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Updated: May 9, 2025
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Detection of Cell-Free DNA in Blood Plasma Samples of Cancer Patients
Published on: September 9, 2020
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Detection of Brain Cancer Using Genome-wide Cell-free DNA Fragmentomes.
Dimitrios Mathios1,2,3, Noushin Niknafs1, Akshaya V Annapragada1
1Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Cancer Discovery
|April 29, 2025
Summary
A novel blood test analyzing cell-free DNA (cfDNA) fragmentomes shows promise for early brain cancer detection. This noninvasive assay accurately identifies gliomas, potentially speeding up diagnosis and improving patient outcomes.
Area of Science:
- Oncology
- Genomics
- Biomarker Discovery
Background:
- Diagnostic delays are common in brain cancer, negatively impacting patient outcomes.
- Developing a blood-based assay could significantly accelerate brain cancer diagnosis.
Purpose of the Study:
- To analyze genome-wide cell-free DNA (cfDNA) fragmentomes for brain cancer detection.
- To evaluate the efficacy of machine learning in identifying brain cancer from cfDNA features.
Main Methods:
- Analysis of cfDNA fragmentome features (fragmentation profiles, repeat landscapes) from plasma samples.
- Machine learning models applied to cfDNA data from patients with and without brain cancer.
- Validation in an independent, prospectively collected cohort.
Main Results:
- Machine learning analysis of cfDNA fragmentome features detected brain cancer across all glioma grades with high accuracy (AUC=0.90).
- Results were successfully validated in an independent cohort.
- Identified cfDNA changes reflect contributions from both glioma cells and altered white blood cell populations.
Conclusions:
- cfDNA fragmentome analysis offers a promising noninvasive approach for brain cancer detection.
- This method has the potential to accelerate diagnosis and improve patient outcomes.
- Further research into cfDNA properties can open new avenues for early cancer detection.
