ArticleAmerican journal of human genetics2018
PubCaseFinder: A Case-Report-Based, Phenotype-Driven Differential-Diagnosis System for Rare Diseases.
Article in American journal of human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 44 citations in OpenAlex.
- A trio-based long-read sequencing workflow identifies a pathogenic transposable element insertion in a previously undiagnosed patient.Journal of human genetics · 2026Article
- Genetic landscape in undiagnosed patients with syndromic hearing loss revealed by whole exome sequencing and phenotype similarity search.Human genetics · 2025Article
- Objectivizing issues in the diagnosis of complex rare diseases: lessons learned from testing existing diagnosis support systems on ciliopathies.BMC medical informatics and decision making · 2024Article
- Performance and clinical utility of a new supervised machine-learning pipeline in detecting rare ciliopathy patients based on deep phenotyping from electronic health records and semantic similarity.Orphanet journal of rare diseases · 2024Article
- Phenotypic similarity-based approach for variant prioritization for unsolved rare disease: a preliminary methodological report.European journal of human genetics : EJHG · 2024Article
- OARD: Open annotations for rare diseases and their phenotypes based on real-world data.American journal of human genetics · 2022Article
- Advances in the development of PubCaseFinder, including the new application programming interface and matching algorithm.Human mutation · 2022Article
- Seven years since the launch of the Matchmaker Exchange: The evolution of genomic matchmaking.Human mutation · 2022Article
- Review
- PhenoApt leverages clinical expertise to prioritize candidate genes via machine learning.American journal of human genetics · 2022Article
- 2022: a pivotal year for diagnosis and treatment of rare genetic diseases.Cold Spring Harbor molecular case studies · 2022Article
- Visualizing the phenotype diversity: a case study of Alexander disease.Genomics & informatics · 2021Article
- Generalizability of Polygenic Risk Scores for Breast Cancer Among Women With European, African, and Latinx Ancestry.JAMA network open · 2021Article
- A pipeline-friendly software tool for genome diagnostics to prioritize genes by matching patient symptoms to literature.Advanced genetics (Hoboken, N.J.) · 2020Article
- AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature.Science translational medicine · 2020Article
- Diagnosis support systems for rare diseases: a scoping review.Orphanet journal of rare diseases · 2020Article
- Article
- Rare, rarer, it still has not happened.Croatian medical journal · 2019Article
- Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.Nucleic acids research · 2019Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently, to speed up the differential-diagnosis process based on symptoms and signs observed from an affected individual in the diagnosis of rare diseases, researchers have developed and implemented phenotype-driven differential-diagnosis systems. The performance of those systems relies on the quantity and quality of underlying databases of disease-phenotype associations (DPAs). Although such databases are often developed by manual curation, they inherently suffer from limited coverage. To address this problem, we propose a text-mining approach to increase the coverage of DPA databases and consequently improve the performance of differential-diagnosis systems. Our analysis showed that a text-mining approach using one million case reports obtained from PubMed could increase the coverage of manually curated DPAs in Orphanet by 125.6%. We also present PubCaseFinder (see Web Resources), a new phenotype-driven differential-diagnosis system in a freely available web application. By utilizing automatically extracted DPAs from case reports in addition to manually curated DPAs, PubCaseFinder improves the performance of automated differential diagnosis. Moreover, PubCaseFinder helps clinicians search for relevant case reports by using phenotype-based comparisons and confirm the results with detailed contextual information.
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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.