Variant prioritization software tools | High-throughput sequencing data analysis
Whole-exome sequencing has become a fundamental tool for the discovery of disease-related genes of familial diseases and the identification of somatic driver variants in cancer. However, finding the causal mutation among the enormous background of individual variability in a small number of samples is still a big challenge.
Identifies causal variants from human sequencing data. Ingenuity Variant Analysis is a web-based application that combines analytical tools and integrated genomics content with user panel, exome, or genome data to rapidly identify and prioritize compelling causal variants using published biological evidence. The software enables prioritization of variants along biologically relevant filter criteria, focus on variants demonstrated to be implicated in the phenotype of interest and to filter variants based on robust statistics for cancer, kindred, and cohort studies.
A three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing studies. This efficient and comprehensive framework successfully narrowed down whole exome variants to very small numbers of candidate variants in the proof-of-concept examples. The proposed framework will play a very useful role in exome sequencing-based discovery of human Mendelian disease genes.
Identifies damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of amino acid substitution (AAS) and aggregative approaches. The software can assay the impact of rare variants to identify rare diseases, and can use both common and rare variants to identify genes involved in common diseases. It includes Pedigree-VAAST (pVAAST), designed for high-throughput sequence data in pedigrees, which allows disease-gene identification.
Enables prioritization of genes and variants in next-generation sequencing (NGS) projects for novel disease-gene discovery or differential diagnostics of Mendelian disease. Exomiser is a suite that contains several different methods for variant prioritization, based on protein-protein interactions and/or phenotype comparisons between a patient and existing human disease databases and model organisms. It provides methods using clinical data, model organism phenotype data, as well as random-walk analysis of protein interactome data to perform prioritization.
Exploits information related to gene function, phenotype, and diseases to rank potentially damaging alleles highlighted by variant-prioritization tools. Phevor is a web application which focuses on single-exome and family trio-based diagnostic analyses with the aim of complementing existing methods. The platform provides a term browser as well as the possibility of link human phenotype ontology (HPO) to five ontologies including the Gene Ontology (GO) or CHEBI.
A pipeline for ranking nonsynonymous single nucleotide variants given a specific phenotype. eXtasy takes into account the putative deleteriousness of the variant, haploinsufficiency predictions of the underlying gene and the similarity of the given gene to known genes in the given phenotype.
Enables researchers to quickly identify and classify disease-relevant variants, and then communicate significant findings in a structured report. A powerful variant analysis and reporting tool, VariantStudio allows researchers to go from human DNA variants to biological insight, fast.