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Updated: Oct 4, 2025
Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids
Published on: June 8, 2019
Serial H3K27M cell-free tumor DNA (cf-tDNA) tracking predicts ONC201 treatment response and progression in diffuse
Evan Cantor1, Kyle Wierzbicki1, Rohinton S Tarapore2
1Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan,USA.
Background:
Diffuse Midline Glioma (DMG) with the H3K27M mutation is a lethal childhood brain cancer, with patients rarely surviving 2 years from diagnosis.
Methods:
We conducted a multi-site Phase 1 trial of the imipridone ONC201 for children with H3K27M-mutant glioma (NCT03416530). Patients enrolled on Arm D of the trial (n = 24) underwent serial lumbar puncture for cell-free tumor DNA (cf-tDNA) analysis and patients on all arms at the University of Michigan underwent serial plasma collection. We performed digital droplet polymerase chain reaction (ddPCR) analysis of cf-tDNA samples and compared variant allele fraction (VAF) to radiographic change (maximal 2D tumor area on MRI).
Results:
Change in H3.3K27M VAF over time ("VAF delta") correlated with prolonged PFS in both CSF and plasma samples. Nonrecurrent patients that had a decrease in CSF VAF displayed a longer progression free survival (P = .0042). Decrease in plasma VAF displayed a similar trend (P = .085). VAF "spikes" (increase of at least 25%) preceded tumor progression in 8/16 cases (50%) in plasma and 5/11 cases (45.4%) in CSF. In individual cases, early reduction in H3K27M VAF predicted long-term clinical response (>1 year) to ONC201, and did not increase in cases of later-defined pseudo-progression.
Conclusion:
Our work demonstrates the feasibility and potential utility of serial cf-tDNA in both plasma and CSF of DMG patients to supplement radiographic monitoring. Patterns of change in H3K27M VAF over time demonstrate clinical utility in terms of predicting progression and sustained response and possible differentiation of pseudo-progression and pseudo-response.
Insights
Monitoring cell-free tumor DNA (cf-tDNA) changes in children with Diffuse Midline Glioma (DMG) can predict treatment response and disease progression. This liquid biopsy approach offers a promising tool to supplement traditional imaging for H3K27M-mutant glioma patients.
Area of Science:
- Pediatric Oncology
- Neuro-oncology
- Molecular Diagnostics
Background:
- Diffuse Midline Glioma (DMG) with H3K27M mutation is a fatal childhood brain cancer.
- Limited survival rates necessitate novel monitoring strategies.
Purpose of the Study:
- To evaluate the utility of serial cell-free tumor DNA (cf-tDNA) analysis in monitoring H3K27M-mutant glioma.
- To correlate cf-tDNA variant allele fraction (VAF) changes with radiographic progression and clinical response.
Main Methods:
- Phase 1 trial of ONC201 in pediatric H3K27M-mutant glioma patients (NCT03416530).
- Serial lumbar punctures for cerebrospinal fluid (CSF) cf-tDNA analysis.
- Serial plasma collection for cf-tDNA analysis.
- Digital droplet PCR (ddPCR) for H3K27M VAF quantification and correlation with MRI findings.
Main Results:
- Changes in H3K27M VAF in CSF and plasma correlated with progression-free survival (PFS).
- Decreased CSF VAF predicted longer PFS (P = .0042); plasma VAF showed a similar trend (P = .085).
- VAF spikes preceded tumor progression in approximately 50% of plasma and 45% of CSF samples.
- Early VAF reduction predicted long-term response to ONC201 and helped differentiate pseudo-progression.
Conclusions:
- Serial cf-tDNA analysis in plasma and CSF is feasible for monitoring DMG patients.
- H3K27M VAF dynamics provide clinical utility in predicting progression and response.
- cf-tDNA monitoring may help differentiate pseudo-progression from true progression.
