SynthesisThe Journal of allergy and clinical immunology2022
Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity.
Synthesis in The Journal of allergy and clinical immunology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Operational Ontology for Oncology (O3): A Professional Society-Based, Multistakeholder, Consensus-Driven Informatics Standard Supporting Clinical and Research Use of Real-World Data From Patients Treated for Cancer.International journal of radiation oncology, biology, physics · 2023Guideline
- Development, Implementation, and Preliminary Results of a Novel Social Network for Rare Disease Communities: Mixed Methods Study.JMIR human factors · 2026Article
- Immune-related actinopathies at the cross-road of immunodeficiency, autoimmunity and autoinflammation.Nature reviews. Immunology · 2026Review
- Exploring the strengths and limitations of AI-driven variant prioritization versus manual curation in inborn errors of immunity.Frontiers in genetics · 2026Article
- Inborn errors of immunity: Manifestation, treatment, and outcome-an ESID registry 1994-2024 report on 30,628 patients.Journal of human immunity · 2025Article
- Human Phenotype Ontology Annotations for Rare Congenital Conditions: Application to Arthrogryposis Multiplex Congenita.American journal of medical genetics. Part A · 2025Article
- MOLGENIS VIP: an end-to-end DNA variant interpretation pipeline for research and diagnostics configurable to support rapid implementation of new methods.NAR genomics and bioinformatics · 2025Article
- Genetic landscape of Romanian children with inborn errors of immunity via gene panels, exome, and genome sequencing.Scientific reports · 2025Article
- The Human Phenotype Ontology in 2024: phenotypes around the world.Nucleic acids research · 2024Article
- CAVaLRi: An Algorithm for Rapid Identification of Diagnostic Germline Variation.Human mutation · 2024Article
- Current genetic diagnostics in inborn errors of immunity.Frontiers in pediatrics · 2024Review
- A Nationwide Study of GATA2 Deficiency in Italy Reveals Novel Symptoms and Genotype-phenotype Association.Journal of clinical immunology · 2023Article
- AutoCore: A network-based definition of the core module of human autoimmunity and autoinflammation.Science advances · 2023Article
- Diffuse alveolar hemorrhage in children with interstitial lung disease: Determine etiologies!Pediatric pulmonology · 2023Article
- Curation and expansion of the Human Phenotype Ontology for systemic autoinflammatory diseases improves phenotype-driven disease-matching.Frontiers in immunology · 2023Article
- Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology.American journal of medical genetics. Part C, Seminars in medical genetics · 2022Article
- The Immune Deficiency and Dysregulation Activity (IDDA2.1 'Kaleidoscope') Score and Other Clinical Measures in Inborn Errors of Immunity.Journal of clinical immunology · 2022Article
- A rapid turnaround gene panel for severe autoinflammation: Genetic results within 48 hours.Frontiers in immunology · 2022Article
- Phenomic Analysis of Chronic Granulomatous Disease Reveals More Severe Integumentary Infections in X-Linked Compared With Autosomal Recessive Chronic Granulomatous Disease.Frontiers in immunology · 2021Article
- Implementation of Early Next-Generation Sequencing for Inborn Errors of Immunity: A Prospective Observational Cohort Study of Diagnostic Yield and Clinical Implications in Dutch Genome Diagnostic Centers.Frontiers in immunology · 2021Observational
Corrections and comments
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Authors and funding
38 authors.
Funding
Abstract
backgroundAccurate, detailed, and standardized phenotypic descriptions are essential to support diagnostic interpretation of genetic variants and to discover new diseases. The Human Phenotype Ontology (HPO), extensively used in rare disease research, provides a rich collection of vocabulary with standardized phenotypic descriptions in a hierarchical structure. However, to date, the use of HPO has not yet been widely implemented in the field of inborn errors of immunity (IEIs), mainly due to a lack of comprehensive IEI-related terms.
objectivesWe sought to systematically review available terms in HPO for the depiction of IEIs, to expand HPO, yielding more comprehensive sets of terms, and to reannotate IEIs with HPO terms to provide accurate, standardized phenotypic descriptions.
methodsWe initiated a collaboration involving expert clinicians, geneticists, researchers working on IEIs, and bioinformaticians. Multiple branches of the HPO tree were restructured and extended on the basis of expert review. Our ontology-guided machine learning coupled with a 2-tier expert review was applied to reannotate defined subgroups of IEIs.
resultsWe revised and expanded 4 main branches of the HPO tree. Here, we reannotated 73 diseases from 4 International Union of Immunological Societies-defined IEI disease subgroups with HPO terms. We achieved a 4.7-fold increase in the number of phenotypic terms per disease. Given the new HPO annotations, we demonstrated improved ability to computationally match selected IEI cases to their known diagnosis, and improved phenotype-driven disease classification.
conclusionsOur targeted expansion and reannotation presents enhanced precision of disease annotation, will enable superior HPO-based IEI characterization, and hence benefit both IEI diagnostic and research activities.
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