Peer-Reviewed Publication
Hum Genet2025;144(2-3):243-251.March 1, 2025Journal Article
Predicting the impact of rare variants on RNA splicing in CAGI6.
Jenny Lord1, Carolina Jaramillo Oquendo1, Htoo A Wai1, Andrew G L Douglas1,2, David J Bunyan1,3, Yaqiong Wang4, Zhiqiang Hu5, Zishuo Zeng6, Daniel Danis7, Panagiotis Katsonis8, Amanda Williams8, Olivier Lichtarge8, Yuchen Chang9,10, Richard D Bagnall9,10, Stephen M Mount11, Brynja Matthiasardottir12,13, Chiaofeng Lin14, Thomas van Overeem Hansen15,16, Raphael Leman17,18, Alexandra Martins19, Claude Houdayer19,20, Sophie Krieger17,18, Constantina Bakolitsa5, Yisu Peng21, Akash Kamandula21, Predrag Radivojac21, Diana Baralle22,23
1Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
2Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
3Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.
4Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.
5University of California, Berkeley, Berkeley, CA, 94720, USA.
6Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08873, USA.
7The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
8Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
9Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia.
10Faculty of Medicine and Health, University of Sydney, Sydney, Australia.
11Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
12Graduate Program in Biological Sciences and Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
13Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD, USA.
14DNAnexus, Mountain View, CA, 94040, USA.
15Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark.
16Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
17Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse, Caen, France.
18Inserm U1245, Cancer Brain and Genomics, Normandie Université, UNICAEN, FHU G4 génomique, Rouen, France.
19Inserm U1245, Cancer Brain and Genomics, Normandie Université, UNIROUEN, FHU G4 génomique, Rouen, France.
20Department of Genetics, Univ Rouen Normandie, INSERM U1245, FHU-G4 Génomique and CHU Rouen, 76000, Rouen, France.
21Khoury College of Computer Sciences, Northeastern University, Boston, MA, 02115, USA.
22Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK. d.baralle@soton.ac.uk.
23Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK. d.baralle@soton.ac.uk.
Abstract
Variants which disrupt splicing are a frequent cause of rare disease that have been under-ascertained clinically. Accurate and efficient methods to predict a variant's impact on splicing are needed to interpret the growing number of variants of unknown significance (VUS) identified by exome and genome sequencing. Here, we present the results of the CAGI6 Splicing VUS challenge, which invited predi…
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