Molecular Landscape of Pediatric Low-Grade Gliomas: Insights From RNA-NGS and Bioinformatic Analysis

Abstract

Pediatric low-grade gliomas (pLGG) are the most common group of childhood brain tumors. Genetic alterations in the RAS-RAF-mitogen-activated protein kinase (MAPK) pathway are the molecular drivers in the vast majority of pLGG. A large proportion of pediatric pLGG are characterized by the presence of fusion genes. An institutional molecular analysis together with an RNA-NGS study was performed to reveal LGG-associated molecular alterations. In our cohort of pLGG patients, molecular alterations were identified in 318 out of 342 cases (92.9%) through a combination of RT-PCR, Sanger sequencing, and NGS methodologies. Fusion events were independently called using three fusion callers: Archer Analysis 6.0 and/or 7.0, Arriba version 2.4, and STAR-Fusion 24. Among these, STAR-Fusion had the lowest sensitivity, detecting rearrangements in only 67% of fusion-positive cases. In contrast, Arriba detected rearrangements in 97.77% of cases, while Archer detected rearrangements in 88.6% of cases. These findings highlight differences in detection efficiency among fusion callers, emphasizing the importance of tool selection in molecular diagnostics. The detection of fusion genes is very important for correct diagnosis, prognosis, and adequate targeted treatment.