ArticleCancers2021
Role of Splicing Regulatory Elements and In Silico Tools Usage in the Identification of Deep Intronic Splicing Variants in Hereditary Breast/Ovarian Cancer Genes.
Article in Cancers, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed, 29 citations in OpenAlex.
- Splice-site variants in neurology: from molecular mechanisms to clinical interpretation - a focused review.Neurogenetics · 2026Review
- Tumor patterns and cancer risk in carriers of TP53 exonic germline variants that alter mRNA splicing.European journal of human genetics : EJHG · 2026Article
- Artificial Intelligence in Rare Diseases: Workflow-Integrated Precision Kidney Care.Clinics and practice · 2026Review
- Investigating the contribution of rare non-coding variants in BRCA1, BRCA2 and PALB2 to hereditary breast cancer.NPJ breast cancer · 2026Article
- Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes.Genome research · 2024Article
- Association Between the rs13306703 and rs8192288 Variants of theDiseases (Basel, Switzerland) · 2024Article
- QR-1011 restores defective ABCA4 splicing caused by multiple severe ABCA4 variants underlying Stargardt disease.Scientific reports · 2024Article
- Characterization and Engineered U1 snRNA Rescue of Splicing Variants in a Turkish Neurodevelopmental Disease Cohort.Human mutation · 2024Article
- Unraveling noncoding DNA variants and epimutations: a paradigm shift in hereditary cancer research.Future oncology (London, England) · 2024Review
- Stargardt disease-associated missense and synonymous ABCA4 variants result in aberrant splicing.Human molecular genetics · 2023Article
- PDIVAS: Pathogenicity predictor for Deep-Intronic Variants causing Aberrant Splicing.BMC genomics · 2023Article
- Introns and Their Therapeutic Applications in Biomedical Researches.Iranian journal of biotechnology · 2023Review
- SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion.Bioinformatics (Oxford, England) · 2023Article
- Splicing Analysis ofHuman mutation · 2023Article
- Computational prediction of human deep intronic variation.GigaScience · 2022Review
- Article
- Minigene-based splicing analysis and ACMG/AMP-based tentative classification of 56 ATM variants.The Journal of pathology · 2022Article
- Phenotype fromGlobal medical genetics · 2022Article
- Identification of an elusive spliceogenic MYBPC3 variant in an otherwise genotype-negative hypertrophic cardiomyopathy pedigree.Scientific reports · 2022Article
- Genetic risk variants for multiple sclerosis are linked to differences in alternative pre-mRNA splicing.Frontiers in immunology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The contribution of deep intronic splice-altering variants to hereditary breast and ovarian cancer (HBOC) is unknown. Current computational in silico tools to predict spliceogenic variants leading to pseudoexons have limited efficiency. We assessed the performance of the SpliceAI tool combined with ESRseq scores to identify spliceogenic deep intronic variants by affecting cryptic sites or splicing regulatory elements (SREs) using literature and experimental datasets. Our results with 233 published deep intronic variants showed that SpliceAI, with a 0.05 threshold, predicts spliceogenic deep intronic variants affecting cryptic splice sites, but is less effective in detecting those affecting SREs. Next, we characterized the SRE profiles using ESRseq, showing that pseudoexons are significantly enriched in SRE-enhancers compared to adjacent intronic regions. Although the combination of SpliceAI with ESRseq scores (considering ∆ESRseq and SRE landscape) showed higher sensitivity, the global performance did not improve because of the higher number of false positives. The combination of both tools was tested in a tumor RNA dataset with 207 intronic variants disrupting splicing, showing a sensitivity of 86%. Following the pipeline, five spliceogenic deep intronic variants were experimentally identified from 33 variants in HBOC genes. Overall, our results provide a framework to detect deep intronic variants disrupting splicing.
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Registered trials
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.