Telethon Undiagnosed Disease Programme: Beyond the Exome

Rare genetic diseases (RGDs) collectively affect millions of individuals worldwide and remain one of the significant challenges in genomic medicine, with almost half of the patients still lacking a molecular diagnosis after Exome Sequencing (ES). The Telethon Undiagnosed Diseases Programme (TUDP) was created to address this diagnostic gap through a nationwide framework of collaboration integrating clinical expertise, standardised phenotyping, and advanced sequencing technologies. During the early phase, TUDP trio-based ES achieved a diagnostic yield of about 50%, consistent with similar project rates. Nonetheless, many cases remained unsolved due to the intrinsic limitations of targeted short-read sequencing. This work aims to increase the diagnostic rate of the unsolved TUDP cohort by implementing new genomic technologies and analytical strategies, including long-read sequencing (LRS), updated re-analysis pipelines, and the detection of non-coding and structurally complex regions. The integration of these approaches into the TUDP workflow has enhanced variant detection and interpretation, enabling the identification of novel pathogenic mechanisms and expanding the spectrum of detectable variants. Overall, this project demonstrates how combining innovative sequencing methods, updated bioinformatic pipelines, and international data-sharing frameworks can transform rare-disease diagnostics. The TUDP thus provides a scalable model for national and European efforts toward a more comprehensive and equitable practice of genomic medicine.