ArticleHuman heredity2012
A combined functional annotation score for non-synonymous variants.
Article in Human heredity, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- Article
- Germline mosaicism in TCF20-associated neurodevelopmental disorders: a case study and literature review.Journal of human genetics · 2025Review
- The disruptive influence of the Ala218Val variant on the ENG protein.microPublication biology · 2025Article
- Proteome-scale characterisation of motif-based interactome rewiring by disease mutations.Molecular systems biology · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Rapid discrimination between deleterious and benign missense mutations in the CAGI 6 experiment.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
- Medulloblastoma group 3 and 4 tumors comprise a clinically and biologically significant expression continuum reflecting human cerebellar development.Cell reports · 2022Article
- Emergence and maintenance of actionable genetic drivers at medulloblastoma relapse.Neuro-oncology · 2022Article
- Novel PRMT7 mutation in a rare case of dysmorphism and intellectual disability.Journal of human genetics · 2022Article
- A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs.BMC genomics · 2021Article
- A domain damage index to prioritizing the pathogenicity of missense variants.Human mutation · 2021Article
- Possible A2E Mutagenic Effects on RPE Mitochondrial DNA from Innovative RNA-Seq Bioinformatics Pipeline.Antioxidants (Basel, Switzerland) · 2020Article
- VIPdb, a genetic Variant Impact Predictor Database.Human mutation · 2019Article
- Elevation in Cell Cycle and Protein Metabolism Gene Transcription in Inactive Colonic Tissue From Icelandic Patients With Ulcerative Colitis.Inflammatory bowel diseases · 2019Article
- Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics.Frontiers in genetics · 2019Review
- RYR1 and CACNA1S genetic variants identified with statin-associated muscle symptoms.Pharmacogenomics · 2018Article
- Rare coding variant analysis in a large cohort of Ashkenazi Jewish families with inflammatory bowel disease.Human genetics · 2018Article
- Article
- What Does This Mutation Mean? The Tools and Pitfalls of Variant Interpretation in Lymphoid Malignancies.International journal of molecular sciences · 2018Review
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7 authors.
Funding
Abstract
aimsNext-generation sequencing has opened the possibility of large-scale sequence-based disease association studies. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, we have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from 2 bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants.
methodsWe used a weighted Z method that combines the probabilistic scores of PolyPhen-2 and SIFT. We defined 2 dataset pairs to train and test CAROL using information from the dbSNP: 'HGMD-PUBLIC' and 1000 Genomes Project databases. The training pair comprises a total of 980 positive control (disease-causing) and 4,845 negative control (non-disease-causing) variants. The test pair consists of 1,959 positive and 9,691 negative controls.
resultsCAROL has higher predictive power and accuracy for the effect of non-synonymous variants than each individual annotation tool (PolyPhen-2 and SIFT) and benefits from higher coverage.
conclusionThe combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences.
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