BJS Open. 2026 Sep 4;10(5):zrag142. doi: 10.1093/bjsopen/zrag142.

ABSTRACT

BACKGROUND: Non-operative management after total neoadjuvant therapy (TNT) has emerged as a potential strategy for patients with locally advanced rectal cancer (LARC) achieving clinical complete response (cCR). Circulating tumour DNA (ctDNA) has been proposed as a systemic biomarker to augment response assessment, but its role in predicting cCR and local regrowth remains uncertain.

METHODS: A systematic review and meta-analysis were performed of studies evaluating ctDNA dynamics in patients with LARC undergoing TNT. PubMed, EMBASE, and Web of Science databases were searched from database inception to 31 March 2026. Primary outcomes were the association between post-TNT ctDNA status and cCR and sustained cCR. Pooled odds ratios (ORs) were calculated using a random-effects model.

RESULTS: Six studies comprising 597 patients were included. ctDNA negativity following TNT was associated with higher likelihood of cCR (OR 8.01; 95% confidence interval (c.i.) 1.43 to 44.90; I2 = 27.0%). The association with sustained cCR was not statistically significant (OR 3.46; 95% c.i. 0.03 to 394.64; I2 = 59.9%). Across studies, post-TNT ctDNA positivity was associated with inferior disease-free, distant recurrence-free, and progression-free survival. ctDNA demonstrated high specificity and positive predictive value for residual disease, but low sensitivity for the detection of residual local disease and local regrowth, with a substantial proportion of patients with residual tumour remaining ctDNA negative at restaging.

CONCLUSION: Post-TNT ctDNA positivity may identify patients at increased risk of adverse oncological outcomes. However, ctDNA negativity was not consistently associated with the absence of residual local disease, limiting its utility as an independent determinant of organ preservation eligibility. ctDNA should be interpreted as a complementary tool for systemic risk stratification alongside established anatomical assessment.

PMID:42832577 | DOI:10.1093/bjsopen/zrag142

Cancer Sci. 2026 Oct 5:10.1111/cas.70552. doi: 10.1111/cas.70552. Online ahead of print.

ABSTRACT

Biliary tract cancer (BTC) is a rare abdominal cancer with poor prognosis. Circulating tumor DNA (ctDNA) analysis with liquid biopsy offers a minimally invasive approach for cancer detection and disease monitoring. Given limited reports, this study aims to evaluate minimal residual disease (MRD) and longitudinal ctDNA monitoring in BTC patients. A total of 124 BTC patients were enrolled, with 111 evaluable for ctDNA analysis using a tumor-informed approach. Baseline tumor tissue and plasma samples were collected for comprehensive genomic profiling (CGP). A customized ctDNA panel was developed based on CGP of resectable BTC tumors and public genomic databases for MRD assessment and longitudinal monitoring. ctDNA sequencing was performed using ultradeep targeted next-generation sequencing. Associations between ctDNA detection and outcomes were analyzed. Preoperative ctDNA detection was associated with advanced pathological stage and significantly worse relapse-free survival (RFS) and overall survival. Using this ctDNA panel, preoperative ctDNA was detected in 51.4% of cases, with TP53, KRAS, ARID1A, and SMAD4 being the most frequently mutated genes. During longitudinal monitoring, 57.8% of patients showed persistent ctDNA positivity or subsequent ctDNA detection before radiological recurrence. RFS was significantly shorter among patients with ctDNA positivity during longitudinal monitoring than among those with undetectable ctDNA (HR = 9.04; 95% CI, 3.56-23.97; p < 0.001). Our customized panel detected BTC-specific mutations in plasma using liquid biopsy, and ctDNA positivity was strongly associated with recurrence and survival outcomes. This panel has the potential to improve MRD assessment and longitudinal monitoring in BTC, enabling earlier intervention and improved patient stratification.

PMID:42831344 | PMC:PMC13636022 | DOI:10.1111/cas.70552

J Liq Biopsy. 2026 Sep 19;14:100496. doi: 10.1016/j.jlb.2026.100496. eCollection 2026 Dec.

ABSTRACT

BACKGROUND: Circulating tumor DNA (ctDNA) analysis has revolutionized minimal residual disease (MRD) monitoring, but conventional tumor-informed amplicon-based sequencing (AMP) is limited by the narrow variant capacity and diversity. Hybrid capture-based sequencing (HYB) is more versatile and enables both tumor-informed and tumor-naïve liquid biopsy profiling.

METHODS: We analytically validated the performance of our novel HYB workflow and VarSURE variant calling pipeline, using reference standards (n = 6), plasma samples of cancer patients (n = 75) and healthy donors (n = 90). Genome-wide (GW) non-mutation features including copy number alterations, fragmentomics, and end-motif signatures were also evaluated to enhance ctDNA-MRD detection. Clinical performance was directly compared against our legacy AMP method (K-TRACK, Gene Solutions), using pre-treatment blood samples across multiple cancers (n = 290) and longitudinal cohorts of colorectal cancer (CRC, n = 64), and hepatocellular carcinoma (HCC, n = 47).

RESULTS: Optimal parameters to maximize assay performance included single-stranded DNA ligation technology, cfDNA input ≥ 15 ng, post-UMI sequencing depth ≥ 2500X, and high number of tracked mutations. In the tumor-informed setting, the HYB workflow was modestly better than the AMP method in detection of pre-treatment ctDNA; addition of GW features was marginally beneficial except in lung cancer. Surveillance ctDNA determined by the HYB workflow had superior sensitivity to predict recurrence in both CRC (AMP: 90.0%, HYB: 100%) and HCC (AMP: 80.0%, HYB: 96.0%). In the tumor-naïve setting, the performance gap widened significantly, and the combined HYB and GW workflow showed the highest performance in baseline ctDNA detection across all cancers, and achieved sensitivity of 90.0% and 92.0% to detect recurrence in CRC and HCC respectively.

CONCLUSIONS: The new methodology offers a streamlined and scalable solution for both comprehensive liquid biopsy profiling and longitudinal MRD tracking in routine clinical practice.

PMID:42830887 | PMC:PMC13634064 | DOI:10.1016/j.jlb.2026.100496

Epigenomics. 2026 Oct 3:1-13. doi: 10.1080/17501911.2026.2740396. Online ahead of print.

ABSTRACT

Plasma cell-free DNA (cfDNA) is fragmented nonrandomly, reflecting the chromatin architecture of its source cells and the nucleases that process it. The fragmentome can therefore provide an indirect readout of cellular regulatory state. This review examines how DNA methylation, chromatin accessibility, nucleosome positioning, protein occupancy, and nuclease activity shape cfDNA fragmentation and considers their implications for oncology. We organize fragmentomic measurements into four classes: coverage and protection, fragment size, fragment-end properties, and diversity and entropy metrics. We discuss the genomic contexts in which these features are informative, including repetitive and transposable elements, and compare platforms by sequencing requirements, feature portability, and the fragment populations captured by different library chemistries. We then review applications in cancer screening, tissue-of-origin inference, molecular subtyping, prognosis, minimal residual disease detection, and treatment response monitoring. A central challenge for clinical translation is attributing fragmentomic changes to their tissue of origin.

PMID:42829334 | DOI:10.1080/17501911.2026.2740396

Clin Chim Acta. 2026 Oct 3:122873. doi: 10.1016/j.cca.2026.122873. Online ahead of print.

ABSTRACT

Liquid biopsy is a minimally invasive approach to early detection and biomarker assessment in gynecological cancers. This structured review synthesizes evidence on circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomal non-coding RNAs, epigenetic markers (methylation and fragmentation), and multi-omics signatures across ovarian, endometrial, cervical, vulvar, and vaginal malignancies. A structured search of PubMed/MEDLINE, Embase, Scopus, Web of Science, and the Cochrane Library identified studies evaluating early detection, predictive and prognostic performance, therapy monitoring, minimal residual disease (MRD) detection, resistance mechanisms, and clinical implementation; each quantitative estimate was assigned an evidence tier reflecting study design and validation status. Multi-omics integration outperforms single-analyte approaches, with a prospective gynecological cohort reporting approximately 82% sensitivity at 97-99% specificity. ctDNA methylation and fragmentomics exceed CA125 in ovarian and endometrial cancers, and cfHPV-DNA shows high specificity in cervical disease. ctDNA dynamics are associated with PARP inhibitor response, MRD status and BRCA reversion-mediated resistance, and detect recurrence before imaging. Reported hazard ratios vary widely but differ in cohort, assay platform and sampling timepoint, and are not directly comparable. Almost all detection estimates derive from retrospective or case-control designs that overestimate performance, and none has been externally and prospectively validated; circulating HPV DNA in cervical cancer is the only marker with prospective trial-level prognostic support. No liquid biopsy assay holds an FDA or EMA indication for any gynecological cancer; pan-tumor clearances exist, but no gynecology-specific companion diagnostic, and no major oncology society recommends use outside clinical trials. Liquid biopsy complements but cannot replace tissue biopsy for diagnosis, subtyping and grading. Randomized trials controlling for lead-time bias are required to establish clinical utility.

PMID:42829044 | DOI:10.1016/j.cca.2026.122873

J Liq Biopsy. 2026 Sep 18;14:100501. doi: 10.1016/j.jlb.2026.100501. eCollection 2026 Dec.

ABSTRACT

INTRODUCTION: Circulating tumor DNA (ctDNA) is a valuable tool for assessing minimal residual disease (MRD) and predicting recurrence in resected non-small cell lung cancer (NSCLC) patients. Combining ctDNA-detection with radiological tumor volume may improve risk stratification.

METHODS: Patients with stage I-III resectable NSCLC were prospectively enrolled in the RESIDUAL study. Plasma samples were collected before surgery (T0), at landmark (10 days after surgery), during surveillance (T2, 20 days, T3, 1 months after surgery and every 3 months for the first year and then at the end of the second year after surgery), and at relapse. Samples were analyzed using Guardant Reveal, a tissue-free methylation-based ctDNA assay. Receiver operating characteristic analysis associated T1 ctDNA status with tumor volume; volume thresholds were calculated via Youden's J, and Cox regression analysis was performed.

RESULTS: Forty-eight patients were enrolled (median age 72 years; 64.6% male). Most had stage I disease (54.2%) and adenocarcinoma histology (79.2%). Median follow-up was 41.8 months, and 19 patients (39.6%) relapsed. Overall ctDNA detection rate was 15.2% across all timepoints. Pre-surgical ctDNA detection was higher in squamous histology and stage II-III disease and was associated with worse disease-free survival (DFS; p = 0.022). Landmark MRD detection was also associated with worse DFS (p = 0.024). Serial surveillance sampling anticipated radiologic recurrence by a median of 2.6 months (range 2.0-7.5). Patients with tumor volume >26,378 mm³ had a significantly higher relapse risk (p < 0.001).

CONCLUSIONS: MRD detection in NSCLC resected patients predicts relapse and poor outcome; integrating ctDNA with tumor volume enhances identification of high-risk patients.

PMID:42828040 | PMC:PMC13631347 | DOI:10.1016/j.jlb.2026.100501

Nat Med. 2026 Oct 2. doi: 10.1038/s41591-026-04673-3. Online ahead of print.

ABSTRACT

Urine biomarkers promise to improve noninvasive detection and molecular characterization of genitourinary malignancies. Here we describe urine random priming and affinity capture of cell-free RNA (cfRNA) fragments for enrichment analysis by sequencing (uRARE-seq), a liquid biopsy method for urine cfRNA profiling, and apply it to 683 urine samples from patients with cancer and controls. Urine cfRNA contained transcripts from genitourinary tissues and, in patients with prostate, kidney or bladder cancer, tumor-derived transcripts. uRARE-seq demonstrated 95% sensitivity at 90% specificity for detecting localized bladder cancer. The method outperformed urine tumor DNA analysis and was unaffected by the presence of field-effect mutations. Urine cfRNA analysis also sensitively detected minimal residual disease and distinguished complete molecular responses after surgery from those after intravesical Bacillus Calmette-Guérin (BCG). Pretreatment urine from complete responders to BCG was enriched for T cell and other immune signatures, suggesting a preexisting antitumor immune response, whereas nonresponders showed higher expression of proliferation-related genes. In pretreatment urine from 114 patients, this biological difference enabled development of a biomarker predicting likelihood of response to BCG versus chemotherapy (area under the curve 0.93) that was strongly associated with risk of recurrence. Urine cfRNA analysis is therefore a promising biomarker approach for bladder cancer and potentially other urologic malignancies, although prospective studies are needed to assess its clinical utility.

PMID:42827132 | DOI:10.1038/s41591-026-04673-3

Clin Chim Acta. 2026 Oct 2;594:122871. doi: 10.1016/j.cca.2026.122871. Online ahead of print.

ABSTRACT

Head and neck cancers (HNCs) represent one of the most prevalent and lethal types of cancer, accounting for 4.7% of annual cancer new cases and 4.9% of cancer-related mortalities. These high prevalence and mortality rates have positioned HNCs as a global health issue. Despite advances in disease treatment methods, the prognosis of patients with advanced or recurrent diseases remains poor. The difficulty of early-stage diagnosis of HNCs is one of the primary contributors to this reduced long-term survival. Currently available diagnostic and disease-monitoring tools, such as tissue biopsy and imaging techniques, are associated with several limitations, including invasiveness, limited repeatability, and limited sensitivity for detecting minimal residual disease (MRD) and microscopic metastases. In recent years, liquid biopsy has emerged as a promising approach, enabling minimally invasive detection of tumor-related biomarkers in body fluids. This review aims to provide a comprehensive overview of the progress and pitfalls of liquid biopsy in the context of HNCs. In this regard, we discuss the principles of liquid biopsy, applicable biomarker types, sample sources, and advanced detection methods. Furthermore, the current status of liquid biopsy in clinical trials of HNCs and the challenges of its clinical translation are also comprehensively explored.

PMID:42826825 | DOI:10.1016/j.cca.2026.122871

J Bone Oncol. 2026 Sep 16;61:100803. doi: 10.1016/j.jbo.2026.100803. eCollection 2026 Dec.

ABSTRACT

Osteosarcoma relapse surveillance remains dominated by scheduled imaging because salvage treatment depends on anatomical confirmation of pulmonary, local or extrapulmonary recurrence. However, radiological recurrence may occur after a biologically active phase in which residual viable disease or micrometastatic progression is already present but not yet localizable. This clinical-translational review reframes postoperative osteosarcoma surveillance as an action-linked decision workflow rather than a comparison of isolated biomarker technologies. Current evidence suggests that tumor-informed circulating tumor DNA (ctDNA) sequencing provides the strongest osteosarcoma-specific minimal residual disease (MRD) signal, with postoperative positivity associated with inferior event-free survival and, in selected patients, molecular detection preceding imaging-confirmed relapse or progression. Cell-free DNA methylation may offer a mutation-independent adjunct, whereas circulating tumor cells, extracellular vesicles and circulating microRNAs remain exploratory signals without validated postoperative surveillance actions. Chest computed tomography (CT) and local magnetic resonance imaging (MRI) remain indispensable for disease localization and treatment planning, while diffusion-weighted imaging, dynamic contrast-enhanced MRI and radiomics currently provide mainly local viability or risk-enrichment information rather than proven surveillance-intervention evidence. The near-term role of integrated biomarkers is therefore not to replace guideline-based imaging, but to define protocolized pathways for molecular-positive/imaging-negative, imaging-positive/molecular-negative, concordant high-risk and concordant low-risk states. Future studies should test whether biomarker-triggered reassessment improves clinically meaningful outcomes, including resectability, second complete remission, clinical trial access, patient burden and survival, rather than simply documenting recurrence earlier.

PMID:42824543 | PMC:PMC13628598 | DOI:10.1016/j.jbo.2026.100803

World J Urol. 2026 Oct 1;44(1):722. doi: 10.1007/s00345-026-06790-7.

ABSTRACT

PURPOSE: To critically appraise circulating tumour DNA (ctDNA) and extrachromosomal DNA (ecDNA) in prostate and bladder cancer, and to define what evidence links the two.

METHODS: Narrative review of search period July-September 2026, supplemented by reference-list and citation screening, covering ctDNA and ecDNA biology, detection and clinical application in prostate and urothelial cancer. The ctDNA-ecDNA interface was appraised using a five-tier evidentiary framework (copy-number gain; structural rearrangement; amplicon-graph reconstruction; phasing/optical mapping; orthogonal validation).

RESULTS: In bladder cancer, the phase 3 IMvigor011 trial validated ctDNA-guided adjuvant atezolizumab (disease-free survival [DFS] HR 0.64; overall survival [OS] HR 0.59), while persistently ctDNA-negative patients had 2-year DFS/OS of 88.4%/97.1% without adjuvant therapy. In prostate cancer, ctDNA positivity and androgen-receptor alterations are strongly prognostic (median OS 29.0 vs. 47.4 months; HR 2.0), but no prospective ctDNA-guided interventional trial exists. ecDNA is present in approximately 36% of urothelial carcinomas and drives oncogene amplification, heterogeneity, immune evasion and resistance. Evidence linking the two is indirect and asymmetric: prostate cancer offers stronger longitudinal ctDNA evidence via plasma AR-ecDNA proxy signatures, whereas bladder cancer shows stronger structural evidence from urinary sediment; no structurally validated blood ecDNA has been reported. This evidence derives predominantly from metastatic cohorts (mCRPC, post-cystectomy bladder cancer), with no established role in earlier-stage or minimal-residual-disease settings.

CONCLUSION: ctDNA is clinically actionable in bladder cancer and prognostic in advanced prostate cancer, whereas ecDNA remains an investigational driver. Structural confirmation of ecDNA in blood, assay standardisation and prospective biomarker-stratified trials are the priorities for the field.

PMID:42823553 | DOI:10.1007/s00345-026-06790-7

Cancer Treat Res Commun. 2026 Oct 1;49:101463. doi: 10.1016/j.ctarc.2026.101463. Online ahead of print.

ABSTRACT

Liquid biopsy has transformed the management of non-small cell lung cancer (NSCLC). However, current plasma-based approaches face inherent limitations in early-stage and low-burden disease, where tumour-derived DNA fractions are frequently below reliable detection thresholds. As lung cancer care shifts toward earlier detection and minimal residual disease assessment, these constraints expose a critical gap in tumour-proximal molecular sampling. This has prompted growing interest in organ-specific liquid biopsy strategies designed to interrogate biological compartments closer to the site of tumour origin. Exhaled breath condensate (EBC), a non-invasive and lung-derived matrix containing airway lining fluid, represents a biologically rational candidate for such an approach. Emerging translational studies demonstrate the feasibility of detecting tumour-associated genomic alterations and nucleic acids within EBC, suggesting potential utility in early detection, molecular profiling, and longitudinal monitoring. However, substantial challenges remain, including pre-analytical standardisation, analytical validation, and prospective clinical evaluation. This narrative review examines the conceptual rationale for lung-specific liquid biopsy, summarises the evolving evidence supporting EBC, and outlines critical and translational steps required to determine whether EBC can become an integral component of lung cancer diagnostics.

PMID:42822136 | DOI:10.1016/j.ctarc.2026.101463

Front Cell Dev Biol. 2026 Sep 14;14:1878092. doi: 10.3389/fcell.2026.1878092. eCollection 2026.

ABSTRACT

Liquid biopsy has emerged as a powerful non-invasive tool in precision oncology, providing real-time insights into tumor evolution, host immune responses, and dynamic changes in the tumor immune microenvironment. By enabling minimally invasive sampling, it can overcome several limitations of conventional tissue biopsy. This review summarizes the major biological sources and components of liquid biopsy, including circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes, and circulating immune cells, and discusses their value as dynamic indicators of interactions during cancer immunotherapy. Particular attention is given to immune-related biomarkers associated with immune checkpoints, immunosuppressive mechanisms, and immune escape, including circulating immune cell populations, and inflammatory cytokine profiles. We further examine their potential applications in predicting treatment response, monitoring immune-related adverse events, assessing minimal residual disease, and detecting acquired resistance. In addition, recent technological advances that are accelerating the clinical translation of liquid biopsy are highlighted, including multi-omics integration, microfluidic platforms. These approaches have improved the sensitivity, accuracy, and multidimensional characterization of tumor- and immune-derived biomarkers. Nevertheless, biological heterogeneity, limited assay standardization, and the lack of large-scale prospective validation studies continue to restrict widespread clinical implementation. Overall, immune-related biomarkers detected through liquid biopsy offer considerable potential for the longitudinal monitoring of the tumor immune microenvironment and may improve non-invasive cancer diagnosis, therapeutic monitoring, and personalized immunotherapy in the era of precision oncology.

PMID:42807637 | PMC:PMC13617286 | DOI:10.3389/fcell.2026.1878092

Front Oncol. 2026 Sep 11;16:1908802. doi: 10.3389/fonc.2026.1908802. eCollection 2026.

ABSTRACT

BACKGROUND: Stage II colon cancer is clinically heterogeneous. Current clinicopathologic risk factors cannot accurately identify patients with residual disease after curative resection. Circulating tumor DNA (ctDNA) has emerged as a promising biomarker for the detection of minimal residual disease (MRD), defined as microscopic residual tumor burden that remains after curative-intent treatment and is not detectable by conventional imaging, and for postoperative risk stratification.

METHODS: This narrative review summarizes the biological basis, analytical approaches, and clinical evidence regarding ctDNA in stage II colon cancer. We particularly emphasize prospective studies and randomized controlled trials.

RESULTS: Postoperative ctDNA positivity is strongly associated with increased recurrence risk and provides superior prognostic stratification compared with conventional clinicopathologic factors. Prospective studies have demonstrated that ctDNA-positive patients experience substantially higher recurrence rates, with the GALAXY study reporting a hazard ratio of 11.99 (95% CI: 8.83-16.27) for disease-free survival among patients with postoperative molecular residual disease. The DYNAMIC trial demonstrated that ctDNA-guided management reduces adjuvant chemotherapy use without compromising recurrence-free survival. However, current evidence suggests an important asymmetry in clinical utility. ctDNA negativity may support treatment de-escalation. In contrast, ctDNA positivity has not yet reliably identified patients who benefit from treatment escalation.

CONCLUSIONS: ctDNA constitutes a robust prognostic biomarker in stage II colon cancer and supports risk-adapted postoperative management. However, its predictive value for guiding treatment escalation remains unproven. Integration with clinicopathologic and molecular features is essential before routine clinical implementation.

PMID:42798930 | PMC:PMC13613144 | DOI:10.3389/fonc.2026.1908802

Cancers (Basel). 2026 Sep 20;18(18):3052. doi: 10.3390/cancers18183052.

ABSTRACT

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, although advances in molecular profiling and artificial intelligence (AI) are now reshaping precision oncology in ways that promise better patient outcomes. This review synthesises contemporary evidence on next-generation biomarkers and AI applications in CRC across multi-omic data integration, liquid biopsy, computational pathology, radiomics and clinical implementation. Several findings stand out. Integrated multi-omic approaches combining genomics, transcriptomics, proteomics, metabolomics and microbiomics outperform single-omic biomarkers for predicting prognosis and treatment response. Machine learning (ML) and deep learning (DL) models achieve clinical-grade performance for molecular biomarker prediction directly from routine histopathology, with a pooled area under the receiver operating characteristic curve (AUROC) of 0.94 for microsatellite instability (MSI) detection. Circulating tumour DNA (ctDNA) monitoring enables minimal residual disease (MRD) detection and real-time treatment guidance, postoperative ctDNA status separating a two-year recurrence-free survival of 91.1% from 50.4%; randomised evidence further shows that ctDNA-guided management can safely reduce adjuvant chemotherapy use in stage II colon cancer. Radiomics and pathomics extract prognostically significant quantitative features from imaging and histopathology, permitting non-invasive tumour characterisation, while multimodal models integrating clinical, genomic, imaging and pathological data support individualised treatment selection. MSI-high (MSI-H) status predicts exceptional immunotherapy benefit, carrying an overall survival hazard ratio of 0.35 against chemotherapy. Considerable difficulties nonetheless persist: harmonising data across institutions, generalising models to diverse populations, algorithmic bias and regulatory frameworks suited to clinical AI. Priorities for the coming years are prospective validation of AI-guided treatment algorithms, integration of spatial transcriptomics and single-cell approaches, federated learning to support multi-institutional collaboration without compromising privacy, and standardised protocols for biomarker testing and interpretation.

PMID:42795017 | PMC:PMC13604706 | DOI:10.3390/cancers18183052

Int J Mol Sci. 2026 Sep 14;27(18):8183. doi: 10.3390/ijms27188183.

ABSTRACT

The detection of circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) is a minimally invasive approach for diagnosing and monitoring cancer. These liquid biopsy-based strategies enable the identification of primary or metastatic tumors and provide valuable information on tumor biology and treatment response. A variety of techniques are employed to analyze components obtained through liquid biopsy. While CTCs are typically detected using cell-based methods, ctDNA is commonly analyzed using highly sensitive molecular approaches, including quantitative PCR (qPCR), digital PCR (dPCR), and next-generation sequencing (NGS). Extracellular vesicles (EVs), which carry tumor-derived nucleic acids, proteins, and other biomolecules, are increasingly investigated as potential biomarkers, while tumor-educated platelets (TEPs) can reflect tumor-associated molecular changes and may provide additional information for cancer detection and monitoring. Furthermore, emerging multi-cancer early detection (MCED) approaches aim to identify molecular signatures associated with multiple cancer types from a single blood sample, highlighting the broader diagnostic potential of liquid biopsy. Due to the high specificity of tumors and somatic mutations, ctDNA serves as a real-time biomarker for tracking cancer progression. The advantages of ctDNA diagnostics include its low invasiveness and its capacity to detect cancer at early stages. In addition to confirming the presence of a tumor, liquid biopsy approaches facilitate the assessment of malignancy and the evaluation of treatment response. In the field of human medicine, ctDNA plays a pivotal role in diagnostic procedures. It is utilized not only for screening tests that detect the presence of cancer but also for the development of targeted treatment protocols for specific patients. These protocols are informed by the detection of genomic alterations and are designed to monitor the response to therapy over the course of treatment. Similarly, CTC, EV, TEP, and MCED approaches are being investigated as complementary tools for cancer detection, molecular characterization, prognosis, and longitudinal disease monitoring. In the domain of veterinary medicine, ctDNA has been instrumental in the diagnosis of various neoplasms, including osteosarcomas, hemangiosarcomas, lymphomas, canine mammary tumors, and melanomas. Other liquid biopsy components, including CTCs and EVs, also show promise for the detection and characterization of tumors in companion animals, although their clinical application remains less developed than in human medicine. Another significant application is in the detection of minimal residual disease (MRD), where a small number of cancer cells remain undetectable by conventional tests, such as blood counts. This underscores the significance of advanced ctDNA analysis. However, challenges persist, including the low concentration of ctDNA in blood, the low ratio of mutated to normal DNA fragments, potential contamination, biological variability, and the need for standardized protocols. This review synthesizes the current knowledge on liquid biopsy, including ctDNA, CTCs, EVs, TEPs, and emerging MCED approaches, and the potential for transferring these technologies from human medicine to animal medicine. Continued research is necessary to enhance the sensitivity and specificity of detection, which could facilitate early cancer diagnosis in animals and improve survival through timely treatment.

PMID:42794612 | PMC:PMC13607009 | DOI:10.3390/ijms27188183

Front Oncol. 2026 Aug 28;16:1907210. doi: 10.3389/fonc.2026.1907210. eCollection 2026.

ABSTRACT

Clonal evolution in hepatocellular carcinoma (HCC), esophageal squamous cell carcinoma (ESCC), and gastric cancer (GC) reflects the interaction of genetic diversification, cell-state plasticity, and tissue-specific selection. Multi-region and single-cell DNA sequencing resolve truncal and subclonal lineages, whereas single-cell and spatial transcriptomics, proteomics, and serial liquid biopsy characterize cellular states, ecological niches, and temporal dynamics. The three cancers differ in dissemination timing, dominant selective pressures, and biomarker maturity: early seeding is best supported in selected HCC cohorts, ESCC is strongly influenced by field cancerization and epithelial-stromal crosstalk, and GC follows subtype- and ecotype-dependent trajectories. We discuss the assumptions and sampling biases that constrain phylogenetic inference, the causal limits of cross-sectional tumor atlases, clonal hematopoiesis, and the incremental value of broad multi-omics over focused assays. Liquid-biopsy detection of minimal residual disease is prognostic, but treatment benefit from marker-guided intervention remains context dependent. Near-term translation requires standardized, decision-linked assays; adaptive therapy and evolutionary steering remain investigational.

PMID:42729528 | PMC:PMC13563159 | DOI:10.3389/fonc.2026.1907210

Open Res Eur. 2026 Apr 3;6:87. doi: 10.12688/openreseurope.23403.1. eCollection 2026.

ABSTRACT

BACKGROUND: Pancreatic cancer and ovarian cancer are very challenging to diagnose at early stages. The endoscopic retrieval of biopsy tissue from a suspected benign or malignant lesion is challenging due to the tissue's nature. Therefore, within the Instand-NGS4P framework, we developed Measurable Residual Disease (MRD) prototypes to analyze blood plasma samples, with the aim of cost-effectively supporting the differential diagnosis of suspected pancreatic or ovarian neoplasms.

METHODS: Our MRD prototypes examine blood plasma for mutations in cell-free DNA in specific genes associated with pancreatic neoplasms or ovarian neoplasms, respectively. Unique molecular identifiers (UMIs) are used to enable bioinformatic error correction. Ultra-deep sequencing is demonstrated on sequencing platforms from two different vendors (Illumina and MGI). We provide detailed information on bioinformatic processing of sequencing data to perform error-correction.

RESULTS: Using commercially available reference standards, we demonstrate stable mutation detection down to a variant allele frequency (VAF) of 0.1%. At a coverage of 4,000x duplex consensus reads, only two false positives were observed, which can be efficiently mitigated using an appropriate filtering strategy.

CONCLUSIONS: The technical usability of our MRD prototype has been clearly demonstrated for stable low-level VAF detection in commercial reference samples.

PMID:42728989 | PMC:PMC13560845 | DOI:10.12688/openreseurope.23403.1

J Mol Diagn. 2026 Sep 11:S1525-1578(26)00156-X. doi: 10.1016/j.jmoldx.2026.08.002. Online ahead of print.

ABSTRACT

Analysis of circulating tumor-DNA (ctDNA) provides a molecular assessment that can complement routine imaging in childhood cancer management. Detailed monitoring of ctDNA levels may provide information on treatment efficacy and resistance, minimal residual disease and allows for early detection of relapse. Here, tumor-informed ctDNA analysis was applied to 90 blood plasma samples collected from eight children with malignant tumors. Four to ten tumor-specific mutations per patient were assessed using SiMSen-Seq, a digital sequencing approach utilizing unique molecular identifiers (UMIs). The effects of individual SiMSen-Seq assays and plasma samples were evaluated in relation to their impact on background error rate, number of detected target molecules and mutant calling using different UMI family size cutoff settings. The use of at least two sequencing reads per UMI provided the best overall performance by generating the highest number of detected target molecules and hence the optimal chance to detect low-frequent mutations. Data were consistent between SiMSen-Seq assays and plasma samples, providing robust ctDNA profiling over time for all patients. In conclusion, the results show that optimal use of UMIs in tumor-informed ctDNA analysis enables sensitive molecular readout that can assist in management of childhood cancers.

PMID:42727690 | DOI:10.1016/j.jmoldx.2026.08.002

Endokrynol Pol. 2026 Sep 11. doi: 10.5603/ep.112817. Online ahead of print.

ABSTRACT

The incidence of thyroid cancer has increased dramatically over the past four decades, making it the most common endocrine malignancy worldwide. Although well-differentiated thyroid carcinomas generally exhibit excellent survival rates following standard surgical and radioactive iodine interventions, the clinical management of high-risk variants, recurrent disease, and indeterminate nodules remains a significant challenge. Historically, the evaluation of thyroid nodules has relied on B-mode ultrasonography and fine-needle aspiration biopsy (FNAB). However, spatial and temporal tumor heterogeneity, coupled with the high rate of indeterminate cytology (Bethesda Categories III and IV), often leads to unnecessary diagnostic thyroidectomies. In recent years, liquid biopsy has emerged as a promising diagnostic approach, offering a non-invasive, dynamic, and comprehensive method for disease monitoring. This comprehensive review evaluates the biological mechanisms and clinical utility of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), extracellular vesicles (EVs), and non-coding RNAs in thyroid oncology. Furthermore, it explores the clinical role of commercial molecular diagnostic panels (e.g., Afirma GSC, ThyroSeq v3) in guiding surgical decisions. This review highlights the diagnostic synergy achieved when these molecular biomarkers are integrated with advanced radiological modalities - including strain elastography, quantitative region-of-interest (ROI) analysis, ACR TI-RADS, and cross-sectional volumetric tracking - as well as nuclear medicine techniques like technetium-99m MIBI scintigraphy. Emerging applications of artificial intelligence and radiomics in image analysis, alongside the concept of minimal residual disease monitoring, are also discussed. Ultimately, we emphasize the need for a multidisciplinary team (MDT) approach in translating these multi-omics and multimodal imaging data into precision medicine, while acknowledging current limitations and charting future directions.

PMID:42725427 | DOI:10.5603/ep.112817

Front Oncol. 2026 Aug 27;16:1919279. doi: 10.3389/fonc.2026.1919279. eCollection 2026.

ABSTRACT

Lung Cancer (LC) continues to be the biggest cause of cancer-related deaths around the world, mostly because of delayed diagnosis. Even if tissue biopsies and circulating tumor DNA (ctDNA) tests have revolutionized clinical management of LC patients, their effectiveness is restricted in settings with lower tumor burden, molecular heterogeneity, and bias in sampling approaches. In this scenario, the epigenetic profiling of cell-free DNA (cfDNA) stands out as a promising, less invasive approach, accurately detect cancer traces. Evidence from stage I-II disease and CT-detected pulmonary nodules supports the diagnostic potential of cfDNA methylation, although further validation in prospective screening cohorts remains necessary. Beyond genomic alterations, cfDNA epigenetic changes, including DNA methylation, chromatin organization, nucleosome positioning, and fragmentation patterns, reflect multi-dimensional complexity of tumor biology. These properties convey both the functional status and the origin of the circulating DNA fragments, accelerating for tumor integrating genomic analysis. Within this group, DNA methylation is the biologically robust and clinically well-established epigenetic marker, as alterations in methylation linked to cancer often occur in the early stages of tumorigenesis and are commonly found across different cancer cell types. Here, we explored the biological and clinical relevance of the epigenetic landscape of cfDNA in LC patients, particularly focusing on DNA methylation-based biomarkers and their evolving applications towards early diagnosis and post-surgical monitoring of minimal residual disease (MRD). We aimed to comprehensively overview analytical approaches for cfDNA methylation analysis, including targeted and genome-wide profiling strategies, and discuss their integration with machine learning (ML) and multi-omics frameworks in order to improve diagnostic performance and clinical applicability in LC management.

PMID:42724581 | PMC:PMC13559918 | DOI:10.3389/fonc.2026.1919279