Advancing Neuropediatric Rare Disease Diagnosis Through Clinical Genome Sequencing

Background: Many patients with rare genetic diseases remain undiagnosed or receive a molecular diagnosis only after years. In this study, we want to evaluate the usefulness of clinical genome sequencing (cGS) in a cohort of complex neuropediatric patients with undiagnosed rare genetic diseases. Methods: Between 2018 and 2022, our Medical Genetics Units in Torino, Trieste and Pavia partnered with the iHope program, a philanthropic initiative by Illumina Inc., with the aim of offering family-based cGS within the Italian National Health Service (Servizio Sanitario Nazionale) diagnostic process. A multidisciplinary team of pediatricians, clinical geneticists, and molecular biologists selected 64 cases. Inclusion criteria consisted of suspicion of an ultra-rare monogenic disease and at least one negative result from a first-tier genetic test. Results: A definitive molecular diagnosis was achieved in 57.8% of the patients. All patients and families underwent clinical re-evaluation to assess the diagnostic relevance of the laboratory findings, which led us to reclassify 10 variants of unknown significance as responsible for the probands' phenotypes. Diagnoses impacted patients' management, enabling palliative care referrals, avoiding unnecessary invasive tests, and guiding follow-up treatments. Conclusions: Our study confirms that the use of cGS in a rare disease setting increased the diagnostic yield even in complex cases where other methods had previously failed. We speculate that introducing cGS as first-tier test within the Italian Servizio Sanitario Nazionale might offer both diagnostic and economic advantages.