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Detection of brain cancer using genome-wide cell-free DNA fragmentomes.

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Detection of brain cancer using genome-wide cell-free DNA fragmentomes. Cancer discovery Mathios, D., Niknafs, N., Annapragada, A. V., Bobeff, E. J., Chiao, E. J., Boyapati, K., Boyapati, K., Short, S., Bartolomucci, A. L., Cristiano, S., Koul, S., Vulpescu, N. A., Ferreira, L., Medina, J. E., Bruhm, D. C., Adleff, V., Podstawka, M., Stanislawska, P., Park, C. K., Huang, J., Gallia, G. L., Brem, H., Mukherjee, D., Caplan, J. M., Weingart, J., Jackson, C. M., Lim, M., Phallen, J., Scharpf, R. B., Velculescu, V. E. 2025

Abstract

Diagnostic delays in patients with brain cancer are common and can impact patient outcome. Development of a blood-based assay for detection of brain cancers could accelerate brain cancer diagnosis. In this study, we analyzed genome-wide cell-free (cfDNA) fragmentomes, including fragmentation profiles and repeat landscapes, from the plasma of individuals with (n=148) or without (n=357) brain cancer. Machine learning analyses of cfDNA fragmentome features detected brain cancer across all grade gliomas (AUC=0.90, 95% CI: 0.87-0.93) and these results were validated in an independent prospectively collected cohort. cfDNA fragmentome changes in patients with gliomas represented a combination of fragmentation profiles from glioma cells and altered white blood cell populations in the circulation. These analyses reveal the properties of cfDNA in patients with brain cancer and open new avenues for noninvasive detection of these individuals.

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