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Shen J, Ding T, Sun X, Yang J, Zhang Y, Wang J, Ge M, Xu H, Xie J, Wang F, Diao F. Comprehensive analysis of genomic complexity in the 5' end coding region of the DMD gene in patients of exons 1-2 duplications based on long-read sequencing. BMC Genomics 2024; 25:292. [PMID: 38504154 PMCID: PMC10949565 DOI: 10.1186/s12864-024-10224-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Dystrophinopathies are the most common X-linked inherited muscle diseases, and the disease-causing gene is DMD. Exonic duplications are a common type of pathogenic variants in the DMD gene, however, 5' end exonic duplications containing exon 1 are less common. When assessing the pathogenicity of exonic duplications in the DMD gene, consideration must be given to their impact on the reading frame. Traditional molecular methods, such as multiplex ligation-dependent probe amplification (MLPA) and next-generation sequencing (NGS), are commonly used in clinics. However, they cannot discriminate the precise physical locations of breakpoints and structural features of genomic rearrangement. Long-read sequencing (LRS) can effectively overcome this limitation. RESULTS We used LRS technology to perform whole genome sequencing on three families and analyze the structural variations of the DMD gene, which involves the duplications of exon 1 and/or exon 2. Two distinct variant types encompassing exon 1 in the DMD Dp427m isoform and/or Dp427c isoform are identified, which have been infrequently reported previously. In pedigree 1, the male individuals harboring duplication variant of consecutive exons 1-2 in the DMD canonical transcript (Dp427m) and exon 1 in the Dp427c transcript are normal, indicating the variant is likely benign. In pedigree 3, the patient carries complex SVs involving exon 1 of the DMD Dp427c transcript showing an obvious phenotype. The locations of the breakpoints and the characteristics of structural variants (SVs) are identified by LRS, enabling the classification of the variants' pathogenicity. CONCLUSIONS Our research sheds light on the complexity of DMD variants encompassing Dp427c/Dp427m promoter regions and emphasizes the importance of cautious interpretation when assessing the pathogenicity of DMD 5' end exonic duplications, particularly in carrier screening scenarios without an affected proband.
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Affiliation(s)
- Jiandong Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, Nanjing, 210029, China.
| | - Taoli Ding
- Yikon Genomics Company, Ltd, Jiangsu Province, Suzhou, 215000, China
| | - Xueping Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, Nanjing, 210029, China
| | - Ji Yang
- Yikon Genomics Company, Ltd, Jiangsu Province, Suzhou, 215000, China
| | - Yue Zhang
- Yikon Genomics Company, Ltd, Jiangsu Province, Suzhou, 215000, China
| | - Jing Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, Nanjing, 210029, China
| | - Mengdi Ge
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, Nanjing, 210029, China
| | - Heng Xu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, Nanjing, 210029, China
| | - Jiazi Xie
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, Nanjing, 210029, China
| | - Fei Wang
- Yikon Genomics Company, Ltd, Jiangsu Province, Suzhou, 215000, China
| | - Feiyang Diao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, Nanjing, 210029, China.
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Xie Z, Liu C, Lu Y, Sun C, Liu Y, Yu M, Shu J, Meng L, Deng J, Zhang W, Wang Z, Lv H, Yuan Y. Exonization of a deep intronic long interspersed nuclear element in Becker muscular dystrophy. Front Genet 2022; 13:979732. [PMID: 36092865 PMCID: PMC9453646 DOI: 10.3389/fgene.2022.979732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
The precise identification of pathogenic DMD variants is sometimes rather difficult, mainly due to complex structural variants (SVs) and deep intronic splice-altering variants. We performed genomic long-read whole DMD gene sequencing in a boy with asymptomatic hyper-creatine kinase-emia who remained genetically undiagnosed after standard genetic testing, dystrophin protein and DMD mRNA studies, and genomic short-read whole DMD gene sequencing. We successfully identified a novel pathogenic SV in DMD intron 1 via long-read sequencing. The deep intronic SV consists of a long interspersed nuclear element-1 (LINE-1) insertion/non-tandem duplication rearrangement causing partial exonization of the LINE-1, establishing a genetic diagnosis of Becker muscular dystrophy. Our study expands the genetic spectrum of dystrophinopathies and highlights the significant role of disease-causing LINE-1 insertions in monogenic diseases.
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Affiliation(s)
- Zhiying Xie
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Chang Liu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Yanyu Lu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Chengyue Sun
- Department of Neurology, Peking University People’s Hospital, Beijing, China
| | - Yilin Liu
- Department of Pathology, Peking Union Medical College Hospital, Beijing, China
| | - Meng Yu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Junlong Shu
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Lingchao Meng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Wei Zhang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing, China
| | - He Lv
- Department of Neurology, Peking University First Hospital, Beijing, China
- *Correspondence: Yun Yuan, ; He Lv,
| | - Yun Yuan
- Department of Neurology, Peking University First Hospital, Beijing, China
- *Correspondence: Yun Yuan, ; He Lv,
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Lambrescu I, Popa A, Manole E, Ceafalan LC, Gaina G. Application of Droplet Digital PCR Technology in Muscular Dystrophies Research. Int J Mol Sci 2022; 23:ijms23094802. [PMID: 35563191 PMCID: PMC9099497 DOI: 10.3390/ijms23094802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Although they are considered rare disorders, muscular dystrophies have a strong impact on people’s health. Increased disease severity with age, frequently accompanied by the loss of ability to walk in some people, and the lack of treatment, have directed the researchers towards the development of more effective therapeutic strategies aimed to improve the quality of life and life expectancy, slow down the progression, and delay the onset or convert a severe phenotype into a milder one. Improved understanding of the complex pathology of these diseases together with the tremendous advances in molecular biology technologies has led to personalized therapeutic procedures. Different approaches that are currently under extensive investigation require more efficient, sensitive, and less invasive methods. Due to its remarkable analytical sensitivity, droplet digital PCR has become a promising tool for accurate measurement of biomarkers that monitor disease progression and quantification of various therapeutic efficiency and can be considered a tool for non-invasive prenatal diagnosis and newborn screening. Here, we summarize the recent applications of droplet digital PCR in muscular dystrophy research and discuss the factors that should be considered to get the best performance with this technology.
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Affiliation(s)
- Ioana Lambrescu
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Alexandra Popa
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Animal Production and Public Health, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 050097 Bucharest, Romania
| | - Emilia Manole
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Laura Cristina Ceafalan
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Gisela Gaina
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Correspondence: ; Tel.: +40-21-319-2732
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