Detection of circulating tumor DNA in early- and late-stage human malignancies

Liquid Biopsy Approaches for Cancer Characterization, Residual Disease Detection, and Therapy Monitoring

Liquid biopsy encompasses a variety of molecular approaches to detect circulating tumor DNA (ctDNA) and has become a powerful tool in the diagnosis and treatment of solid tumors. Current applications include comprehensive genomic profiling for identifying targetable mutations and therapeutic resistance mechanisms, with emerging applications in minimal residual disease detection and treatment response monitoring. Increasingly, the potential for liquid biopsy in guiding treatment decisions is under active investigation through prospective clinical trials using ctDNA-adaptive interventions in patients with early-stage and metastatic cancers. Limitations arise on the basis of the sensitivity and feasibility of individual liquid biopsy assays; nonetheless, emerging technologies set the stage for improving these shortcomings. As the global oncology community continues to ascertain the clinical value of liquid biopsy across the continuum of patient care, this minimally invasive approach heralds a significant advancement in the promise of precision oncology.

[Molecular testing and liquid biopsies in colorectal cancer]

BACKGROUND

The introduction of new DNA sequencing technologies has led to the discovery of many prognostically and predictively relevant biomarkers in tumor tissue and blood from patients with colorectal cancer.

OBJECTIVES

Presentation of meaningful tissue-based molecular pathological diagnostics and discussion of the clinical application of circulating tumor DNA (ctDNA) from liquid biopsies in colorectal cancer.

MATERIALS AND METHODS

Evaluation of existing literature and congress publications, discussion of post hoc analyses of clinical studies and expert recommendations.

RESULTS

In Union for International Cancer Control (UICC) stages II/III, the tissue-based evaluation of microsatellite instability (MSI-H) contributes to individual therapy optimization through advice on adjuvant chemotherapy (colon cancer, UICC II) or, if necessary, individual neo-adjuvant therapy concepts via the use of immunotherapy (colon, rectal cancer, UICC II/III). From liquid biopsies, ctDNA was associated with minimal residual disease, which influences disease-free survival. In the metastatic stage (UICC IV), tissue-based determination of RAS and BRAF V600E mutations, MSI‑H and in the near future also HER2/neu overexpression should be performed. Broader molecular diagnostics to optimize first-line therapy (molecular hyperselection) shows little additional benefit. ctDNA can be used for longitudinal monitoring of clonal tumor evolution or as an alternative to invasive diagnostics in patients.

CONCLUSIONS

Molecular pathological diagnostics from tissue and blood complement each other and should be used in a targeted and meaningful way according to the underlying question.

Circulating Tumor DNA in Addition to Fecal Immunochemical Test in a Dual-Test Colorectal Cancer Screening Approach

BACKGROUND

Early detection is paramount when reducing incidence and mortality of colorectal cancer (CRC). Current population-based screening programs primarily use fecal immunochemical test (FIT) to allocate individuals for colonoscopy although low specificity challenges colonoscopy capacities. We aimed to assess the potential of circulating tumor (ct)DNA markers for early CRC detection in a dual-test CRC screening approach among FIT positive individuals.

METHODS

Plasma samples from 774 FIT positive (≥100 ng Hemoglobin/mL) individuals from the Danish CRC screening program were analyzed for hypermethylated DNA in the genes Branched Chain Amino-acid Transaminase 1 (BCAT1), Ikaros-Family Zinc Finger transcription 1 (IKZF1), and Interferon Regulator Factor 4 (IRF4). Multivariate logistic regression models were generated adding the ctDNA markers and age to the FIT value. The dual-test approach was benchmarked to FIT at specific thresholds.

RESULTS

The dual-test approach improved CRC detection compared to the FIT alone (AUC of 87.2 [95% CI, 82.9-91.4] vs AUC of 72.5 [95% CI, 67.0-77.9]). This was also seen when adding advanced adenomas to the outcome resulting in AUCs of 71.8 [95% CI, 67.8-75.8] for the dual-test approach compared to 65.5 [95% CI, 61.3-69.7] for the FIT model alone. Benchmarking the dual-test approach at FIT cut-offs between 100 and 600 ng Hb/mL showed a potential for either reducing the colonoscopy requirement by up to 56% or increasing CRC detection by up to 28%.

CONCLUSIONS

As increasing FIT cutoff will decrease CRC detection rate, application of the ctDNA panel can increase the sensitivity and specificity in a dual-test approach among asymptomatic individuals.

Circulating tumor DNA monitoring in advanced mutated melanoma (LIQUID-MEL)

Introduction

Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of metastatic melanoma, but a percentage of patients did not show benefit. Circulating tumor DNA (ctDNA) has emerged as a potential non-invasive tool for monitoring disease evolution and treatment response. The present study aimed to evaluate the clinical utility of ctDNA dynamics in patients with metastatic melanoma receiving ICIs, while exploring its role in the oncological course.

Materials and methods

The LIQUID-MEL study is a prospective, single-centre pilot study including patients with BRAF/NRAS-mutant metastatic melanoma. ctDNA was quantified using digital droplet PCR (ddPCR) at four different time points. Uni- and multivariable Cox regression models were used to assess the correlation between shedding and progression-free survival (PFS), and overall survival (OS).

Results

Overall, 23 patients were included. At baseline, ctDNA was detectable in 5/23 (21.7 %) cases. Baseline ctDNA shedding was associated with shorter PFS (3.88 months vs. 0.69 months, p=0.012). A strong numerical trend was observed also in OS (12.66 months vs. 2.53 months, p=0.287). Shedding at baseline did not demonstrate independent prognostic or predictive value in the uni- and multivariable analysis. The longitudinal analysis revealed intriguing patterns of ctDNA shedding in individual patients.

Conclusion

ctDNA detectability and its dynamic changes during treatment may have potential clinical utility in patients with metastatic melanoma, offering a valuable non-invasive tool for monitoring disease and treatment response. The small sample size limited the statistical power of the analysis. Further studies with larger cohorts are needed to validate its role in routine clinical practice.

ctDNA detection in cerebrospinal fluid and plasma and mutational concordance with the primary tumor in a multicenter prospective study of patients with glioma

BACKGROUND

Cerebrospinal fluid (CSF) stands as an easily accessible reservoir for circulating tumor DNA (ctDNA) analysis in patients with central nervous system (CNS) tumors, although evidence is still limited. Our aim was to prospectively evaluate the feasibility of detecting ctDNA for mutational analysis in CSF and plasma in patients with glioma.

METHODS

This was a prospective study of patients with glioma diagnosed at four third-level hospitals in Spain. A customized next-generation sequencing (NGS) eight-gene panel (IDH1, IDH2, ATRX, TP53, PTEN, PIK3CA, EGFR, BRAF) was used in paired CSF, plasma and tumor samples. Mutation concordance occurred when the same pathogenic gene variant was detected in tumor and ctDNA. The prognostic value of ctDNA and that of its median variant allele frequency (mVAF) were analyzed.

RESULTS

Between February 2017 and March 2020, 37 patients with glioma were enrolled. The 32 patients with analyzable CSF samples comprised patients with new diagnosis (n = 23) and relapse (n = 9); World Health Organization fifth Edition types: IDH-mutant astrocytoma (n = 10), IDH-mutant oligodendroglioma (n = 6) and IDH-wildtype glioblastoma (n = 16); CSF-ctDNA-positive: 19/32 (59%); and CSF-ctDNA-negative: 13/32 (41%). CSF mutation numbers were 1 (10/19), 2 (7/19) and 3 (2/19). Frequencies of CSF-ctDNA-mutated genes were EGFR (8/19, 42%), PTEN (7/19, 37%), TP53 (6/19, 32%), IDH1 (5/19, 26%) and PIK3CA (4/19, 21%). Tumor-CSF mutation concordance was found in 16/19 (84%). Progression-free and overall survival were significantly shorter in ctDNA-positive patients with VAF equal to or greater than the mVAF compared with ctDNA-positive patients with VAF lower than the mVAF. No association was found between ctDNA in CSF and distance to closest CSF reservoir, tumor size or IDH status. ctDNA was detected in 2 of 14 (14%) individual plasma samples, in both cases concordant with the primary tumor.

CONCLUSION

CSF is a reliable reservoir for ctDNA analyses in patients with glioma. ctDNA is detectable in plasma although at a lower rate. Larger, prospective studies should be conducted to refine the potential role of liquid biopsy in this disease.

Modulating cell-free DNA biology as the next frontier in liquid biopsies

Technical advances over the past two decades have enabled robust detection of cell-free DNA (cfDNA) in biological samples. Yet, higher clinical sensitivity is required to realize the full potential of liquid biopsies. This opinion article argues that to overcome current limitations, the abundance of informative cfDNA molecules - such as circulating tumor DNA (ctDNA) - collected in a sample needs to increase. To accomplish this, new methods to modulate the biological processes that govern cfDNA production, trafficking, and clearance in the body are needed, informed by a deeper understanding of cfDNA biology. Successful development of such methods could enable a major leap in the performance of liquid biopsies and vastly expand their utility across the spectrum of clinical care.

Circulating tumor DNA dynamic variation predicts sotorasib efficacy in KRASp.G12C-mutated advanced non-small cell lung cancer

BACKGROUND

The objective of this study was to investigate the correlation between circulating tumor DNA (ctDNA) KRAS G12C-mutation dynamic variations and treatment outcomes in patients with advanced non-small cell lung cancer (NSCLC) receiving sotorasib therapy in a real-world setting.

METHODS

Peripheral blood samples were prospectively collected from 32 patients at baseline, at cycle 3, and then at each radiologic assessment during sotorasib treatment. Both tissue and plasma samples were analyzed by using ultra-deep, customized next-generation sequencing (NGS) assays. Plasma samples from 27 of 32 patients also were analyzed by digital polymerase chain reaction analysis, and ctDNA dynamic variations were correlated with radiologic responses and patients' clinical outcomes.

RESULTS

A significant correlation between NGS and digital polymerase chain reaction-detected KRAS G12C variant allelic fractions (p < .001) was observed. Patients who achieved clearance of KRAS G12C-mutant ctDNA levels had a significant improvement in the objective response rate (80% vs. 8%; p < .001), median progression-free survival (7.9 vs. 2.8 months; p < .001), and median overall survival (16.8 vs. 6.4 months; p < .001) compared with those who did not achieve clearance. The clearance of ctDNA was the only prognostic factor significantly associated with both median progression-free survival (hazard ratio, 0.15; 95% confidence interval, 0.04-0.48) and median overall survival (hazard ratio, 0.09; 95% confidence interval, 0.02-0.45) in multivariable analysis. Moreover, a dynamic increase in the KRAS G12C median variant allele fraction anticipated radiologic disease progression in 70% of patients who were evaluable at the resistance time point.

CONCLUSIONS

This study demonstrated that early clearance of KRAS G12C-mutant ctDNA predicted the clinical benefit of sotorasib in patients with advanced NSCLC, suggesting that dynamic monitoring of ctDNA levels also may anticipate sotorasib resistance.

Circulating Tumor DNA in the Surgical Management of Cancer: A Review of Clinical Trials to Understand Future Impact on Multidisciplinary Practice

BackgroundCirculating tumor DNA (ctDNA) has been proposed as a surrogate for solid tumor tissue biopsies. Our study evaluated trends of clinical trials that assess the role of ctDNA in surgical oncology.MethodsThe ClinicalTrials.gov database was queried for clinical trial that evaluated the use of ctDNA in the management of patients who underwent curative resections for solid tumor malignancies. Studies were categorized based on the phase of operative care were ctDNA was assessed and further stratified based on surgical application. Descriptive statistics were utilized to describe trends of included trials.ResultsOf 382,298 clinical trials, our study identified 68 trials (2014-2021). The majority of these trials were phase 2 (82.4%) and actively recruiting (63.2%). The most commonly studied malignancies were breast (20.0%), colon (17.1%) and lung (14.3%) cancers. Majority of trials assessed ctDNA utility in preoperative prognostication (52.9%) and in postoperative adjuvant therapy candidacy (16.2%).DiscussionThere have been significant strides in the use of ctDNA in surgical oncology including preoperative prognostication, postoperative surveillance, and risk stratification for adjuvant therapy. In recognizing the dynamic landscape of clinical trials, multidisciplinary oncology teams can be better informed to anticipate the clinical implications of ctDNA within their practice.

Promoter hypermethylation of SFRP1 is an allele fraction-dependent prognostic biomarker in metastatic pancreatic ductal adenocarcinoma

Introduction

Metastatic pancreatic ductal adenocarcinoma (PDAC) is highly lethal. Promoter hypermethylation of SFRP1 (phSFRP1) in cell-free DNA is an established prognostic biomarker in PDAC. We used digital droplet PCR (ddPCR) to examine whether the prognostic impact of phSFRP1 was allele fraction (AF) dependent.

Methods

Prospectively collected plasma samples were analyzed blinded. Dual-strand methylation ddPCR assays were designed for SFRP1, with single-strand assay for the reference gene EPHA3. Patients were stratified into unmethylated SFRP1 (umSFRP1), low phSFRP1 AF (phSFRP1low), and high phSFRP1 AF (phSFRP1high). Survival was assessed with Kaplan-Meier curves. The 3-, 6-, and 12-month absolute risk difference (ARD) was calculated, and performance assessed with ROC analyses.

Results

Overall, 354 patients were included. Patients with umSFRP1 (n=137) had a mOS of 9.1 months compared to 7.2 months in phSFRP1low (n=78) and 3.4 months in phSFRP1high (n=143, P<0.01). phSFRP1high was associated with increased mortality at 3 (ARD 26%, 95%CI: 15, 37), 6 (ARD 37%, 95%CI: 26, 48), and 12 months (ARD 23%, 95%CI: 14, 33). phSFRP1low was associated with increased mortality at 12 months (ARD 13%, 95%CI: 2, 25) but not at 3 (ARD -3%, 95%CI: -13, 8) or 6 months (ARD 3%, 95%CI: -10, 17). phSFRP1 significantly improved performance in predicting mortality compared to only clinical variables (AUC: 0.70-0.71 vs. 0.54-0.57).

Discussion

Patients with phSFRP1high had significantly shorter survival than phSFRP1low or umSFRP1, indicating AF-dependent prognostic effects. phSFRP1low had a worse prognosis than umSFRP1 at only 12 months, indicating dynamic changes. This could help personalize the treatment of PDAC.

A novel KRAS exon 2 drop-off digital PCR assay for mutation detection in cell-free DNA of cancer patients

BACKGROUND

KRAS exon 2 mutations are highly prevalent in human malignancies, making them attractive targets for detection and monitoring in cell-free DNA (cfDNA) of cancer patients. Drop-off assays designed for digital polymerase chain reaction (ddPCR drop-off) span entire mutational hotspots and detect any mutated allele within the covered region, overcoming a major limitation of mutation-specific ddPCR assays. We therefore set out to develop a novel KRAS codon 12/13 ddPCR drop-off assay for the robust, highly sensitive and specific detection of KRAS exon 2 hotspot mutations in cfDNA.

METHODS

We designed, optimized and extensively validated a KRAS codon 12/13 ddPCR drop-off assay. We compared assay performance to a commercially available KRAS multiplex assay. For clinical validation, we analyzed plasma samples collected from patients with KRAS-mutated gastrointestinal malignancies.

RESULTS

Limit of detection of the newly established ddPCR drop-off assay was 0.57 copies/µL, limit of blank was 0.13 copies/µ. The inter-assay precision (r2) was 0.9096. Our newly developed KRAS ddPCR drop-off assay accurately identified single nucleotide variants in 35/36 (97.2%) of circulating tumor DNA-positive samples from the patient validation cohort. Assay cross-validation showed that the newly established KRAS codon 12/13 ddPCR drop-off assay outperformed a commercially available KRAS multiplex ddPCR assay in terms of specificity. Moreover, the newly developed assay proved to be suitable for multiplexing with mutation-specific probes.

CONCLUSION

We developed and clinically validated a highly accurate ddPCR drop-off assay for KRAS exon 2 hot-spot detection in cfDNA with broad applicability for clinic and research.

Diagnostic value of genetic and epigenetic biomarker panels for colorectal cancer detection: a systematic review

PURPOSE

Exploration of effective screening methods is imperative to improve current screening for colorectal cancer (CRC). Our aim was to systematically search the literature to identify and assess the diagnostic accuracy of both genetic and epigenetic biomarker panels for CRC detection using liquid biopsies for circulating tumour DNA (ctDNA) from stool, blood, or urine.

METHODS

A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) with searches in Medline, Embase, CENTRAL, and Web Of Science from inception up to March 20, 2025, using pre-defined keywords. Study quality assessment was performed using QUADAS-2 tool (Quality Assessment for Diagnostic Accuracy Studies 2). Primary and secondary outcomes were panel performance (sensitivity and specificity) for CRC, advanced precancerous lesions (APL), and staging of disease.

RESULTS

Forty-four studies were included. Exceptional performance for both CRC (sensitivity and specificity) and APL (sensitivity) was displayed by biomarker panels including methylated SDC2 with methylated SFRP1/2 (CRC: 91.5%/97.3%, APL: 89.2%) or methylated TFPI2 (CRC: 94.9%/98.1%, APL: 100%), and a 5-biomarker panel of mutational targets APC, Bat-26, KRAS, L-DNA, and p53 (CRC: 91.0%/93.0%, APL: 82.0%). Suboptimal APL sensitivities up to 57.0% were exhibited by Cologuard and variant panels (including KRAS, methylated BMP3, methylated NDRG4, FIT), and 47.8% for combinations including methylated SEPT9.

CONCLUSIONS

High-performance, candidate ctDNA biomarker panels with exceptional diagnostic accuracy for both CRC and APL have been identified. Further work should focus on the development of large-scale studies to justify their clinical implementation.

ctDNA and Recurrence Risk for Adjuvant De-Escalation in HPV-Positive Oropharyngeal Carcinoma: A Secondary Analysis of the DART Phase 3 Randomized Clinical Trial

Importance

The De-escalated Adjuvant Radiation Therapy (DART) phase 3 randomized clinical trial (RCT) showed that in patients with human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma, postoperative minimal residual disease (MRD), detected through circulating tumor HPV DNA (ctHPVDNA), was associated with a higher risk of disease progression. When considered along with pathologic factors, postoperative ctHPVDNA assessment may improve patient selection for adjuvant treatment de-escalation; however, more data are needed to demonstrate how it may be used in personalizing treatment intensity.

Objective

To determine the association of postoperative MRD status with progression-free survival (PFS) after surgery for HPV-associated oropharyngeal squamous cell carcinoma.

Design, Setting, and Participants

This was a secondary analysis of the DART RCT, which was conducted from October 2016 to August 2020 in multiple sites in the US. Participants from the de-escalated adjuvant radiation therapy group and the standard of care group with available blood specimen data were included. Reports from 3-month posttreatment surveillance visits were used to assess associations and outcomes. Data analyses were performed from March 2023 to March of 2025.

Interventions

The DART group received 30 to 36 Gy of radiation therapy in 1.5 to 1.8 Gy twice daily, plus docetaxel, 15 mg/m2, on days 1 and 8. The standard of care group received 60 Gy with or without weekly cisplatin, 40 mg/m2.

Main Outcome and Measure

PFS.

Results

The analysis included 140 patients (mean [SD] age, 59.1 [8.4] years; 12 [8.6%] females and 128 [91.4%] males; 97 [69.3%] with no smoking history); characteristics were similar to the overall DART RCT population. Of these, 17 patients (12.1%) had postoperative MRD (13 of 96 [13.5%] receiving DART and 4 of 44 [9.1%] receiving standard of care). For all patients, postoperative MRD positivity was strongly associated with worsened PFS at 24 months (MRD positivity, 69.5%; MRD negativity, 95.9%; hazard ratio [HR], 0.19; 95% CI, 0.06-0.59). MRD positivity was associated with PFS when evaluating only those patients in the DART group, where 24-month PFS was 68.4% compared to 92.6% for MRD-negative patients (HR, 0.28; 95% CI, 0.08-0.93). Three months after completion of all treatment, 8 of 117 patients (6.8%) had detectable ctHPVDNA, whereas 109 of 117 (93.2%) did not, and detection was highly associated with PFS (HR, 20.48; 95% CI, 6.91-60.67).

Conclusions and Relevance

This secondary analysis of the DART RCT found that patients with detectable ctHPVDNA after surgery had a higher risk of disease progression. When added to the pathologic factors considered, ctHPVDNA assessment may improve selection of patients for treatment de-escalation. In addition, the 3-month posttreatment time point, early in surveillance, may identify a sizable portion of patients with progression and may guide intervention and surveillance after surgery for HPV-associated oropharyngeal squamous cell carcinoma.

Trial Registration

ClinicalTrials.gov Identifier: NCT02908477.

The Application of Circulating Tumour DNA (ctDNA) in the Diagnosis, Prognosis, and Treatment Monitoring of Gynaecological and Breast Cancers (Review)

Gynaecological cancers, including endometrial, ovarian, and cervical cancers as well as breast cancer, despite numerous studies, still constitute a challenge for modern oncology. For this reason, research aimed at the application of modern diagnostic methods that are useful in early detection, prognosis, and treatment monitoring deserves special attention, Great hopes are currently being placed on the use of liquid biopsy (LB), which examines various tumour components, including cell-free RNA (cfRNA), circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), exosomes, and tumour-educated platelets (TEPs). LB has shown promise as a minimally invasive means of early diagnosis of cancers, detection of recurrence, prediction of therapy response, treatment monitoring, and drug selection. The integration of this test into clinical practice in modern oncology is challenging, but offers many benefits, including reducing the risks associated with invasive procedures, improving diagnostic and therapeutic efficacy, and improving the quality of life of oncology patients. The aim of this review is to present recent reports on the use of ctDNA in diagnosing, predicting the outcome of, and monitoring the treatment of gynaecological and breast cancers.

Immunotherapy for resectable lung cancer

Lung cancer remains a significant global health challenge, demanding innovative treatment strategies. Immune checkpoint blockade has revolutionized cancer care, leading to improved survival across advanced malignancies and has now become a standard therapy for earlier stage, resectable lung cancer. This review article consolidates the current landscape and future prospects of neoadjuvant and perioperative immunotherapy in lung cancer. The authors outline key findings from clinical trials in resectable lung cancer, including early efficacy, safety profiles, and emerging impact on disease recurrence, and overall survival. Additionally, this review elucidates the challenges encountered, including patient selection criteria, optimal treatment schedules, immune-related adverse events, and impact on surgery. This comprehensive analysis amalgamates current evidence with future directions, providing a roadmap for clinicians, researchers, and stakeholders to navigate the dynamic realm of immunotherapy for surgically resectable lung cancer.

A field resource for the glioma cerebrospinal fluid proteome: Impacts of resection and location on biomarker discovery

BACKGROUND

While serial sampling of glioma tissue is rarely performed prior to recurrence, cerebrospinal fluid (CSF) is an underutilized longitudinal source of candidate glioma biomarkers for understanding therapeutic impacts. However, the impact of key variables to consider in longitudinal CSF samples for monitoring biomarker discovery, including anatomical location and post-surgical changes, remains unknown.

METHODS

Aptamer-based proteomics was performed on 147 CSF samples from 74 patients; 71 of whom had grade 2-4 astrocytomas or grade 2-3 oligodendrogliomas. This included pre- versus post-resection intracranial CSF samples obtained at early (1-16 days; n = 20 patients) or delayed (86-153 days; n = 11 patients) time points for patients with glioma. Paired lumbar versus intracranial glioma CSF samples were also obtained (n = 14 patients).

RESULTS

Significant differences were identified in the CSF proteome between lumbar, subarachnoid, and ventricular CSF in patients with gliomas. Importantly, we found that resection had a significant, evolving longitudinal impact on the CSF proteome, with distinct sets of proteins present at different time points since resection. Our analysis of serial intracranial CSF samples suggests the early potential for disease monitoring and evaluation of pharmacodynamic impact of targeted therapies, such as bevacizumab and immunotherapies.

CONCLUSIONS

The intracranial glioma CSF proteome serves as a rich and dynamic reservoir of potential biomarkers that can be used to evaluate the effects of resection and other therapies over time. All data within this study, including detailed individual clinical annotations, are shared as a resource for the neuro-oncology community to collectively address these unanswered questions and further understand glioma biology through CSF proteomics.

Circulating tumor DNA laboratory processes and clinical applications in nasopharyngeal carcinoma

Circulating tumor DNA (ctDNA), a subset of cell-free DNA (cfDNA), originates from primary tumors and metastatic lesions in cancer patients, often carrying genomic variations identical to those of the primary tumor. ctDNA analysis via liquid biopsy has proven to be a valuable biomarker for early cancer detection, minimal residual disease (MRD) assessment, monitoring tumor recurrence, and evaluating treatment efficacy. However, despite advancements in ctDNA analysis technologies, standardized protocols for its extraction and detection have yet to be established. Each step of the process-from pre-analytical variables to detection techniques-significantly impacts the accuracy and reliability of ctDNA analysis. This review examines recent developments in ctDNA detection methods, focusing on pre-analytical factors such as specimen types, collection tubes, centrifugation protocols, and storage conditions, alongside high-throughput and ultra-sensitive detection technologies. It also briefly discusses the clinical potential of liquid biopsy in nasopharyngeal carcinoma (NPC).

Research trends and hotspots of circulating tumor DNA in colorectal cancer: a bibliometric study

Introduction

Colorectal cancer (CRC) is the third most common cancer worldwide and the second leading cause of cancer-related deaths. The current standard of care for patients with early-stage CRC includes surgical resection and, in selected patients, adjuvant chemotherapy. Circulating tumor DNA (ctDNA) testing is an important component of liquid biopsy, and with the development of testing technology, its value for clinical application has attracted widespread attention. The aim of this study was to help researchers review what has been achieved and better understand the direction of future research through bibliometric analysis.

Methods

We used the Web of Science Core Collection database to search for ctDNA in CRC-related articles published between 2014 - 2023. Bibliometric analyses of major keywords, authors, countries, institutions, literature and journals in the field were performed using CiteSpace and VOSviewer.

Results

The number of publications in the field has continued to increase over the last decade. The United States has the highest number of publications, and Italian research scholars have made outstanding contributions. Cancers is the journal with the highest number of publications.

Conclusion

This study systematically summarizes the research findings in the field of ctDNA in CRC from 2014 to 2023 and describes the research hotspots and trends worldwide that can guide future research.

Current treatment landscape for patients with non-small cell lung cancer with common EGFR mutations

Common EGFR mutations including exon-19 deletions and the L858R point mutation in exon 21 constitute predominant actionable genomic alterations in individuals with non-small cell lung cancer (NSCLC). The introduction of EGFR tyrosine kinase inhibitors (TKIs) has fundamentally changed the treatment landscape for such patients by improving both progression-free survival (PFS) and overall survival (OS). Among EGFR-TKIs, third-generation agents such as osimertinib have shown marked efficacy and favorable safety profiles and have become the standard of care in the first-line setting. The combination of osimertinib with platinum-based chemotherapy has recently been shown to improve PFS compared with osimertinib monotherapy in the FLAURA2 trial. Similarly, the MARIPOSA trial demonstrated clinical benefit of the combination of the EGFR-MET bispecific antibody, amivantamab, with the third-generation EGFR-TKI, lazertinib, further supporting the use of combination therapies as first-line treatment for EGFR-mutated NSCLC. Despite these advances, however, challenges such as brain metastases remain substantial barriers to successful treatment outcomes. Management of patients with such metastases often requires a multidisciplinary approach that integrates systemic treatment with local interventions such as radiation therapy. Finally, circulating tumor DNA has emerged as a promising biomarker for real-time monitoring of treatment response and evolution of drug resistance mechanisms. Analysis of such biomarkers can facilitate dynamic and personalized therapeutic adjustments, potentially improving outcomes. This review provides a comprehensive overview of the latest clinical evidence supporting therapeutic advances in the management of EGFR-mutated NSCLC, emphasizing the importance of tailoring treatment strategies based on tumor biology, patient-specific factors, and evolving therapeutic options.

Prognostic significance of circulating tumor DNA alterations in advanced renal cell carcinoma from SCRUM-Japan MONSTAR-SCREEN: a nationwide genomic profiling project

BACKGROUND

Circulating tumor DNA (ctDNA) is a promising tool for diagnosing and predicting cancer prognosis. However, its clinical utility in metastatic renal cell carcinoma (mRCC) remains unclear, particularly in terms of clinical prognosis.

METHODS

We enrolled 124 patients with mRCC in the MONSTAR-SCREEN study (UMIN 000036749) between August 2019 and February 2022, a national observational ctDNA-based screening study, and performed ctDNA sequencing before and at the time of resistance to systemic therapy.

RESULTS

ctDNA were assessed in 178 samples containing 432 mutations. The most frequently altered genes at baseline were VHL (25.0%), PBRM1 (10.9%), TERT2 (8.7%), BAP1 (8.7%), and MTOR (7.6%). Patients receiving first-line therapy with tumor fraction (TF) < 1.2% showed significantly better progression-free survival than those with TF ≥ 1.2% (Hazard ratio (HR) = 0.467; 95% CI 0.229-0.979; p = 0.0425). BAP1 mutational status of ctDNA at baseline led to poor OS (HR = 0.4867; 95% CI 0.322-0.736; p = 0.0003). Serial ctDNA analysis showed that 46.8% of patients developed new ctDNA mutations at disease progression, which was linked to shorter time to progression (p = 0.046).

CONCLUSIONS

Our findings demonstrated that ctDNA profiling is feasible in mRCC and can predict disease progression after treatment.

Integrating Plasma Cell-Free DNA Fragment End Motif and Size with Genomic Features Enables Lung Cancer Detection

Early detection of lung cancer is important for improving patient survival rates. Liquid biopsy using whole-genome sequencing of cell-free DNA (cfDNA) offers a promising avenue for lung cancer screening, providing a potential alternative or complementary approach to current screening modalities. Here, we aimed to develop and validate an approach by integrating fragment and genomic features of cfDNA to enhance lung cancer detection accuracy across diverse populations. Deep learning-based classifiers were trained using comprehensive cfDNA fragmentomic features from participants in multi-institutional studies, including a Korean discovery dataset (218 patients with lung cancer and 2,559 controls), a Korean validation dataset (111 patients with lung cancer and 1,136 controls), and an independent Caucasian validation cohort (50 patients with lung cancer and 50 controls). In the discovery dataset, classifiers using fragment end motif by size, a feature that captures both fragment end motif and size profiles, outperformed standalone fragment end motif and fragment size classifiers, achieving an area under the curve (AUC) of 0.917. The ensemble classifier integrating fragment end motif by size and genomic coverage achieved an improved performance, with an AUC of 0.937. This performance extended to the Korean validation dataset and demonstrated ethnic generalizability in the Caucasian validation cohort. Overall, the development of a deep learning-based classifier integrating cfDNA fragmentomic and genomic features in this study highlights the potential for accurate lung cancer detection across diverse populations. Significance: Evaluating fragment-based features and genomic coverage in cell-free DNA offers an accurate lung cancer screening method, promising improvements in early cancer detection and addressing challenges associated with current screening methods.

ctDNA variations according to treatment intensity in first-line metastatic colorectal cancer

BACKGROUND

Circulating tumor DNA variations (∆ctDNA) were reported to be associated with treatment efficacy in metastatic colorectal cancer (mCRC). The present study evaluated ∆ctDNA according to first-line treatment intensity.

METHODS

Patients from two prospective ctDNA collections were divided into Group ≤ 2 drugs and Group ≥ 3 drugs. ∆ctDNA were analysed from baseline to cycle 3 or 4 (C3-4) according to three predefined subgroups: ∆ctDNA ≥ 80%_ undetectable, ∆ctDNA ≥ 80%_ detectable, and ∆ctDNA < 80%. Impact of ∆ctDNA on progression-free survival (PFS) and overall survival (OS) were analysed.

RESULTS

Pretreatment ctDNA was detected in 129/152 (84.9%) of patients. A ∆ctDNA ≥ 80%_undetectable was more frequent in Group ≥ 3 than ≤ 2 drugs (respectively 51.5% vs. 32.7%, p = 0.015). Patients with ∆ctDNA ≥ 80%_undetectable had longer survival than other ∆ctDNA subgroups, in Group ≥ 3 drugs (mPFS 11.5 vs 7.8 vs 6.3 months, p = 0.02: mOS 30.2 vs 18.1 vs 16.4 month, p = 0.04) and in Group ≤ 2 drugs (mPFS 8.4 vs 6.0 vs 5.3 months, p = 0.05; mOS 29.6 vs 14.6 vs 14.6 months, p = 0.007).

DISCUSSION

Early ∆ctDNA are associated to treatment intensity in first line mCRC with a significant impact on prognosis.

Cost-effective shallow genome-wide sequencing for profiling plasma cfDNA signatures to enhance lung cancer detection

BACKGROUND

Lung cancer (LC) screening via low-dose computed tomography (LDCT) faces challenges including high false-positive rates and low patient compliance. Circulating tumor DNA (ctDNA)-based tests offer a minimally invasive alternative but are limited by high costs and low sensitivity, particularly in early-stage detection. This study introduces a cost-effective, shallow genome-wide sequencing approach for LC detection by profiling multiple cell-free DNA (cfDNA) signatures.

METHODS

We developed a multimodal cfDNA assay with shallow sequencing coverage (0.5×) that integrates fragmentomic, nucleosome, end-motif, and copy number alteration analyses. A machine-learning model trained on a discovery cohort (99 LC patients, 168 healthy controls) and validated on an independent cohort (58 LC patients, 71 controls) demonstrated robust performance.

RESULTS

The ensemble model exhibited outstanding performance, achieving an AUC of 0.97 and a specificity of 92% in both the discovery and validation cohorts, with sensitivities of 94% and 90%, respectively. Notably, it outperformed hotspot mutation-based assays and the multi-cancer SPOT-MAS assay in sensitivity across all LC stages.

CONCLUSIONS

This assay provides a cost-effective, accurate, and minimally invasive method for LC detection, addressing the limitations of current screening methods. It represents a promising complementary tool to improve early detection and patient outcomes in LC.

Establishment of xenografts and methods to evaluate tumor burden for the three most frequent subclasses of pediatric-type diffuse high grade gliomas

PURPOSE

We aimed to expand and refine the experimental models for pediatric-type diffuse high grade gliomas (pHGG) and the methods to follow up disease progression in mouse pHGG xenografts.

METHODS

Using whole exome sequencing and immunoassays we characterized pHGG primary cultures and xenografts established at hospital SJD Barcelona. We obtained tumor samples and serial CSF samples from mouse xenografts. To assess tumor progression, we evaluated: (1) mouse weight, (2) human cell counts in brain paraffin sections, and (3) tumor DNA amount, quantified through droplet digital polymerase chain reaction (ddPCR) in paraffin sections and cerebrospinal fluid (CSF).

RESULTS

We established 15 experimental models of three pHGG subclasses, four of which engrafted in mice. Xenografts HSJD-DIPG-007 and HSJD-DMG-005 are diffuse midline glioma (DMG) H3 K27-altered, HSJD-GBM-002 is an H3 G34-mutant diffuse hemispheric glioma, and HSJD-GBM-001 is an H3-wildtype and IDH-wildtype pHGG. ddPCR quantification of human H3F3A K27M, H3F3A G34R, and ACVR1 R206H in paraffin samples is linear and sufficiently sensitive. We required a preamplification step to detect H3F3A K27M in CSF. In HSJD-DIPG-007 xenografts, human cell counts correlated with H3F3A amounts in paraffin for the whole engraftment period. Weight loss correlated with human cell counts and H3F3A amounts in paraffin. Serial collection of CSF was feasible, but H3F3A amounts in the CSF correlated only with weight loss.

CONCLUSION

The developed methods contribute to the preclinical field of pHGG and introduce for the first time the concept of liquid biopsy in mice, which still needs improvement regarding its use as a preclinical biomarker.

The Efficacy of Liquid Biopsy of Total cfDNA for Predicting Systemic Metastasis in Japanese Patients With Oral Squamous Cell Carcinoma

BACKGROUND

The use of liquid biopsy of total cell-free DNA (cfDNA) to identify otherwise undetectable cancers has attracted interest; however, its efficacy remains unknown. We explored whether analysis using total cfDNA is efficacious for Japanese patients with oral squamous cell carcinoma (OSCC).

METHODS

We collected total cfDNA from nine patients with OSCC preoperatively, 1 month postoperatively, and every 3 months thereafter to analyze this association. We used a target DNA sequence for genetic mutation analysis of tumor tissues collected from 33 patients, including the aforementioned nine patients.

RESULTS

Patients with good disease control showed negligible changes in preoperative and postoperative total cfDNA concentrations. A rapid increase in total cfDNA concentration was observed in patients who developed systemic metastases. Patients whose tumor tissue DNA showed genetic mutations had the same mutations in preoperative circulating tumor DNA.

CONCLUSIONS

Our data suggested that analyzing total cfDNA is efficacious for patients with OSCC.

Cerebrospinal fluid circulating tumor DNA profiling for risk stratification and matched treatment of central nervous system metastases

Genomic profiling of central nervous system (CNS) metastases has the potential to guide treatments. In the present study, we included 584 patients with non-small-cell lung cancer and CNS metastases and performed a comprehensive analysis of cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) with clinicopathological annotation. CSF ctDNA-positive detection was independently associated with shorter survival than negative detection (hazard ratio (HR) = 1.9, 95% confidence interval (CI) = 1.56-2.39; P < 0.0001). Matched tumor-CSF analysis characterized the CSF private molecular features causing poor survival (HR = 1.64, 95% CI = 1.15-2.32, P = 0.006). A multimetric CSF ctDNA prognostic model integrating CSF ctDNA features and clinical factors was developed for risk-stratifying CNS metastases and validated in an independent cohort. Among patients with treatment histories available, those positive for a driver alteration by CSF ctDNA showed a survival benefit from CSF-matched therapy (HR = 0.78, 95% CI = 0.65-0.92, P = 0.003). Longitudinal monitoring by CSF identified CNS-specific resistant mechanisms and a second matched targeted therapy indicating improved survival (HR = 0.56, 95% CI = 0.35-0.91, P = 0.018). These findings support the clinical value of CSF ctDNA for risk-stratifying CNS metastases and guiding therapy.

Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection

Genomic analyses of cell-free DNA (cfDNA) in plasma are enabling noninvasive blood-based biomarker approaches to cancer detection and disease monitoring. Current approaches for identification of circulating tumour DNA typically use targeted tumour-specific mutations or methylation analyses. An emerging approach is based on the recognition of altered genome-wide cfDNA fragmentation in patients with cancer. Recent studies have revealed a multitude of characteristics that can affect the compendium of cfDNA fragments across the genome, collectively called the 'cfDNA fragmentome'. These changes result from genomic, epigenomic, transcriptomic and chromatin states of an individual and affect the size, position, coverage, mutation, structural and methylation characteristics of cfDNA. Identifying and monitoring these changes has the potential to improve early detection of cancer, especially using highly sensitive multi-feature machine learning approaches that would be amenable to broad use in populations at increased risk. This Review highlights the rapidly evolving field of genome-wide analyses of cfDNA characteristics, their comparison to existing cfDNA methods, and recent related innovations at the intersection of large-scale sequencing and artificial intelligence. As the breadth of clinical applications of cfDNA fragmentome methods have enormous public health implications for cancer screening and personalized approaches for clinical management of patients with cancer, we outline the challenges and opportunities ahead.

Salivary biomarkers: a promising approach for predicting immunotherapy response in head and neck cancers

Head and neck cancers, including cancers of the mouth, throat, voice box, salivary glands, and nose, are a significant global health issue. Radiotherapy and surgery are commonly used treatments. However, due to treatment resistance and disease recurrence, new approaches such as immunotherapy are being explored. Immune checkpoint inhibitors (ICIs) have shown promise, but patient responses vary, necessitating predictive markers to guide appropriate treatment selection. This study investigates the potential of non-invasive biomarkers found in saliva, oral rinses, and tumor-derived exosomes to predict ICI response in head and neck cancer patients. The tumor microenvironment significantly impacts immunotherapy efficacy. Oral biomarkers can provide valuable information on composition, such as immune cell presence and checkpoint expression. Elevated tumor mutation load is also associated with heightened immunogenicity and ICI responsiveness. Furthermore, the oral microbiota may influence treatment outcomes. Current research aims to identify predictive salivary biomarkers. Initial studies indicate that tumor-derived exosomes and miRNAs present in saliva could identify immunosuppressive pathways and predict ICI response. While tissue-based markers like PD-L1 have limitations, combining multiple oral fluid biomarkers could create a robust panel to guide treatment decisions and advance personalized immunotherapy for head and neck cancer patients.

Utilizing ctDNA to discover mechanisms of resistance to targeted therapies in patients with metastatic NSCLC: towards more informative trials

Advances in targeted therapies for patients with non-small-cell lung cancer have substantially improved the outcomes of those with actionable alterations in certain oncogenic driver genes. However, acquired resistance to these targeted therapies remains a major challenge. Understanding the mechanisms underlying acquired resistance will be crucial for the development of strategies that might either overcome this effect or delay the onset. Circulating tumour DNA, owing to the need for only minimally invasive sampling and a potential role as both a prognostic and predictive biomarker, is increasingly being used in both research and clinical practice. Several studies have explored the landscape of acquired resistance to targeted therapies using this approach. However, the methodologies of the published studies vary widely, and several major challenges remain in addressing the practical difficulties associated with these methods. These challenges currently limit the depth of research insight provided by the available data. In this Perspective, we review clinical reports describing the use of circulating tumour DNA to detect mechanisms of acquired resistance to targeted therapies, predominantly in patients with advanced-stage non-small-cell lung cancer, and highlight key unresolved questions with the aim of moving towards more-informative research studies.

Circulating tumor DNA in human papillomavirus-associated oropharyngeal cancer management: A systematic review

OBJECTIVE

Circulating tumor DNA (ctDNA) has emerged as a promising tool in the treatment of HPV-associated oropharyngeal squamous cell cancer (OPSCC). This systematic review sought to answer the question: what is the current role of ctDNA in the diagnosis, treatment, and surveillance of HPV-associated OPSCC?

DATA SOURCES

Medline (Ovid), Embase (Ovid), Scopus.

REVIEW METHODS

Original articles studying the role of ctDNA in the diagnosis or surveillance of HPV-associated OPSCC were eligible for inclusion. Two authors independently reviewed studies for inclusion and abstracted data, including study design, characterization of liquid biopsy technology, and diagnostic outcomes.

RESULTS

After a preliminary screening of 441 studies, 23 were selected for inclusion. Ten studies were conducted retrospectively, and 13 were conducted prospectively. In these studies, diagnostic testing included plasma-based droplet digital polymerase chain reaction (ddPCR, n = 13), quantitative PCR (qPCR, n = 4), digital PCR (dPCR, n = 3), next-generation sequencing (NGS) (n = 3), or a ctDNA detection kit (n = 1). Diagnostic outcomes were reported for pre-diagnosis (n = 1), pre-treatment (n = 17), during treatment (n = 6), and surveillance/recurrence (n = 11) timepoints. Test sensitivities ranged from 20.6 %-100 % pre-treatment and 72 %-100 % during surveillance, while test specificities ranged from 95 %-100 % pre-treatment and 87.2 %-100 % during surveillance.

CONCLUSION

The majority of studied ctDNA technologies allow for detection of HPV-associated OPSCC with high diagnostic accuracy. However, heterogeneity is introduced by test type and assay used. These findings highlight the utility, as well as limitations, of ctDNA in the diagnosis, treatment monitoring, and surveillance of HPV-associated OPSCC. Future studies and clinical consensus will need to address acceptable diagnostic accuracy thresholds for clinical use.

Personalized Tumor-Specific Amplified DNA Junctions in Peripheral Blood of Patients with High-Grade Gliomas

PURPOSE

Monitoring disease progression in patients with high-grade gliomas (HGG) is challenging due to treatment-related changes in imaging and the requirement for neurosurgical intervention to obtain diagnostic tissue. DNA junctions in HGG often amplify oncogenes, making these DNA fragments potentially more abundant in blood than monoallelic mutations. In this study, we piloted a cell-free DNA approach for disease detection in the plasma of patients with HGG by leveraging patient-specific DNA junctions associated with oncogene amplifications.

EXPERIMENTAL DESIGN

Whole-genome sequencing of grade 3 or 4 isocitrate dehydrogenase-mutant or wild-type astrocytomas was utilized to identify amplified junctions. Individualized qPCR assays were developed using patient-specific primers designed for the amplified junction. ctDNA levels containing these junctions were measured in patient plasma samples.

RESULTS

Unique amplified junctions were evaluated by individualized semi-qPCR assays in presurgical plasma of 18 patients, 15 with tumor-associated focal amplifications and three without tumor-associated focal amplifications. high copy-number junctions were robustly detected in the plasma of 14 of 15 (93.3%) patients with amplified junctions and none of the controls. Changes in junction abundance correlated with disease trajectory in serial plasma samples from five patients, including increased abundance of amplified junctions preceding radiographic disease progression.

CONCLUSIONS

In patients with grade 3 or 4 astrocytomas who had tumor-associated amplifications, patient-specific amplified junctions were successfully detected in assayed plasma from most patients. Longitudinal analysis of plasma samples correlated with disease trajectory, including cytoreduction and progression.

Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling

Differentiating sequencing errors from true variants is a central genomics challenge, calling for error suppression strategies that balance costs and sensitivity. For example, circulating cell-free DNA (ccfDNA) sequencing for cancer monitoring is limited by sparsity of circulating tumor DNA, abundance of genomic material in samples and preanalytical error rates. Whole-genome sequencing (WGS) can overcome the low abundance of ccfDNA by integrating signals across the mutation landscape, but higher costs limit its wide adoption. Here, we applied deep (~120×) lower-cost WGS (Ultima Genomics) for tumor-informed circulating tumor DNA detection within the part-per-million range. We further leveraged lower-cost sequencing by developing duplex error-corrected WGS of ccfDNA, achieving 7.7 × 10-7 error rates, allowing us to assess disease burden in individuals with melanoma and urothelial cancer without matched tumor sequencing. This error-corrected WGS approach will have broad applicability across genomics, allowing for accurate calling of low-abundance variants at efficient cost and enabling deeper mapping of somatic mosaicism as an emerging central aspect of aging and disease.

Performance Comparison of Droplet Digital PCR and Next-Generation Sequencing for Circulating Tumor DNA Detection in Non-Metastatic Rectal Cancer

BACKGROUND AND OBJECTIVES

Circulating tumor DNA (ctDNA) can potentially identify rectal cancer patients benefiting from neoadjuvant and adjuvant therapy. This study compared droplet digital PCR (ddPCR) and next-generation sequencing (NGS) for ctDNA detection in localized rectal cancer before and after surgery.

METHODS

Pre-therapy plasma and rectal tumor samples were collected from a development group (n = 41) and a validation group (n = 26). Mutations in tumor samples were identified using NGS, and ctDNA detection was performed with both ddPCR and NGS. Recurrence was assessed 1 year after surgery in the development group.

RESULTS

In the development group, ddPCR detected ctDNA in 24/41 (58.5%) and NGS panel in 15/41 (36.6%; p = 0.00075) of the baseline plasma. In the validation group, 21/26 (80.8%) patients had detectable ctDNA in the pre-therapy plasma. A positive ctDNA result was associated with higher clinical tumor stage and with lymph node positivity as detected by MRI. Postoperative ddPCR did not detect ctDNA before most recurrences.

CONCLUSIONS

We demonstrated a practical oligomarker ctDNA test for localized rectal cancer suitable for clinical workflow, and that ddPCR detects ctNA from pre-therapy plasma at a satisfactory level in advanced rectal cancers. Detecting ctDNA with ddPCR may help to assess the local severity, but the clinical utility of this approach should be evaluated in clinical trials.

Intra-clustering analysis reveals tissue-specific mutational patterns

BACKGROUND AND OBJECTIVE

The identification of tissue-specific mutational patterns associated with cancer is challenging due to the low frequency of certain mutations and the high variability among tumors within the same cancer type. To address the inter-tumoral heterogeneity issue, our study aims to uncover infrequent mutational patterns by proposing a novel intra-clustering analysis.

METHODS

A Network Graph of 8303 patients and 198 genes was constructed using single-point-mutation data from The Cancer Genome Atlas (TCGA). Patient-gene groups were retrieved with the parallel use of two separate methodologies based on the: (a) Barber's modularity index, and (b) network dynamics. An intra-clustering analysis was employed to explore the patterns within smaller patient subgroups in two phases: i) to determine the significant presence of a gene with a cancer type using the Fisher's exact test and ii) to determine gene-to-gene patterns using multiple correspondence analysis and DISCOVER. The results are followed by a Benjamini-Hochberg false discovery rate of 5%.

RESULTS

This analysis was applied over 24 statistically meaningful groups of 2619 patients spanning 21 cancer types and it recovered 42 mutational patterns that are not reported in the TCGA consortium publications. Notably, our findings: (i) suggest that AMER1 mutations are a putative separative element between colon and rectal adenocarcinomas, (ii) highlight the significant presence of RAC1 in head and neck squamous cell carcinoma (iii) suggest that EP300 mutations in head and neck squamous cell carcinoma are irrelevant of the HPV status of the patients and (iv) show that mutational-based clusters can contain patients with contrasting genetic alterations.

CONCLUSIONS

The proposed intra-clustering analysis extracted statistically significant relationships within clusters, uncovering putative clinically relevant connections and disentangling mutational heterogeneity.

Liquid biopsy in breast cancer: a practical guide for surgeons

Breast cancer remains a global health challenge, requiring innovative strategies for early detection, diagnosis, treatment monitoring, and recurrence detection. Liquid biopsy-leveraging circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), microRNAs (miRNAs), exosomes, immune-based biomarkers, and tumor-educated platelets (TEPs)-has emerged as a promising tool to address these needs. CTCs and ctDNA provide critical insights into tumor heterogeneity, therapeutic targets, and resistance mechanisms, while miRNAs, exosomes, and other non-CTC-based markers reflect the tumor microenvironment and offer potential biomarkers for disease progression. Importantly, liquid biopsy offers distinct advantages in early detection and precise diagnosis, as well as in identifying therapeutic resistance in real time, allowing clinicians to adapt treatment strategies effectively. The non-invasive nature of liquid biopsy further enables real-time tumor monitoring, paving the way for personalized treatment approaches. However, several challenges hinder its routine clinical adoption, including technical complexity, economic constraints, and variations in detection sensitivity due to low biomarker abundance. Additionally, a lack of standardization in methodology and interpretation limits its widespread application. Rigorous standardization and clinical validation are essential to address these barriers, ensuring equitable access across diverse healthcare settings and transforming breast cancer care for millions worldwide. Future directions include integrating artificial intelligence and multi-omic approaches to enhance diagnostic accuracy and clinical utility.

Liquid biopsies for the monitoring of gliomas and brain metastases in adults

Clinical evaluation and MR imaging are currently the cornerstone of brain tumor progression monitoring. However, this is complicated by the occurrence of treatment effects such as pseudoprogression and radionecrosis. While essential for patient management, the distinction from true progression remains a significant challenge. Moreover, MR imaging provides limited real-time insights into tumor heterogeneity, genetic divergence, and treatment resistance. Although surgical histopathological biopsies can yield additional valuable information, they are not always conclusive, invasive, and therefore, not suitable for longitudinal measurements. In the era of precision medicine, there is a critical need for minimally invasive, accurate, and cost-effective monitoring methods for both primary brain tumors and brain metastases. Liquid biopsies have emerged as a potential candidate. Various analytes, including circulating nucleic acids, extracellular vesicles, platelet RNAs, and circulating tumor cells, can be obtained from whole blood and its derivatives, as well as other body fluids such as cerebrospinal fluid. In this narrative review, we outline the potential of liquid biopsies for the management of gliomas and brain metastases in adults and emphasize their utility in monitoring disease progression and treatment response. We discuss the most studied biofluids and analytes, along with their respective advantages and downsides. Furthermore, we address key considerations for future research and biobanking to pave the way for clinical implementation.

Liquid biopsy in lung cancer

Precision medicine based on biomarkers, such as genetic abnormalities and PD-L1 expression, has been established for the treatment of nonsmall cell lung cancer. Recently, liquid biopsy has emerged as a valuable and minimally invasive alternative. This method analyzes blood and other bodily fluids to detect cancer-related genetic abnormalities and molecular residual disease (MRD). Liquid biopsy, which includes testing for circulating tumor cells, circulating tumor DNA (ctDNA), and microRNA (miRNA), offers several advantages over conventional methods. It is minimally invasive, can be performed repeatedly, and provides crucial information for early cancer diagnosis, genotyping, and treatment monitoring. Elevated ctDNA levels and miRNA markers show promise for early diagnosis. Liquid biopsy complements traditional tissue biopsy during genotyping, particularly when tumor samples are insufficient. Tests such as Cobas® EGFR Mutation Test v2 and Guardant360® CDx have been shown to be effective in detecting genetic mutations and guiding treatment decisions. Although the accuracy of liquid biopsy is still lower than that of tissue biopsy, its clinical utility continues to improve. For cancer prediction recurrence and treatment monitoring, ctDNA analysis can detect MRD earlier than conventional imaging, offering potential benefits for treatment adjustment and early relapse detection. The continuous development and validation of liquid biopsy methods are essential for improving personalized lung cancer treatment strategies.

Present progress in biomarker discovery of endometrial cancer by multi-omics approaches

Endometrial cancer (EC), a prevalent and intricate disease, is associated with a poor prognosis among gynecological malignancies. Its incidence rising globally underscores the urgent need for biomarkers detection in both research and clinical settings. Over the past decade, we've witnessed rapid advancements in biological methodologies and techniques. A multitude of omics technologies, encompassing genomic/transcriptomic sequencing and proteomic/metabolomic mass spectrometry, have been extensively employed to analyze both tissue and liquid samples derived from EC patients. The integration of multi-omics data has not only broadened our understanding of the disease but also unearthed valuable biomarkers specific to EC. This review encapsulates the recent progress and future prospects in the application of multi-omics technologies in EC research, emphasizing the potential of multi-omics in uncovering novel biomarkers and enhancing clinical assessments.

Liquid Biopsy as a New Tool for Diagnosis and Monitoring in Renal Cell Carcinoma

Renal cell carcinoma (RCC) presents a significant diagnostic challenge, particularly in small renal masses. The search for non-invasive screening methods and biomarkers has directed research toward liquid biopsy, which focuses on microRNAs (miRNAs), exosomes, and circulating tumor cells (CTCs). miRNAs are small non-coding RNA molecules that show considerable dysregulation in RCC, and they have potential for both diagnostic and prognostic applications. Research has highlighted their utility on biofluids, such as plasma, serum, and urine, in detecting RCC and characterizing its subtypes. Promising miRNA signatures have been associated with overall survival, suggesting their potential importance in the management of RCC. Exosomes, which carry a variety of molecular components, including miRNAs, are emerging as valuable biomarkers, whereas CTCs, released from primary tumors into the bloodstream, provide critical information on cancer progression. However, translation of these findings into clinical practice requires additional validation and standardization through large-scale studies and robust evidence. Although there are currently no approved diagnostic tests for RCC, the future potential of liquid biopsy in monitoring, treatment decision-making, and outcome prediction in patients with this disease is significant. This review examined and discussed recent developments in liquid biopsy for RCC, assessing both the strengths and limitations of these approaches for managing this disease.

Monitoring circulating tumor DNA by recurrent hotspot mutations in bladder cancer

BACKGROUND

Liquid biopsy can evaluate minimally residual disease. Hotspot mutations are also common in non-coding regions among the MIBC patients. We evaluated the status of MIBC with hotspot mutations with cfDNA.

METHODS

Tumor and blood from MIBC patients were collected prospectively. We evaluate the VAF of mutations (TERT, PLEKHS1, ADGRG6 and WDR74) with digital PCR in tumor and cfDNA as somatic mutation. We originally designed and validated primers and probes. VAF of cfDNA and clinical imaging were matched. This study was approved by the Institutional Review Board (#2022-157).

RESULT

37 MIBC patients were enrolled and 28 (76%) patients had any hotspot. Among the 21 patients of follow-up cohort, cfDNA predicted recurrence 58 days earlier than the diagnosis by CT scan. Furthermore, the detection of ctDNA at the first visit after radical cystectomy was associated with recurrence free survival (P = 0.0043) and overall survival (P = 0.017). The patient who received neoadjuvant chemotherapy (NAC) and diagnosed as ypT0 belonged to the nonrecurrence group with negative ctDNA.

CONCLUSION

Hotspot mutation is promising biomarker to predict earlier recurrence than CT-scan. Multiple detection of mutations in cfDNA contributes to reliable recurrence prediction.

Circulating tumor DNA strongly predicts efficacy of chemotherapy plus immune checkpoint inhibitors in patients with advanced gastro-esophageal adenocarcinoma

BACKGROUND

Efficacy of 2nd line treatment in advanced gastric or gastro-esophageal junction (GEJ) adenocarcinoma remains limited with no identified strong predictor of treatment efficacy. We evaluated the prognostic value of circulating tumor DNA (ctDNA) in predicting the efficacy of immune checkpoint inhibitors (ICI) plus chemotherapy in the randomized PRODIGE 59-FFCD 1707-DURIGAST trial.

METHODS

ctDNA was evaluated before treatment (baseline) and at 4 weeks (before the third cycle of treatment, C3) using droplet-digital PCR assays based on the detection of CpG methylation.

RESULTS

Progression-free survival (PFS) and overall survival (OS) were shorter in patients with a high (>1.1 ng/mL) versus low (<1.1 ng/mL) ctDNA concentration at baseline (2.3 vs. 5.8 months; HR = 2.19; 95% CI, 1.09-4.41; p = 0.03 and 4.5 vs. 12.9 months; HR = 2.73; 95% CI, 1.29-5.75; p < 0.01), respectively, after adjustment for identified prognostic variables. Patients with a ctDNA decrease ≤75% between baseline and C3 versus a ctDNA decrease >75% had a worse objective response rate (p = 0.007), shorter PFS (2.2 vs. 7.4 months, HR = 1.90; 95% CI, 1.03-3.51; p = 0.04) and OS (6.6 vs 16.0 months; HR = 2.18; 95% CI, 1.09-4.37; p = 0.03).

CONCLUSIONS

An early decrease in ctDNA concentration is a strong predictor of the therapeutic efficacy of ICI plus chemotherapy in advanced gastric/GEJ adenocarcinoma. Clinical Trial Information NCT03959293 (DURIGAST).

DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches

Breast cancer remains one of the most common cancers in women worldwide. Early detection is critical for improving patient outcomes, yet current screening methods have limitations. Therefore, there is a pressing need for more sensitive and specific approaches to detect breast cancer in its earliest stages. Liquid biopsy has emerged as a promising non-invasive method for early cancer detection and management. DNA methylation, an epigenetic alteration that often precedes genetic changes, has been observed in precancerous or early cancer stages, making it a valuable biomarker. This review explores the role of DNA methylation in breast cancer and its potential for developing blood-based tests. We discuss advancements in DNA methylation detection methods, recent discoveries of potential DNA methylation biomarkers from both single-omics and multi-omics integration studies, and the role of machine learning in enhancing diagnostic accuracy. Challenges and future directions are also addressed. Although challenges remain, advances in multi-omics integration and machine learning continue to enhance the clinical potential of methylation-based biomarkers. Ongoing research is crucial to further refine these approaches and improve early detection and patient outcomes.

Blood-based biomarkers in pancreatic ductal adenocarcinoma: developments over the last decade and what holds for the future- a review

Pancreatic Ductal Adenocarcinoma (PDAC) accounts for a significant burden of global cancer deaths worldwide. The dismal outcomes associated with PDAC can be overcome by detecting the disease early and developing tools that predict response to treatment, allowing the selection of the most optimal treatment. Over the last couple of years, significant progress has been made in the development of novel biomarkers that aid in diagnosis, prognosis, treatment selection, and monitoring response. Blood-based biomarkers offer an alternative to tissue-based diagnosis and offer immense potential in managing PDAC. In this review, we have discussed the advances in blood-based biomarkers in PDAC, such as DNA (mutations and methylations), RNA, protein biomarkers and circulating tumor cells (CTC) over the last decade and also elucidated all aspects of practical implementation of these biomarkers in clinical practice. We have also discussed implementing multiomics utilizing more than one biomarker and targeted therapies that have been developed using these biomarkers.

Next-generation sequencing in cancer diagnosis and treatment: clinical applications and future directions

Next-generation sequencing (NGS) has emerged as a pivotal technology in the field of oncology, transforming the approach to cancer diagnosis and treatment. This paper provides a comprehensive overview of the integration of NGS into clinical settings, emphasizing its significant contributions to precision medicine. NGS enables detailed genomic profiling of tumors, identifying genetic alterations that drive cancer progression and facilitating personalized treatment plans targeting specific mutations, thereby improving patient outcomes. This capability facilitates the development of personalized treatment plans targeting specific mutations, leading to improved patient outcomes and the potential for better prognosis. The application of NGS extends beyond identifying actionable mutations; it is instrumental in detecting hereditary cancer syndromes, thus aiding in early diagnosis and preventive strategies. Furthermore, NGS plays a crucial role in monitoring minimal residual disease, offering a sensitive method to detect cancer recurrence at an early stage. Its use in guiding immunotherapy by identifying biomarkers that predict response to treatment is also highlighted. Ethical issues related to genetic testing, such as concerns around patient consent and data privacy, are also important considerations that need to be addressed for the broader implementation of NGS. These include the complexities of data interpretation, the need for robust bioinformatics support, cost considerations, and ethical issues related to genetic testing. Addressing these challenges is essential for the widespread adoption of NGS. Looking forward, advancements such as single-cell sequencing and liquid biopsies promise to further enhance the precision of cancer diagnostics and treatment. This review emphasizes the transformative impact of NGS in oncology and advocates for its incorporation into routine clinical practice to promote molecularly driven cancer care.

Upfront liquid biopsy in patients with advanced solid tumors who were not feasible for tissue-based next-generation sequencing

BACKGROUND

Liquid biopsy has been developed as an alternative to tissue-based sequencing for detecting genomic alterations in solid tumors. However, the clinical utility of liquid biopsy in patients with solid tumors for whom tissue-based next-generation sequencing (NGS) is infeasible has not been well-characterized, particularly in previously untreated individuals.

METHODS

This prospective study evaluated the clinical impact of liquid biopsy, focusing on six solid tumor types. Overall, 109 patients were enrolled and underwent liquid biopsy using Guardant360 (Guardant Health, Redwood City, CA, USA). Among these, 94 (86.3%) patients were previously untreated.

RESULTS

The most common cancer type was non-small cell lung cancer (n = 57, 52.3%), followed by pancreatic (n = 35, 32.1%), biliary tract (n = 8, 7.3%), gastric (n = 5, 4.6%), colorectal (n = 3, 2.8%), and triple-negative breast (n = 1, 0.9%) cancers. The success rate of liquid biopsy was 99.1%, and the median turnaround time from blood collection to results was 7 days (range: 5-22 days). Actionable alterations were detected in 31 (28.4%) patients, and 8.3% of them received matched therapy based on alterations identified by liquid biopsy. Among previously untreated patients, actionable mutations were identified in 29.8%, and 8.5% received matched therapy.

CONCLUSIONS

In patients with advanced solid tumors for which tissue-based NGS is not feasible, performing upfront liquid biopsy could lead to the detection of actionable alterations and help guide targeted therapies.

CLINICAL TRIAL REGISTRY

UMIN Clinical Trials Registry (UMIN000041722).

Biological profile of breast cancer brain metastasis

Breast cancer is one of the leading causes of death worldwide. The aggressive behaviour of breast tumor results from their metastasis. Notably, the brain tissue is one of the common regions of metastasis, thereby reducing the overall survival of patients. Moreover, the metastatic tumors demonstrate poor response or resistance to therapies. In addition, breast cancer brain metastasis provides the poor prognosis of patients. Therefore, it is of importance to understand the mechanisms in breast cancer brain metastasis. Both cell lines and animal models have been developed for the evaluation of breast cancer brain metastasis. Moreover, different tumor microenvironment components and other factors such as lymphocytes and astrocytes can affect brain metastasis. The breast cancer cells can disrupt the blood-brain barrier (BBB) during their metastasis into brain, developing blood-tumor barrier to enhance carcinogenesis. The breast cancer brain metastasis can be increased by the dysregulation of chemokines, STAT3, Wnt, Notch and PI3K/Akt. On the other hand, the effective therapeutics have been developed for the brain metastasis such as introduction of nanoparticles. Moreover, the disruption of BBB by ultrasound can increase the entrance of bioactive compounds to the brain tissue. In order to improve specificity and selectivity, the nanoparticles for the delivery of therapeutics and crossing over BBB have been developed to suppress breast cancer brain metastasis.

Application of EGFR-TKIs in brain tumors, a breakthrough in future?

Brain tumors, both primary and secondary, represent a significant clinical challenge due to their high mortality and limited treatment options. Primary brain tumors, such as gliomas and meningiomas, and brain metastases from cancers such as non-small cell lung cancer and breast cancer require innovative therapeutic strategies. Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR -TKIs) have emerged as a promising treatment option, particularly for tumors harboring EGFR mutations. This review examines the use of EGFR-TKIs in brain tumors, highlighting both laboratory and clinical research findings. In primary brain tumors and brain metastases, EGFR-TKIs have shown potential in controlling tumor growth and improving patient outcomes. Advanced applications, such as nano-formulated EGFR-TKIs and combination therapies with other pathway inhibitors, are being investigated to improve efficacy and overcome resistance. Challenges such as treatment-related events, resistance mechanisms and blood-brain barrier penetration remain significant hurdles. Addressing tumor heterogeneity through personalized medicine approaches is critical to optimizing EGFR-TKI therapies. This review highlights the need for continued research to refine these therapies and improve survival for patients with brain tumors.

Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling

Shallow genome-wide cell-free DNA sequencing holds great promise for noninvasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single-nucleotide variations (SNVs) are, however, much harder to identify with low sequencing depth due to sequencing errors. Here, we present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which leverages RCA and consensus calling based on genome-wide long-read nanopore sequencing to enable simultaneous multimodal tumor fraction (TF) estimation through SNVs, CNAs, and fragmentomics. The efficacy of NanoRCS is tested on 18 cancer patient samples and seven healthy controls, demonstrating its ability to reliably detect TFs as low as 0.24%. In vitro experiments confirm that SNV measurements are essential for detecting TFs below 3%. NanoRCS provides an opportunity for cost-effective and rapid sample processing, which aligns well with clinical needs, particularly in settings where quick and accurate cancer monitoring is essential for personalized treatment strategies.

Liquid Biopsy as a Diagnostic and Monitoring Tool in Glioblastoma

Glioblastoma (GBM) is the most prevalent and aggressive primary central nervous system (CNS) tumor in adults. GBMs exhibit genetic and epigenetic heterogeneity, posing difficulties in surveillance and being associated with high rates of recurrence and mortality. Nevertheless, due to the high infiltrating ability of glioblastoma cells, and regardless of the considerable progress made in radiotherapeutic, chemotherapeutic, and surgical protocols, the treatment of GBM is still inefficient. Conventional diagnostic approaches, such as neuroimaging techniques and tissue biopsies, which are invasive maneuvers, present certain challenges and limitations in providing real-time information, and are incapable of differentiating pseudo-progression related to treatment from real tumor progression. Liquid biopsy, the analysis of biomarkers such as nucleic acids (DNA/RNA), circulating tumor cells (CTCs), extracellular vesicles (EVs), or tumor-educated platelets (TEPs) that are present in body fluids, provides a minimally invasive and dynamic method of diagnosis and continuous monitoring for GBM. It represents a new preferred approach that enables a superior manner to obtain data on possible tumor risk, prognosis, and recurrence assessment. This article is a literature review that aims to provide updated information about GBM biomarkers in body fluids and to analyze their clinical efficiency.