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Wang Y, Wen X, Shen XM, Di L, Sun Y, Li Y, Zhang S, Wen Q, Wang J, Duo J, Huang Y, Lu Y, Xu M, Wang M, Chen H, Zhu W, Da Y. A rare complex structural variant of novel intragenic inversion combined with reciprocal translocation t(X;1)(p21.2;p13.3) in Duchenne muscular dystrophy. Neuromuscul Disord 2024; 39:24-29. [PMID: 38714145 DOI: 10.1016/j.nmd.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 05/09/2024]
Abstract
Structural variants (SVs) are infrequently observed in Duchenne muscular dystrophy (DMD), a condition mainly marked by deletions and point mutations in the DMD gene. SVs in DMD remain difficult to reliably detect due to the limited SV-detection capacity of conventionally used short-read sequencing technology. Herein, we present a family, a boy and his mother, with clinical signs of muscular dystrophy, elevated creatinine kinase levels, and intellectual disability. A muscle biopsy from the boy showed dystrophin deficiency. Routine molecular techniques failed to detect abnormalities in the DMD gene, however, dystrophin mRNA transcripts analysis revealed an absence of exons 59 to 79. Subsequent long-read whole-genome sequencing identified a rare complex structural variant, a 77 kb novel intragenic inversion, and a balanced translocation t(X;1)(p21.2;p13.3) rearrangement within the DMD gene, expanding the genetic spectrum of dystrophinopathy. Our findings suggested that SVs should be considered in cases where conventional molecular techniques fail to identify pathogenic variants.
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Affiliation(s)
- Yaye Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Xinmei Wen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Xin-Ming Shen
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
| | - Li Di
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yanan Sun
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yun Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Shu Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Qi Wen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Jingsi Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Jianying Duo
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yue Huang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yan Lu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Min Xu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Min Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Hai Chen
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Wenjia Zhu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China
| | - Yuwei Da
- Department of Neurology, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing 100053, China.
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Pluta N, Hoffjan S, Zimmer F, Köhler C, Lücke T, Mohr J, Vorgerd M, Nguyen HHP, Atlan D, Wolf B, Zaum AK, Rost S. Homozygous Inversion on Chromosome 13 Involving SGCG Detected by Short Read Whole Genome Sequencing in a Patient Suffering from Limb-Girdle Muscular Dystrophy. Genes (Basel) 2022; 13:genes13101752. [PMID: 36292638 PMCID: PMC9601614 DOI: 10.3390/genes13101752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/15/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
New techniques in molecular genetic diagnostics now allow for accurate diagnosis in a large proportion of patients with muscular diseases. Nevertheless, many patients remain unsolved, although the clinical history and/or the muscle biopsy give a clear indication of the involved genes. In many cases, there is a strong suspicion that the cause must lie in unexplored gene areas, such as deep-intronic or other non-coding regions. In order to find these changes, next-generation sequencing (NGS) methods are constantly evolving, making it possible to sequence entire genomes to reveal these previously uninvestigated regions. Here, we present a young woman who was strongly suspected of having a so far genetically unsolved sarcoglycanopathy based on her clinical history and muscle biopsy. Using short read whole genome sequencing (WGS), a homozygous inversion on chromosome 13 involving SGCG and LINC00621 was detected. The breakpoint in intron 2 of SGCG led to the absence of γ-sarcoglycan, resulting in the manifestation of autosomal recessive limb-girdle muscular dystrophy 5 (LGMDR5) in the young woman.
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Affiliation(s)
- Natalie Pluta
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sabine Hoffjan
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany
- Correspondence:
| | - Frederic Zimmer
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Cornelia Köhler
- Department of Neuropaediatrics, University Children’s Hospital, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Thomas Lücke
- Department of Neuropaediatrics, University Children’s Hospital, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Jennifer Mohr
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44789 Bochum, Germany
| | - Matthias Vorgerd
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44789 Bochum, Germany
| | | | - David Atlan
- Phenosystems SA, 1440 Braine le Chateau, Belgium
| | - Beat Wolf
- iCoSys, University of Applied Sciences Western Switzerland, 1700 Fribourg, Switzerland
| | - Ann-Kathrin Zaum
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- Medical Genetics Center (MGZ), 80335 Munich, Germany
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Zaum AK, Nanda I, Kress W, Rost S. Detection of pericentric inversion with breakpoint in DMD by whole genome sequencing. Mol Genet Genomic Med 2022; 10:e2028. [PMID: 35912688 PMCID: PMC9544221 DOI: 10.1002/mgg3.2028] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/25/2022] [Accepted: 07/08/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Dystrophinopathies caused by variants in the DMD gene are a well-studied muscle disease. The most common type of variant in DMD are large deletions. Very rarely reported forms of variants are chromosomal translocations, inversions and deep intronic variants (DIVs) because they are not detectable by standard diagnostic techniques (sequencing of coding sequence, copy number variant detection). This might be the reason that some clinically and histologically proven dystrophinopathy cases remain unsolved. METHODS We used whole genome sequencing (WGS) to screen the entire DMD gene for variants in one of two brothers suffering from typical muscular dystrophy with strongly elevated creatine kinase levels. RESULTS Although a pathogenic DIV could not be detected, we were able to identify a pericentric inversion with breakpoints in DMD intron 44 and Xq13.3, which could be confirmed by Sanger sequencing in the index as well as in his brother and mother. As this variation affects a major part of DMD it is most likely disease causing. CONCLUSION Our findings elucidate that WGS is capable of detecting large structural rearrangements and might be suitable for the genetic diagnostics of dystrophinopathies in the future. In particular, inversions might be a more frequent cause for dystrophinopathies as anticipated and should be considered in genetically unsolved dystrophinopathy cases.
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Affiliation(s)
- Ann-Kathrin Zaum
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Indrajit Nanda
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Wolfram Kress
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Simone Rost
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Odaira K, Kawashima F, Tamura S, Suzuki N, Tokoro M, Hayakawa Y, Suzuki A, Kanematsu T, Okamoto S, Takagi A, Katsumi A, Matsushita T, Shima M, Nogami K, Kojima T, Hayakawa F. F9 mRNA splicing aberration due to a deep Intronic structural variation in a patient with moderate hemophilia B. Thromb Res 2022; 213:91-96. [DOI: 10.1016/j.thromres.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/03/2022] [Accepted: 03/11/2022] [Indexed: 10/18/2022]
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Waldrop MA, Moore SA, Mathews KD, Darbro BW, Medne L, Finkel R, Connolly AM, Crawford TO, Drachman D, Wein N, Habib AA, Krzesniak-Swinarska MA, Zaidman CM, Collins JJ, Jokela M, Udd B, Day JW, Ortiz-Guerrero G, Statland J, Butterfield RJ, Dunn DM, Weiss RB, Flanigan KM. Intron mutations and early transcription termination in Duchenne and Becker muscular dystrophy. Hum Mutat 2022; 43:511-528. [PMID: 35165973 PMCID: PMC9901284 DOI: 10.1002/humu.24343] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 11/11/2022]
Abstract
DMD pathogenic variants for Duchenne and Becker muscular dystrophy are detectable with high sensitivity by standard clinical exome analyses of genomic DNA. However, up to 7% of DMD mutations are deep intronic and analysis of muscle-derived RNA is an important diagnostic step for patients who have negative genomic testing but abnormal dystrophin expression in muscle. In this study, muscle biopsies were evaluated from 19 patients with clinical features of a dystrophinopathy, but negative clinical DMD mutation analysis. Reverse transcription-polymerase chain reaction or high-throughput RNA sequencing methods identified 19 mutations with one of three pathogenic pseudoexon types: deep intronic point mutations, deletions or insertions, and translocations. In association with point mutations creating intronic splice acceptor sites, we observed the first examples of DMD pseudo 3'-terminal exon mutations causing high efficiency transcription termination within introns. This connection between splicing and premature transcription termination is reminiscent of U1 snRNP-mediating telescripting in sustaining RNA polymerase II elongation across large genes, such as DMD. We propose a novel classification of three distinct types of mutations identifiable by muscle RNA analysis, each of which differ in potential treatment approaches. Recognition and appropriate characterization may lead to therapies directed toward full-length dystrophin expression for some patients.
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Affiliation(s)
- Megan A. Waldrop
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205,Department of Neurology, The Ohio State University, Columbus, OH 43205,Department of Pediatrics, The Ohio State University, Columbus, OH 43205
| | - Steven A. Moore
- Department of Pathology, The University of Iowa, Iowa City, IA, 52242
| | | | | | - Livja Medne
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Anne M. Connolly
- Department of Neurology, Washington University, Saint Louis, MO 63110
| | | | | | - Nicolas Wein
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205
| | | | | | - Craig M. Zaidman
- Department of Neurology, Washington University, Saint Louis, MO 63110
| | - James J. Collins
- Department of Pediatric Neurology, Mercy Hospitals, Springfield, MO 65804
| | - Manu Jokela
- Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland,Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland
| | - Bjarne Udd
- Neuromuscular Research Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - John W. Day
- Department of Neurology, University of Minnesota Medical Center, Minneapolis, MN 55454
| | | | - Jeff Statland
- Department of Neurology, University of Kansas, Kansas City, KS
| | - Russell J. Butterfield
- Department of Pediatrics, The University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Diane M. Dunn
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Robert B. Weiss
- Department of Pediatrics, The University of Utah School of Medicine, Salt Lake City, UT 84112,Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Kevin M. Flanigan
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH 43205,Department of Neurology, The Ohio State University, Columbus, OH 43205,Department of Pediatrics, The Ohio State University, Columbus, OH 43205
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6
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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Integrating Whole-Genome Sequencing in Clinical Genetics: A Novel Disruptive Structural Rearrangement Identified in the Dystrophin Gene ( DMD). Int J Mol Sci 2021; 23:ijms23010059. [PMID: 35008485 PMCID: PMC8744749 DOI: 10.3390/ijms23010059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
While in most patients the identification of genetic alterations causing dystrophinopathies is a relatively straightforward task, a significant number require genomic and transcriptomic approaches that go beyond a routine diagnostic set-up. In this work, we present a Becker Muscular Dystrophy patient with elevated creatinine kinase levels, progressive muscle weakness, mild intellectual disability and a muscle biopsy showing dystrophic features and irregular dystrophin labelling. Routine molecular techniques (Southern-blot analysis, multiplex PCR, MLPA and genomic DNA sequencing) failed to detect a defect in the DMD gene. Muscle DMD transcript analysis (RT-PCR and cDNA-MLPA) showed the absence of exons 75 to 79, seen to be present at the genomic level. These results prompted the application of low-coverage linked-read whole-genome sequencing (WGS), revealing a possible rearrangement involving DMD intron 74 and a region located upstream of the PRDX4 gene. Breakpoint PCR and Sanger sequencing confirmed the presence of a ~8 Mb genomic inversion. Aberrant DMD transcripts were subsequently identified, some of which contained segments from the region upstream of PRDX4. Besides expanding the mutational spectrum of the disorder, this study reinforces the importance of transcript analysis in the diagnosis of dystrophinopathies and shows how WGS has a legitimate role in clinical laboratory genetics.
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8
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Abstract
The DMD gene is the largest in the human genome, with a total intron content exceeding 2.2Mb. In the decades since DMD was discovered there have been numerous reported cases of pseudoexons (PEs) arising in the mature DMD transcripts of some individuals, either as the result of mutations or as low-frequency errors of the spliceosome. In this review, I collate from the literature 58 examples of DMD PEs and examine the diversity and commonalities of their features. In particular, I note the high frequency of PEs that arise from deep intronic SNVs and discuss a possible link between PEs induced by distal mutations and the regulation of recursive splicing.
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Affiliation(s)
- Niall P Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University and Perron Institute, Perth, Australia
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9
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Xu Y, Wang H, Xiao B, Wei W, Liu Y, Ye H, Ying X, Chen Y, Liu X, Ji X, Sun Y. Novel noncontiguous duplications identified with a comprehensive mutation analysis in the DMD gene by DMD gene-targeted sequencing. Gene 2017; 645:113-118. [PMID: 29273555 DOI: 10.1016/j.gene.2017.12.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/01/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022]
Abstract
Genomic rearrangements, such as intragenic deletions and duplications, are the most prevalent types of mutation in the DMD gene, and DMD mutations underlie Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Using multiplex ligation dependent probe amplification (MLPA) and DMD gene-targeted sequencing, we performed a molecular characterization of two cases of complex noncontiguous duplication rearrangements that involved inverted duplications. The breakpoint sequences were analyzed to investigate the mechanisms of the rearrangement. The two cases shared the same duplication events (Dup-nml-Dup/inv), and both involved microhomology and small insertions at the breakpoints. Additionally, in case 1, SNP sequencing results indicated that the de novo duplication mutation arose in the allele that originated from the grandfather. This study has identified a novel type of DMD complex rearrangement and provides insight into the molecular basis of this genomic rearrangement.
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Affiliation(s)
- Yan Xu
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Huanhuan Wang
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Bing Xiao
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Wei Wei
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Yu Liu
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Hui Ye
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Xiaomin Ying
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Yingwei Chen
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqing Liu
- Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China; Department of Pediatric Neurology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xing Ji
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China.
| | - Yu Sun
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China.
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10
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Normal and altered pre-mRNA processing in the DMD gene. Hum Genet 2017; 136:1155-1172. [DOI: 10.1007/s00439-017-1820-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
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11
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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12
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Yatsenko AN, Georgiadis AP, Röpke A, Berman AJ, Jaffe T, Olszewska M, Westernströer B, Sanfilippo J, Kurpisz M, Rajkovic A, Yatsenko SA, Kliesch S, Schlatt S, Tüttelmann F. X-linked TEX11 mutations, meiotic arrest, and azoospermia in infertile men. N Engl J Med 2015; 372:2097-107. [PMID: 25970010 PMCID: PMC4470617 DOI: 10.1056/nejmoa1406192] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The genetic basis of nonobstructive azoospermia is unknown in the majority of infertile men. METHODS We performed array comparative genomic hybridization testing in blood samples obtained from 15 patients with azoospermia, and we performed mutation screening by means of direct Sanger sequencing of the testis-expressed 11 gene (TEX11) open reading frame in blood and semen samples obtained from 289 patients with azoospermia and 384 controls. RESULTS We identified a 99-kb hemizygous loss on chromosome Xq13.2 that involved three TEX11 exons. This loss, which was identical in 2 patients with azoospermia, predicts a deletion of 79 amino acids within the meiosis-specific sporulation domain SPO22. Our subsequent mutation screening showed five novel TEX11 mutations: three splicing mutations and two missense mutations. These mutations, which occurred in 7 of 289 men with azoospermia (2.4%), were absent in 384 controls with normal sperm concentrations (P=0.003). Notably, five of those TEX11 mutations were detected in 33 patients (15%) with azoospermia who received a diagnosis of azoospermia with meiotic arrest. Meiotic arrest in these patients resembled the phenotype of Tex11-deficient male mice. Immunohistochemical analysis showed specific cytoplasmic TEX11 expression in late spermatocytes, as well as in round and elongated spermatids, in normal human testes. In contrast, testes of patients who had azoospermia with TEX11 mutations had meiotic arrest and lacked TEX11 expression. CONCLUSIONS In our study, hemizygous TEX11 mutations were a common cause of meiotic arrest and azoospermia in infertile men. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- Alexander N Yatsenko
- From the Departments of Obstetrics, Gynecology, and Reproductive Sciences (A.N.Y., A.P.G., J.S., A. Rajkovic, S.A.Y.) and Urology (T.J.), University of Pittsburgh School of Medicine, and the Department of Biological Sciences, University of Pittsburgh, Kenneth P. Dietrich School of Arts and Sciences (A.J.B.) - all in Pittsburgh; the Institute of Human Genetics (A. Röpke, F.T.) and Center of Reproductive Medicine and Andrology (B.W., S.K., S.S.), University of Münster, Münster, Germany; and the Department of Reproductive Biology and Stem Cells, Institute of Human Genetics, Polish Academy of Sciences, Poznań (M.O., M.K.)
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Baskin B, Stavropoulos DJ, Rebeiro PA, Orr J, Li M, Steele L, Marshall CR, Lemire EG, Boycott KM, Gibson W, Ray PN. Complex genomic rearrangements in the dystrophin gene due to replication-based mechanisms. Mol Genet Genomic Med 2014; 2:539-47. [PMID: 25614876 PMCID: PMC4303224 DOI: 10.1002/mgg3.108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 01/01/2023] Open
Abstract
Genomic rearrangements such as intragenic deletions and duplications are the most prevalent type of mutations in the dystrophin gene resulting in Duchenne and Becker muscular dystrophy (D/BMD). These copy number variations (CNVs) are nonrecurrent and can result from either nonhomologous end joining (NHEJ) or microhomology-mediated replication-dependent recombination (MMRDR). We characterized five DMD patients with complex genomic rearrangements using a combination of MLPA/mRNA transcript analysis/custom array comparative hybridization arrays (CGH) and breakpoint sequence analysis to investigate the mechanisms for these rearrangements. Two patients had complex rearrangements that involved microhomologies at breakpoints. One patient had a noncontiguous insertion of 89.7 kb chromosome 4 into intron 43 of DMD involving three breakpoints with 2–5 bp microhomology at the junctions. A second patient had an inversion of exon 44 flanked by intronic deletions with two breakpoint junctions each showing 2 bp microhomology. The third patient was a female with an inherited deletion of exon 47 in DMD on the maternal allele and a de novo noncontiguous duplication of exons 45–49 in DMD and MID1 on the paternal allele. The other two patients harbored complex noncontiguous duplications within the dystrophin gene. We propose a replication-based mechanisms for all five complex DMD rearrangements. This study identifies additional underlying mechanisms in DMD, and provides insight into the molecular bases of these genomic rearrangements.
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Affiliation(s)
- Berivan Baskin
- Department of Immunology, Genetics and Pathology, The Rudbeck Laboratory, Uppsala University Uppsala, Sweden ; The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada ; Department of Laboratory Medicine and Pathology, University of Toronto Toronto, Ontario, Canada ; Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Paige A Rebeiro
- The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Jennifer Orr
- Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Martin Li
- Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Leslie Steele
- Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada ; Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada
| | - Edmond G Lemire
- Division of Medical Genetics, Royal University Hospital & University of Saskatchewan Saskatoon, Saskatchewan, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario Ottawa, Ontario, Canada
| | - William Gibson
- Department of Medical Genetics, Child and Family Research Institute, The University of British Columbia Vancouver, British Columbia, Canada
| | - Peter N Ray
- The Centre for Applied Genomics, The Hospital for Sick Children Toronto, Ontario, Canada ; Division of Molecular Genetics, The Hospital for Sick Children Toronto, Ontario, Canada ; Department of Molecular Genetics, The University of Toronto Toronto, Ontario, Canada
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15
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Gedicke-Hornung C, Behrens-Gawlik V, Reischmann S, Geertz B, Stimpel D, Weinberger F, Schlossarek S, Précigout G, Braren I, Eschenhagen T, Mearini G, Lorain S, Voit T, Dreyfus PA, Garcia L, Carrier L. Rescue of cardiomyopathy through U7snRNA-mediated exon skipping in Mybpc3-targeted knock-in mice. EMBO Mol Med 2013; 5:1128-45. [PMID: 23716398 PMCID: PMC3721478 DOI: 10.1002/emmm.201202168] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 04/19/2013] [Accepted: 04/19/2013] [Indexed: 11/26/2022] Open
Abstract
Exon skipping mediated by antisense oligoribonucleotides (AON) is a promising therapeutic approach for genetic disorders, but has not yet been evaluated for cardiac diseases. We investigated the feasibility and efficacy of viral-mediated AON transfer in a Mybpc3-targeted knock-in (KI) mouse model of hypertrophic cardiomyopathy (HCM). KI mice carry a homozygous G>A transition in exon 6, which results in three different aberrant mRNAs. We identified an alternative variant (Var-4) deleted of exons 5–6 in wild-type and KI mice. To enhance its expression and suppress aberrant mRNAs we designed AON-5 and AON-6 that mask splicing enhancer motifs in exons 5 and 6. AONs were inserted into modified U7 small nuclear RNA and packaged in adeno-associated virus (AAV-U7-AON-5+6). Transduction of cardiac myocytes or systemic administration of AAV-U7-AON-5+6 increased Var-4 mRNA/protein levels and reduced aberrant mRNAs. Injection of newborn KI mice abolished cardiac dysfunction and prevented left ventricular hypertrophy. Although the therapeutic effect was transient and therefore requires optimization to be maintained over an extended period, this proof-of-concept study paves the way towards a causal therapy of HCM.
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Affiliation(s)
- Christina Gedicke-Hornung
- Department of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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16
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Abstract
Antisense-mediated exon skipping to restore the disrupted dystrophin reading frame is currently in clinical trials for Duchenne muscular dystrophy. This chapter describes the rationale of this approach and gives an overview of in vitro and in vivo experiments with antisense oligonucleotides and antisense genes. Finally, an overview of clinical trials is given and outstanding questions and hurdles are discussed.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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17
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Trump N, Cullup T, Verheij JBGM, Manzur A, Muntoni F, Abbs S, Jungbluth H. X-linked myotubular myopathy due to a complex rearrangement involving a duplication of MTM1 exon 10. Neuromuscul Disord 2011; 22:384-8. [PMID: 22153990 DOI: 10.1016/j.nmd.2011.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 11/11/2011] [Accepted: 11/16/2011] [Indexed: 11/18/2022]
Abstract
X-linked myotubular myopathy is a predominantly severe congenital myopathy with central nuclei on muscle biopsy due to mutations in the MTM1 gene encoding myotubularin. We report a boy with typical features of X-linked myotubular myopathy. Sequencing of the MTM1 gene did not reveal any causative mutations. Subsequent MLPA analysis identified a duplication of MTM1 exon 10 both in the patient and his mother. Additional quantitative fluorescent PCR and long-range PCR revealed an additional large deletion (2536bp) within intron 10, 143bp downstream of exon 10, and confirmed the duplication of exon 10. Our findings suggest that complex rearrangements have to be considered in typically affected males with X-linked myotubular myopathy.
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Affiliation(s)
- N Trump
- DNA Laboratory, GSTS Pathology, Guy's Hospital, London, UK.
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18
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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.
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Affiliation(s)
- Kevin M Flanigan
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, Ohio, USA
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19
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Khelifi MM, Ishmukhametova A, Khau Van Kien P, Thorel D, Méchin D, Perelman S, Pouget J, Claustres M, Tuffery-Giraud S. Pure intronic rearrangements leading to aberrant pseudoexon inclusion in dystrophinopathy: a new class of mutations? Hum Mutat 2011; 32:467-75. [PMID: 21305657 DOI: 10.1002/humu.21471] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 01/20/2011] [Indexed: 12/12/2022]
Abstract
We report on two unprecedented cases of pseudoexon (PE) activation in the DMD gene resulting from pure intronic double-deletion events that possibly involve microhomology-mediated mechanisms. Array comparative genomic hybridization analysis and direct genomic sequencing allowed us to elucidate the causes of the pathological PE inclusion detected in the RNA of the patients. In the first case (Duchenne phenotype), we showed that the inserted 387-bp PE was originated from an inverted ∼57 kb genomic region of intron 44 flanked by two deleted ∼52 kb and ∼1 kb segments. In the second case (Becker phenotype), we identified in intron 56 two small deletions of 592 bp (del 1) and 29 bp (del 2) directly flanking a 166-bp PE located in very close proximity (134 bp) to exon 57. The key role of del 1 in PE activation was established by using splicing reporter minigenes. However, the analysis of mutant constructs failed to identify cis elements that regulate the inclusion of the PE and suggested that other splicing regulatory factors may be involved such as RNA structure. Our study introduces a new class of mutations in the DMD gene and emphasizes the potential role of underdetected intronic rearrangements in human diseases.
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Baskin B, Gibson WT, Ray PN. Duchenne muscular dystrophy caused by a complex rearrangement between intron 43 of the DMD gene and chromosome 4. Neuromuscul Disord 2011; 21:178-82. [DOI: 10.1016/j.nmd.2010.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 11/15/2010] [Indexed: 10/18/2022]
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21
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Rimessi P, Fabris M, Bovolenta M, Bassi E, Falzarano S, Gualandi F, Rapezzi C, Coccolo F, Perrone D, Medici A, Ferlini A. Antisense modulation of both exonic and intronic splicing motifs induces skipping of a DMD pseudo-exon responsible for x-linked dilated cardiomyopathy. Hum Gene Ther 2010; 21:1137-46. [PMID: 20486769 DOI: 10.1089/hum.2010.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Antisense-mediated exon skipping has proven to be efficacious for subsets of Duchenne muscular dystrophy mutations. This approach is based on targeting specific splicing motifs that interfere with the spliceosome assembly by steric hindrance. Proper exon recognition by the splicing machinery is thought to depend on exonic splicing enhancer sequences, often characterized by purine-rich stretches, representing potential targets for antisense-mediated exon skipping. We identified and functionally characterized two purine-rich regions located within dystrophin intron 11 and involved in splicing regulation of a pseudo-exon. A functional role for these sequences was suggested by a pure intronic DMD deletion causing X-linked dilated cardiomyopathy through the prevalent cardiac incorporation of the aberrant pseudo-exon, marked as Alu-exon, into the dystrophin transcript. The first splicing sequence is contained within the pseudo-exon, whereas the second is localized within its 3' intron. We demonstrated that the two sequences actually behave as splicing enhancers in cell-free splicing assays because their deletion strongly interferes with the pseudo-exon inclusion. Cell-free results were then confirmed in myogenic cells derived from the patient with X-linked dilated cardiomyopathy, by targeting the identified motifs with antisense molecules and obtaining a reduction in dystrophin pseudo-exon recognition. The splicing motifs identified could represent target sequences for a personalized molecular therapy in this particular DMD mutation. Our results demonstrated for the first time the role of intronic splicing sequences in antisense modulation with implications in exon skipping-mediated therapeutic approaches.
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Affiliation(s)
- Paola Rimessi
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Italy.
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22
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Bauman J, Jearawiriyapaisarn N, Kole R. Therapeutic potential of splice-switching oligonucleotides. Oligonucleotides 2010; 19:1-13. [PMID: 19125639 DOI: 10.1089/oli.2008.0161] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Alternative splicing enables a single pre-messenger RNA transcript to yield multiple protein isoforms, making it a major contributor to the diversity of the proteome. While this process is essential for normal development, aberrations in alternative splicing are the cause of a multitude of human diseases. Methods for manipulating alternative splicing would thus be of therapeutic value. Chemically modified antisense oligonucleotides that alter alternative splicing by directing splice site selection have been developed to achieve this end. These splice-switching oligonucleotides (SSOs) have been applied to correct aberrant splicing, induce expression of a therapeutic splice variant, or induce expression of a novel therapeutic splice variant in a number of disease-relevant genes. Recently, in vivo efficacy of SSOs has been reported using animal disease models, as well as in results from the first clinical trial.
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Affiliation(s)
- John Bauman
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
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23
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Stapelbroek JM, van Erpecum KJ, Klomp LWJ, Houwen RHJ. Liver disease associated with canalicular transport defects: current and future therapies. J Hepatol 2010; 52:258-71. [PMID: 20034695 DOI: 10.1016/j.jhep.2009.11.012] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Bile formation at the canalicular membrane is a delicate process. This is illustrated by inherited liver diseases due to mutations in ATP8B1, ABCB11, ABCB4, ABCC2 and ABCG5/8, all encoding hepatocanalicular transporters. Effective treatment of these canalicular transport defects is a clinical and scientific challenge that is still ongoing. Current evidence indicates that ursodeoxycholic acid (UDCA) can be effective in selected patients with PFIC3 (ABCB4 deficiency), while rifampicin reduces pruritus in patients with PFIC1 (ATP8B1 deficiency) and PFIC2 (ABCB11 deficiency), and might abort cholestatic episodes in BRIC (mild ATP8B1 or ABCB11 deficiency). Cholestyramine is essential in the treatment of sitosterolemia (ABCG5/8 deficiency). Most patients with PFIC1 and PFIC2 will benefit from partial biliary drainage. Nevertheless liver transplantation is needed in a substantial proportion of these patients, as it is in PFIC3 patients. New developments in the treatment of canalicular transport defects by using nuclear receptors as a target, enhancing the expression of the mutated transporter protein by employing chaperones, or by mutation specific therapy show substantial promise. This review will focus on the therapy that is currently available as well as on those developments that are likely to influence clinical practice in the near future.
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Affiliation(s)
- Janneke M Stapelbroek
- Department of Paediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
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24
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Dhir A, Buratti E. Alternative splicing: role of pseudoexons in human disease and potential therapeutic strategies. FEBS J 2010; 277:841-55. [PMID: 20082636 DOI: 10.1111/j.1742-4658.2009.07520.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
What makes a nucleotide sequence an exon (or an intron) is a question that still lacks a satisfactory answer. Indeed, most eukaryotic genes are full of sequences that look like perfect exons, but which are nonetheless ignored by the splicing machinery (hence the name 'pseudoexons'). The existence of these pseudoexons has been known since the earliest days of splicing research, but until recently the tendency has been to view them as an interesting, but rather rare, curiosity. In recent years, however, the importance of pseudoexons in regulating splicing processes has been steadily revalued. Even more importantly, clinically oriented screening studies that search for splicing mutations are beginning to uncover a situation where aberrant pseudoexon inclusion as a cause of human disease is more frequent than previously thought. Here we aim to provide a review of the mechanisms that lead to pseudoexon activation in human genes and how the various cis- and trans-acting cellular factors regulate their inclusion. Moreover, we list the potential therapeutic approaches that are being tested with the aim of inhibiting their inclusion in the final mRNA molecules.
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Affiliation(s)
- Ashish Dhir
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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25
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Abstract
PURPOSE OF REVIEW Duchenne muscular dystrophy is a progressive muscle degenerative disease caused by dystrophin mutations. The purpose of this review is to highlight two emerging therapies designed to repair the primary genetic defect, called 'exon skipping' and 'nonsense codon suppression'. RECENT FINDINGS A drug, PTC124, was identified that suppresses nonsense codon translation termination. PTC124 can lead to restoration of some dystrophin expression in human Duchenne muscular dystrophy muscles with mutations resulting in premature stops. Two drugs developed for exon skipping, PRO051 and AVI-4658, result in the exclusion of exon 51 from mature mRNA. They can restore the translational reading frame to dystrophin transcripts from patients with a particular subset of dystrophin gene deletions and lead to some restoration of dystrophin expression in affected boys' muscle in vivo. Both approaches have concluded phase I trials with no serious adverse events. SUMMARY These novel therapies that act to correct the primary genetic defect of dystrophin deficiency are among the first generation of therapies tailored to correct specific mutations in humans. Thus, they represent paradigm forming approaches to personalized medicine with the potential to lead to life changing treatment for those affected by Duchenne muscular dystrophy.
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26
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Chou LS, Liu CSJ, Boese B, Zhang X, Mao R. DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: neurofibromatosis type 1 gene as a model. Clin Chem 2009; 56:62-72. [PMID: 19910506 DOI: 10.1373/clinchem.2009.132639] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND The introduction and use of next-generation sequencing (NGS) techniques have taken genomic research into a new era; however, implementing such powerful techniques in diagnostics laboratories for applications such as resequencing of targeted disease genes requires attention to technical issues, including sequencing template enrichment, management of massive data, and high interference by homologous sequences. METHODS In this study, we investigated a process for enriching DNA samples that uses a customized high-density oligonucleotide microarray to enrich a targeted 280-kb region of the NF1 (neurofibromin 1) gene. The captured DNA was sequenced with the Roche/454 GS FLX system. Two NF1 samples (CN1 and CN2) with known genotypes were tested with this protocol. RESULTS Targeted microarray capture may also capture sequences from nontargeted regions in the genome. The capture specificity estimated for the targeted NF1 region was approximately 60%. The de novo Alu insertion was partially detected in sample CN1 by additional de novo assembly with 50% base-match stringency; the single-base deletion in sample CN2 was successfully detected by reference mapping. Interferences by pseudogene sequences were removed by means of dual-mode reference-mapping analysis, which reduced the risk of generating false-positive data. The risk of generating false-negative data was minimized with higher sequence coverage (>30x). CONCLUSIONS We used a clinically relevant complex genomic target to evaluate a microarray-based sample-enrichment process and an NGS instrument for clinical resequencing purposes. The results allowed us to develop a systematic data-analysis strategy and algorithm to fit potential clinical applications.
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Affiliation(s)
- Lan-Szu Chou
- Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, UT 84108-1221, USA
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27
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Le Roy F, Charton K, Lorson CL, Richard I. RNA-targeting approaches for neuromuscular diseases. Trends Mol Med 2009; 15:580-91. [PMID: 19906562 DOI: 10.1016/j.molmed.2009.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 09/25/2009] [Accepted: 10/08/2009] [Indexed: 12/16/2022]
Abstract
Although most molecular therapy strategies for genetic diseases are based on gene replacement, interesting alternative approaches target RNA. These strategies rely on the modification of the mutated gene's expression in vivo by modulating pre-mRNA splicing, mRNA stability or mRNA translation. Here, we review recent progress using these RNA-based approaches in the field of muscle and muscle-related genetic diseases. Different molecular tools, including modified antisense oligonucleotides, pre-mRNA trans-splicing molecules, ribozymes or chemical compounds have been used successfully on patient cells or animal models of disease. These diverse strategies show tremendous therapeutic potential and several clinical trials have been initiated with Duchenne muscular dystrophy patients with promising results.
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Affiliation(s)
- Florence Le Roy
- Généthon, CNRS/UEVE UMR8587 LAMBE, 1, rue de l'Internationale, 91000 Evry, France
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28
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Aartsma-Rus A, van Ommen GJB. Progress in therapeutic antisense applications for neuromuscular disorders. Eur J Hum Genet 2009; 18:146-53. [PMID: 19809477 DOI: 10.1038/ejhg.2009.160] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Neuromuscular disorders are a frequent cause of chronic disability in man. They often result from mutations in single genes and are thus, in principle, well suited for gene therapy. However, the tissues involved (muscle and the central nervous system) are post-mitotic, which poses a challenge for most viral vectors. In some cases, alternative approaches may use small molecules, for example, antisense oligonucleotides (AONs). These do not deliver a new gene, but rather modulate existing gene products or alter the utilization of pathways. For Duchenne muscular dystrophy, this approach is in early phase clinical trials, and for two other common neuromuscular disorders (spinal muscular atrophy and myotonic dystrophy), significant preclinical advances have recently been made.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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29
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Zhang F, Carvalho CMB, Lupski JR. Complex human chromosomal and genomic rearrangements. Trends Genet 2009; 25:298-307. [PMID: 19560228 DOI: 10.1016/j.tig.2009.05.005] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 05/14/2009] [Accepted: 05/19/2009] [Indexed: 01/08/2023]
Abstract
Copy number variation (CNV) is a major source of genetic variation among humans. In addition to existing as benign polymorphisms, CNVs can also convey clinical phenotypes, including genomic disorders, sporadic diseases and complex human traits. CNV results from genomic rearrangements that can represent simple deletion or duplication of a genomic segment, or be more complex. Complex chromosomal rearrangements (CCRs) have been known for some time but their mechanisms have remained elusive. Recent technology advances and high-resolution human genome analyses have revealed that complex genomic rearrangements can account for a large fraction of non-recurrent rearrangements at a given locus. Various mechanisms, most of which are DNA-replication-based, for example fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR), have been proposed for generating such complex genomic rearrangements and are probably responsible for CCR.
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Affiliation(s)
- Feng Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, and Texas Children's Hospital, Houston, TX 77030, USA
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30
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Regional genomic instability predisposes to complex dystrophin gene rearrangements. Hum Genet 2009; 126:411-23. [PMID: 19449031 DOI: 10.1007/s00439-009-0679-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 04/29/2009] [Indexed: 10/20/2022]
Abstract
Mutations in the dystrophin gene (DMD) cause Duchenne and Becker muscular dystrophies and the majority of cases are due to DMD gene rearrangements. Despite the high incidence of these aberrations, little is known about their causative molecular mechanism(s). We examined 792 DMD/BMD clinical samples by oligonucleotide array-CGH and report on the junction sequence analysis of 15 unique deletion cases and three complex intragenic rearrangements to elucidate potential underlying mechanism(s). Furthermore, we present three cases with intergenic rearrangements involving DMD and neighboring loci. The cases with intragenic rearrangements include an inversion with flanking deleted sequences; a duplicated segment inserted in direct orientation into a deleted region; and a splicing mutation adjacent to a deletion. Bioinformatic analysis demonstrated that 7 of 12 breakpoints combined among 3 complex cases aligned with repetitive sequences, as compared to 4 of 30 breakpoints for the 15 deletion cases. Moreover, the inversion/deletion case may involve a stem-loop structure that has contributed to the initiation of this rearrangement. For the duplication/deletion and splicing mutation/deletion cases, the presence of the first mutation, either a duplication or point mutation, may have elicited the deletion events in an attempt to correct preexisting mutations. While NHEJ is one potential mechanism for these complex rearrangements, the highly complex junction sequence of the inversion/deletion case suggests the involvement of a replication-based mechanism. Our results support the notion that regional genomic instability, aided by the presence of repetitive elements, a stem-loop structure, and possibly preexisting mutations, may elicit complex rearrangements of the DMD gene.
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