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

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 detection. 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) and 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.

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000001445	The dataset for “Detection of brain cancer using genome-wide cell-free DNA fragmentomes” includes 310 bam files from whole genome next-generation sequencing on the Illumina Novaseq 6000. The dataset analyzed include plasma cfDNA samples from patients with cancer, patients with neurological conditions, and healthy individuals.	Illumina NovaSeq 6000	310

Publications	Citations
Detection of Brain Cancer Using Genome-wide Cell-free DNA Fragmentomes. Mathios D, Niknafs N, Annapragada AV, Bobeff EJ, Chiao EJ, Boyapati K, Boyapati K, Short S, Bartolomucci AL, Cristiano S, Koul S, Vulpescu NA, Ferreira L, Medina JE, Bruhm DC, Adleff V, Podstawka M, Stanisławska P, Park CK, Huang J, Gallia GL, Brem H, Mukherjee D, Caplan JM, Weingart J, Jackson CM, Lim M, Phallen J, Scharpf RB, Velculescu VE. Cancer Discov 15: 2025 1593-1608	3

Publications

Citations

Detection of Brain Cancer Using Genome-wide Cell-free DNA Fragmentomes.
Mathios D, Niknafs N, Annapragada AV, Bobeff EJ, Chiao EJ, Boyapati K, Boyapati K, Short S, Bartolomucci AL, Cristiano S, Koul S, Vulpescu NA, Ferreira L, Medina JE, Bruhm DC, Adleff V, Podstawka M, Stanisławska P, Park CK, Huang J, Gallia GL, Brem H, Mukherjee D, Caplan JM, Weingart J, Jackson CM, Lim M, Phallen J, Scharpf RB, Velculescu VE. Cancer Discov 15: 2025 1593-1608