ArticleNature genetics2023
Aberrant splicing prediction across human tissues.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 88 citations in OpenAlex.
- Reanalysis of genomic data doubles the diagnostic yield for Welsh patients recruited to the UK 100,000 Genomes Project.European journal of human genetics : EJHG · 2026Article
- Minigene-based characterization and classification of splice-associated variants in succinate dehydrogenase B.NPJ precision oncology · 2026Article
- Validation structures for sequence variants of uncertain significance in hereditary cancer.European journal of human genetics : EJHG · 2026Review
- Review
- Advances and challenges of splicing prediction with AI.Nature genetics · 2026Review
- Improving splice site usage prediction with SPLAIRE.bioRxiv : the preprint server for biology · 2026Article
- Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- Pathogenicity prediction for noncanonical splice-altering variants based on multimodal feature fusion.Briefings in bioinformatics · 2026Article
- NCBoost v2: a classifier for non-coding single-nucleotide variants in Mendelian diseases.Bioinformatics (Oxford, England) · 2026Article
- Prime editor-based high-throughput screening reveals functional synonymous mutations in human cells.Nature biotechnology · 2026Article
- Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.Cell genomics · 2026Article
- CDsyn: A comprehensive database for deleterious human synonymous variation prediction.iScience · 2026Article
- MDGA2 homozygous loss-of-function variants cause developmental and epileptic encephalopathy.American journal of human genetics · 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
- Causal splicing variants revealed by deep-learning integration of single-cell sQTL mapping under influenza infection.Research square · 2026Article
- Article
- Synonymous and non-synonymous variants at splice junctions can disrupt splicing and are frequently linked to disease associated loss of function genes.BMC genomics · 2025Article
- Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Aberrant splicing is a major cause of genetic disorders but its direct detection in transcriptomes is limited to clinically accessible tissues such as skin or body fluids. While DNA-based machine learning models can prioritize rare variants for affecting splicing, their performance in predicting tissue-specific aberrant splicing remains unassessed. Here we generated an aberrant splicing benchmark dataset, spanning over 8.8 million rare variants in 49 human tissues from the Genotype-Tissue Expression (GTEx) dataset. At 20% recall, state-of-the-art DNA-based models achieve maximum 12% precision. By mapping and quantifying tissue-specific splice site usage transcriptome-wide and modeling isoform competition, we increased precision by threefold at the same recall. Integrating RNA-sequencing data of clinically accessible tissues into our model, AbSplice, brought precision to 60%. These results, replicated in two independent cohorts, substantially contribute to noncoding loss-of-function variant identification and to genetic diagnostics design and analytics.
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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.