ArticleNucleic acids research2014
In silico prediction of splice-altering single nucleotide variants in the human genome.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 321 papers.
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Who cites it
321 citing papers in PubMed.
- HiFIseek: Gene-specific enrichment of high-impact mutations in associated genomic regions.PLoS computational biology · 2026Article
- Rapid minigene workflow for functional reclassification of splicing variants in hereditary cancer diagnostics.Journal of medical genetics · 2026Article
- Splice-site variants in neurology: from molecular mechanisms to clinical interpretation - a focused review.Neurogenetics · 2026Review
- Identification ofGenes · 2026Article
- Abnormal ClC-3/TMEM9-mediated endosomal ion transport in CLCN3-associated neurodevelopmental disease.EMBO molecular medicine · 2026Article
- Asparagine Synthetase Deficiency: Neuropathological Evidence of Disrupted Cortical Development.JIMD reports · 2026Article
- Phenotypic Expansion ofGenes · 2026Article
- Integration of Machine Learning-Based Pathogenicity Prediction and Phenotype Matching Improves Variant Prioritization in Rare Clinical Testing.Current issues in molecular biology · 2026Article
- Multi-modal data integration reveals functionally credible predictive biomarkers in ovarian cancer.Genome medicine · 2026Article
- MuSA: a Nextflow pipeline for deep, reproducible annotation and clinical ranking of genomic variants.BMC bioinformatics · 2026Article
- Genetic causes of the lissencephaly spectrum: insights from chromosomal microarray and clinical/whole-exome sequencing.Croatian medical journal · 2026Article
- Comparative fine-mapping of breast cancer susceptibility loci using summary statistics methods and multinomial regression.medRxiv : the preprint server for health sciences · 2026Article
- Identification of novel biallelic mutations in CFAP53 associated with fetal situs inversus totalis and literature review.Journal of applied genetics · 2026Review
- Genetic background shapes AI-predicted variant effects.bioRxiv : the preprint server for biology · 2026Article
- Large-scale exome analyses reveal new rare variant contributions in amyotrophic lateral sclerosis.Nature genetics · 2026Article
- A novel phenotype-guided genome analysis pipeline for variant discovery.NPJ genomic medicine · 2026Article
- CDsyn: A comprehensive database for deleterious human synonymous variation prediction.iScience · 2026Article
- De novo variants in the splicing factor gene SF3B1 are associated with neurodevelopmental disorders.Nature communications · 2026Article
- Article
- Assessment of paralogue annotation for improving diagnostic accuracy inFrontiers in genetics · 2026Article
261 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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Abstract
In silico tools have been developed to predict variants that may have an impact on pre-mRNA splicing. The major limitation of the application of these tools to basic research and clinical practice is the difficulty in interpreting the output. Most tools only predict potential splice sites given a DNA sequence without measuring splicing signal changes caused by a variant. Another limitation is the lack of large-scale evaluation studies of these tools. We compared eight in silico tools on 2959 single nucleotide variants within splicing consensus regions (scSNVs) using receiver operating characteristic analysis. The Position Weight Matrix model and MaxEntScan outperformed other methods. Two ensemble learning methods, adaptive boosting and random forests, were used to construct models that take advantage of individual methods. Both models further improved prediction, with outputs of directly interpretable prediction scores. We applied our ensemble scores to scSNVs from the Catalogue of Somatic Mutations in Cancer database. Analysis showed that predicted splice-altering scSNVs are enriched in recurrent scSNVs and known cancer genes. We pre-computed our ensemble scores for all potential scSNVs across the human genome, providing a whole genome level resource for identifying splice-altering scSNVs discovered from large-scale sequencing studies.
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