Optimising diagnosis in children with short stature: an integrated clinical and NGS approach.

Short stature (SS) is one of the most frequent reasons for referral to paediatric endocrinologists. Linear growth is a multifactorial process, with genetic variation representing the principal determinant of height differences. Between 2018 and 2022, 102 children referred to our clinic for growth failure were identified as having SS of unknown aetiology. The cohort comprised 57 children with idiopathic GH deficiency (GHD-SS) and 45 with idiopathic short stature (ISS). Children born small for gestational age and those with known genetic conditions were excluded. All patients underwent a single next-generation sequencing (NGS) analysis using a custom-designed targeted gene panel for SS. When variants were detected, segregation analysis was performed through parental testing. The overall diagnostic yield of NGS was 14.9%, with variants considered causative of the SS phenotype detected in 14.3% of GHD-SS patients and 15.6% of ISS patients. Detection rates were comparable between isolated GHD and combined pituitary hormone deficiency. Among ISS patients, a genetic diagnosis was achieved in 23.8% of familial cases and in 8.7% of sporadic cases. Variants of uncertain significance were identified in approximately half of the cohort. In conclusion, a first-line targeted NGS approach, applied in routine clinical practice to a carefully selected cohort of children with SS of unknown aetiology, demonstrated a competitive diagnostic yield. Accurate phenotypic assessment remains critical to improving the diagnostic performance of molecular testing and refining the aetiological evaluation of SS. Moreover, identification of the underlying genetic cause provides valuable insights for predicting clinical evolution and guiding therapeutic strategies.