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VariBench specifications

Information


Unique identifier OMICS_04625
Name VariBench
Restrictions to use None
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Mauno Vihinen

Publications for VariBench

VariBench citations

 (8)
library_books

Mapping genetic variations to three dimensional protein structures to enhance variant interpretation: a proposed framework

2017
Genome Med
PMCID: 5735928
PMID: 29254494
DOI: 10.1186/s13073-017-0509-y

[…] HGMD [], and OMIM [], or somatic mutations, such as the Cancer Genome Atlas (TCGA) [] and COSMIC []. Carefully selected benchmark datasets to develop and test prediction methods have been collected: VariBench [] and VariSNP [].Few prediction methods are purely based on 3D structural information, with the exception of FoldX [], which uses an empirical scoring function to predict the change in prot […]

library_books

Evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines

2017
Genome Biol
PMCID: 5704597
PMID: 29179779
DOI: 10.1186/s13059-017-1353-5

[…] aset that is perfectly balanced (balanced dataset * in Additional file : Figure S3). We also detected evidence for potential type 2 circularity for algorithms such as MetaSVM/LR and MCAP (balanced vs varibench for MetaSVM, MetaLR, and MCAP, bootstrap p value < 0.0001; Additional file : Figure S3). Thus, caution should be used in interpreting scores using algorithms such as FATHMM as the prediction […]

library_books

PhD SNPg: a webserver and lightweight tool for scoring single nucleotide variants

2017
Nucleic Acids Res
PMCID: 5570245
PMID: 28482034
DOI: 10.1093/nar/gkx369

[…] ther comparison of the performance of PhD-SNPg, CADD and FATHMM-MKL in predicting the impact of coding variants, we scored the three algorithms on a dataset of nonsynonymous SNVs (AllToolScores) from VariBench (). This test confirmed that PhD-SNPg performs similarly to CADD and better than FATHMM-MKL ().Finally, we also evaluated the ability of PhD-SNPg to predict the effect of non-coding variants […]

library_books

Computational assessment of feature combinations for pathogenic variant prediction

2016
PMCID: 4947862
PMID: 27468419
DOI: 10.1002/mgg3.214

[…] variants for both sets is shown in Fig. S1. The overlap of the training and validation datasets to the existing datasets ExoVar (Li et al. ), HumVar (Adzhubei et al. ), SwissVar (Mottaz et al. ), and VariBench (protein tolerance dataset 1) (Nair and Vihinen ) is shown in Fig. S2. The handling of variants with missing data is described in Data S1. The complete datasets are available upon request to […]

library_books

Increased Aggregation Is More Frequently Associated to Human Disease Associated Mutations Than to Neutral Polymorphisms

2015
PLoS Comput Biol
PMCID: 4560525
PMID: 26340370
DOI: 10.1371/journal.pcbi.1004374

[…] er and metabolic diseases. In order to probe the potential of protein aggregation as a disease-modifying factor, we here analyze a curated set of polymorphisms and disease-associated mutations from a VariBench subset[] for which structural information is available (5480 pathogenic and 1015 neutral mutations).Protein aggregation is determined by short aggregation prone regions (APRs) that are gener […]

library_books

Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process

2015
Biomed Res Int
PMCID: 4461748
PMID: 26106619
DOI: 10.1155/2015/923491

[…] iousness score. Although SIFT and Polyphen are highly cited tools, comparative analyses carried out by Thusberg et al. and Shihab et al. found FATHMM, MutPred, and SNPs&GO to perform better using the VariBench benchmarking dataset containing missense mutations [, ]. For predicting the effects of noncoding variants, FATHMM-MKL [], GWAVA [], and/or CADD [] should be used. Also Human Splice Finder (l […]

Citations

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VariBench institution(s)
Institute of Biomedical Technology, University of Tampere, Finland; BioMediTech, Tampere, Finland; Department of Experimental Medical Science, Lund University, Lund, Sweden
VariBench funding source(s)
Sigrid Juselius Foundation; Tampere City's Science Fellowship; Competitive Research Funding of the Tampere University Hospital; Biocenter Finland

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