Abstract
Aneuploidy, an abnormal number of chromosomes, is a hallmark of cancer and has been proposed as an initiating event in tumorigenesis. In glioblastoma (GBM), a highly aggressive brain tumor, cells almost universally display gain of chromosome 7 and loss of chromosome 10. However, it remains unclear whether these alterations arise de novo during malignant transformation or reflect pre-existing chromosomal instability in normal brain tissue. Here, we used single-nucleus whole-genome sequencing (snWGS) on 225 NeuN-negative (non-neuronal) cortical nuclei from 12 healthy individuals and 6 GBM patients, including matched tumor cores and non-tumor brain regions. In healthy brains, approximately 15% of glial nuclei harbored somatic aneuploidies, most often involving chromosome arms, with recurrent 16p alterations detected in up to 3% of nuclei from both healthy controls and GBM non-tumor tissue. These findings establish 16p is a hotspot of structural variation in adult glia. Non-tumor regions in GBM patients closely resembled healthy controls in aneuploidy burden and chromosomal instability metrics and lacked hallmark tumor alterations. In contrast, GBM tumors exhibited significantly elevated aneuploidy (~50%), enrichment for canonical chromosomal instability-driven events, and sex-specific karyotype patterns, consistent with transformation-associated chromosomal instability. Thus, aneuploidy is a recurrent but constrained feature of normal adult glia, whereas chromosome instability and GBM-defining aneuploidies emerge only during malignant transformation.