ArticlePloS one2020
Phenogenon: Gene to phenotype associations for rare genetic diseases.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed, 9 citations in OpenAlex.
- A Hypergraph powered approach to Phenotype-driven Gene Prioritization and Rare Disease Prediction.Scientific reports · 2025Article
- Enhancing the Accuracy of Human Phenotype Ontology Identification: Comparative Evaluation of Multimodal Large Language Models.Journal of medical Internet research · 2025Article
- Next-generation phenotyping of inherited retinal diseases from multimodal imaging with Eye2Gene.Nature machine intelligence · 2025Article
- Prediction of causative genes in inherited retinal disorder from fundus photography and autofluorescence imaging using deep learning techniques.The British journal of ophthalmology · 2021Article
- Genes underlying the evolution of tetrapod testes size.BMC biology · 2021Article
Corrections and comments
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Authors and funding
11 authors at 7 institutions in 2 countries.
Funding
Abstract
As high-throughput sequencing is increasingly applied to the molecular diagnosis of rare Mendelian disorders, a large number of patients with diverse phenotypes have their genetic and phenotypic data pooled together to uncover new gene-phenotype relations. We introduce Phenogenon, a statistical tool that combines, Human Phenotype Ontology (HPO) annotated patient phenotypes, gnomAD allele population frequency, and Combined Annotation Dependent Depletion (CADD) score for variant pathogenicity, in order to jointly predict the mode of inheritance and gene-phenotype associations. We ran Phenogenon on our cohort of 3,290 patients who had undergone whole exome sequencing. Among the top associations, we recapitulated previously known, such as "SRD5A3-Abnormal full-field electroretinogram-recessive" and "GRHL2 -Nail dystrophy-recessive", and discovered one potentially novel, "RRAGA-Abnormality of the skin-dominant". We also developed an interactive web interface available at https://phenogenon.phenopolis.org to visualise and explore the results.
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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.