PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

@article{Bendl2016PredictSNP2AU,
  title={PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions},
  author={J. Bendl and M. Musil and J. Stourac and J. Zendulka and J. Damborsk{\'y} and J. Brezovsky},
  journal={PLoS Computational Biology},
  year={2016},
  volume={12}
}
An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been… Expand
A review study: Computational techniques for expecting the impact of non-synonymous single nucleotide variants in human diseases.
TLDR
The most popular and recent unique tools that predict pathogenic variations and Meta-tool that merge some of them for enhancing their predictive power are introduced and the most common fundamental criteria for performance assessment of predictive tools are addressed. Expand
parSMURF, a High Performance Computing tool for the genome-wide detection of pathogenic variants
Several prediction problems in Computational Biology and Genomic Medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples canExpand
parSMURF, a high-performance computing tool for the genome-wide detection of pathogenic variants
Abstract Background Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, wherebyExpand
VIPdb, a genetic Variant Impact Predictor Database
TLDR
This database will help researchers and clinicians explore appropriate tools, and inform the development of improved methods, in the genetic Variant Impact Predictor Database (VIPdb). Expand
Refinement of evolutionary medicine predictions based on clinical evidence for the manifestations of Mendelian diseases
TLDR
The evolutionary variation analysis approach described here is the first to enable the highly specific identification of likely disease-causing missense variations that have not yet been associated with any clinical phenotype. Expand
Web-Based Bioinformatics Predictors: Recommendations to Assess Lysosomal Cholesterol Trafficking Diseases-Related Genes.
TLDR
It is found that the best prediction tool for the NPC1, NPC2, and LIPA variants was MutPred1 for exonic regions and HSF and SROOGLE for intronic regions and splice sites. Expand
DNA damage is a major cause of sequencing errors, directly confounding variant identification
TLDR
It is shown that false positive variants can account for more than 70% of identified somatic variations, rendering conventional detection methods inadequate for accurate determination of low allelic variants. Expand
Comparison and integration of computational methods for deleterious synonymous mutation prediction
TLDR
An ensemble model, named Prediction of Deleterious Synonymous Mutation (PrDSM), is established, which averages the ratings generated by the three most accurate predictors, and outperformed the reviewed tools for the prediction of deleterious synonymous mutations. Expand
MoBiDiC Prioritization Algorithm, a Free, Accessible, and Efficient Pipeline for Single-Nucleotide Variant Annotation and Prioritization for Next-Generation Sequencing Routine Molecular Diagnosis.
TLDR
A variant-prioritization tool, the MoBiDiCprioritized algorithm (MPA), based on curated interpretation of data on previously reported variants, biological assumptions, and splice and missense predictors, and is used to prioritize all types of single-nucleotide variants. Expand
Genetic variants in mRNA untranslated regions
TLDR
How the correct use and interpretation of public GWAS repositories could lead to a better understanding of etiopathogenetic mechanisms and the generation of robust biological hypothesis as starting point for further functional studies are discussed. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 71 REFERENCES
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
TLDR
This study constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated prediction tools, and returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. Expand
A general framework for estimating the relative pathogenicity of human genetic variants
TLDR
The ability of CADD to prioritize functional, deleterious and pathogenic variants across many functional categories, effect sizes and genetic architectures is unmatched by any current single-annotation method. Expand
A method to predict the impact of regulatory variants from DNA sequence
TLDR
It is shown that deltaSVM accurately predicts the impact of SNPs on DNase I sensitivity in their native genomic contexts and accurately predicted the results of dense mutagenesis of several enhancers in reporter assays, and it is predicted new risk-conferring SNPs for several autoimmune diseases. Expand
Annotation of functional variation in personal genomes using RegulomeDB.
TLDR
A novel approach and database, RegulomeDB, which guides interpretation of regulatory variants in the human genome, which includes high-throughput, experimental data sets from ENCODE and other sources, as well as computational predictions and manual annotations to identify putative regulatory potential and identify functional variants. Expand
Bioinformatics for personal genome interpretation
TLDR
The most important developments in the field are reviewed--the databases and bioinformatics tools that will be of utmost importance in the concerted effort to interpret the human variome. Expand
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
TLDR
The ANNOVAR tool to annotate single nucleotide variants and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP is developed. Expand
An integrated map of genetic variation from 1,092 human genomes
TLDR
It is shown that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. Expand
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease
TLDR
A use case of HaploReg is illustrated for attention deficit hyperactivity disorder (ADHD)-associated SNPs with putative brain regulatory mechanisms, and the number of chromatin state maps to 127 reference epigenomes is greatly expanded. Expand
Performance of mutation pathogenicity prediction methods on missense variants
TLDR
The overall best performing methods in this study were SNPs&GO and MutPred, with accuracies reaching 0.82 and 0.81, respectively. Expand
The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity
TLDR
It is shown that comparative evaluations of predictors that do not address two types of circularity may erroneously conclude that circularity confounded tools are most accurate among all tools, and may even outperform optimized combinations of tools. Expand
...
1
2
3
4
5
...