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Silk M, de Sá A, Olshansky M, Ascher DB. Insights from Spatial Measures of Intolerance to Identifying Pathogenic Variants in Developmental and Epileptic Encephalopathies. Int J Mol Sci 2023; 24:ijms24065114. [PMID: 36982187 PMCID: PMC10049344 DOI: 10.3390/ijms24065114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) are a group of epilepsies with early onset and severe symptoms that sometimes lead to death. Although previous work successfully discovered several genes implicated in disease outcomes, it remains challenging to identify causative mutations within these genes from the background variation present in all individuals due to disease heterogeneity. Nevertheless, our ability to detect possible pathogenic variants has continued to improve as in silico predictors of deleteriousness have advanced. We investigate their use in prioritising likely pathogenic variants in epileptic encephalopathy patients’ whole exome sequences. We showed that the inclusion of structure-based predictors of intolerance improved upon previous attempts to demonstrate enrichment within epilepsy genes.
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Affiliation(s)
- Michael Silk
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Alex de Sá
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, VIC 3010, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, QLD 4072, Australia
| | - Moshe Olshansky
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - David B. Ascher
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Parkville, VIC 3052, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Parkville, VIC 3010, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane City, QLD 4072, Australia
- Correspondence: ; Tel.: +61-7-336-53891
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