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Wu K, Bu F, Wu Y, Zhang G, Wang X, He S, Liu MF, Chen R, Yuan H. Exploring noncoding variants in genetic diseases: from detection to functional insights. J Genet Genomics 2024; 51:111-132. [PMID: 38181897 DOI: 10.1016/j.jgg.2024.01.001] [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: 11/05/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.
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Affiliation(s)
- Ke Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Gen Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China.
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Efthymiou S, Lemmers RJLF, Vishnu VY, Dominik N, Perrone B, Facchini S, Vegezzi E, Ravaglia S, Wilson L, van der Vliet PJ, Mishra R, Reyaz A, Ahmad T, Bhatia R, Polke JM, Srivastava MP, Cortese A, Houlden H, van der Maarel SM, Hanna MG, Bugiardini E. Optical Genome Mapping for the Molecular Diagnosis of Facioscapulohumeral Muscular Dystrophy: Advancement and Challenges. Biomolecules 2023; 13:1567. [PMID: 38002249 PMCID: PMC10669274 DOI: 10.3390/biom13111567] [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: 08/18/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 11/26/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is the second most common muscular dystrophy in adults, and it is associated with local D4Z4 chromatin relaxation, mostly via the contraction of the D4Z4 macrosatellite repeat array on chromosome 4q35. In this study, we aimed to investigate the use of Optical Genome Mapping (OGM) as a diagnostic tool for testing FSHD cases from the UK and India and to compare OGM performance with that of traditional techniques such as linear gel (LGE) and Pulsed-field gel electrophoresis (PFGE) Southern blotting (SB). A total of 6 confirmed and 19 suspected FSHD samples were processed with LGE and PFGE, respectively. The same samples were run using a Saphyr Genome-Imaging Instrument (1-color), and the data were analysed using custom EnFocus FSHD analysis. OGM was able to confirm the diagnosis of FSHD1 in all FSHD1 cases positive for SB (n = 17), and D4Z4 sizing highly correlated with PFGE-SB (p < 0.001). OGM correctly identified cases with mosaicism for the repeat array contraction (n = 2) and with a duplication of the D4Z4 repeat array. OGM is a promising new technology able to unravel structural variants in the genome and seems to be a valid tool for diagnosing FSHD1.
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Affiliation(s)
- Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (S.E.); (N.D.); (B.P.); (L.W.); (H.H.)
| | - Richard J. L. F. Lemmers
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands (S.M.v.d.M.)
| | - Venugopalan Y. Vishnu
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India; (V.Y.V.); (R.M.); (A.R.); (R.B.); (M.P.S.)
| | - Natalia Dominik
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (S.E.); (N.D.); (B.P.); (L.W.); (H.H.)
| | - Benedetta Perrone
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (S.E.); (N.D.); (B.P.); (L.W.); (H.H.)
| | - Stefano Facchini
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (S.E.); (N.D.); (B.P.); (L.W.); (H.H.)
| | - Elisa Vegezzi
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (E.V.); (S.R.)
| | | | - Lindsay Wilson
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (S.E.); (N.D.); (B.P.); (L.W.); (H.H.)
| | - Patrick J. van der Vliet
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands (S.M.v.d.M.)
| | - Rinkle Mishra
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India; (V.Y.V.); (R.M.); (A.R.); (R.B.); (M.P.S.)
| | - Alisha Reyaz
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India; (V.Y.V.); (R.M.); (A.R.); (R.B.); (M.P.S.)
| | - Tanveer Ahmad
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India; (V.Y.V.); (R.M.); (A.R.); (R.B.); (M.P.S.)
| | - Rohit Bhatia
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India; (V.Y.V.); (R.M.); (A.R.); (R.B.); (M.P.S.)
| | - James M. Polke
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, London WC1N 3BG, UK;
| | - Mv Padma Srivastava
- Department of Neurology, All India Institute of Medical Sciences, New Delhi 110029, India; (V.Y.V.); (R.M.); (A.R.); (R.B.); (M.P.S.)
| | - Andrea Cortese
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (S.E.); (N.D.); (B.P.); (L.W.); (H.H.)
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (E.V.); (S.R.)
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (S.E.); (N.D.); (B.P.); (L.W.); (H.H.)
| | - Silvère M. van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands (S.M.v.d.M.)
| | - Michael G. Hanna
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (S.E.); (N.D.); (B.P.); (L.W.); (H.H.)
| | - Enrico Bugiardini
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK; (S.E.); (N.D.); (B.P.); (L.W.); (H.H.)
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