Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity
Haimel, Matthias (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences (Vienna))
Pazmandi, Julia (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences (Vienna))
Heredia, Raú Jiménez (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences (Vienna))
Dmytrus, Jasmin (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences (Vienna))
Bal, Sevgi Köstel (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences (Vienna))
Zoghi, Samaneh (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences (Vienna))
van Daele, Paul (Erasmus University Medical Center (Rotterdam))
Briggs, Tracy A. (University of Manchester)
Wouters, Carine (University Hospitals Leuven (Bèlgica))
Bader-Meunier, Brigitte (Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE) (Paris))
Aeschlimann, Florence A. (Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE),(Paris))
Caorsi, Roberta (IRCCS Istituto Giannina Gaslini, Genova)
Eleftheriou, Despina (Hospital for Children NHS Foundation Trust (London))
Hoppenreijs, Esther (Radboud University Medical Centre (Nijmegen))
Salzer, Elisabeth (Medical University of Vienna)
Bakhtiar, Shahrzad (Goethe University)
Derfalvi, Beata (Dalhousie University/IWK Health Centre Halifax)
Saettini, Francesco (University of Milano Bicocca)
Kusters, Maaike A. A. (Hospital for Children NHS Foundation Trust)
Elfeky, Reem (Hospital for Children NHS Foundation Trust (London))
Trück, Johannes (University Children's Hospital Zurich)
Rivière, Jacques G.. (Hospital Universitari Vall d'Hebron. Institut de Recerca)
van der Burg, Mirjam (Leiden University Medical Center)
Gattorno, Marco (IRCCS Istituto Giannina Gaslini (Genova))
Seidel, Markus G. (Medical University Graz)
Burns, Siobhan (Royal Free Hospital NHS Foundation Trust)
Warnatz, Klaus (University of Freiburg)
Hauck, Fabian (Ludwig-Maximilians-Universität München (Munich))
Brogan, Paul (Hospital for Children NHS Foundation Trust (London))
Gilmour, Kimberly C. (Hospital for Children NHS Foundation Trust (London))
Schuetz, Catharina (Technische Universität Dresden)
Simon, Anna (Radboud University Nijmegen Medical Centre)
Bock, Christoph (Medical University of Vienna)
Hambleton, Sophie (Newcastle University)
de Vries, Esther (Elisabeth-Tweesteden Hospital (Tilburg))
Robinson, Peter N. (The Jackson Laboratory for Genomic Medicine (Farmington))
van Gijn, Marielle (University Medical Center Groningen)
Boztug, Kaan (Medical University of Vienna)
Universitat Autònoma de Barcelona

Fecha:	2021
Resumen:	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.
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, i la comunicació pública de l'obra, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original. No es permet la creació d'obres derivades.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Materia:	Diagnostic support ; Disease classification ; Genetic analysis ; HPO ; Immunodeficiencies ; Inborn errors of immunity ; Ontology ; Patient matching ; Phenotype ; Rare diseases
Publicado en:	The Journal of Allergy and Clinical Immunology, Vol. 149 (may 2021) , p. 369-378, ISSN 1097-6825

DOI: 10.1016/j.jaci.2021.04.033
PMID: 33991581

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