Inborn errors of immunity (IEI) are a heterogeneous group of disorders caused by monogenic defects and encompassing more than 500 disease-causing genes, as catalogued in the International Union of Immunological Societies (IUIS) 2024 classification. Genetic diagnosis is essential for understanding disease pathophysiology and guiding therapeutic decision-making; however, a substantial proportion of patients remain undiagnosed even after comprehensive genomic analyses, including targeted gene panel testing and whole-exome sequencing. The functional interpretation of variants of uncertain significance (VUS) represents a major unresolved challenge in this field. To address this, we implemented an integrative multi-omics approach combining targeted RNA sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS)-based proteomics and applied this strategy to cases that had not achieved a diagnosis through conventional genomic analysis. This workflow enabled cross-platform evaluation of aberrant gene expression, splicing dysregulation, and protein-level alterations, thereby providing functional evidence to support VUS reclassification. As a result, we achieved an incremental diagnostic yield of 6% (4 of 70 cases). In this presentation, we describe our implementation strategy and outcomes and discuss the clinical impact of multi-omics approaches and future perspectives for their broader application in IEI diagnostics.
