ArticleNature methods2014
Phen-Gen: combining phenotype and genotype to analyze rare disorders.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
99 citing papers in PubMed, 1 synthesis or guideline pooled it, 155 citations in OpenAlex.
- Computational resources associating diseases with genotypes, phenotypes and exposures.Briefings in bioinformatics · 2019Pooled it
- Evaluation of Presumably Disease Causing SCN1A Variants in a Cohort of Common Epilepsy Syndromes.PloS one · 2016Trial
- Article
- Comparison of missing data handling methods for variant pathogenicity predictors.NAR genomics and bioinformatics · 2025Article
- geneEX: An Integrated Phenotype-Driven Algorithm for Rapid Identification of Causative Variants in Monogenic Disorders.Molecular genetics & genomic medicine · 2025Article
- Few shot learning for phenotype-driven diagnosis of patients with rare genetic diseases.NPJ digital medicine · 2025Article
- Single-cell data combined with phenotypes improves variant interpretation.BMC genomics · 2025Article
- Atlas of imprinted and allele-specific DNA methylation in the human body.Nature communications · 2025Article
- Data simulation to optimize frameworks for genome-wide association studies in diverse populations.Frontiers in genetics · 2025Article
- Clinical signatures of genetic epilepsies precede diagnosis in electronic medical records of 32,000 individuals.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.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
- Article
- diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype.Bioinformatics (Oxford, England) · 2023Article
- IMPROVE-DD: Integrating multiple phenotype resources optimizes variant evaluation in genetically determined developmental disorders.HGG advances · 2023Article
- Phenotype-aware prioritisation of rare Mendelian disease variants.Trends in genetics : TIG · 2022Review
- Predicting genes from phenotypes using human phenotype ontology (HPO) terms.Human genetics · 2022Article
- Phenotype-driven approaches to enhance variant prioritization and diagnosis of rare disease.Human mutation · 2022Review
- PheNominal: an EHR-integrated web application for structured deep phenotyping at the point of care.BMC medical informatics and decision making · 2022Article
- Network-Based Methods for Approaching Human Pathologies from a Phenotypic Point of View.Genes · 2022Review
39 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce Phen-Gen, a method that combines patients' disease symptoms and sequencing data with prior domain knowledge to identify the causative genes for rare disorders. Simulations revealed that the causal variant was ranked first in 88% of cases when it was a coding variant-a 52% advantage over a genotype-only approach-and Phen-Gen outperformed other existing prediction methods by 13-58%. If disease etiology was unknown, the causal variant was assigned the top rank in 71% of simulations. Phen-Gen is available at http://phen-gen.org/.
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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.