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Dawes R, Bournazos AM, Bryen SJ, Bommireddipalli S, Marchant RG, Joshi H, Cooper ST. SpliceVault predicts the precise nature of variant-associated mis-splicing. Nat Genet 2023; 55:324-332. [PMID: 36747048 PMCID: PMC9925382 DOI: 10.1038/s41588-022-01293-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/15/2022] [Indexed: 02/08/2023]
Abstract
Even for essential splice-site variants that are almost guaranteed to alter mRNA splicing, no current method can reliably predict whether exon-skipping, cryptic activation or multiple events will result, greatly complicating clinical interpretation of pathogenicity. Strikingly, ranking the four most common unannotated splicing events across 335,663 reference RNA-sequencing (RNA-seq) samples (300K-RNA Top-4) predicts the nature of variant-associated mis-splicing with 92% sensitivity. The 300K-RNA Top-4 events correctly identify 96% of exon-skipping events and 86% of cryptic splice sites for 140 clinical cases subject to RNA testing, showing higher sensitivity and positive predictive value than SpliceAI. Notably, RNA re-analyses showed we had missed 300K-RNA Top-4 events for several clinical cases tested before the development of this empirical predictive method. Simply, mis-splicing events that happen around a splice site in RNA-seq data are those most likely to be activated by a splice-site variant. The SpliceVault web portal allows users easy access to 300K-RNA for informed splice-site variant interpretation and classification.
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Affiliation(s)
- Ruebena Dawes
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Adam M Bournazos
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Samantha J Bryen
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Rhett G Marchant
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Himanshu Joshi
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- The Children's Medical Research Institute, Sydney, New South Wales, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Sydney, New South Wales, Australia.
- Discipline of Child and Adolescent Health, Faculty of Health and Medicine, University of Sydney, Sydney, New South Wales, Australia.
- The Children's Medical Research Institute, Sydney, New South Wales, Australia.
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