ArticleNucleic acids research2013
Exploring functional variant discovery in non-coding regions with SInBaD.
Article in Nucleic acids research, 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, 27 citations in OpenAlex.
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- VIPdb, a genetic Variant Impact Predictor Database.Human mutation · 2019Article
- Global inference of disease-causing single nucleotide variants from exome sequencing data.BMC bioinformatics · 2016Article
- Role of non-coding sequence variants in cancer.Nature reviews. Genetics · 2016Review
- dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions.Database : the journal of biological databases and curation · 2016Article
- The genetics of human autoimmune disease: A perspective on progress in the field and future directions.Journal of autoimmunity · 2015Review
- Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data.Scientific reports · 2015Article
- Genome-wide analysis of noncoding regulatory mutations in cancer.Nature genetics · 2014Article
- Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.PLoS genetics · 2014Article
- GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications.Nucleic acids research · 2013Article
- Prediction of deleterious nonsynonymous single-nucleotide polymorphism for human diseases.TheScientificWorldJournal · 2013Review
- Spatiotemporal Control of microRNA-Target Interactions.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The thousand genomes project and many similar ongoing large-scale sequencing efforts require new methods to predict functional variants in both coding and non-coding regions in order to understand phenotype and genotype relationships. We report the design of a new model SInBaD (Sequence-Information-Based-Decision-model) which relies on nucleotide conservation information to evaluate any annotated human variant in all known exons, introns, splice junctions and promoter regions. SInBaD builds separate mathematical models for promoters, exons and introns, using the human disease mutations annotated in human gene mutation database as the training dataset for functional variants. The ten-fold cross validation shows high prediction accuracy. Validations on test datasets, demonstrate that variants predicted as functional have a significantly higher occurrence in cancer patients. We also applied our model to variants found in four different individual human genomes to identify a set of functional variants, which might be of interest for further studies. Scores for any possible variants for all annotated genes are available under http://tingchenlab.cmb.usc.edu/sinbad/. SInBaD supports the current standard format of genotyping, the variant call files (VCF 4.0), making it easy to integrate it into any existing next-generation sequencing pipeline. The accuracy of SNP detection poses the only limitation to the use of SInBaD.
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