 55.9%). Abnormal MLPA results correlated with CA mismatch and low melting temperature (≤75°C). False-positive events for large gene rearrangements involving a single exon in DMD accounted for approximately 15% (11/75). Therefore, careful design of MLPA probes is required to avoid false-positive results.
Collapse
|
20
|
Russell M, Roberts AE, Abrams DJ, Murphy AM, Towbin JA, Chung WK. How to effectively utilize genetic testing in the care of children with cardiomyopathies. PROGRESS IN PEDIATRIC CARDIOLOGY 2015. [DOI: 10.1016/j.ppedcard.2015.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
21
|
Abstract
Mutations in the DMD gene result in Duchenne or Becker muscular dystrophy due to absent or altered expression of the dystrophin protein. The more severe Duchenne muscular dystrophy typically presents around ages 2 to 5 with gait disturbance, and historically has led to the loss of ambulation by age 12. It is important for the practicing pediatrician, however, to be aware of other presenting signs, such as delayed motor or cognitive milestones, or elevated serum transaminases. Becker muscular dystrophy is milder, often presenting after age 5, with ambulation frequently preserved past 20 years and sometimes into late decades.
Collapse
Affiliation(s)
- Nicolas Wein
- The Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Lindsay Alfano
- The Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA; Department of Physical Therapy, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Kevin M Flanigan
- The Center for Gene Therapy, The Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA; Department of Pediatrics, Ohio State University, 700 Children's Drive, Columbus, OH 43205, USA; Department of Neurology, Ohio State University, 700 Children's Drive, Columbus, OH 43205, USA.
| |
Collapse
|
22
|
Xp21 deletion in female patients with intellectual disability: Two new cases and a review of the literature. Eur J Med Genet 2015; 58:341-5. [PMID: 25917374 DOI: 10.1016/j.ejmg.2015.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/08/2015] [Indexed: 11/20/2022]
Abstract
Xp21 continuous gene deletion syndrome is characterized by complex glycerol kinase deficiency (GK), adrenal hypoplasia congenital (NROB1), intellectual disability and/or Duchenne muscular dystrophy (DMD). The clinical features depend on the size of the deletion, as well as on the number and the nature of the encompassed genes. More than 100 male patients have been reported so far, while only a few cases of symptomatic female carriers have been described. We report here detailed clinical features and X chromosome inactivation analysis in two unrelated female patients with overlapping Xp21 deletions presenting with intellectual disability and inconstant muscular symptoms.
Collapse
|
23
|
Nallamilli BRR, Ankala A, Hegde M. Molecular diagnosis of Duchenne muscular dystrophy. ACTA ACUST UNITED AC 2014; 83:9.25.1-29. [PMID: 25271841 DOI: 10.1002/0471142905.hg0925s83] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Duchenne Muscular Dystrophy (DMD) is an X-linked inherited neuromuscular disorder caused by mutations in the dystrophin gene (DMD; locus Xp21.2). The mutation spectrum of DMD is unique in that 65% of causative mutations are intragenic deletions, with intragenic duplications and point mutations (along with other sequence variants) accounting for 6% to 10% and 30% to 35%, respectively. The strategy for molecular diagnostic testing for DMD involves initial screening for deletions/duplications using microarray-based comparative genomic hybridization (array-CGH) followed by full-sequence analysis of DMD for sequence variants. Recently, next-generation sequencing (NGS)-based targeted gene analysis has become clinically available for detection of point mutations and other sequence variants (small insertions, deletions, and indels). This unit initially discusses the strategic algorithm for establishing a molecular diagnosis of DMD and later provides detailed protocols of current molecular diagnostic methods for DMD, including array-CGH, PCR-based Sanger sequencing, and NGS-based sequencing assay.
Collapse
|
24
|
Chen C, Ma H, Zhang F, Chen L, Xing X, Wang S, Zhang X, Luo Y. Screening of Duchenne muscular dystrophy (DMD) mutations and investigating its mutational mechanism in Chinese patients. PLoS One 2014; 9:e108038. [PMID: 25244321 PMCID: PMC4171529 DOI: 10.1371/journal.pone.0108038] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a common X-linked recessive disease of muscle degeneration and death. In order to provide accurate and reliable genetic counseling and prenatal diagnosis, we screened DMD mutations in a cohort of 119 Chinese patients using multiplex ligation-dependent probe amplification (MLPA) and denaturing high performance liquid chromatography (DHPLC) followed by Sanger sequencing. In these unrelated DMD patients, we identified 11 patients with DMD small mutations (9.2%) and 81 patients with DMD deletions/duplications (del/dup) (68.1%), of which 64 (79.0%) were deletions, 16 (19.8%) were duplications, and one (1.2%) was both deletion and duplication. Furthermore, we analyzed the frequency of DMD breakpoint in the 64 deletion cases by calculating exon-deletion events of certain exon interval that revealed a novel mutation hotspot boundary. To explore why DMD rearrangement breakpoints were predisposed to specific regions (hotspot), we precisely characterized junction sequences of breakpoints at the nucleotide level in 21 patients with exon deleted/duplicated in DMD with a high-resolution SNP microarray assay. There were no exactly recurrent breakpoints and there was also no significant difference between single-exon del/dup and multiple-exon del/dup cases. The data from the current study provided a comprehensive strategy to detect DMD mutations for clinical practice, and identified two deletion hotspots at exon 43–55 and exon 10–23 by calculating exon-deletion events of certain exon interval. Furthermore, this is the first study to characterize DMD breakpoint at the nucleotide level in a Chinese population. Our observations provide better understanding of the mechanism for DMD gene rearrangements.
Collapse
Affiliation(s)
- Chen Chen
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Hongwei Ma
- Department of Developing Pediatrics, Shengjing Hospital, China Medical University, Shenyang, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Lu Chen
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xuesha Xing
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Shusen Wang
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Luo
- The Research Center for Medical Genomics, Key Laboratory of Medical Cell Biology, Chinese Ministry of Education, College of Basic Medical Science, China Medical University, Shenyang, China
- * E-mail:
| |
Collapse
|
25
|
|
26
|
Nigro V, Piluso G. Spectrum of muscular dystrophies associated with sarcolemmal-protein genetic defects. Biochim Biophys Acta Mol Basis Dis 2014; 1852:585-93. [PMID: 25086336 DOI: 10.1016/j.bbadis.2014.07.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/19/2014] [Accepted: 07/23/2014] [Indexed: 01/31/2023]
Abstract
Muscular dystrophies are heterogeneous genetic disorders that share progressive muscle wasting. This may generate partial impairment of motility as well as a dramatic and fatal course. Less than 30 years ago, the identification of the genetic basis of Duchenne muscular dystrophy opened a new era. An explosion of new information on the mechanisms of disease was witnessed, with many thousands of publications and the characterization of dozens of other genetic forms. Genes mutated in muscular dystrophies encode proteins of the plasma membrane and extracellular matrix, several of which are part of the dystrophin-associated complex. Other gene products localize at the sarcomere and Z band, or are nuclear membrane components. In the present review, we focus on muscular dystrophies caused by defects that affect the sarcolemmal and sub-sarcolemmal proteins. We summarize the nature of each disease, the genetic cause, and the pathogenic pathways that may suggest future treatment options. We examine X-linked Duchenne and Becker muscular dystrophies and the autosomal recessive limb-girdle muscular dystrophies caused by mutations in genes encoding sarcolemmal proteins. The mechanism of muscle damage is reviewed starting from disarray of the shock-absorbing dystrophin-associated complex at the sarcolemma and activation of inflammatory response up to the final stages of fibrosis. We trace only a part of the biochemical, physiopathological and clinical aspects of muscular dystrophy to avoid a lengthy list of different and conflicting observations. We attempt to provide a critical synthesis of what we consider important aspects to better understand the disease. In our opinion, it is becoming ever more important to go back to the bedside to validate and then translate each proposed mechanism. This article is part of a Special Issue entitled: Neuromuscular Diseases: Pathology and Molecular Pathogenesis.
Collapse
Affiliation(s)
- Vincenzo Nigro
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, via Luigi De Crecchio 7, 80138 Napoli, Italy; Telethon Institute of Genetics and Medicine (TIGEM), via Pietro Castellino 111, 80131 Napoli, Italy.
| | - Giulio Piluso
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, via Luigi De Crecchio 7, 80138 Napoli, Italy; Telethon Institute of Genetics and Medicine (TIGEM), via Pietro Castellino 111, 80131 Napoli, Italy
| |
Collapse
|
27
|
Nguyen K, Putoux A, Busa T, Cordier M, Sigaudy S, Till M, Chabrol B, Michel-Calemard L, Bernard R, Julia S, Malzac P, Labalme A, Missirian C, Edery P, Popovici C, Philip N, Sanlaville D. Incidental findings on array comparative genomic hybridization: detection of carrier females of dystrophinopathy without any family history. Clin Genet 2014; 87:488-91. [DOI: 10.1111/cge.12421] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/23/2014] [Accepted: 05/05/2014] [Indexed: 01/19/2023]
Affiliation(s)
- K. Nguyen
- Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille France
| | - A. Putoux
- Service de Génétique; Hospices Civils de Lyon; Lyon France
- CNRL, INSERM U1028, CNRS UMR5292; Université Claude Bernard Lyon 1; Lyon France
| | - T. Busa
- Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille France
| | - M.P. Cordier
- Service de Génétique; Hospices Civils de Lyon; Lyon France
| | - S. Sigaudy
- Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille France
| | - M. Till
- Service de Génétique; Hospices Civils de Lyon; Lyon France
| | - B. Chabrol
- Service de Pédiatrie et Neuropédiatrie; Hôpital d'enfants de la Timone; Marseille France
| | - L. Michel-Calemard
- Service d'Endocrinologie Moléculaire et Maladies Rares; Hospices Civils de Lyon; Lyon France
| | - R. Bernard
- Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille France
| | - S. Julia
- Service de Génétique; CHU de Toulouse; Toulouse France
| | - P. Malzac
- Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille France
- UMR 7268 ADES; Aix-Marseille Université-EFS-CNRS; Marseille France
| | - A. Labalme
- Service de Génétique; Hospices Civils de Lyon; Lyon France
| | - C. Missirian
- Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille France
| | - P. Edery
- Service de Génétique; Hospices Civils de Lyon; Lyon France
- CNRL, INSERM U1028, CNRS UMR5292; Université Claude Bernard Lyon 1; Lyon France
| | - C. Popovici
- Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille France
| | - N. Philip
- Département de Génétique Médicale; Hôpital d'enfants de la Timone; Marseille France
| | - D. Sanlaville
- Service de Génétique; Hospices Civils de Lyon; Lyon France
- CNRL, INSERM U1028, CNRS UMR5292; Université Claude Bernard Lyon 1; Lyon France
| |
Collapse
|
28
|
Shawky RM, Elsayed SM, Todorov T, Zibert A, Alawbathani S, Schmidt HHJ. Non-deletion mutations in Egyptian patients with Duchenne muscular dystrophy. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2014. [DOI: 10.1016/j.ejmhg.2014.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
|
29
|
De novo mutation in DMD gene in a patient with combined hemophilia A and Duchenne muscular dystrophy. Int J Hematol 2013; 99:184-7. [DOI: 10.1007/s12185-013-1488-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 11/26/2013] [Accepted: 11/26/2013] [Indexed: 10/25/2022]
|
30
|
Jarmin S, Kymalainen H, Popplewell L, Dickson G. New developments in the use of gene therapy to treat Duchenne muscular dystrophy. Expert Opin Biol Ther 2013; 14:209-30. [PMID: 24308293 DOI: 10.1517/14712598.2014.866087] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Duchenne muscular dystrophy (DMD) is a lethal X-linked inherited disorder characterised by progressive muscle weakness, wasting and degeneration. Although the gene affected in DMD was identified over 25 years ago, there is still no effective treatment. AREAS COVERED Here we review some of the genetic-based strategies aimed at amelioration of the DMD phenotype. A number of Phase II/III clinical trials of antisense oligonucleotide-induced exon skipping for restoration of the open reading frame (ORF) of the DMD gene have recently been completed. The potential strategies for overcoming the hurdles that appear to prevent exon skipping becoming an effective treatment for DMD currently are discussed. EXPERT OPINION The applicability of exon skipping as a therapy to DMD is restricted and the development of alternative strategies that are more encompassing is needed. The rapid pre-clinical advances that are being made in the field of adeno-associated virus (AAV)-based delivery of micro-dystrophin would address this. The obstacles to be faced with gene replacement strategies would include the need for high viral titres, efficient muscle targeting and avoidance of immune response to vector and transgene. The new emerging field of gene editing could potentially provide permanent correction of the DMD gene and the feasibility of such an approach to DMD is discussed.
Collapse
Affiliation(s)
- Susan Jarmin
- Royal Holloway University of London , Egham, Surrey , UK
| | | | | | | |
Collapse
|
31
|
Askree SH, Chin ELH, Bean LH, Coffee B, Tanner A, Hegde M. Detection limit of intragenic deletions with targeted array comparative genomic hybridization. BMC Genet 2013; 14:116. [PMID: 24304607 PMCID: PMC4235222 DOI: 10.1186/1471-2156-14-116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/12/2013] [Indexed: 11/24/2022] Open
Abstract
Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered.
Collapse
Affiliation(s)
| | | | | | | | | | - Madhuri Hegde
- Emory Genetics Laboratory, Department of Human Genetics, Emory University, 2165 N Decatur Road, Decatur, GA 30033, USA.
| |
Collapse
|
32
|
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]
|
33
|
Targeted next-generation sequencing as a comprehensive test for patients with and female carriers of DMD/BMD: a multi-population diagnostic study. Eur J Hum Genet 2013; 22:110-8. [PMID: 23756440 DOI: 10.1038/ejhg.2013.82] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/20/2013] [Accepted: 03/20/2013] [Indexed: 11/08/2022] Open
Abstract
Duchenne and Becker muscular dystrophies (DMD/BMD) are the most commonly inherited neuromuscular disease. However, accurate and convenient molecular diagnosis cannot be achieved easily because of the enormous size of the dystrophin gene and complex causative mutation spectrum. Such traditional methods as multiplex ligation-dependent probe amplification plus Sanger sequencing require multiple steps to fulfill the diagnosis of DMD/BMD. Here, we introduce a new single-step method for the genetic analysis of DMD patients and female carriers in real clinical settings and demonstrate the validation of its accuracy. A total of 89 patients, 18 female carriers and 245 non-DMD patients were evaluated using our targeted NGS approaches. Compared with traditional methods, our new method yielded 99.99% specificity and 98.96% sensitivity for copy number variations detection and 100% accuracy for the identification of single-nucleotide variation mutations. Additionally, this method is able to detect partial deletions/duplications, thus offering precise personal DMD gene information for gene therapy. We detected novel partial deletions of exons in nine samples for which the breakpoints were located within exonic regions. The results proved that our new method is suitable for routine clinical practice, with shorter turnaround time, higher accuracy, and better insight into comprehensive genetic information (detailed breakpoints) for ensuing gene therapy.
Collapse
|
34
|
Marquis-Nicholson R, Prosser D, Love JM, Love DR. Gene Dosage Analysis in a Clinical Environment: Gene-Targeted Microarrays as the Platform-of-Choice. ACTA ACUST UNITED AC 2013; 2:51-62. [PMID: 27605180 PMCID: PMC5003480 DOI: 10.3390/microarrays2020051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 01/11/2023]
Abstract
The role of gene deletion and duplication in the aetiology of disease has become increasingly evident over the last decade. In addition to the classical deletion/duplication disorders diagnosed using molecular techniques, such as Duchenne Muscular Dystrophy and Charcot-Marie-Tooth Neuropathy Type 1A, the significance of partial or whole gene deletions in the pathogenesis of a large number single-gene disorders is becoming more apparent. A variety of dosage analysis methods are available to the diagnostic laboratory but the widespread application of many of these techniques is limited by the expense of the kits/reagents and restrictive targeting to a particular gene or portion of a gene. These limitations are particularly important in the context of a small diagnostic laboratory with modest sample throughput. We have developed a gene-targeted, custom-designed comparative genomic hybridisation (CGH) array that allows twelve clinical samples to be interrogated simultaneously for exonic deletions/duplications within any gene (or panel of genes) on the array. We report here on the use of the array in the analysis of a series of clinical samples processed by our laboratory over a twelve-month period. The array has proven itself to be robust, flexible and highly suited to the diagnostic environment.
Collapse
Affiliation(s)
- Renate Marquis-Nicholson
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, P.O. Box 110031, Auckland 1148, New Zealand.
| | - Debra Prosser
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, P.O. Box 110031, Auckland 1148, New Zealand.
| | - Jennifer M Love
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, P.O. Box 110031, Auckland 1148, New Zealand.
| | - Donald R Love
- Diagnostic Genetics, LabPLUS, Auckland City Hospital, P.O. Box 110031, Auckland 1148, New Zealand.
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| |
Collapse
|
35
|
Arnold WD, Flanigan KM. A practical approach to molecular diagnostic testing in neuromuscular diseases. Phys Med Rehabil Clin N Am 2013; 23:589-608. [PMID: 22938877 DOI: 10.1016/j.pmr.2012.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Molecular diagnosis is an important aspect in the care of patients with neuromuscular disorders. Because of the rapidly evolving nature of the field, the approach to obtaining a molecular diagnosis may be challenging. This article provides a general approach to molecular diagnostic testing while reviewing the principles of genetics and genetic disorders and the indications and limitations of testing methods in common hereditary neuromuscular disorders.
Collapse
Affiliation(s)
- W David Arnold
- Division of Neuromuscular Disorders, Department of Neurology, Wexner Medical Center at the Ohio State University, The Ohio State University, 395 W. 12th Avenue, 7th Floor, Columbus, OH 43210, USA.
| | | |
Collapse
|
36
|
Hukuda ME, Escorcio R, Fernandes LAY, de Carvalho EV, Caromano FA. Evaluation Scale Development, Reliability for Sitting and Standing From the Chair for Duchenne Muscular Dystrophy. J Mot Behav 2013; 45:117-26. [DOI: 10.1080/00222895.2012.760513] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
37
|
Marquis-Nicholson R, Doherty E, Love JM, Lan CC, George AM, Thrush A, Love DR. Array-based Identification of Copy Number Changes in a Diagnostic Setting: Simultaneous gene-focused and low resolution whole human genome analysis. Sultan Qaboos Univ Med J 2013; 13:69-79. [PMID: 23573385 DOI: 10.12816/0003198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 09/06/2012] [Accepted: 10/06/2012] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVES The aim of this study was to develop and validate a comparative genomic hybridisation (CGH) array that would allow simultaneous targeted analysis of a panel of disease genes and low resolution whole genome analysis. METHODS A bespoke Roche NimbleGen 12x135K CGH array (Roche NimbleGen Inc., Madison, Wisconsin, USA) was designed to interrogate the coding regions of 66 genes of interest, with additional widely-spaced backbone probes providing coverage across the whole genome. We analysed genomic deoxyribonucleic acid (DNA) from 20 patients with a range of previously characterised copy number changes and from 8 patients who had not previously undergone any form of dosage analysis. RESULTS The custom-designed Roche NimbleGen CGH array was able to detect known copy number changes in all 20 patients. A molecular diagnosis was also made for one of the additional 4 patients with a clinical diagnosis that had not been confirmed by sequence analysis, and carrier testing for familial copy number variants was successfully completed for the remaining four patients. CONCLUSION The custom-designed CGH array described here is ideally suited for use in a small diagnostic laboratory. The method is robust, accurate, and cost-effective, and offers an ideal alternative to more conventional targeted assays such as multiplex ligation-dependent probe amplification.
Collapse
|
38
|
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.
Collapse
|
39
|
Evolution of Molecular Diagnosis of Duchenne Muscular Dystrophy. J Mol Neurosci 2013; 50:314-6. [DOI: 10.1007/s12031-013-9971-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
|
40
|
Vasson A, Leroux C, Orhant L, Boimard M, Toussaint A, Leroy C, Commere V, Ghiotti T, Deburgrave N, Saillour Y, Atlan I, Fouveaut C, Beldjord C, Valleix S, Leturcq F, Dodé C, Bienvenu T, Chelly J, Cossée M. Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes. Eur J Hum Genet 2013; 21:977-87. [PMID: 23340513 PMCID: PMC3746255 DOI: 10.1038/ejhg.2012.279] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/31/2012] [Accepted: 11/13/2012] [Indexed: 11/09/2022] Open
Abstract
The frequency of disease-related large rearrangements (referred to as copy-number mutations, CNMs) varies among genes, and search for these mutations has an important place in diagnostic strategies. In recent years, CGH method using custom-designed high-density oligonucleotide-based arrays allowed the development of a powerful tool for detection of alterations at the level of exons and made it possible to provide flexibility through the possibility of modeling chips. The aim of our study was to test custom-designed oligonucleotide CGH array in a diagnostic laboratory setting that analyses several genes involved in various genetic diseases, and to compare it with conventional strategies. To this end, we designed a 12-plex CGH array (135k; 135 000 probes/subarray) (Roche Nimblegen) with exonic and intronic oligonucleotide probes covering 26 genes routinely analyzed in the laboratory. We tested control samples with known CNMs and patients for whom genetic causes underlying their disorders were unknown. The contribution of this technique is undeniable. Indeed, it appeared reproducible, reliable and sensitive enough to detect heterozygous single-exon deletions or duplications, complex rearrangements and somatic mosaicism. In addition, it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints. All of these points, associated with the possibility of a simultaneous analysis of several genes and scalability 'homemade' make it a valuable tool as a new diagnostic approach of CNMs.
Collapse
Affiliation(s)
- Aurélie Vasson
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Biochimie et Génétique Moléculaire, Hôpital Cochin, APHP, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
|
42
|
The medical genetics of dystrophinopathies: Molecular genetic diagnosis and its impact on clinical practice. Neuromuscul Disord 2013; 23:4-14. [DOI: 10.1016/j.nmd.2012.09.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 08/23/2012] [Accepted: 09/04/2012] [Indexed: 01/01/2023]
|
43
|
Juan-Mateu J, Gallano P, Trujillo-Tiebas MJ. Recomendaciones de buena práctica para el diagnóstico genético de las distrofias musculares de Duchenne y de Becker. Med Clin (Barc) 2012; 139:307-12. [DOI: 10.1016/j.medcli.2012.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/08/2012] [Accepted: 02/09/2012] [Indexed: 01/15/2023]
|
44
|
Ishmukhametova A, Khau Van Kien P, Méchin D, Thorel D, Vincent MC, Rivier F, Coubes C, Humbertclaude V, Claustres M, Tuffery-Giraud S. Comprehensive oligonucleotide array-comparative genomic hybridization analysis: new insights into the molecular pathology of the DMD gene. Eur J Hum Genet 2012; 20:1096-100. [PMID: 22510846 DOI: 10.1038/ejhg.2012.51] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We report on the effectiveness of a custom-designed oligonucleotide-based comparative genomic hybridization microarray (array-CGH) to interrogate copy number across the entire 2.2-Mb genomic region of the DMD gene and its applicability in diagnosis. The high-resolution array-CGH, we developed, successfully detected a series of 42 previously characterized large rearrangements of various size, localization and type (simple or complex deletions, duplications, triplications) and known intronic CNVs/Indels. Moreover, the technique succeeded in identifying a small duplication of only 191 bp in one patient previously negative for DMD mutation. Accurate intronic breakpoints localization by the technique enabled subsequent junction fragments identification by sequencing in 86% of cases (all deletion cases and 62.5% of duplication cases). Sequence examination of the junctions supports a role of microhomology-mediated processes in the occurrence of DMD large rearrangements. In addition, the precise knowledge of the sequence context at the breakpoints and analysis of the resulting consequences on maturation of pre-mRNA contribute to elucidating the cause of discrepancies in phenotype/genotype correlations in some patients. Thereby, the array-CGH proved to be a highly efficient and reliable diagnostic tool, and the new data it provides will have many potential implications in both, clinics and research.
Collapse
|
45
|
A wide methodological approach to identify a large duplication in CFTR gene in a CF patient uncharacterised by sequencing analysis. J Cyst Fibros 2012; 10:412-7. [PMID: 21852204 DOI: 10.1016/j.jcf.2011.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 06/17/2011] [Accepted: 06/18/2011] [Indexed: 02/03/2023]
Abstract
BACKGROUND PCR-based diagnostic procedures are not able to characterise 6% of CF alleles. Recently, the application of array-CGH and of CFTR mRNA analysis has allowed the identification of new copy number mutations and splicing defects, that account for 2% and 13% of CF alleles, respectively, in the Italian population. METHODS Here, we report the characterisation of a large duplication in CFTR gene through different methods: MLPA assay, RT-PCR and high-resolution array-CGH. RESULTS We identified a large duplication, involving exons 6b-16, in a patient heterozygous for F508del mutation. This duplication produces an abnormal transcript with an out of frame addition of 2244 nucleotides and leads to the insertion of 8 amino-acid residues in the protein, followed by a stop codon. CONCLUSIONS We propose a wide methodological approach based on MLPA assay, RT-PCR and high-resolution array-CGH to routinely analyse CF patients uncharacterised for one or both CFTR alleles.
Collapse
|
46
|
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.
Collapse
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.)
| |
Collapse
|
47
|
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.
Collapse
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
| |
Collapse
|
48
|
Arai T, Oh-ishi T, Yamamoto H, Nunoi H, Kamizono J, Uehara M, Kubota T, Sakurai T, Kizaki T, Ohno H. Copy number variations due to large genomic deletion in X-linked chronic granulomatous disease. PLoS One 2012; 7:e27782. [PMID: 22383943 PMCID: PMC3287986 DOI: 10.1371/journal.pone.0027782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 10/25/2011] [Indexed: 01/15/2023] Open
Abstract
Mutations in genes for any of the six subunits of NADPH oxidase cause chronic granulomatous disease (CGD), but almost 2/3 of CGD cases are caused by mutations in the X-linked CYBB gene, also known as NAD (P) H oxidase 2. Approximately 260 patients with CGD have been reported in Japan, of whom 92 were shown to have mutations of the CYBB gene and 16 to have chromosomal deletions. However, there has been very little detailed analysis of the range of the deletion or close understanding of the disease based on this. We therefore analyzed genomic rearrangements in X-linked CGD using array comparative genomic hybridization analysis, revealing the extent and the types of the deletion genes. The subjects were five Japanese X-linked CGD patients estimated to have large base deletions of 1 kb or more in the CYBB gene (four male patients, one female patient) and the mothers of four of those patients. The five Japanese patients were found to range from a patient exhibiting deletions only of the CYBB gene to a female patient exhibiting an extensive DNA deletion and the DMD and CGD phenotype manifested. Of the other three patients, two exhibited CYBB, XK, and DYNLT3 gene deletions. The remaining patient exhibited both a deletion encompassing DNA subsequent to the CYBB region following intron 2 and the DYNLT3 gene and a complex copy number variation involving the insertion of an inverted duplication of a region from the centromere side of DYNLT3 into the deleted region.
Collapse
Affiliation(s)
- Takashi Arai
- Department of Clinical Research, Saitama Children's Medical Center, Saitama, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Bovolenta M, Scotton C, Falzarano MS, Gualandi F, Ferlini A. Rapid, comprehensive analysis of the dystrophin transcript by a custom micro-fluidic exome array. Hum Mutat 2012; 33:572-81. [DOI: 10.1002/humu.22017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 12/20/2011] [Indexed: 11/08/2022]
|
50
|
Flanigan KM, Dunn D, Larsen CA, Medne L, Bönnemann CB, Weiss RB. Becker muscular dystrophy due to an inversion of exons 23 and 24 of the DMD gene. Muscle Nerve 2011; 44:822-5. [PMID: 22006698 DOI: 10.1002/mus.22226] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The use of hybridization-based methods for Duchenne muscular dystrophy (DMD) mutation analysis is increasingly common. We report a case of Becker muscular dystrophy in which discrepant results between a polymerase chain reaction (PCR)-based single-condition amplification/internal primer (SCAIP) and a comparative genomic hybridization assay incompletely characterized the mutation (an inversion of exons 23 and 24). These results demonstrate the limits of sensitivity and specificity of both tests, and highlight the need for more detailed analysis when intronic deletions are detected by comparative genome hybridization methods.
Collapse
Affiliation(s)
- Kevin M Flanigan
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA
| | | | | | | | | | | |
Collapse
|