Journal article
Saturation mutagenesis-reinforced functional assays for disease-related genes
Cell, Vol.187(23), pp.6707-6724.e22
11/2024
DOI: 10.1016/j.cell.2024.08.047
PMCID: PMC11568926
PMID: 39326416
Abstract
Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods are obstacles for achieving genome-wide resolution of variants in disease-related genes. Our framework, saturation mutagenesis-reinforced functional assays (SMuRF), offers simple and cost-effective saturation mutagenesis paired with streamlined functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for all possible coding single-nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Overall, our approach enables variant-to-function insights for disease genes in a cost-effective manner that can be broadly implemented by standard research laboratories.
Details
- Title: Subtitle
- Saturation mutagenesis-reinforced functional assays for disease-related genes
- Creators
- Kaiyue Ma - Shanghai Jiao Tong UniversityShushu Huang - Yale UniversityKenneth K Ng - Yale UniversityNicole J Lake - Yale UniversitySoumya Joseph - University of IowaJenny Xu - University of New HavenAngela Lek - Muscular Dystrophy AssociationLin GeKeryn G Woodman - Center for ChildrenKatherine E Koczwara - Yale UniversityJustin Cohen - Yale UniversityVincent Ho - Yale UniversityChristine L O'Connor - Yale School of MedicineMelinda A Brindley - University of GeorgiaKevin P Campbell - University of IowaMonkol Lek - Yale University
- Resource Type
- Journal article
- Publication Details
- Cell, Vol.187(23), pp.6707-6724.e22
- DOI
- 10.1016/j.cell.2024.08.047
- PMID
- 39326416
- PMCID
- PMC11568926
- NLM abbreviation
- Cell
- ISSN
- 0092-8674
- eISSN
- 1097-4172
- Publisher
- CELL PRESS
- Grant note
- ML Bio SolutionsMuscular Dystrophy Association: 629095 Chan Zuckerberg Initiative Science Diversity Leadership Award: 2022-309740 National Institute of Neurological Disorders and Stroke of the National Institutes of Health: P50NS053672 National Institute of Allergy and Infectious Diseases of the National Institutes of Health: R01AI139238 Muscular Dystrophy Association Development Grant: MDA 963708 Chris Carrino Foundation: NIH/5F32AR079892-02 NCI Cancer Center Support Grant: NIH P30 CA016359
We thank Sander Pajusalu and Heather Best for their efforts, which helped lead to this project. We thank In-Hyun Park, Ira Hall, and Carrie Lucas for serving on K.M.'s PhD thesis committee and their suggestions regarding this study. We thank Nicholas Johnson and the GRASP LGMD consortium for granting us access to their deidentified patient data, which was funded by ML Bio Solutions. We thank Stephen Tapscott for the gift of MB135 cells. This work is supported by a grant to M.L. from the Muscular Dystrophy Association (629095) for "improved clinical interpretation of rare variants in muscle diseases." M.L. is supported by Chan Zuckerberg Initiative Science Diversity Leadership Award (2022-309740) . K.P.C. is an investigator of the Howard Hughes Medical Institute. Research reported in this publication was in part supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under Award Number P50NS053672 (K.P.C.) . M.A.B. was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award number R01AI139238 (M.A.B.) . S.H. is supported by a Muscular Dystrophy Association Development Grant (MDA 963708) . J.C. is supported by The Chris Carrino Foundation for FSHD and NIH/5F32AR079892-02. We thank Yale Flow Cytometry for their assistance with FFC and FACS services. The Core is supported in part by an NCI Cancer Center Support Grant #NIH P30 CA016359.
- Language
- English
- Electronic publication date
- 09/19/2024
- Date published
- 11/2024
- Academic Unit
- Neurology; Molecular Physiology and Biophysics; Iowa Neuroscience Institute
- Record Identifier
- 9984721144202771
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