ArticleGenomics, proteomics & bioinformatics2013
Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences.
Article in Genomics, proteomics & bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 28 citations in OpenAlex.
- Small genetic variation affecting mRNA isoforms associated with marbling and meat color in beef cattle.Functional & integrative genomics · 2022Article
- Functional assessment of somatic STK11 variants identified in primary human non-small cell lung cancers.Carcinogenesis · 2021Article
- Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing.Frontiers in genetics · 2020Article
- Massive computational identification of somatic variants in exonic splicing enhancers using The Cancer Genome Atlas.Cancer medicine · 2019Article
- Pan-cancer repository of validated natural and cryptic mRNA splicing mutations.F1000Research · 2018Article
- Prevalence and spectrum of germline rare variants in BRCA1/2 and PALB2 among breast cancer cases in Sarawak, Malaysia.Breast cancer research and treatment · 2017Article
- In silico prioritization and further functional characterization of SPINK1 intronic variants.Human genomics · 2017Article
- A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer.BMC medical genomics · 2016Article
- Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning.Molecular oncology · 2016Article
- 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 of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis.F1000Research · 2014Review
- Mutational screening of splicing factor genes in cases with autosomal dominant retinitis pigmentosa.Molecular vision · 2014Article
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Authors and funding
6 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Information theory-based methods have been shown to be sensitive and specific for predicting and quantifying the effects of non-coding mutations in Mendelian diseases. We present the Shannon pipeline software for genome-scale mutation analysis and provide evidence that the software predicts variants affecting mRNA splicing. Individual information contents (in bits) of reference and variant splice sites are compared and significant differences are annotated and prioritized. The software has been implemented for CLC-Bio Genomics platform. Annotation indicates the context of novel mutations as well as common and rare SNPs with splicing effects. Potential natural and cryptic mRNA splicing variants are identified, and null mutations are distinguished from leaky mutations. Mutations and rare SNPs were predicted in genomes of three cancer cell lines (U2OS, U251 and A431), which were supported by expression analyses. After filtering, tractable numbers of potentially deleterious variants are predicted by the software, suitable for further laboratory investigation. In these cell lines, novel functional variants comprised 6-17 inactivating mutations, 1-5 leaky mutations and 6-13 cryptic splicing mutations. Predicted effects were validated by RNA-seq analysis of the three aforementioned cancer cell lines, and expression microarray analysis of SNPs in HapMap cell lines.
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