ArticleAdvances in bioinformatics2016
Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions.
Article in Advances in bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Imaging flow cytometry-based cellular screening elucidates pathophysiology in individuals with Variants of Uncertain Significance.Genome medicine · 2025Article
- Evaluation of pathogenicity of WT1 intron variants by in vitro splicing analysis.Clinical and experimental nephrology · 2024Article
- Functional analysis of theAnimal biotechnology · 2024Article
- Combined bioinformatic and splicing analysis of likely benign intronic and synonymous variants reveals evidence for pathogenicity.Genetics in medicine open · 2024Article
- All reported non-canonical splice site variants in GLA cause aberrant splicing.Clinical and experimental nephrology · 2023Article
- Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications.Genome biology · 2023Article
- Aberrant splicing caused by exonic single nucleotide variants positioned 2nd or 3rd to the last nucleotide in the COL4A5 gene.Clinical and experimental nephrology · 2023Article
- Prevalence, parameters, and pathogenic mechanisms for splice-altering acceptor variants that disrupt the AG exclusion zone.HGG advances · 2022Article
- Craniofacial, dental, and molecular features of Pyle disease in a South African child.BDJ open · 2022Article
- Empirical prediction of variant-activated cryptic splice donors using population-based RNA-Seq data.Nature communications · 2022Article
- Identification of novel single-nucleotide variants altering RNA splicing of PKD1 and PKD2.Journal of human genetics · 2022Article
- Article
- Internal Standardization of the Interpretation and Reporting of Sequence Variants in Hematologic Neoplasms.Molecular diagnosis & therapy · 2021Article
- A novel synonymous variant in exon 1 ofBone reports · 2021Article
- Use of RNA‑sequencing to detect abnormal transcription of the collagen α‑2 (VI) chain gene that can lead to Bethlem myopathy.International journal of molecular medicine · 2021Article
- Article
- Machine learning based CRISPR gRNA design for therapeutic exon skipping.PLoS computational biology · 2021Article
- Molecular characterization of hemophilia B patients in Colombia.Molecular genetics & genomic medicine · 2020Article
- Variation benchmark datasets: update, criteria, quality and applications.Database : the journal of biological databases and curation · 2020Article
- ClinGen Myeloid Malignancy Variant Curation Expert Panel recommendations for germline RUNX1 variants.Blood advances · 2019Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The increasing diagnostic use of gene sequencing has led to an expanding dataset of novel variants that lie within consensus splice junctions. The challenge for diagnostic laboratories is the evaluation of these variants in order to determine if they affect splicing or are merely benign. A common evaluation strategy is to use in silico analysis, and it is here that a number of programmes are available online; however, currently, there are no consensus guidelines on the selection of programmes or protocols to interpret the prediction results. Using a collection of 222 pathogenic mutations and 50 benign polymorphisms, we evaluated the sensitivity and specificity of four in silico programmes in predicting the effect of each variant on splicing. The programmes comprised Human Splice Finder (HSF), Max Entropy Scan (MES), NNSplice, and ASSP. The MES and ASSP programmes gave the highest performance based on Receiver Operator Curve analysis, with an optimal cut-off of score reduction of 10%. The study also showed that the sensitivity of prediction is affected by the level of conservation of individual positions, with in silico predictions for variants at positions -4 and +7 within consensus splice sites being largely uninformative.
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Registered trials
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