Early genomic testing prevents years of inconclusive visits for pediatric patients

For many families, eight years of uncertainty meant repeated specialist visits, inconclusive genetic tests and the growing fear that a clear answer might never come. For nearly half of the children enrolled in the Telethon Undiagnosed Disease Program (TUDP), that wait is now over.

A study published in Genetics in Medicine Open, the journal of the American College of Medical Genetics and Genomics, presents the results of the TUDP across its first eight years (2016–2023), covering more than 1,300 pediatric cases evaluated at 22 specialist centers in Italy. The findings show that a structured national genomic program for rare disease diagnosis can be more effective than fragmented clinical efforts and can be implemented by the national health system.

The numbers: A diagnostic yield among the highest worldwide

The program, coordinated by the Telethon Institute of Genetics and Medicine (TIGEM), achieved a definitive genetic diagnosis in 49 % of enrolled children, a diagnostic yield that compares favourably with other undiagnosed disease initiatives worldwide. Pathogenic variants were identified across 330 genes, reflecting the wide genetic diversity of childhood-onset rare conditions. More than 70 % of causative variants were de novo, arising spontaneously with no prior family history.

For families enrolled, a diagnosis was typically delivered within 12 to 18 months of entry. For children born after the TUDP's 2016 launch, early access to this pathway meant avoiding years of inconclusive testing altogether.

More than a result: What a diagnosis actually means

In severe pediatric rare diseases, a molecular diagnosis is not just a clinical label. In this cohort, it brought an end to a diagnostic odyssey that often lasted almost a decade, allowed accurate genetic counselling and informed reproductive choices. It also guided clinical management and, in a growing number of cases, opened access to targeted therapies such as antisense oligonucleotides, gene therapy and precision pharmacology

"Behind every percentage point there is a child and a family who have waited, sometimes for a decade, for a single word: a name. A molecular diagnosis changes the trajectory of a life, not only in terms of medicine but in terms of hope, identity, and connection to a global community of patients and researchers working on the same diseases" comments Vincenzo Nigro, TUDP Coordinator at TIGEM and professor of Genetics at the University of Campania 'Luigi Vanvitelli'.

The TUDP model: Rigorous selection, national network, continuous reanalysis

The TUDP differs from routine clinical genomics in its strict enrollment, limited to children under 18 with severe, complex phenotypes that remain undiagnosed after prior genomic testing: all cases are reviewed through a national network of clinicians from participating centers and TIGEM scientists.

All samples are processed centrally at TIGEM in Pozzuoli, using trio-based exome sequencing as entry-level testing and further genomic technologies applied when needed. Unsolved cases are not considered closed: through regular reanalysis of genomic data, and the continuous expansion of disease-gene knowledge, the program has increased its diagnostic yield over time, showing that genomic data can become informative. Systematic reanalysis of unsolved cases has already increased the overall diagnostic yield by more than 17% among previously negative cases.

Gene discovery: From diagnosis to new knowledge

The TUDP is not only a diagnostic service, but it has also become an important source of new scientific discovery. During the study period, it contributed to the identification of 16 previously unknown disease-causing genes, validated through international collaborations and functional studies in model organisms. A further 14 candidate genes are currently under validation. These findings underscore both the progress achieved and how much of the genetic basis of rare diseases remains uncharacterized.

Collaboration with the Matchmaker Exchange platform enabled identification of patients worldwide carrying variants in the same newly discovered genes, accelerating the evidence needed to establish causality. To date, the TUDP has generated 74 publications, including original research articles, case reports, phenotypic expansions, and therapeutic studies.

A striking recent example is the identification of 11 probands with de novo variants in RNU4-2, a non-coding RNA gene recently linked to a newly recognized neurodevelopmental disorder (ReNU syndrome), made possible precisely through the TUDP's systematic reanalysis strategy.

Part of an international rare disease network

The TUDP operates within, and contributes to, an international network devoted to rare diseases. It is a full member of the Undiagnosed Diseases Network International (UDNI) and a partner in the European Commission-funded Solve-RD project, which has reanalyzed TUDP datasets through European Reference Networks. Patient phenotypic data are shared via PhenomeCentral, Decipher, and ClinVar, enabling cross-border matchmaking and accelerating gene–disease associations.

Following diagnosis, families are supported through InfoRare, Fondazione Telethon's free information service, which provides guidance on referral centers, patient associations, clinical trials, and condition-specific scientific developments.

Next steps for the TUDP

The 2016–2023 results establish the TUDP as a national reference program for rare pediatric genomic medicine. In the current phase the entry-level testing is represented by trio whole genome sequencing, integrating artificial intelligence tools for variant classification. Additional tools are whole genome long-read sequencing and optical mapping for structurally complex unresolved cases, as well as RNA sequencing to detect deep intronic and splicing variants, and pilot initiatives for personalized treatments.

Unsolved cases are not failures. They represent an important scientific resource and a shared responsibility. As genomic technologies and biological knowledge evolve, many of today's unsolved cases are likely to become tomorrow's diagnoses and, in some instances, the basis for new therapies"

Vincenzo Nigro, University of Campania 'Luigi Vanvitelli'

See the complete list of the Clinical Structures involved.