ArticleScientific reports2016
iFish: predicting the pathogenicity of human nonsynonymous variants using gene-specific/family-specific attributes and classifiers.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 29 citations in OpenAlex.
- Functional Profiling ofCirculation. Genomic and precision medicine · 2025Article
- Comparative analysis of in-silico tools in identifying pathogenic variants in dominant inherited retinal diseases.Human molecular genetics · 2024Article
- Enhancing missense variant pathogenicity prediction with protein language models using VariPred.Scientific reports · 2024Article
- Improving the clinical interpretation of missense variants in X linked genes using structural analysis.Journal of medical genetics · 2022Article
- Predicting deleterious missense genetic variants via integrative supervised nonnegative matrix tri-factorization.Scientific reports · 2021Article
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- IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions.Bioinformatics (Oxford, England) · 2020Article
- MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals.Genomics, proteomics & bioinformatics · 2020Article
- REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification.Scientific reports · 2019Article
- Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016.Human mutation · 2019Article
- ATP1A3 mosaicism in families with alternating hemiplegia of childhood.Clinical genetics · 2019Article
- DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants.Nucleic acids research · 2018Article
- AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder.Database : the journal of biological databases and curation · 2018Article
- Article
- Genomic mosaicism in paternal sperm and multiple parental tissues in a Dravet syndrome cohort.Scientific reports · 2017Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate prediction of the pathogenicity of genomic variants, especially nonsynonymous single nucleotide variants (nsSNVs), is essential in biomedical research and clinical genetics. Most current prediction methods build a generic classifier for all genes. However, different genes and gene families have different features. We investigated whether gene-specific and family-specific customized classifiers could improve prediction accuracy. Customized gene-specific and family-specific attributes were selected with AIC, BIC, and LASSO, and Support Vector Machine classifiers were generated for 254 genes and 152 gene families, covering a total of 5,985 genes. Our results showed that the customized attributes reflected key features of the genes and gene families, and the customized classifiers achieved higher prediction accuracy than the generic classifier. The customized classifiers and the generic classifier for other genes and families were integrated into a new tool named iFish (integrated Functional inference of SNVs in human, http://ifish.cbi.pku.edu.cn). iFish outperformed other methods on benchmark datasets as well as on prioritization of candidate causal variants from whole exome sequencing. iFish provides a user-friendly web-based interface and supports other functionalities such as integration of genetic evidence. iFish would facilitate high-throughput evaluation and prioritization of nsSNVs in human genetics research.
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