Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden
Open accessAbstract
Sequencing of cell-free DNA in the blood of cancer patients (liquid biopsy) provides attractive opportunities for early diagnosis, assessment of treatment response, and minimally invasive disease monitoring. To unlock liquid biopsy analysis for pediatric tumors with few genetic aberrations, we introduce an integrated genetic/epigenetic analysis method and demonstrate its utility on 241 deep whole-genome sequencing profiles of 95 patients with Ewing sarcoma and 31 patients with other pediatric sarcomas. Our method achieves sensitive detection and classification of circulating tumor DNA in peripheral blood independent of any genetic alterations. Moreover, we benchmark different metrics for cell-free DNA fragmentation analysis, and we introduce the LIQUORICE algorithm for detecting circulating tumor DNA based on cancer-specific chromatin signatures. Finally, we combine several fragmentation-based metrics into an integrated machine learning classifier for liquid biopsy analysis that exploits widespread epigenetic deregulation and is tailored to cancers with low mutation rates. Clinical associations highlight the potential value of cfDNA fragmentation patterns as prognostic biomarkers in Ewing sarcoma. In summary, our study provides a comprehensive analysis of circulating tumor DNA beyond recurrent genetic aberrations, and it renders the benefits of liquid biopsy more readily accessible for childhood cancers.
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Application of WGS in longitudinal MRD detection remains challenging due to relatively high sequencing cost and lower sensitivity compared to NGS-based ctDNA panel detection.
“Nevertheless, the application of WGS in longitudinal MRD detection remains challenging due to its relatively high sequencing cost and lower sensitivity, compared to NGS-based ctDNA panel detection.”
From Tumor-informed deep sequencing of ctDNA detects minimal residual disease and predicts relapse in osteosarcoma (2024) · cites this paper as [17]
The Results section (page not provided) states that deep cfDNA whole-genome sequencing is costly as a routine diagnostic assay. It does not establish that WGS has lower sensitivity than NGS-based ctDNA panels for longitudinal MRD detection; its reported sensitivity comparison is against other genetic methods, not targeted panels. (LLM, conf=0.88)
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Integrated, Longitudinal Analysis of Cell-free DNA in Uveal Melanoma
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- Authors
- Peneder, P., Stütz, A. M., Surdez, D., Krumbholz, M., Semper, S., Chicard, M., Sheffield, N. C., Pierron, G., Lapouble, E., Tötzl, M., Ergüner, B., Barreca, D., Rendeiro, A. F., Agaimy, A., Boztug, H., Engstler, G., Dworzak, M., Bernkopf, M., Taschner-Mandl, S., Ambros, I. M., Myklebost, O., Marec-Bérard, P., Burchill, S. A., Brennan, B., Strauss, S. J., Whelan, J., Schleiermacher, G., Schaefer, C., Dirksen, U., Hutter, C., Boye, K., Ambros, P. F., Delattre, O., Metzler, M., Bock, C., & Tomazou, E. M.
- Affiliations
- St. Anna Children's Cancer Research Institute (AT)
- Inserm (FR)
- Universitätsklinikum Erlangen (DE)
- University of Virginia (US)
- Institut Curie (FR)
- Austrian Academy of Sciences (AT)
- St Anna Children's Hospital (AT)
- Oslo University Hospital (NO)
- St James's University Hospital (GB)
- Royal Manchester Children's Hospital (GB)
- University College Hospital (GB)
- Essen University Hospital (DE)
- Corresponding author
- Bock, Christoph
- Tomazou, Eleni M.
- ORCID
- Peneder, Peter
- Stütz, Adrian M.
- Surdez, Didier
- Krumbholz, Manuela
- Chicard, Mathieu
- Sheffield, Nathan C.
- Pierron, Gaelle
- Lapouble, Eve
- Tötzl, Marcus
- Ergüner, Bekir
- Barreca, Daniele
- Rendeiro, André F.
- Agaimy, Abbas
- Engstler, Gernot
- Dworzak, Michael
- Bernkopf, Marie
- Taschner-Mandl, Sabine
- Ambros, Inge M.
- Myklebost, Ola
- Burchill, Susan Ann
- Brennan, Bernadette
- Strauss, Sandra J.
- Whelan, Jeremy
- Schleiermacher, Gudrun
- Schaefer, Christiane
- Dirksen, Uta
- Hutter, Caroline
- Boye, Kjetil
- Ambros, Peter F.
- Delattre, Olivier
- Metzler, Markus
- Bock, Christoph
- Tomazou, Eleni M.
- Venue
- Nature Communications
- Published
- 2021-05-28
- Volume
- 12
- Issue
- 1
- Pages
- 3230-3230
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC8163828
- OpenAlex
- W3165287952
- Cited by
- 200
- References
- 82
- Citations by year
- 2026: 26 · 2025: 39 · 2024: 38 · 2023: 45 · 2022: 39 · 2021: 12 · 2020: 1
- FWCI
- 13.63
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- NORA - Norwegian Open Research Archives (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- Zurich Open Repository and Archive (University of Zurich) (submittedVersion, cc-by)
- Zurich Open Repository and Archive (University of Zurich)
- Funders
- Kreftforeningen
- European Commission (HORIZON2020, 602856)
- Vienna Science and Technology Fund (LS18-049)
- Austrian Science Fund (V 506, I 2798)
- Oesterreichische Nationalbank (17876)
- Ligue Contre le Cancer
- Deutsche Krebshilfe (#108128, 70112018, DKH 108128, 70113419)
- H2020 European Research Council (679146)
- 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 › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- liquid biopsy, cell-free DNA, childhood cancer, Ewing sarcoma, pediatric sarcoma, low mutational burden, cfDNA fragmentation, chromatin signatures, epigenetic dysregulation, prognostic factors, machine learning classifiers
- MeSH terms
- Whole Genome Sequencing, Liquid Biopsy, Circulating Tumor DNA, Adolescent, Adult, Bone Neoplasms, Child, Child, Preschool, DNA Mutational Analysis, Female, Humans, Infant, Male, Middle Aged, Mutation, Sarcoma, Ewing, Biomarkers, Tumor, Case-Control Studies, Young Adult
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