Curation and expansion of the Human Phenotype Ontology for systemic autoinflammatory diseases improves phenotype-driven disease-matching

Willem Maassen, Geertje Legger, Ovgu Kul Cinar, Paul van Daele, Marco Gattorno, Brigitte Bader-Meunier, Carine Wouters, Tracy Briggs, Lennart Johansson, Joeri van der Velde, Morris Swertz, Ebun Omoyinmi, Esther Hoppenreijs, Alexandre Belot, Despina Eleftheriou, Roberta Caorsi, Florence Aeschlimann, Guilaine Boursier, Paul Brogan, Matthias HaimelMarielle van Gijn

Research output: Contribution to journalArticlepeer-review


INTRODUCTION: Accurate and standardized phenotypic descriptions are essential in diagnosing rare diseases and discovering new diseases, and the Human Phenotype Ontology (HPO) system was developed to provide a rich collection of hierarchical phenotypic descriptions. However, although the HPO terms for inborn errors of immunity have been improved and curated, it has not been investigated whether this curation improves the diagnosis of systemic autoinflammatory disease (SAID) patients. Here, we aimed to study if improved HPO annotation for SAIDs enhanced SAID identification and to demonstrate the potential of phenotype-driven genome diagnostics using curated HPO terms for SAIDs.

METHODS: We collected HPO terms from 98 genetically confirmed SAID patients across eight different European SAID expertise centers and used the LIRICAL (Likelihood Ratio Interpretation of Clinical Abnormalities) computational algorithm to estimate the effect of HPO curation on the prioritization of the correct SAID for each patient.

RESULTS: Our results show that the percentage of correct diagnoses increased from 66% to 86% and that the number of diagnoses with the highest ranking increased from 38 to 45. In a further pilot study, curation also improved HPO-based whole-exome sequencing (WES) analysis, diagnosing 10/12 patients before and 12/12 after curation. In addition, the average number of candidate diseases that needed to be interpreted decreased from 35 to 2.

DISCUSSION: This study demonstrates that curation of HPO terms can increase identification of the correct diagnosis, emphasizing the high potential of HPO-based genome diagnostics for SAIDs.

Original languageEnglish
Article number1215869
JournalFrontiers in Immunology
Publication statusPublished - 12 Sept 2023


  • genome diagnostics
  • Human Phenotype Ontology (HPO)
  • systemic autoinflammatory disorders (SAIDs)
  • variant interpretation
  • whole exome sequencing (WES)


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