ArticleGenes2020
An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data.
Article in Genes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 67 citations in OpenAlex.
- A recurrentBiochemistry and biophysics reports · 2026Article
- Integration of Machine Learning-Based Pathogenicity Prediction and Phenotype Matching Improves Variant Prioritization in Rare Clinical Testing.Current issues in molecular biology · 2026Article
- Artificial Intelligence in Rare Diseases: Workflow-Integrated Precision Kidney Care.Clinics and practice · 2026Review
- A novel phenotype-guided genome analysis pipeline for variant discovery.NPJ genomic medicine · 2026Article
- Application of qualifying variants for genomic analysis.Bioinformatics (Oxford, England) · 2026Article
- Accelerate the discovery of genetic variants in mitochondrial diseases with Variant prIOritization using Latent spAce.Briefings in bioinformatics · 2025Article
- An optimized variant prioritization process for rare disease diagnostics: recommendations for Exomiser and Genomiser.Genome medicine · 2025Article
- Clinical and data-driven optimization of Genomiser for rare disease patients: experience from the Hong Kong Genome Project.Briefings in bioinformatics · 2025Article
- Improving automated deep phenotyping through large language models using retrieval-augmented generation.Genome medicine · 2025Article
- Identification of technically challenging variants: Whole-genome sequencing improves diagnostic yield in patients with high clinical suspicion of rare diseases.HGG advances · 2025Article
- Evaluating seven bioinformatics platforms for tertiary analysis of genomic data from whole exome sequencing in a pilot group of patients.Advances in laboratory medicine · 2025Article
- Article
- Next-generation phenotyping of inherited retinal diseases from multimodal imaging with Eye2Gene.Nature machine intelligence · 2025Article
- Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals.Mammalian genome : official journal of the International Mammalian Genome Society · 2024Review
- Tissue-aware interpretation of genetic variants advances the etiology of rare diseases.Molecular systems biology · 2024Article
- 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
- Diagnostic elusiveness of pathogenic variants in cases of autosomal recessive diseases.European journal of human genetics : EJHG · 2024Article
- Aspirin-exacerbated respiratory disease is associated with variants in filaggrin, epithelial integrity, and cellular interactions.The journal of allergy and clinical immunology. Global · 2024Article
- Standards of NGS Data Sharing and Analysis in Ataxias: Recommendations by the NGS Working Group of the Ataxia Global Initiative.Cerebellum (London, England) · 2024Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 3 countries.
Funding
Abstract
Next-generation sequencing has revolutionized rare disease diagnostics, but many patients remain without a molecular diagnosis, particularly because many candidate variants usually survive despite strict filtering. Exomiser was launched in 2014 as a Java tool that performs an integrative analysis of patients' sequencing data and their phenotypes encoded with Human Phenotype Ontology (HPO) terms. It prioritizes variants by leveraging information on variant frequency, predicted pathogenicity, and gene-phenotype associations derived from human diseases, model organisms, and protein-protein interactions. Early published releases of Exomiser were able to prioritize disease-causative variants as top candidates in up to 97% of simulated whole-exomes. The size of the tested real patient datasets published so far are very limited. Here, we present the latest Exomiser version 12.0.1 with many new features. We assessed the performance using a set of 134 whole-exomes from patients with a range of rare retinal diseases and known molecular diagnosis. Using default settings, Exomiser ranked the correct diagnosed variants as the top candidate in 74% of the dataset and top 5 in 94%; not using the patients' HPO profiles (i.e., variant-only analysis) decreased the performance to 3% and 27%, respectively. In conclusion, Exomiser is an effective support tool for rare Mendelian phenotype-driven variant prioritization.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.