Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity

Accurate, 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...

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Detalhes bibliográficos
Autores: Haimel, Matthias, Pazmandi, Julia, Heredia, Raú Jiménez, Dmytrus, Jasmin, Bal, Sevgi Köstel, Zoghi, Samaneh, van Daele, Paul, Briggs, Tracy A., Wouters, Carine, Bader-Meunier, Brigitte, Aeschlimann, Florence A., Caorsi, Roberta, Eleftheriou, Despina, Hoppenreijs, Esther, Salzer, Elisabeth, Bakhtiar, Shahrzad, Derfalvi, Beata, Saettini, Francesco|||0000-0003-0767-3905, Kusters, Maaike A.|||0000-0001-7601-9822, Elfeky, Reem, Trück, Johannes, Rivière, Jacques G.|||0000-0003-1055-2063, van der Burg, Mirjam, Gattorno, Marco, Seidel, Markus G., Burns, Siobhan|||0000-0002-3356-9506, Warnatz, Klaus|||0000-0002-1172-865X, Hauck, Fabian, Brogan, Paul, Gilmour, Kimberly C., Schuetz, Catharina, Simon, Anna, Bock, Christoph, Hambleton, Sophie, de Vries, Esther, Robinson, Peter N.|||0000-0002-0736-9199, Van Gijn, Marielle, Boztug, Kaan
Formato: artículo
Fecha de publicación:2021
País:España
Recursos:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:280557
Acesso em linha:https://ddd.uab.cat/record/280557
https://dx.doi.org/urn:doi:10.1016/j.jaci.2021.04.033
Access Level:acceso abierto
Palavra-chave:Diagnostic support
Disease classification
Genetic analysis
HPO
Immunodeficiencies
Inborn errors of immunity
Ontology
Patient matching
Phenotype
Rare diseases
Descrição
Resumo:Accurate, 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. We 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. We 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. We 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. Our 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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