Subtype-specific evolutionary constraints shape the genomic architecture of adult diffuse gliomas

Diffuse gliomas are the most common malignant primary brain tumors in adults and exhibit substantial clinical and biological heterogeneity. The 2021 WHO Classification integrates histologic and molecular features to define adult-type diffuse gliomas as astrocytoma (AST), IDH-mutant; oligodendroglioma (ODG), IDH-mutant and 1p/19q-codeleted; and glioblastoma (GBM), IDH-wildtype. Although prior TCGA and other whole-exome sequencing studies have characterized key genomic features of pan-gliomas, the temporal ordering and evolutionary heterogeneity of genomic events across subtypes remain incompletely understood. Here, we analyzed whole-genome sequencing data from 814 tumor samples across 798 patients spanning glioblastoma and lower-grade gliomas. Tumors were reclassified based on IDH1/2 mutation and 1p/19q codeletion status. Using a novel computational framework to infer subclonal architecture and event timing, we identified distinct evolutionary trajectories across glioma subtypes. GBM exhibited highly heterogeneous evolutionary paths driven by early copy-number alterations affecting major oncogenic pathways, with whole-genome duplication (WGD) emerging later in a subset of tumors. In contrast, ODG followed a tightly constrained evolutionary program initiated by early IDH mutation and 1p/19q codeletion, with relatively few subsequent alterations, including CIC and FUBP1 mutations and infrequent WGD. AST displayed an intermediate, stepwise trajectory characterized by early TP53 and IDH1 mutations, followed by ATRX loss and gradual accumulation of copy-number alterations. TP53 mutations occurred as the earliest clonal events in GBM and AST but were rare and late in ODG.De novo evolutionary modeling further revealed two distinct trajectories within GBM and AST. GBM segregated into one group driven by early, diverse copy-number alterations and a second group following a mutation-anchored, stepwise evolution marked by recurrent chromosome 20 gain. AST similarly divided into an early, cascade TP53 -driven evolutionary trajectory characterized by progressive TP53 allelic imbalance and significantly worse survival. In contrast, a second group exhibited a more heterogeneous evolutionary route involving early alterations in chromatin and transcriptional regulators.Together, these findings define subtype-specific temporal constraints and evolutionary heterogeneity across diffuse gliomas, providing clinically relevant insights into early clonal events that may inform prognostic stratification and guide precision therapeutic strategies.