AbstractTheFGFR1gene encoding fibroblast growth factor receptor 1 has emerged as a frequently altered oncogene in the pathogenesis of multiple low-grade neuroepithelial tumor (LGNET) subtypes including pilocytic astrocytoma, dysembryoplastic neuroepithelial tumor (DNT), rosette-forming glioneuronal tumor (RGNT), and extraventricular neurocytoma (EVN). These activatingFGFR1alterations in LGNET can include tandem duplication of the exons encoding the intracellular tyrosine kinase domain, in-frame gene fusions most often withTACC1as the partner, or hotspot missense mutations within the tyrosine kinase domain (either at p.N546 or p.K656). However, the specificity of these differentFGFR1events for the various LGNET subtypes and accompanying genetic alterations are not well defined. Here we performed comprehensive genomic and epigenomic characterization on a diverse cohort of 30 LGNET withFGFR1alterations. We identified that RGNT harbors a distinct epigenetic signature compared to other LGNET withFGFR1alterations, and is uniquely characterized byFGFR1kinase domain hotspot missense mutations in combination with eitherPIK3CAorPIK3R1mutation, often with accompanyingNF1orPTPN11mutation. In contrast, EVN harbors its own distinct epigenetic signature and is characterized byFGFR1-TACC1fusion as the solitary pathogenic alteration. Additionally, DNT and pilocytic astrocytoma are characterized by either kinase domain tandem duplication or hotspot missense mutations, occasionally with accompanyingNF1orPTPN11mutation, but lacking the accompanyingPIK3CAorPIK3R1mutation that characterizes RGNT. The glial component of LGNET withFGFR1alterations typically has a predominantly oligodendroglial morphology, and many of the pilocytic astrocytomas withFGFR1alterations lack the biphasic pattern, piloid processes, and Rosenthal fibers that characterize pilocytic astrocytomas withBRAFmutation or fusion. Together, this analysis improves the classification and histopathologic stratification of LGNET withFGFR1alterations.