Phenolyzer: phenotype-based prioritization of candidate genes for human diseases

By Hui Yang, Peter N. Robinson, Kai Wang. Nature Methods, 2015

362 citations recorded by the source corpus.

Prior biological knowledge and phenotype information may help to identify disease genes from human whole-genome and whole-exome sequencing studies. We developed Phenolyzer (http://phenolyzer.usc.edu), a tool that uses prior information to implicate genes involved in diseases. Phenolyzer exhibits superior performance over competing methods for prioritizing Mendelian and complex disease genes, based on disease or phenotype terms entered as free text.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5a7ee9aaa0de81c51c330691ec4e180eaa3e0f75

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Citations in the corpus

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. (2016, background): “Phenotype-Driven Prioritization of Non-coding Variants We and others have previously shown that phenotypic information can effectively boost the prioritization of disease-associated genes.(1,61,62) Regulatory mutations can lead to identical or similar phenotypic abnormalities as”
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR (2015, methodology): “…on the basis of their association with the input disease or phenotype term, where the association is calculated by integrating multiple disease-gene databases, disease-phenotype databases, disease ontology databases and gene-gene interaction databases through a machine-learning framework 27 .”
Settling the score: variant prioritization and Mendelian disease (2017, methodology): “Phenotype analysis tools such as the Phenotype-Driven Variant Ontological Re-ranking tool (Phevor) 80 and Phenolyzer 78 can evaluate qualitative HPO-based phenotype descriptions such as ‘lethargy, seizures and hepatomegaly’ and use the broader structure of the HPO and its gene–symptom linkages in…”