Circulating Plasma Tumor DNA Is Superior to Plasma Tumor RNA Detection in Ewing Sarcoma Patients
Open accessAbstract
The detection of tumor-specific nucleic acids from blood increasingly is being used as a method of liquid biopsy and minimal residual disease detection. However, achieving high sensitivity and high specificity remains a challenge. Here, we perform a direct comparison of two droplet digital PCR (ddPCR)-based detection methods, circulating plasma tumor RNA and circulating plasma tumor DNA (ptDNA), in blood samples from newly diagnosed Ewing sarcoma patients. First, we developed three specific ddPCR-based assays to detect EWS-FLI1 or EWS-ERG fusion transcripts, which naturally showed superior sensitivity to DNA detection on in vitro control samples. Next, we identified the patient-specific EWS-FLI1 or EWS-ERG breakpoint from five patient tumor samples and designed ddPCR-based, patient-specific ptDNA assays for each patient. These patient-specific assays show that although plasma tumor RNA can be detected in select newly diagnosed patients, positive results are low and statistically unreliable compared with ptDNA assays, which reproducibly detect robust positive results across most patients. Furthermore, the unique disease biology of Ewing sarcoma enabled us to show that most cell-free RNA is not tumor-derived, although cell-free-DNA burden is affected strongly by tumor-derived DNA burden. Here, we conclude that, even with optimized highly sensitive and specific assays, tumor DNA detection is superior to RNA detection in Ewing sarcoma patients.
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Plasma tumor DNA appears more reproducible than plasma tumor RNA in Ewing sarcoma.
“Similarly, plasma tumor DNA appears more reproducible than plasma tumor RNA in Ewing sarcoma”
From Signals Alongside Scans: A Genomics-Guided Framework for Liquid Biopsy in Bone and Soft-Tissue Sarcomas (2026) · cites this paper as [37]
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- Authors
- Bodlak, A., Chang, K., Channel, J., Treece, A. L., Donaldson, N., Cost, C. R., Garrington, T. P., Greffe, B., Luna-Fineman, S., Sopfe, J., Loeb, D. M., & Hayashi, M.
- Affiliations
- University of Colorado Denver (US)
- University of Houston (US)
- Albert Einstein College of Medicine (US)
- University of Colorado Anschutz (US)
- Corresponding author
- Hayashi, Masanori
- ORCID
- Venue
- The Journal of Molecular Diagnostics
- Publisher
- Elsevier BV
- Published
- 2021-07
- Volume
- 23
- Issue
- 7
- Pages
- 872-881
- ISSN
- 1525-1578 (ISSN-L)
- PMC
- PMC8261897
- OpenAlex
- W3154075702
- Cited by
- 12
- References
- 46
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 5 · 2023: 2 · 2022: 2
- FWCI
- 0.90
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Journal of Molecular Diagnostics (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of Colorado
- National Institutes of Health (K12HD068372)
- Saint Baldricks Foundation
- Hyundai Hope On Wheels
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Sarcoma Diagnosis and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Extracellular vesicles in disease
- Keywords
- Ewing sarcoma, circulating tumor DNA, circulating tumor RNA, liquid biopsy, droplet digital PCR, EWS-FLI1 fusion, minimal residual disease, cell-free RNA, cell-free DNA, sensitivity and specificity
- MeSH terms
- Circulating Tumor DNA, Adolescent, Child, Female, Humans, Male, RNA, Neoplasm, Sarcoma, Ewing, Transcription Factors, Translocation, Genetic, Biomarkers, Tumor, Reproducibility of Results, Oncogene Proteins, Fusion, Polymerase Chain Reaction, RNA-Binding Protein EWS, Proto-Oncogene Protein c-fli-1
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