ArticleBMC bioinformatics2010
A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 18 citations in OpenAlex.
- The Influence of a Genetic Variant inInternational journal of molecular sciences · 2024Article
- Delineation of the Germline and Somatic Mutation Interaction Landscape in Triple-Negative and Non-Triple-Negative Breast Cancer.International journal of genomics · 2020Article
- Assessment of Diagnostic Outcomes of RNA Genetic Testing for Hereditary Cancer.JAMA network open · 2019Article
- Integrating Germline and Somatic Mutation Information for the Discovery of Biomarkers in Triple-Negative Breast Cancer.International journal of environmental research and public health · 2019Article
- Mapping the Germline and Somatic Mutation Interaction Landscape in Indolent and Aggressive Prostate Cancers.Journal of oncology · 2019Article
- The Splicing Factor hnRNPA1 Regulates Alternate Splicing of the MYLK Gene.American journal of respiratory cell and molecular biology · 2018Article
- Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer.Scientific reports · 2014Article
- Validation of predicted mRNA splicing mutations using high-throughput transcriptome data.F1000Research · 2014Article
- Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences.Genomics, proteomics & bioinformatics · 2013Article
- Article
- Identification of cis-regulatory sequence variations in individual genome sequences.Genome medicine · 2011Article
- Compensatory signals associated with the activation of human GC 5' splice sites.Nucleic acids research · 2011Article
- Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites.BMC bioinformatics · 2011Article
- An integrative genomics approach to biomarker discovery in breast cancer.Cancer informatics · 2011Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPolymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelian diseases, the implication of such events in multi-genic disorders is yet to be well understood. We have developed a new tool (SpliceScan II) for predicting the effects of genetic variants on splicing and cis-regulatory elements. The novel Bayesian non-canonical 5'GC splice site (SS) sensor used in our tool allows inference on non-canonical exons.
resultsOur tool performed favorably when compared with the existing methods in the context of genes linked to the Autism Spectrum Disorder (ASD). SpliceScan II was able to predict more aberrant splicing isoforms triggered by the mutations, as documented in DBASS5 and DBASS3 aberrant splicing databases, than other existing methods. Detrimental effects behind some of the polymorphic variations previously associated with Alzheimer's and breast cancer could be explained by changes in predicted splicing patterns.
conclusionsWe have developed SpliceScan II, an effective and sensitive tool for predicting the detrimental effects of genomic variants on splicing leading to Mendelian and complex hereditary disorders. The method could potentially be used to screen resequenced patient DNA to identify de novo mutations and polymorphic variants that could contribute to a genetic disorder.
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