ArticleBMC bioinformatics2011
Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- An elevated level of interleukin-17A in a Senegalese malaria cohort is associated with rs8193038 IL-17A genetic variant.BMC infectious diseases · 2024Article
- Predicting functional consequences of SNPs on mRNA translation via machine learning.Nucleic acids research · 2023Article
- Bioinformatic analysis of KIT juxtamembrane domain mutations in Syrian GIST patients: jigsaw puzzle completed.Journal of the Egyptian National Cancer Institute · 2023Article
- Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance.International journal of molecular sciences · 2022Review
- What's Wrong in a Jump? Prediction and Validation of Splice Site Variants.Methods and protocols · 2021Review
- Genetic regulation of antibody responsiveness to immunization in substrains of BALB/c mice.Immunology and cell biology · 2019Article
- Architecture of polymorphisms in the human genome reveals functionally important and positively selected variants in immune response and drug transporter genes.Human genomics · 2018Article
- Genomic and Bioinformatics Approaches for Analysis of Genes Associated With Cancer Risks Following Exposure to Tobacco Smoking.Frontiers in public health · 2018Review
- Identification of functional single nucleotide polymorphisms in the branchpoint site.Human genomics · 2017Article
- ATM mutations and E-cadherin expression define sensitivity to EGFR-targeted therapy in colorectal cancer.Oncotarget · 2017Article
- Angiopoietin receptor TEK mutations underlie primary congenital glaucoma with variable expressivity.The Journal of clinical investigation · 2016Article
- Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.Advances in experimental medicine and biology · 2016Article
- Alternative Splicing in Alzheimer's Disease.Journal of Parkinson's disease and Alzheimer's disease · 2015Article
- SNPlice: variants that modulate Intron retention from RNA-sequencing data.Bioinformatics (Oxford, England) · 2015Article
- In silico tools for splicing defect prediction: a survey from the viewpoint of end users.Genetics in medicine : official journal of the American College of Medical Genetics · 2014Review
- The Association between Polymorphismsin Insulin and Obesity Related Genesand Risk of Colorectal Cancer.Iranian journal of cancer prevention · 2013Review
- SNP Discovery through Next-Generation Sequencing and Its Applications.International journal of plant genomics · 2012Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSome single nucleotide polymorphisms (SNPs) are known to modify the risk of developing certain diseases or the reaction to drugs. Due to next generation sequencing methods the number of known human SNPs has grown. Not all SNPs lead to a modified protein, which may be the origin of a disease. Therefore, the recognition of functional SNPs is needed. Because most SNP annotation tools look for SNPs which lead to an amino acid exchange or a premature stop, we designed a new tool called AASsites which searches for SNPs which modify splicing.
resultsAASsites uses several gene prediction programs and open reading frame prediction to compare the wild type (wt) and the variant gene sequence. The results of the comparison are combined by a handmade rule system to classify a change in splicing as "likely, probable, unlikely". Having received good results from tests with SNPs known for changing the splicing pattern we checked 80,000 SNPs from the human genome which are located near splice sites for their ability to change the splicing pattern of the gene and hereby result in a different protein. We identified 301 "likely" and 985 "probable" classified SNPs with such characteristics. Within this set 33 SNPs are described in the ssSNP Target database to cause modified splicing.
conclusionsWith AASsites single SNPs can be checked for those causing splice modifications. Screening 80,000 known human SNPs we detected about 1,200 SNPs which probably modify splicing. AASsites is available at http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar using any web browser.
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