ArticleHuman mutation2016
Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel).
Article in Human mutation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers, 1 of them a synthesis that pooled it.
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Who cites it
91 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).Genetics in medicine : official journal of the American College of Medical Genetics · 2022Guideline
- aiDIVA - hybrid AI for rare disease diagnostics using evidence-based, machine learning and language models.NPJ genomic medicine · 2026Article
- Semantic embedding of variant effect annotations enables rapid and accurate pathogenicity prediction with VUS.Life.Scientific reports · 2026Article
- Calibration of in-frame indel variant effect predictors for clinical variant classification.bioRxiv : the preprint server for biology · 2026Article
- Proteome-Wide Analysis of Human Deletions.Proteins · 2026Article
- Leveraging protein language models and a scoring function for indel characterization and transfer learning.Patterns (New York, N.Y.) · 2026Article
- Mutations altering the DNA binding domains of the human RAD52 protein exert distinct effects on homologous recombination repair in Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2026Article
- MENDELSEEK: An algorithm that predicts mendelian genes and elucidates what makes them special.PLoS computational biology · 2026Article
- PON-Del predictor for sequence retaining protein deletions.PLoS computational biology · 2026Article
- Cancer mutations in RAD51 and its paralogues.PloS one · 2026Article
- The Performance ofHuman mutation · 2026Article
- Assessment of In-Frame Indel Variants in an Unsolved Cohort of Inherited Retinal Diseases Using Machine Learning.Human mutation · 2026Article
- Identification of Novel Susceptibility Genes for Early-Onset Colorectal Cancer Through Germline Rare Variant Burden Testing.Cancers · 2025Article
- MutAnt: mutation annotation tool predicts deleteriousness of missense mutations and improves mutation calling from transcriptomics.Human genetics · 2025Article
- Trio exome sequencing of an optic nerve hypoplasia cohort reveals evidence for polygenic architecture.Ophthalmic genetics · 2025Article
- The Role ofmedRxiv : the preprint server for health sciences · 2025Article
- Structural and energetic analysis of stabilizing indel mutations.bioRxiv : the preprint server for biology · 2024Article
- The genetic landscape of autism spectrum disorder in an ancestrally diverse cohort.NPJ genomic medicine · 2024Article
- Expanding the genotypic and phenotypic spectra with a novel variant in the ciliopathy gene,Ophthalmic genetics · 2024Article
- Synergic activity of FGFR2 and MEK inhibitors in the treatment of FGFR2-amplified cancers of unknown primary.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Insertion/deletion variants (indels) alter protein sequence and length, yet are highly prevalent in healthy populations, presenting a challenge to bioinformatics classifiers. Commonly used features--DNA and protein sequence conservation, indel length, and occurrence in repeat regions--are useful for inference of protein damage. However, these features can cause false positives when predicting the impact of indels on disease. Existing methods for indel classification suffer from low specificities, severely limiting clinical utility. Here, we further develop our variant effect scoring tool (VEST) to include the classification of in-frame and frameshift indels (VEST-indel) as pathogenic or benign. We apply 24 features, including a new "PubMed" feature, to estimate a gene's importance in human disease. When compared with four existing indel classifiers, our method achieves a drastically reduced false-positive rate, improving specificity by as much as 90%. This approach of estimating gene importance might be generally applicable to missense and other bioinformatics pathogenicity predictors, which often fail to achieve high specificity. Finally, we tested all possible meta-predictors that can be obtained from combining the four different indel classifiers using Boolean conjunctions and disjunctions, and derived a meta-predictor with improved performance over any individual method.
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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.