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Liquid Biopsies in Oncology—3rd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Oncology".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 6226

Editors


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Guest Editor
Fox Chase Cancer Center, Philadelphia, PA 19111, USA
Interests: breast cancer; circulating tumor cells (CTCs); cell-free DNA (cfDNA); cell-tumor DNA (ctDNA); liquid biopsies; genetic variants
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Clinical and Experimental Medicine, University of Study of Foggia, 71122 Foggia, Italy
Interests: precision medicine; personalized medicine; cancer genomics; genomics; liquid biopsy; molecular diagnostic; laboratory medicine; clinical molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the era of precision oncology, tumor molecular characterization plays a key role in selecting the right treatment for each patient at the right time. Technological advances, particularly next-generation sequencing (NGS), have paved the way to personalized medicine, reducing the time and costs required to assess the tumor’s genetic profile. Unfortunately, in some cases, tumor biopsies are not feasible, due to insufficient or inaccessible material. The use of liquid biopsies has revolutionized the standard clinical approach by allowing the detection of different circulating molecules in the bloodstream and other body fluids, which may have a key role in diagnosing and monitoring the evolution of the tumor, and evaluating the response or resistance to the treatment. Since their FDA approval in 2016, for a therapy-guiding blood-based test to detect EGFR mutations in lung cancer patients, liquid biopsies are emerging as the standard of care. Liquid biopsies have several advantages, including minimal invasiveness and repeatability, which could guarantee a dynamic picture of the tumor and the chance to monitor pharmacological responses to the biopsy.

We invite scientists to submit original research focused on the application of liquid biopsies as an innovative tool in cancer diagnosis and monitoring, as well as its possible application in clinical practice. Articles may also be focused on understanding how circulating molecules offer new therapeutic strategies in cancer treatment. Review articles that describe the state of the art on this topic are also encouraged. This Special Issue, focusing on liquid biopsies in oncology, includes the use of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), circulating tumor RNAs (ctRNAs) as well as miRNAs, and extracellular vesicles (EVs). The topics of interest for this Special Issue include, but are not limited to, the following:

  • Liquid biopsy for cancer screening, diagnosis, prognosis, follow-up and therapeutic management of tumors;
  • Liquid biopsy for stratification and monitoring of cancer patients;
  • Liquid biopsy for the detection of actionable oncogenic mutations in cancers;
  • Liquid biopsy targeting ctDNA for molecular diagnosis of cancer;
  • Clinical validity and utility of ctDNA and ctRNA for tumor analysis;
  • Extracellular vesicle biomarkers;
  • New techniques to evaluate cell-free molecules;
  • Liquid biopsy on exosome for cancer diagnosis;
  • Liquid biopsies and epigenetics.

Dr. Sandra V. Fernandez
Dr. Carmela Paolillo
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • precision oncology
  • personalized therapy
  • cancer biomarkers
  • liquid biopsy
  • biological fluids
  • circulating molecules
  • circulating tumor cells
  • CTCs
  • ctDNA
  • ctRNA
  • cell-free DNA
  • cfDNA
  • NGS
  • circulating miRNAs
  • exosomes
  • extracellular vesicles

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Published Papers (3 papers)

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Research

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24 pages, 6586 KB  
Article
Off-Target-Based Tumor Fraction Estimation from Targeted Sequencing Shows Concordance with Orthogonal Methods Across Advanced Solid Tumors
by Samantha O. Hasenleithner, Shilpa Rao, Jian Q. Yu, Yinfei Tan, Fathima Sheriff, Jennifer S. Winn, Hossein Borghaei, Martin J. Edelman, Anshu Giri, Igor Astsaturov, Mariusz Wasik, Philipp J. Jost and Sandra V. Fernandez
Int. J. Mol. Sci. 2026, 27(13), 6078; https://doi.org/10.3390/ijms27136078 - 7 Jul 2026
Viewed by 564
Abstract
Circulating tumor DNA fraction (ctFraction) has emerged as an important biomarker for assessing tumor burden and monitoring treatment response in patients with cancer. In this study, we compared ctFraction estimates generated by ichorCNA, Fragle low-pass whole-genome sequencing (Fragle LP-WGS), Fragle off-target, and OTTER, [...] Read more.
Circulating tumor DNA fraction (ctFraction) has emerged as an important biomarker for assessing tumor burden and monitoring treatment response in patients with cancer. In this study, we compared ctFraction estimates generated by ichorCNA, Fragle low-pass whole-genome sequencing (Fragle LP-WGS), Fragle off-target, and OTTER, a proprietary algorithm from Tempus AI. Plasma samples from 33 patients with advanced solid tumors were analyzed using a ctDNA assay targeting 150 cancer-associated genes, and ctFraction estimates generated by the different methods were compared. Fragle off-target demonstrated the highest concordance with Fragle LP-WGS (rho = 0.903), followed by OTTER (rho = 0.698) and ichorCNA (rho = 0.696), while OTTER and ichorCNA showed strong agreement (rho = 0.826). Mean VAF (mVAF) significantly correlated with all ctFraction estimates, with the strongest association observed for ichorCNA (rho = 0.910), followed by OTTER (rho = 0.865), Fragle LP-WGS (rho = 0.680), and Fragle off-target (rho = 0.658). Longitudinal analysis of 20 patients at baseline and after two cycles of treatment demonstrated strong correlations between changes in ctFraction (ΔctFraction) and mean ΔVAF for both ichorCNA and Fragle off-target (r = 0.955 and r = 0.906, respectively). Overall, these findings demonstrate that ctFraction estimates derived from copy-number- and fragmentomic-based approaches show strong concordance across advanced solid tumors and significantly correlate with mVAF, a commonly used measure of ctDNA abundance. Fragle off-target, in particular, provides an efficient strategy for ctFraction estimation directly from existing targeted sequencing data, eliminating the need for additional sequencing. Larger prospective studies are warranted to further evaluate Fragle off-target clinical utility for treatment monitoring and outcome prediction. Full article
(This article belongs to the Special Issue Liquid Biopsies in Oncology—3rd Edition)
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14 pages, 1747 KB  
Article
Dissecting Tumor Heterogeneity by Liquid Biopsy—A Comparative Analysis of Post-Mortem Tissue and Pre-Mortem Liquid Biopsies in Solid Neoplasias
by Tatiana Mögele, Kathrin Hildebrand, Aziz Sultan, Sebastian Sommer, Lukas Rentschler, Maria Kling, Irmengard Sax, Matthias Schlesner, Bruno Märkl, Martin Trepel, Maximilian Schmutz and Rainer Claus
Int. J. Mol. Sci. 2025, 26(15), 7614; https://doi.org/10.3390/ijms26157614 - 6 Aug 2025
Cited by 6 | Viewed by 2219
Abstract
Tumor heterogeneity encompasses genetic, epigenetic, and phenotypic diversity, impacting treatment response and resistance. Spatial heterogeneity occurs both inter- and intra-lesionally, while temporal heterogeneity results from clonal evolution. High-throughput technologies like next-generation sequencing (NGS) enhance tumor characterization, but conventional biopsies still do not adequately [...] Read more.
Tumor heterogeneity encompasses genetic, epigenetic, and phenotypic diversity, impacting treatment response and resistance. Spatial heterogeneity occurs both inter- and intra-lesionally, while temporal heterogeneity results from clonal evolution. High-throughput technologies like next-generation sequencing (NGS) enhance tumor characterization, but conventional biopsies still do not adequately capture genetic heterogeneity. Liquid biopsy (LBx), analyzing circulating tumor DNA (ctDNA), provides a minimally invasive alternative, offering real-time tumor evolution insights and identifying resistance mutations overlooked by tissue biopsies. This study evaluates the capability of LBx to capture tumor heterogeneity by comparing genetic profiles from multiple metastatic lesions and LBx samples. Eight patients from the Augsburger Longitudinal Plasma Study with various types of cancer provided 56 postmortem tissue samples, which were compared against pre-mortem LBx-derived circulating-free DNA sequenced by NGS. Tissue analyses revealed significant mutational diversity (4–12 mutations per patient, VAFs: 1.5–71.4%), with distinct intra- and inter-lesional heterogeneity. LBx identified 51 variants (4–17 per patient, VAFs: 0.2–31.1%), which overlapped with mutations from the tissue samples by 33–92%. Notably, 22 tissue variants were absent in LBx, whereas 18 LBx-exclusive variants were detected (VAFs: 0.2–2.8%). LBx effectively captures tumor heterogeneity, but should be used in conjunction with tissue biopsies for comprehensive genetic profiling. Full article
(This article belongs to the Special Issue Liquid Biopsies in Oncology—3rd Edition)
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Review

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24 pages, 1012 KB  
Review
Circulating Tumor DNA as a Biomarker for Precision Medicine in Prostate Cancer: A Systematic Review
by Nouhaila Chanhih, Abdelilah Laraqui, Salma Hassine, Ahmed Ameur, Larbi Hamedoun, Hicham El Annaz, Rachid Abi, Mohamed Rida Tagajdid, Idriss Lahlou Amine, Khalid Ennibi, Abdelaziz Benjouad and Lamiae Belayachi
Int. J. Mol. Sci. 2025, 26(22), 11049; https://doi.org/10.3390/ijms262211049 - 15 Nov 2025
Cited by 7 | Viewed by 2764
Abstract
Circulating tumor DNA (ctDNA) profiling offers non-invasive insights for personalized prostate cancer management. This systematic review provides the first comprehensive appraisal of ctDNA assay methods, genomic targets, and their clinical correlations and proposes practical recommendations to guide future standardization and validation. We searched [...] Read more.
Circulating tumor DNA (ctDNA) profiling offers non-invasive insights for personalized prostate cancer management. This systematic review provides the first comprehensive appraisal of ctDNA assay methods, genomic targets, and their clinical correlations and proposes practical recommendations to guide future standardization and validation. We searched PubMed, ScienceDirect, Scopus, and the Cochrane Library starting December 2024 following PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines. From 229 records, 44 studies (10,631 patients) met the inclusion criteria. Plasma ctDNA analyzed by NGS predominantly profiled TP53 (72.7%), AR (70.4%), BRCA1/2 (61.3%), ATM (50%), RB1 (47.7%), and PTEN (41%). ctDNA positivity and specific key alterations correlated with poorer overall and progression-free survival. BRCA1/2-mutant patients benefited from Olaparib plus Abiraterone, while persistent alterations predicted early progression. Beyond synthesizing existing evidence, we identify key gaps, such as inconsistent reporting of variant allele fractions, limited diversity in study populations, and underexplored rare alterations. We recommend unified reporting standards (e.g., variant allele frequency thresholds and panel composition) and prioritized prospective trials to validate high-impact targets. These steps will accelerate the integration of ctDNA into routine precision oncology practice worldwide. Full article
(This article belongs to the Special Issue Liquid Biopsies in Oncology—3rd Edition)
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