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Lochmüller H, Bönnemann CG. The First Decade of Journal of Neuromuscular Diseases: Supporting and Advancing the Rapidly Evolving Field of Translational Research. J Neuromuscul Dis 2024; 11:1-3. [PMID: 38189763 PMCID: PMC10789322 DOI: 10.3233/jnd-249000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2023] [Indexed: 01/09/2024]
Affiliation(s)
- Hanns Lochmüller
- Children’s Hospital of Eastern Ontario Research Institute; Division of Neurology, Department of Medicine, The Ottawa Hospital; and Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - Carsten G. Bönnemann
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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Ma K, Ng KK, Huang S, Lake NJ, Xu J, Lek A, Ge L, Woodman KG, Koczwara KE, Ho V, O’Connor CL, Joseph S, Brindley MA, Campbell KP, Lek M. Deep Mutational Scanning in Disease-related Genes with Saturation Mutagenesis-Reinforced Functional Assays (SMuRF). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548370. [PMID: 37873263 PMCID: PMC10592615 DOI: 10.1101/2023.07.12.548370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods hamper crowd-sourcing approaches toward genome-wide resolution of variants in disease-related genes. Our framework, Saturation Mutagenesis-Reinforced Functional assays (SMuRF), addresses these issues by offering simple and cost-effective saturation mutagenesis, as well as streamlining functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for over 99.8% of all possible coding single nucleotide variants and resolved 310 clinically reported variants of uncertain significance with high confidence, enhancing clinical variant interpretation in dystroglycanopathies. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Our approach opens new directions for enabling variant-to-function insights for disease genes in a manner that is broadly useful for crowd-sourcing implementation across standard research laboratories.
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Affiliation(s)
- Kaiyue Ma
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Kenneth K. Ng
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Shushu Huang
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Nicole J. Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Jenny Xu
- Yale University, New Haven, CT, USA
| | - Angela Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Muscular Dystrophy Association, Chicago, IL, USA
| | - Lin Ge
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, National Center for Children’s Health, Beijing Children’s Hospital, Capital Medical University, Beijing, China
| | - Keryn G. Woodman
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Vincent Ho
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Soumya Joseph
- Howard Hughes Medical Institute, Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Molecular Physiology and Biophysics and Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Melinda A. Brindley
- Department of Infectious Diseases, Department of Population Health, University of Georgia, Athens, GA, USA
- Senior Authors
| | - Kevin P. Campbell
- Howard Hughes Medical Institute, Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Molecular Physiology and Biophysics and Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
- Senior Authors
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Senior Authors
- Lead Contact
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