Rare-ID: Genomic Diagnosis in Symptomatic Neonates and Young Infants with Complex Clinical Phenotypes: A Descriptive Cohort Study

Background/Objectives: Genomic sequencing can shorten the diagnostic pathway for selected symptomatic neonates and young infants, but evidence from such cohorts should not be extrapolated to population newborn screening. This study describes molecular findings and potential clinical implications in 25 unrelated patients younger than 6 months at referral with heterogeneous, predominantly neurological phenotypes and no established molecular diagnosis. Methods: The first 17 patients underwent whole-exome sequencing (WES), and the subsequent 8 underwent whole-genome sequencing (WGS) under sequential laboratory protocols; allocation was not randomized, and the study was not designed to compare platforms. Results: Pathogenic or likely pathogenic findings providing a definitive or likely molecular diagnosis were identified in 7/25 patients (28.0%; 95% confidence interval [CI], 14.3–47.6), including sequence variants, one 20q13.33 deletion, and mosaic trisomy 9. An additional RANBP2 variant was interpreted as a susceptibility-associated finding in a patient with infection-related encephalitis, yielding clinically relevant findings in 8/25 patients (32.0%; 95% CI, 17.2–51.6). Three definitive diagnoses involved disorders with established disease-specific management considerations; however, patient-level treatment changes, turnaround times, and outcomes were not systematically assessed. Conclusions: These findings support the diagnostic value of genomic testing in selected symptomatic neonates and young infants, while the small, heterogeneous cohort, sequential non-equivalent workflows, and incomplete outcome data preclude conclusions about comparative WES/WGS performance or population newborn screening.