Can a Liquid Biopsy Detect Circulating Tumor DNA With Low-passage Whole-genome Sequencing in Patients With a Sarcoma? A Pilot Evaluation
Open accessAbstract
BACKGROUND: A liquid biopsy is a test that evaluates the status of a disease by analyzing a sample of bodily fluid, most commonly blood. In recent years, there has been progress in the development and clinical application of liquid biopsy methods to identify blood-based, tumor-specific biomarkers for many cancer types. However, the implementation of these technologies to aid in the treatment of patients who have a sarcoma remains behind other fields of cancer medicine. For this study, we chose to evaluate a sarcoma liquid biopsy based on circulating tumor DNA (ctDNA). All human beings have normal cell-free DNA (cfDNA) circulating in the blood. In contrast with cfDNA, ctDNA is genetic material present in the blood stream that is derived from a tumor. ctDNA carries the unique genomic fingerprint of the tumor with changes that are not present in normal circulating cfDNA. A successful ctDNA liquid biopsy must be able to target these tumor-specific genetic alterations. For instance, epidermal growth factor receptor (EGFR) mutations are common in lung cancers, and ctDNA liquid biopsies are currently in clinical use to evaluate the status of disease in patients who have a lung cancer by detecting EGFR mutations in the blood. As opposed to many carcinomas, sarcomas do not have common recurrent mutations that could serve as the foundation to a ctDNA liquid biopsy. However, many sarcomas have structural changes to their chromosomes, including gains and losses of portions or entire chromosomes, known as copy number alterations (CNAs), that could serve as a target for a ctDNA liquid biopsy. Murine double minute 2 (MDM2) amplification in select lipomatous tumors or parosteal osteosarcoma is an example of a CNA due to the presence of extra copies of a segment of the long arm of chromosome 12. Since a majority of sarcomas demonstrate a complex karyotype with numerous CNAs, a blood-based liquid biopsy strategy that searches for these CNAs may be able to detect the presence of sarcoma ctDNA. Whole-genome sequencing (WGS) is a next-generation sequencing technique that evaluates the entire genome. The depth of coverage of WGS refers to how detailed the sequencing is, like higher versus lower power on a microscope. WGS can be performed with high-depth sequencing (that is, > 60×), which can detect individual point mutations, or low-depth sequencing (that is, 0.1× to 5×), referred to as low-passage whole-genome sequencing (LP-WGS), which may not detect individual mutations but can detect structural chromosomal changes including gains and losses (that is, CNAs). While similar strategies have shown favorable early results for specific sarcoma subtypes, LP-WGS has not been evaluated for applicability to the broader population of patients who have a sarcoma. QUESTIONS/PURPOSES: Does an LP-WGS liquid biopsy evaluating for CNAs detect ctDNA in plasma samples from patients who have sarcomas representing a variety of histologic subtypes? METHODS: This was a retrospective study conducted at a community-based, tertiary referral center. Nine paired (plasma and formalin-fixed paraffin-embedded [FFPE] tissue) and four unpaired (plasma) specimens from patients who had a sarcoma were obtained from a commercial biospecimen bank. Three control specimens from individuals who did not have cancer were also obtained. The paired and unpaired specimens from patients who had a sarcoma represented a variety of sarcoma histologic subtypes. cfDNA was extracted, amplified, and quantified. Libraries were prepared, and LP-WGS was performed using a NextSeq 500 next-generation sequencing machine at a low depth of sequencing coverage (∼1×). The ichorCNA bioinformatics algorithm, which was designed to detect CNAs from low-depth genomic sequencing data, was used to analyze the data. In contrast with the gold standard for diagnosis in the form of histopathologic analysis of a tissue sample, this test does not discriminate between sarcoma subtypes but detects the presence of tumor-derived CNAs within the ctDNA in the blood that should not be present in a patient who does not have cancer. The liquid biopsy was positive for the detection of cancer if the ichorCNA algorithm detected the presence of ctDNA. The algorithm was also used to quantitatively estimate the percent ctDNA within the cfDNA. The concentration of ctDNA was then calculated from the percent ctDNA relative to the total concentration of cfDNA. The CNAs of the paired FFPE tissue and plasma samples were graphically visualized using aCNViewer software. RESULTS: This LP-WGS liquid biopsy detected ctDNA in 9 of 13 of the plasma specimens from patients with a sarcoma. The other four samples from patients with a sarcoma and all serum specimens from patients without cancer had no detectable ctDNA. Of those 9 patients with positive liquid biopsy results, the percent ctDNA ranged from 6% to 11%, and calculated ctDNA quantities were 0.04 to 5.6 ng/mL, which are levels to be expected when ctDNA is detectable. CONCL
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Low-pass or ultra-low-pass WGS has the advantage of genome-wide CNA detection without requiring predefined mutation panels, making it conceptually attractive for complex-karyotype sarcomas.
“Its main advantage is genome-wide CNA detection without requiring predefined mutation panels, making it conceptually attractive for complex-karyotype sarcomas [ 33 ].”
From Signals Alongside Scans: A Genomics-Guided Framework for Liquid Biopsy in Bone and Soft-Tissue Sarcomas (2026) · cites this paper as [33]
Broad plasma panels, CNA-based WGS, methylation-based assays, cfRNA approaches, and CTC-based strategies remain more exploratory or proof-of-concept in most sarcoma subtypes, particularly when applied to low-volume MRD or routine surveillance settings.
“In contrast, broad plasma panels, CNA-based WGS, methylation-based assays, cfRNA approaches, and CTC-based strategies remain more exploratory or proof-of-concept in most sarcoma subtypes, particularly when applied to low-volume MRD or routine surveillance settings [ 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ].”
From Signals Alongside Scans: A Genomics-Guided Framework for Liquid Biopsy in Bone and Soft-Tissue Sarcomas (2026) · cites this paper as [33]
Commercial or large-panel plasma profiling may identify clinically relevant alterations in selected advanced cases.
“Commercial or large-panel plasma profiling may identify clinically relevant alterations in selected advanced cases, but variable tissue–plasma concordance, low tumor fraction, and inconsistent copy-number detection limit its use as a general surveillance strategy [ 32 , 33 , 34 , 35 , 36 ].”
From Signals Alongside Scans: A Genomics-Guided Framework for Liquid Biopsy in Bone and Soft-Tissue Sarcomas (2026) · cites this paper as [33]
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Cites
Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., del Angel, G., Levy‐Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., et al. (2013) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1110s43 · Cited by 6,687 · see citing works
Liquid biopsy and minimal residual disease - latest advances and implications for cure
Pantel, K., & Alix-Panabières, C. (2019) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-019-0187-3 · Cited by 1,110 · see citing works
Enhanced detection of circulating tumor DNA by fragment size analysis
Mouliere, F. C., Chandrananda, D., Piskorz, A., Moore, E. K., Morris, J., Ahlborn, L. B., Mair, R. J., Goranova, T., Marass, F., Heider, K., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aat4921 · Cited by 1,071 · see citing works
Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
Abeshouse, A., Adebamowo, C., Adebamowo, S. N., Akbani, R., Akeredolu, T., Ally, A., Anderson, M. L., Anur, P., Appelbaum, E. L., Armenia, J., et al. (2017) · Cell · doi:10.1016/j.cell.2017.10.014 · Cited by 1,069 · see citing works
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors
Adalsteinsson, V. A., Ha, G., Freeman, S. S., Choudhury, A. D., Stover, D. G., Parsons, H. A., Gydush, G., Reed, S. C., Rotem, D., Rhoades, J., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00965-y · Cited by 1,035 · see citing works
Merker, J. D., Oxnard, G. R., Compton, C., Diehn, M., Hurley, P., Lazar, A. J., Lindeman, N., Lockwood, C. M., Rai, A. J., Schilsky, R. L., et al. (2018) · Journal of Clinical Oncology · doi:10.1200/jco.2017.76.8671 · Cited by 959 · see citing works
Shern, J. F., Chen, L., Chmielecki, J., Wei, J. S., Patidar, R., Rosenberg, M. W., Ambrogio, L., Auclair, D., Wang, J., Song, Y. K., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0639 · Cited by 742 · see citing works
Perry, J. A., Kiezun, A., Tonzi, P., Van Allen, E. M., Carter, S. L., Baca, S. C., Cowley, G. S., Bhatt, A. S., Rheinbay, E., Pedamallu, C. S., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419260111 · Cited by 481 · see citing works
Genome-Informed Targeted Therapy for Osteosarcoma
Sayles, L. C., Breese, M. R., Koehne, A. L., Leung, S. G., Lee, A. G., Liu, H.-Y., Spillinger, A., Shah, A. T., Tanasa, B., Straessler, K., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-1152 · Cited by 452 · see citing works
Shulman, D. S., Klega, K., Imamovic-Tuco, A., Clapp, A., Nag, A., Thorner, A. R., Van Allen, E., Ha, G., Lessnick, S. L., Gorlick, R., et al. (2018) · British Journal of Cancer · doi:10.1038/s41416-018-0212-9 · Cited by 149 · see citing works
Klega, K. S., Imamović, A., Ha, G., Clapp, A. N., Meyer, S. C., Ward, A., Clinton, C., Nag, A., Allen, E. M. V., Mullen, E. A., et al. (2018) · JCO Precision Oncology · doi:10.1200/po.17.00285 · Cited by 139 · see citing works
Using cfDNA and ctDNA as Oncologic Markers: A Path to Clinical Validation
Dao, J., Conway, P., Subramani, B., Meyyappan, D., Russell, S., & Mahadevan, D. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241713219 · Cited by 107 · see citing works
Genomic EWSR1 Fusion Sequence as Highly Sensitive and Dynamic Plasma Tumor Marker in Ewing Sarcoma
Krumbholz, M., Hellberg, J., Steif, B., Bäuerle, T., Gillmann, C., Fritscher, T., Agaimy, A., Frey, B., Juengert, J., Wardelmann, E., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-3028 · Cited by 96 · see citing works
Assessment of circulating tumor DNA in pediatric solid tumors: The promise of liquid biopsies
Abbou, S. D., Shulman, D. S., DuBois, S. G., & Crompton, B. D. (2019) · Pediatric Blood & Cancer · doi:10.1002/pbc.27595 · Cited by 72 · see citing works
Non‐invasive detection of genome‐wide somatic copy number alterations by liquid biopsies
Heitzer, E., Ulz, P., Geigl, J. B., & Speicher, M. R. (2015) · Molecular Oncology · doi:10.1016/j.molonc.2015.12.004 · Cited by 70 · see citing works
Cho, M.-S., Park, C. H., Lee, S., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0230622 · Cited by 69 · see citing works
Detection of Circulating Tumor DNA in Patients With Leiomyosarcoma With Progressive Disease
Hemming, M. L., Klega, K. S., Rhoades, J., Ha, G., Acker, K. E., Andersen, J. L., Thai, E., Nag, A., Thorner, A. R., Raut, C. P., et al. (2019) · JCO Precision Oncology · doi:10.1200/po.18.00235 · Cited by 60 · see citing works
Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients
Tsui, D. W. Y., Cheng, M. L., Shady, M., Yang, J. L., Stephens, D. P., Won, H. H., Srinivasan, P., Huberman, K. H., Meng, F., Jing, X., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00898-8 · Cited by 58 · see citing works
Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors
Christodoulou, E., Yellapantula, V., O’Halloran, K., Xu, L., Berry, J. L., Cotter, J. A., Zdanowicz, A., Mascarenhas, L., Amatruda, J. F., Ostrow, D., et al. (2023) · npj Precision Oncology · doi:10.1038/s41698-023-00357-0 · Cited by 55 · see citing works
The Emerging Role of Liquid Biopsies in Revolutionising Cancer Diagnosis and Therapy
Shegekar, T., Vodithala, S., & Juganavar, A. (2023) · Cureus · doi:10.7759/cureus.43650 · Cited by 55 · see citing works
Application of liquid biopsy in bone and soft tissue sarcomas: Present and future
Li, X., Seebacher, N. A., Hornicek, F. J., Xiao, T., & Duan, Z. (2018) · Cancer Letters · doi:10.1016/j.canlet.2018.09.012 · Cited by 53 · see citing works
Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma
Negri, G. L., Grande, B. M., Delaidelli, A., El-Naggar, A. M., Cochrane, D. R., Lau, C. C., Triche, T. J., Moore, R. A., Jones, S. J. M., Montpetit, A., et al. (2019) · The Journal of Pathology · doi:10.1002/path.5319 · Cited by 48 · see citing works
Li, C., Shao, J., Li, P., Feng, J., Li, J., & Wang, C. (2023) · Cancer Letters · doi:10.1016/j.canlet.2023.216365 · Cited by 40 · see citing works
Liquid Biopsies in Sarcoma Clinical Practice: Where Do We Stand?
van der Laan, P., van Houdt, W. J., van den Broek, D. A., Steeghs, N., & van der Graaf, W. T. A. (2021) · Biomedicines · doi:10.3390/biomedicines9101315 · Cited by 30 · see citing works
Liquid Biopsy: A New Translational Diagnostic and Monitoring Tool for Musculoskeletal Tumors
Hadjimichael, A. C., Pergaris, A., Kaspiris, A., Foukas, A. F., & Theocharis, S. E. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222111526 · Cited by 25 · see citing works
de la Vega, L. L., Hovelson, D. H., Cani, A. K., et al. (2016) · Human Pathology · doi:10.1016/j.humpath.2016.09.004 · Cited by 19 · see citing works
Demoret, B., Gregg, J., Liebner, D. A., Tinoco, G., Lenobel, S., & Chen, J. L. (2019) · Cancers · doi:10.3390/cancers11121829 · Cited by 18 · see citing works
Mihály, D., Nagy, N., Papp, G., Pápai, Z., & Sápi, Z. (2018) · Diagnostic Pathology · doi:10.1186/s13000-018-0756-2 · Cited by 17 · see citing works
Cell-free tumour DNA analysis detects copy number alterations in gastro-oesophageal cancer patients
Wallander, K., Eisfeldt, J., Lindblad, M., Nilsson, D., Billiau, K., Asl, H. F., Nordenskjöld, M., Liedén, A., & Tham, E. (2021) · PLoS ONE · doi:10.1371/journal.pone.0245488 · Cited by 17 · see citing works
Liquid biopsies in primary and secondary bone cancers
Ucci, A., Rucci, N., & Ponzetti, M. (2022) · Cancer Drug Resistance · doi:10.20517/cdr.2022.17 · Cited by 14 · see citing works
Arshad, J., Barreto‐Coelho, P., Jonczak, E., Freire, A. P. E., D’Amato, G. Z., & Trent, J. C. (2020) · Journal of Immunotherapy and Precision Oncology · doi:10.36401/jipo-20-3 · Cited by 13 · see citing works
Application of high-resolution genomic profiling in the differential diagnosis of liposarcoma
Koczkowska, M., Lipska-Ziętkiewicz, B. S., Iliszko, M., et al. (2017) · Molecular Cytogenetics · doi:10.1186/s13039-017-0309-5 · Cited by 12 · see citing works
Renault, V., Tost, J., Pichon, F., Renault, S., Letouzé, É., Imbeaud, S., Zucman‐Rossi, J., Deleuze, J., & How‐Kit, A. (2017) · PLoS ONE · doi:10.1371/journal.pone.0189334 · Cited by 9 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- Edge SB, Byrd DR, Compton CC, Fritz AG, Greene FL, Trotti A, eds. AJCC Cancer Staging Manual. 7th ed. Springer; 2010.
- Jain S, Xu R, Prieto VG, Lee P. Molecular classification of soft tissue sarcomas and its clinical applications. Int J Clin Exp Pathol. 2010;3:416-428.
- WHO Classification of Tumours Editorial Board. WHO Classification of Tumours Soft Tissue and Bone Tumours. 5 th ed. IARC Press; 2020.
Cited by
Sorted by citations
Joch, S., Smolle, M. A., Kashofer, K., Thüringer, A., Szkandera, J., Benesch, M., El-Heliebi, A., Liegl-Atzwanger, B., Leithner, A., & Seidel, M. G. (2024) · Oncology Research and Treatment · doi:10.1159/000543223 · Cited by 2 · see citing works
Alabid, I., Yousef, A. J., Patni, M. M., Aloti, R. A., Qassim, Z. A.-A. M., Alothman-Agha, A. A., Hamdy, H. A., Noury, F. M., & Abdelfattah, M. T. (2026) · Cells · doi:10.3390/cells15141271
- Authors
- Anderson, C. J., Yang, H., Parsons, J., Ahrens, W. A., Jagosky, M. H., Hsu, J. H., Patt, J. C., Kneisl, J. S., & Steuerwald, N. M.
- Affiliations
- Atrium Health Wake Forest Baptist (US)
- Levine Cancer Institute, Atrium Health Wake Forest Baptist, Charlotte, NC, USA
- Venue
- Clinical Orthopaedics & Related Research
- Published
- 2024-06-21
- Volume
- 483
- Issue
- 1
- Pages
- 39-48
- ISSN
- 0009-921X (ISSN-L)
- 1528-1132
- PMC
- PMC11658723
- OpenAlex
- W4399880655
- Cited by
- 10
- References
- 33
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 2
- FWCI
- 1.99
- Type
- journal article
- Language
- en
- Open access
- green
- pmc.ncbi.nlm.nih.gov
- Locations
- Clinical Orthopaedics and Related Research (publishedVersion)
- PubMed Central (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed (publishedVersion)
- 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, circulating tumor DNA, sarcoma, copy number alterations, tumor genomic alterations, MDM2 amplification, parosteal osteosarcoma, lipomatous tumor, tumor-specific biomarkers, tumor heterogeneity, treatment response monitoring
- MeSH terms
- Whole Genome Sequencing, Liquid Biopsy, Circulating Tumor DNA, Adult, Aged, DNA Mutational Analysis, Female, Humans, Male, Middle Aged, Mutation, Pilot Projects, Predictive Value of Tests, Sarcoma, Biomarkers, Tumor
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