Cell-Free DNA as a Diagnostic and Prognostic Biomarker in Pediatric Rhabdomyosarcoma
Open accessAbstract
PURPOSE: Total cell-free DNA (cfDNA) and tumor-derived cfDNA (ctDNA) can be used to study tumor-derived genetic aberrations. We analyzed the diagnostic and prognostic potential of cfDNA and ctDNA, obtained from pediatric patients with rhabdomyosarcoma. METHODS: cfDNA was isolated from diagnostic plasma samples from 57 patients enrolled in the EpSSG RMS2005 study. To study the diagnostic potential, shallow whole genome sequencing (shWGS) and cell-free reduced representation bisulphite sequencing (cfRRBS) were performed in a subset of samples and all samples were tested using droplet digital polymerase chain reaction to detect methylated RASSF1A ( RASSF1A-M). Correlation with outcome was studied by combining cfDNA RASSF1A-M detection with analysis of our rhabdomyosarcoma-specific RNA panel in paired cellular blood and bone marrow fractions and survival analysis in 56 patients. RESULTS: At diagnosis, ctDNA was detected in 16 of 30 and 24 of 26 patients using shallow whole genome sequencing and cfRRBS, respectively. Furthermore, 21 of 25 samples were correctly classified as embryonal by cfRRBS. RASSF1A-M was detected in 21 of 57 patients. The presence of RASSF1A-M was significantly correlated with poor outcome (the 5-year event-free survival [EFS] rate was 46.2% for 21 RASSF1A-M ‒positive patients, compared with 84.9% for 36 RASSF1A-M ‒negative patients [ P < .001]). RASSF1A-M positivity had the highest prognostic effect among patients with metastatic disease. Patients both negative for RASSF1A-M and the rhabdomyosarcoma-specific RNA panel (28 of 56 patients) had excellent outcome (5-year EFS 92.9%), while double-positive patients (11/56) had poor outcome (5-year EFS 13.6%, P < .001). CONCLUSION: Analyzing ctDNA at diagnosis using various techniques is feasible in pediatric rhabdomyosarcoma and has potential for clinical use. Measuring RASSF1A-M in plasma at initial diagnosis correlated significantly with outcome, particularly when combined with paired analysis of blood and bone marrow using a rhabdomyosarcoma-specific RNA panel.
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Dynamic longitudinal change may be more informative than end-treatment values alone in pediatric sarcomas.
“In pediatric sarcomas specifically, prior studies showed that ctDNA detectability and prognostic impact can vary by subtype, disease burden, and assay design (e.g., fusion-based vs. broader panels), suggesting that dynamic longitudinal change may be more informative than end-treatment values alone [38,39].”
From Circulating Tumor DNA and microRNA–Based Liquid Biopsy for Longitudinal Treatment Monitoring and Recurrence Prediction in Pediatric Sarcomas: A Prospective Cohort Study (2026) · cites this paper as [39]
The Results (RASSF1A-M During Treatment and Clinical Follow-Up; page unavailable) show that ctDNA usually became undetectable early in treatment. The Discussion (page unavailable) proposes earlier, repeated sampling as a possible way to develop a prognostic marker. The paper does not establish that longitudinal change is more informative than end-treatment values, and its findings concern rhabdomyosarcoma rather than pediatric sarcomas generally. (LLM, conf=0.83)
Experimental — accuracy not yet measuredIn pediatric sarcomas, ctDNA detectability and prognostic impact can vary by subtype, disease burden, and assay design (e.g., fusion-based vs. broader panels).
“In pediatric sarcomas specifically, prior studies showed that ctDNA detectability and prognostic impact can vary by subtype, disease burden, and assay design (e.g., fusion-based vs. broader panels), suggesting that dynamic longitudinal change may be more informative than end-treatment values alone [38,39].”
From Circulating Tumor DNA and microRNA–Based Liquid Biopsy for Longitudinal Treatment Monitoring and Recurrence Prediction in Pediatric Sarcomas: A Prospective Cohort Study (2026) · cites this paper as [39]
The Results (Diagnostic Potential of Various Molecular Techniques for Detecting ctDNA; no page available) report that RASSF1A-M detection differed by rhabdomyosarcoma subtype and metastatic status. The Results and Discussion also describe differences among assays and stronger prognostic value in metastatic patients. The paper does not compare fusion-based ctDNA assays with broader panels, and its findings concern rhabdomyosarcoma rather than pediatric sarcomas generally. (LLM, conf=0.86)
Experimental — accuracy not yet measured
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- [23]De Koker R, Van Paemel R, De Wilde B, et al: A versatile method for circulating cell-free DNA methylome profiling by reduced representation bisulfite sequencing. https://www.biorxiv.org/content/10.1101/663195v2, 2019 · DOI
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- Authors
- Lak, N. S. M., van Zogchel, L. M. J., Zappeij-Kannegieter, L., Javadi, A., van Paemel, R., Vandeputte, C., De Preter, K., De Wilde, B., Chicard, M., Iddir, Y., Schleiermacher, G., Ruhen, O., Shipley, J., Fiocco, M., Merks, J. H. M., van Noesel, M. M., van der Schoot, C. E., Tytgat, G. A. M., & Stutterheim, J.
- Affiliations
- Sanquin (NL)
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Sanquin Research Department, Amsterdam, the Netherlands
- Translational Oncogenomics and Bioinformatics Lab, Department of Biomolecular Medicine & Cancer Research Institute Ghent, Ghent University Hospital, Ghent, Belgium
- Ghent University Hospital (BE)
- Inserm (FR)
- Institut Curie (FR)
- Institute of Cancer Research (GB)
- Leiden University (NL)
- Princess Máxima Center (NL)
- Corresponding author
- Stutterheim, Janine
- ORCID
- Venue
- JCO Precision Oncology
- Published
- 2023-01
- Volume
- 7
- Issue
- 7
- Pages
- e2200113-e2200113
- ISSN
- 2473-4284 (ISSN-L)
- PMC
- PMC9928631
- OpenAlex
- W4317477271
- Cited by
- 25
- References
- 39
- Citations by year
- 2026: 6 · 2025: 8 · 2024: 7 · 2023: 4
- FWCI
- 4.61
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- JCO Precision Oncology (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Leiden Repository (Leiden University) (submittedVersion, cc-by-nc-nd)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by-nc-nd)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- Universiteit Gent
- Topics
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Sarcoma Diagnosis and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Acute Lymphoblastic Leukemia research
- Keywords
- pediatric rhabdomyosarcoma, cell-free DNA, circulating tumor DNA, prognostic factors, diagnostic biomarkers, plasma DNA, event-free survival, embryonal rhabdomyosarcoma, bone marrow, metastatic disease, liquid biopsy
- MeSH terms
- Cell-Free Nucleic Acids, Child, Humans, Prognosis, Rhabdomyosarcoma, RNA, Biomarkers
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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