ArticleBMC bioinformatics2017
An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 79 citations in OpenAlex.
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- PON-Del predictor for sequence retaining protein deletions.PLoS computational biology · 2026Article
- The impact of AI on modern oncology from early detection to personalized cancer treatment.NPJ precision oncology · 2026Review
- Clinical description, genetic analysis and characterization of two NLRP12 heterozygous VUS variants.Frontiers in immunology · 2026Article
- Assessment of In-Frame Indel Variants in an Unsolved Cohort of Inherited Retinal Diseases Using Machine Learning.Human mutation · 2026Article
- A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins.Nature communications · 2025Article
- Description and phenotype of a novel C5 gene mutation and a novel combination: family report and literature review.Frontiers in immunology · 2025Review
- Evaluating the Performance ofCombinatorial chemistry & high throughput screening · 2025Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Global prevalence of hereditary thrombotic thrombocytopenic purpura determined by genetic analysis.Blood advances · 2024Article
- VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome.Nucleic acids research · 2024Article
- Widening the infantile hypotonia with psychomotor retardation and characteristic Facies-1 Syndrome's clinical and molecular spectrum through NALCNFrontiers in genetics · 2024Article
- Somatic ARAF mutations in pediatric Langerhans cell histiocytosis: clinicopathologic, genetic and functional profiling.Clinical and experimental medicine · 2023Article
- PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants.Nucleic acids research · 2023Article
- Predicting pathogenicity from non-coding mutations.Nature biomedical engineering · 2023Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundSmall insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome.
resultsWe present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk.
conclusionsFATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome.
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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.