ArticleHuman mutation2021
Benchmarking deep learning splice prediction tools using functional splice assays.
Article in Human mutation, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 107 citations in OpenAlex.
- Tumor patterns and cancer risk in carriers of TP53 exonic germline variants that alter mRNA splicing.European journal of human genetics : EJHG · 2026Article
- Tackling non-canonical splicing in arrhythmogenic cardiomyopathy to reduce the uncertain significance variants burden.Journal of translational medicine · 2026Article
- DeepSAP: improved RNA-seq alignment by integrating transcriptome guidance with transformer-based splice junction scoring.Genome biology · 2026Article
- RNA Sequencing Resolves Cryptic Pathogenic Variants in Mitochondrial Disease.Annals of clinical and translational neurology · 2026Article
- A novel phenotype-guided genome analysis pipeline for variant discovery.NPJ genomic medicine · 2026Article
- The actionable transcriptome: a framework for incorporating RNA sequencing into precision oncology.Nature reviews. Clinical oncology · 2026Review
- Genetic and Molecular Characterization of Treacher Collins Syndrome in Three Mexican Families.International journal of molecular sciences · 2026Article
- Expansion of Molecular and Clinical Aspects of EPS8L2 (DFNB106)-Associated Hearing Loss Emphasizes a Potential Therapeutic Window.Molecular neurobiology · 2026Article
- Detection of alternative splicing: deep sequencing or deep learning?Briefings in bioinformatics · 2026Article
- Article
- Coexisting With Humans: Genomic and Behavioral Consequences in a Small and Isolated Bear Population.Molecular biology and evolution · 2025Article
- Genome-wide functional annotation and interpretation of splicing variants: toward RNA-targeted therapies.Journal of human genetics · 2025Review
- Hidden Splicing Variants in Inherited Retinal Degeneration: Discovery and Functional Insight.Investigative ophthalmology & visual science · 2025Article
- Unraveling the Functional Impact of Splicing Variants in Inherited Hearing Disorders Through Minigene Splicing Assays.Biomedicines · 2025Article
- Clinical and data-driven optimization of Genomiser for rare disease patients: experience from the Hong Kong Genome Project.Briefings in bioinformatics · 2025Article
- Article
- New genetic diagnoses for inherited retinal dystrophies by integrating splicing tools into NGS pipelines.NPJ genomic medicine · 2025Article
- Unraveling the complex genetic landscape of OTOF-related hearing loss: a deep dive into cryptic variants and haplotype phasing.Molecular medicine (Cambridge, Mass.) · 2025Article
- A series of reviews in familial cancer: genetic cancer risk in context variants of uncertain significance in MMR genes: which procedures should be followed?Familial cancer · 2025Review
- Establishment and clinical significance of genetic factor screening method for patients with nonobstructive azoospermia based on whole exon sequencing technology.Translational andrology and urology · 2025Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hereditary disorders are frequently caused by genetic variants that affect pre-messenger RNA splicing. Though genetic variants in the canonical splice motifs are almost always disrupting splicing, the pathogenicity of variants in the noncanonical splice sites (NCSS) and deep intronic (DI) regions are difficult to predict. Multiple splice prediction tools have been developed for this purpose, with the latest tools employing deep learning algorithms. We benchmarked established and deep learning splice prediction tools on published gold standard sets of 71 NCSS and 81 DI variants in the ABCA4 gene and 61 NCSS variants in the MYBPC3 gene with functional assessment in midigene and minigene splice assays. The selection of splice prediction tools included CADD, DSSP, GeneSplicer, MaxEntScan, MMSplice, NNSPLICE, SPIDEX, SpliceAI, SpliceRover, and SpliceSiteFinder-like. The best-performing splice prediction tool for the different variants was SpliceRover for ABCA4 NCSS variants, SpliceAI for ABCA4 DI variants, and the Alamut 3/4 consensus approach (GeneSplicer, MaxEntScacn, NNSPLICE and SpliceSiteFinder-like) for NCSS variants in MYBPC3 based on the area under the receiver operator curve. Overall, the performance in a real-time clinical setting is much more modest than reported by the developers of the tools.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.