Single nucleotide polymorphism prioritization software tools | Genome-wide association study data analysis
Although there are millions of SNPs deposited in public SNP databases, only a small proportion of them are functional polymorphisms that contribute to disease phenotypes. Thus, prioritizing SNPs based on their phenotypic risks is essential for association studies. Assessment of the risk requires access to a variety of heterogeneous biological databases and analytical tools.
Provides a statistical framework to test associations between any type of perturbation of biological processes and the occurrence of disease. MEGA-V identifies gene sets with a significantly higher number of variants in a cohort of interest (cohort A) as compared to a control cohort (cohort B) or a random distribution generated using Monte Carlo. Gene sets are predefined by the user and they can be group of genes involved in the same biological processes, Gene Ontology groups, or genes associated to the same disease.
Provides a toolkit for organize, annotate, and select single nucleotide polymorphisms (SNPs). SNPinfo is composed of three pipelines and three additional tools. The platform can be used for either small or large-scale SNP selection and it aims especially designed for association studies. It uses both functional prediction and Genome Wide Association Studies (GWAS) results to select not only SNPs included in the GWAS, but also functional SNPs in dbSNP.
A tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.
Permits the selection of tags from empirical data to rank-order them according to proxy count. Tagger employs single-marker or specified multimarker tests. It enables to record the statistical tests to be done on the tags chosen. This tool is useful to conduct single-marker tests, specified multimarker tests or exhaustive tests. It allows the assessment of tag single nucleotide polymorphisms (SNPs) from genotype data.
Allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature of FASTSNP is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents.
Selects the maximally informative set of common single-nucleotide polymorphisms (tagSNPs) to assay in candidate-gene association studies. ldSelect is an algorithm that identifies sets of tagSNPs in a candidate gene, such that all polymorphisms above a specified frequency threshold either are directly assayed or exceed a specified level of r2 with an assayed polymorphism.
Allows users to query pairwise linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs). LDlink is a web-based LD analysis tool providing access to several bioinformatics modules. The software integrates expanded population reference sets, updated functional annotations, and interactive output to explore possible functional variants in high LD. It can facilitate mapping of disease susceptibility regions and assist researchers in characterizing functional variants based on genotype-phenotype associations with potential clinical utility.