Standardised Human Phenotype Ontology Annotation Enables High Quality Phenotypic Data Capture in a Real-World Common Variable Immunodeficiency Cohort

BackgroundPatients with Common Variable Immunodeficiency (CVID) exhibit diverse clinical manifestations, indicating heterogeneity in pathogenic mechanisms. Systematic application of standardised phenotyping in large cohorts is essential to dissect this heterogeneity. The Human Phenotype Ontology (HPO) provides a structured framework for capturing and comparing disease phenotypes. ObjectiveTo evaluate the implementation and outcomes of HPO-based phenotyping in CVID patients enrolled for whole-genome sequencing in a large national adult primary immunodeficiency cohort. MethodsWe developed a web-based Phenotype Capture Tool and delivered structured clinician training to standardise HPO annotation. Numerical laboratory parameters were mapped to corresponding HPO terms to enrich patient records. ResultsWe coded the phenotypes of 526 CVID patients across 11 UK centres. Clinician training increased phenotype granularity and improved phenotyping consistency between clinicians. We assigned 883 unique HPO terms across the cohort and applied logical rules to the terms to classify patients into an infection-only group and a complex phenotype group (42% vs 58%, respectively). Patients in the complex phenotype group were significantly more likely to have reduced switched memory and expanded CD21low B cells, as well as pathogenic variants in IUIS-listed genes overall and pathogenic NFKB1 variants specifically. Having a pathogenic variant in an IUIS-listed gene was associated with Autoimmune hemolytic anemia and having a pathogenic NFKB1 variant specifically was associated with Autoimmune neutropenia. ConclusionThis is the first study to systematically collect granular HPO-coded phenotypes in a large real-world CVID cohort, refining the CVID landscape and providing a comprehensive CVID HPO term set relevant for international research. Clinical ImplicationHPO allows systematic capture of CVID phenotypes with low inter-clinician variability and improves comparison of cohorts, enhancing identification of disease heterogeneity essential to support genotype-phenotype studies and targeted therapeutic strategies. Capsule summaryHPO-based phenotyping of 526 CVID patients improved annotation quality, identifying immunological and genetic associations with clinical manifestations, distinguishing infection-only from complex disease and refining clinical characterisation to support international collaboration.