ESMO recommendations on the use of circulating tumour DNA assays for patients with cancer: a report from the ESMO Precision Medicine Working Group

Radiomic markers associated with clinical benefit in patients with radiographic progression of advanced uveal melanoma on tebentafusp

STUDY AIM

Tebentafusp, a bispecific fusion protein consisting of affinity-enhanced T cell receptor fused to anti-CD3 effector, has shown overall survival (OS) benefits across all RECIST response categories, including progressive disease (PD). In a phase 2 trial (NCT02570308) for advanced uveal melanoma (mUM), 35 % of PD patients experienced ≥ 0.5 log ctDNA reduction, resulting in a median overall survival (OS) of ∼17 months, compared to ∼8 months in the non-ctDNA reduction group.

METHODS

A total of 34 of 127 2L+ mUM patients with PD were split into two groups based on absence or presence of ctDNA reduction (≥0.5 log reduction). Lesions from CT and MRI scans were analyzed using radiomics features at baseline and week eight, yielding two machine-learning-derived patient signatures (16 features). Performance of per-patient analysis (n = 32) and per-lesion analysis (n = 148) was assessed using ROC AUC (95 % confidence interval [CI]).

RESULTS

In the per-patient analysis, a volumetric signature classified patients into groups with ROC AUC of 0.71 [0.53-0.90] with 63 % specificity and 81 % sensitivity at the optimal threshold (0.57). In the per-lesion analysis, a radiomic signature reached an ROC AUC of 0.70 [0.58-0.81] with 66 % specificity and 74 % sensitivity at the optimal threshold (0.53). Group B had lower baseline tumor lesion volume (ROC AUC=0.65), distinct baseline (ROC AUC=0.66), and change by week eight (ROC AUC=0.66/0.69 on CT/MRI) in tumor heterogeneity.

CONCLUSION

Radiomic analysis accurately predicted ctDNA reduction in PD patients at both the patient and lesion level. The most influential predictor was decreased tumor heterogeneity observed on CT/MRI.

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.

Discovery of mutations predictive of survival benefit from immunotherapy in first-line NSCLC: A retrospective machine learning study of IMpower150 liquid biopsy data

Predictive biomarker identification in cancer treatment has traditionally relied on pre-defined analyses, limiting discoveries to expected biomarkers and potentially overlooking novel ones predictive of therapy response. In this work, we develop a novel machine-learning approach capable of exploring full landscape of mutations and combinations and identify potentially new predictive biomarkers for chemoimmunotherapy. Utilizing the liquid biopsy dataset from 313 non-small cell lung cancer (NSCLC) patients in the Phase 3 Impower150 trial (NCT02366143), we developed the HRdiffRF algorithm with a novel hazard ratio-splitting criterion. Predictive mutations and combinations were identified for overall survival (OS) improvement with atezolizumab plus bevacizumab plus carboplatin and paclitaxel (ABCP) compared to bevacizumab plus carboplatin and paclitaxel (BCP). Our analysis confirms the predictive role of KRAS mutations and reveals the predictive value of PTPRD and SMARCA4 mutations in chemoimmunotherapy efficacy. Unlike other KRAS wild-type NSCLC patients, NSCLC patients with KRAS wild-type status and mutations in FAT1, ERBB2, or PTPRD may benefit from chemoimmunotherapy, while NTRK3 and GNAS mutations could negatively impact survival. Patients harboring concurrent KRAS and KEAP1 mutations may not benefit from chemoimmunotherapy. These findings highlight the complex genetic factors influencing treatment response for chemoimmunotherapy in NSCLC. In summary, the proposed machine-learning tool identified potential predictive biomarkers for first-line chemoimmunotherapy in NSCLC and can be readily applied to other tumor types and studies. It can also be extended to explore predictive biomarkers beyond mutations.

The biological and technical challenges facing utilizing circulating tumor DNA in non-metastatic breast cancer patients

Breast cancer is one of the most prevalent cancers and has emerged as a major global challenge. Circulating tumor DNA (ctDNA), a liquid biopsy method, overcomes the accessibility limitations of tissue-based testing and is widely used for monitoring minimal residual disease and molecular relapse, predicting prognosis, evaluating the response of neoadjuvant therapy, and optimizing treatment decisions in non-metastatic breast cancer. However, the application of ctDNA still faces many challenges. Here, we survey the clinical applications of ctDNA in non-metastatic breast cancer and discuss the significant biological and technical challenges of utilizing ctDNA. Importantly, we investigate potential avenues for addressing the challenges. In addition, emerging technologies, including fragmentomics detection, methylation sequencing, and long-read sequencing, have clinical potential and could be a future direction. Proper utilization of machine learning facilitates the identification of meaningful patterns from complex fragment and methylation profiles of ctDNA. There is still a lack of clinical trials focused on the subsets of ctDNA (e.g., circulating mitochondrial DNA), ctDNA-inferred drug-resistant clonal evolution, tumor heterogeneity, and ctDNA-guided clinical decision-making in non-metastatic breast cancer. Due to regional differences in the number of registered clinical trials, it is essential to enhance communication and foster global collaboration to advance the field.

Cell-Free DNA: Features and Attributes Shaping the Next Frontier in Liquid Biopsy

Cell-free DNA (cfDNA) is changing the face of liquid biopsy as a minimally invasive tool for disease detection and monitoring, with its main applications in oncology and prenatal testing, and rising roles in transplant patient monitoring. However, the processes of cfDNA biogenesis, fragmentation, and clearance are complex and require further investigation. Evidence suggests that cfDNA production relates to mechanisms of cell death and DNA repair, both of which further influence fragment size and its applicability as a biomarker. An emerging domain, cfDNA fragmentomics is being explored for advancing the field of diagnostics using non-mutational signatures such as fragment size ratios and methylation patterns. Thus, this review examines structural diversity in cfDNA with various fragment sizes. In examining these cfDNA subsets, we discuss their distinct biological origins and potential clinical utility. Development of sequencing methodologies has broadened the application of cfDNA in diagnosing cancers and organ-specific pathologies, as well as directing personalized therapies. This has been achieved by identifying and uncovering different subsets of cfDNA in biofluids using different methodologies and biofluids. Different cfDNA subsets provide important insights regarding genomic and epigenetic features, enhancing the understanding of gene regulation, tissue-specific functions, and disease progression. Advancement of these key areas further asserts increasing clinical relevance for the use of cfDNA as a biomarker. Continued exploration of cfDNA subsets is expected to drive further innovation in liquid biopsy and its integration into routine clinical practice.

Circulating tumour DNA and circulating tumour cells in bladder cancer - from discovery to clinical implementation

Liquid biopsies, indicating the sampling of body fluids rather than solid-tissue biopsies, have the potential to revolutionize cancer care through personalized, noninvasive disease detection and monitoring. Circulating tumour DNA (ctDNA) and circulating tumour cells (CTCs) are promising blood-based biomarkers in bladder cancer. Results from several studies have shown the clinical potential of ctDNA and CTCs in bladder cancer for prognostication, treatment-response monitoring, and early detection of minimal residual disease and disease recurrence. Following successful clinical trial evaluation, assessment of ctDNA and CTCs holds the potential to transform the therapeutic pathway for patients with bladder cancer - potentially in combination with the analysis of urinary tumour DNA - through tailored treatment guidance and optimized disease surveillance.

Fragmentomics profiling and quantification of plasma Epstein-Barr virus DNA enhance prediction of future nasopharyngeal carcinoma

Fragmentomics analysis of plasma autosomal DNA has shown promise in cancer diagnostics. Here we evaluated the clinical utility of plasma Epstein-Barr virus (EBV) DNA fragmentomics analysis for nasopharyngeal carcinoma (NPC) screening. Among our prospective cohort of approximately 20,000 subjects that underwent two rounds of screening, we analyzed the first-round blood samples of subjects who tested positive for EBV DNA via polymerase chain reaction (PCR) (n = 558). We found that those who subsequently developed NPC in the second round exhibited a distinctive mononucleosomal size pattern, an NPC-associated end motif (specifically, a depletion of CC-motif) and aberrations in methylation identified through fragmentomics-based methylation analysis (FRAGMA). Subjects with these aberrant fragmentomics features and higher quantity of EBV DNA had a relative risk of 87.1 times greater for developing NPC in the second round compared to subjects tested negative for EBV DNA on PCR. These results demonstrate plasma DNA fragmentomics could predict future cancer risk.

Liquid Biopsy in Solid Tumours: An Overview

The advent of personalised and precision medicine has radically modified the management and the clinical outcome of cancer patients. However, the expanding number of predictive, prognostic, and diagnostic biomarkers has raised the need for simple, noninvasive, quicker, but equally efficient tests for molecular profiling. In this complex scenario, the adoption of liquid biopsy, particularly circulating tumour DNA (ctDNA), has been a real godsend for many cancer patients who would otherwise have been denied the benefits of targeted treatments. Undeniably, ctDNA analysis has several advantages over conventional tissue-based analysis. One advantage is that it can guide treatment decision making, especially when tissue samples are scarce or totally unavailable. Indeed, a simple blood test can inform clinicians on patients' response or resistance to targeted therapies, help them monitor minimal residual disease (MRD) after surgical resections, and facilitate them with early cancer detection and interception. Finally, an equally important advantage is that ctDNA analysis can help decipher temporal and spatial tumour heterogeneity, a mechanism highly responsible for therapeutic resistance. In this review, we gathered and analysed current evidence on the clinical usefulness of ctDNA analysis in solid tumours.

Gene expression analysis in circulating tumour cells to determine resistance to CDK4/6 inhibitors plus endocrine therapy in HR + /HER2- metastatic breast cancer patients

BACKGROUND

Metastatic breast cancer (BC) is the main cause of cancer-related mortality in women worldwide. HR + /HER2- BC patients are treated with endocrine therapy (ET), but therapeutic resistance is common. The combination of cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) with ET was approved for metastatic BC patients and extended the median progression-free survival to 24 months. This therapy is not always effective, and in every patient, resistance ultimately occurs, but the underlying resistance mechanisms remain unclear. To address this gap, we explored circulating tumour cells (CTCs) as biomarkers to assess treatment response and resistance in metastatic HR + /HER2- BC patients receiving CDK4/6i plus ET.

METHODS

In total, 53 HR + /HER2- metastatic BC patients who received a CDK4/6i plus ET as first-line treatment were analysed, including samples from internal and external validation cohorts. CTCs were isolated using the negative enrichment approach RosetteSep (STEMCELL Technologies) or positive immunomagnetic selection targeting EpCAM, EGFR, and HER2 (AdnaTest EMT-2/StemCell Select™, QIAGEN). RNA was extracted from CTCs and PBMCs for nCounter analysis (Pancancer pathways panel) in a discovery phase. Subsequent validation was performed by RT-qPCR.

RESULTS

CTC gene expression analysis revealed that non responder patients (those who experienced disease progression before 180 days) exhibited elevated PRKCB (p-value: 0.011), MAPK3 (p-value: 0.006) and STAT3 (p-value: 0.008) expression, while responders showed increased CDK6 (p-value: 0.011) and CCND1 (p-value: 0.035) expression at baseline. CTC transcriptional characterization revealed a gene expression signature (STAT3highPRKCBhighCDK6low) that accurately classified HR + /HER2- metastatic BC patients who responded to CDK4/6i plus ET, regardless of the CTC isolation method (AUC > 0.8). CTC characterization at progression also identified biomarkers linked to therapy resistance, including the epigenetic regulators EZH2 and HDAC6 and the cell cycle regulator CDC7, which could guide the selection of subsequent therapy lines. The expression of the CDK4 and STAT3 genes in CTCs was associated with progression-free survival and overall survival, respectively. Likewise, the presence of ≥ one CTC after one cycle of therapy predicts a worse prognosis.

CONCLUSIONS

CTC gene expression provides information about treatment outcomes in HR + /HER2- metastatic BC patients receiving CDK4/6i plus ET and could guide personalized strategies and improve prognosis.

Circulating tumor DNA Clearance as a Predictive Biomarker of Pathologic Complete Response in Patients with Solid Tumors Treated with Neoadjuvant Immune-Checkpoint Inhibitors: a Systematic Review and Meta-Analysis

BACKGROUND

In patients with solid tumors undergoing neoadjuvant immune checkpoint inhibitor (ICI) therapy, identifying biomarkers to predict pathologic complete response (pCR) preoperatively could enhance treatment modulation. Circulating tumor DNA (ctDNA) clearance is a potential predictor of pCR, though its analytical and clinical validity has yet to be established. This systematic review and meta-analysis aims to assess the role of ctDNA clearance as a predictor of pCR in patients with solid tumors treated with neoadjuvant ICIs.

MATERIALS AND METHODS

A systematic search of PubMed, EMBASE and conference proceedings up to 5 August 2024 was carried out to identify phase 1b, 2 or 3 clinical trials investigating ctDNA clearance and pCR in patients with solid tumors and detectable ctDNA, undergoing neoadjuvant therapy with ICIs. Using a bivariate model, we estimated the pooled sensitivity and specificity of ctDNA clearance in predicting pCR, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and diagnostic odds ratio (DOR), with 95% Confidence Intervals (CI).

RESULTS

Thirteen trials involving 380 patients with detectable ctDNA at baseline were included. ctDNA was assessed with a tumor-informed approach in 11 (85%) trials. Overall, 38% of patients achieved pCR and 73% had ctDNA clearance before/at the surgery. Pooled sensitivity was 0.98 (95% CI: 0.86, 1.00), specificity was 0.53 (95% CI: 0.37, 0.69), PLR was 2.09 (95% CI: 1.48, 2.93), NLR was 0.04 (95% CI: 0.01, 0.26), DOR was 57.36 (95% CI: 8.12, 405.12). Significant heterogeneity was observed across studies (I2 ∼70% for all metrics), indicating considerable variability in the diagnostic performance.

CONCLUSION

The lack of ctDNA clearance may identify patients unlikely to have a pCR. Instead, the confirmatory power of ctDNA clearance is limited by low specificity and high heterogeneity due to the variability of the assays, and warrants further study. Therefore, clinicians should not rely on the use of ctDNA clearance to inform treatment decisions in the neoadjuvant setting.

Reporting of molecular test results from cell-free DNA analyses: expert consensus recommendations from the 2023 European Liquid Biopsy Society ctDNA Workshop

The implementation of circulating tumor DNA (ctDNA) in the diagnostic routine may enable non-invasive predictive biomarker testing and treatment optimization in patients who lack a suitable tumor specimen, have failed previous molecular analysis or are clinically ineligible for (re-)biopsy procedures. As the interpretation and reporting are more complex for ctDNA than conventional tissue-based NGS, there is a need for specific guidelines. These will offer support for the reporting of ctDNA test results and will facilitate optimal communication of liquid biopsy findings between diagnostic laboratories and the medical oncology team. Aiming to generate guidelines based on real-world experiences and broad perspectives, we organized a European Liquid Biopsy Society (ELBS) ctDNA workshop, in which forty-four experts and key stakeholders from different molecular diagnostics laboratories, oncology and pathology departments, as well as an IVDR specialist, convened to address significant challenges associated with the reporting of liquid biopsy test results. This report delineates the resulting consensus recommendations for ctDNA test reporting with underlying rationale and background information.

Benefits of Combining Circulating Tumor DNA With Tissue and Longitudinal Circulating Tumor DNA Genotyping in Advanced Solid Tumors: SCRUM-Japan MONSTAR-SCREEN-1 Study

PURPOSE

The utility of capturing heterogeneity by circulating tumor DNA (ctDNA) genotyping combined with tissue analysis or applying it in a sequential manner remains uncertain.

METHODS

We assessed the clinical value of ctDNA genotyping using data from 2,187 patients with advanced solid tumors enrolled in SCRUM-Japan MONSTAR-SCREEN-1, a nationwide cancer genome screening project, which examined ctDNA from longitudinally collected blood samples and tumor tissue samples (UMIN 000036749).

RESULTS

Among 667 patients with both baseline ctDNA and tissue genotyping results, 51 (7.6%) had actionable biomarkers identified exclusively through ctDNA genotyping. The most frequent targets of genotype-matched therapy guided by solely ctDNA were immune checkpoint, estrogen receptor, and poly(ADP-ribose) polymerase (PARP). Comparison of objective response rates (ORRs) and progression-free survival (PFS) between patients treated based on tissue versus ctDNA alone showed no significant difference, with ORRs of 34.0% versus 23.1% (P = .54) and a median PFS of 11.5 versus 13.8 months (hazard ratio [HR], 1.4 [95% CI, 0.72 to 2.80]), respectively. Among 924 patients undergoing sequential ctDNA genotyping, the detection of actionable biomarkers increased from 63.2% to 72.5% following subsequent ctDNA. Targets for genotype-matched therapy guided by subsequent ctDNA alone commonly included PARP, immune checkpoint, and BRAF. The ORR was 23.2% and 26.7% (P = .75), and the median PFS was 5.2 and. 3.7 months (HR, 1.5 [95% CI, 0.79 to 2.80]) for genotype-matched therapy based on initial versus subsequent ctDNA alone, respectively.

CONCLUSION

Combining ctDNA with tissue analysis, followed by sequential ctDNA assessments, effectively enhances the identification of actionable biomarkers. This strategy facilitates clinically beneficial, genetically informed therapies, underscoring its significant value in precision oncology.

LIBELULE: A Randomized Phase III Study to Evaluate the Clinical Relevance of Early Liquid Biopsy in Patients With Suspicious Metastatic Lung Cancer

OBJECTIVES

Genomic profiling is a major component for first-line treatment decisions in patients with NSCLC and the timeliness of biomarker testing is essential to improve time to treatment initiation (TTI) or avoid inappropriate treatment.

METHODS

The phase III LIquid Biopsy for the Early detection of LUng cancer Lesion trial (NCT03721120) included patients with radiological suspicion of advanced lung cancer. They were randomized (1:1), the control arm receiving diagnostic procedures according to each center's practice, and the liquid biopsy arm with additional testing performed at the first visit using the InVisionFirst-Lung assay. Treatment initiation and type were defined according to the European Society for Medical Oncology guidelines. Primary endpoint was the time from randomization to initiation of appropriate treatment on the basis of informative genomic and pathological results in the intention-to-treat population.

RESULTS

A total of 319 patients were enrolled (liquid biopsy [LB]: 161; control: 158). The median age was 68 years, 28.8% were non-smokers, 18.1% had a performance status of 2 or higher, and 56.7% had adenocarcinoma. In the LB arm, 81% of patients had circulating tumor DNA findings. The mean TTI was not significantly reduced (LB: 29.0 d; control 34 d (p = 0.26)). Sensitivity analyses found a shorter TTI in patients from the LB arm who received systemic treatment (LB: 29.1 d; control: 38.9 d, p = 0.01), in patients with advanced non-squamous NSCLC (LB: 29.5 d; control: 40.3 d, p = 0.01), and in patients with first-line targetable alterations (LB: 21d; control 37.4 d) (p = 0.004). Time to contributory genomic results was significantly reduced (LB: 17.9 d; control: 25.6 d, p < 0.001).

CONCLUSION

Early liquid biopsy testing did not significantly shorten the TTI in unselected patients referred for suspected advanced lung cancer. Nevertheless, it could reduce the TTI in patients eligible for systemic treatment, particularly for those with actionable alterations.

Japan society of clinical oncology position paper on appropriate clinical use of molecular residual disease (MRD) testing

Although the 5-year relative survival rates for resectable solid tumors have improved over the past few years, the risk of postoperative recurrence necessitates effective monitoring strategies. Recent advancements in molecular residual disease (MRD) testing based on circulating tumor DNA (ctDNA) analysis have shown considerable promise in the context of predicting recurrence; however, significant barriers to widespread clinical implementation remain-mainly, low awareness among healthcare professionals, high costs, and lack of standardized assays and comprehensive evidence. This position paper, led by the Japan Society of Clinical Oncology, aims to establish a common framework for the appropriate clinical use of MRD testing in a tumor type-agnostic manner. It synthesizes currently available evidence, reviews region-specific clinical trends, addresses critical clinical questions related to MRD testing, and offers recommendations to guide healthcare professionals, biotechnology and pharmaceutical companies, and regulatory authorities. These recommendations were developed based on a voting process involving 15 expert members, ensuring a consensus-driven approach. These findings underscore the importance of collaborative efforts among various stakeholders in enhancing the clinical utility of MRD testing. This project aimed to foster consensus and provide clear guidelines to support the advancement of precision medicine in oncology and improve patient outcomes in the context of perioperative care.

Prognostic value of assessing ctDNA in patients with endometrial carcinoma - an international multicenter study

OBJECTIVE

At present, no reliable blood-based biomarkers have been established for patients with endometrial cancer. Liquid biopsies, which can detect circulating tumor DNA (ctDNA), provide a non-invasive way to assess prognosis, monitor tumor evolution and treatment response. We aimed to examine the feasibility and performance of ctDNA as a prognostic tool in a multi-center cohort of EC patients with matched tumor samples.

METHODS

Blood plasma samples were collected preoperatively from 83 patients at three European cancer centers. Circulating cell-free DNA (cfDNA) was isolated and analyzed using the Oncomine™ Pan-Cancer cell-free assay. Tumor tissue from 56 of the 83 patients was subjected to whole-exome sequencing, and clinical data were collected for oncological outcome assessment.

RESULTS

The mean input of cfDNA was 8.17 ng (range 1.47-29.12 ng). Sixteen (19.3 %) patients were considered ctDNA positive with mutations in one or more genes. Most alterations detected in plasma were concordant with mutations found in the matched tumor for the paired cases. The preoperative presence of ctDNA was associated with a significantly higher rate of recurrence (37.5 % vs 11.9 %, P = 0.024). Although eight of the 14 (57 %) patients with recurrence were negative for ctDNA at diagnosis, positive ctDNA status remained an independent predictor of recurrence also when controlling for other known histopathologic risk factors (HR 5.49, 95 % CI 1.5-20, P = 0.010).

CONCLUSIONS

Our results demonstrated the feasibility of using an off-the-shelf gene panel to detect ctDNA in patients with endometrial cancer. ctDNA positivity was significantly associated with worse oncological outcomes.

Mutational profiling using liquid biopsy to guide targeted therapy in patients with metastatic cancer

Liquid biopsy gained significant interest in the area of cancer management. This study aims to evaluate the effectiveness of molecular testing using ctDNA (circulating tumor DNA) to; detect genetic alterations, screen for abnormalities, identify mutations associated with treatment sensitivity or resistance and guide therapy decision for several types of cancer in patients with metastasis. A total of 85 samples were collected from 74 patients recruited at our center, as part of their routine clinical follow-up. 17 different cancer types were analyzed. Genetic testing was conducted in patients with metastasis after failure of standard treatments. Sequencing was conducted in plasma-ctDNA samples; and when it was possible on the tumor tissue as well. Our analysis revealed that 88% (65 patients) of patients were eligible for treatment guidance using liquid biopsy. Among them, 64% (47 patients) received an FDA-approved drug, and treatment decisions were based on molecular testing using ctDNA. Somatic gene mutations were detected in 89% (66 patients) of the patients tested; 81% (60 patients) of patients had at least two mutations, 8% (6 patients) had only one mutation and 11% (8 patients) had no detected mutations. Interestingly, among the genes tested, BRCA2, EGFR, MSH6, and NF1 were the most frequently mutated in our patients. Our study highlights the potential benefits of personalized medicine through a non-invasive genetic testing across patients with metastasis regardless of the cancer types. Moreover, our study identified the frequent occurrence of specific gene mutations across various types of cancer, which paves the way for considering targeted therapies that could be applicable to multiple cancer types, rather than being restricted to just a few.

Circulating tumor DNA in endometrial cancer: clinical significance and implications

Circulating tumor DNA (ctDNA) is a promising non-invasive tool that has been demonstrated to be a clinically useful biomarker in several tumor types for risk stratification, prognosis, and early detection of recurrence. However, there are limited data on the clinical utility of ctDNA in endometrial cancer (EC) compared with other solid tumors. The evolution of EC management through the integration of molecular characterization into the treatment algorithm has intensified the need to develop more effective predictive biomarkers to optimize treatment and reduce clinical toxicities. Given its non-invasive nature and its ability to represent and complement tumor multiclonal spatial and temporal heterogeneity, ctDNA could act as a valid surrogate for tissue sampling. In addition to plasma ctDNA detection being associated with clinicopathologic features of tumor aggressiveness at pre-operative assessment, an association with reduced disease-free survival and overall survival has been observed in patients with detectable ctDNA. Moreover, the half-life of ctDNA is significantly shorter than CA125, and plasma levels are reported to be completely cleared from the blood within 1 week from surgical debulking. Therefore, ctDNA may serve as a dynamic biomarker for occult microscopic residual disease when assessed within the first 4 to 8 weeks after eradicative surgery. Few studies have reported high sensitivity of ctDNA in detecting disease recurrence at longitudinal follow-up, although there are limited data comparing ctDNA and traditional serum biomarkers (CA125 and HE4) in identifying recurrence. In the perspective of personalized oncology, ctDNA may potentially help improve adjuvant therapeutic management by escalating/de-escalating treatment based on ctDNA detection after surgery, during maintenance, or in the recurrent/metastatic setting, in addition to acting as a sensitive biomarker for early detection of recurrence. Several challenges hinder the use of ctDNA in EC, including the lack of standardized protocols, the low mutational burden, tumor heterogeneity, and background normal DNA, which limit assay sensitivity and specificity. In addition, the high cost of ctDNA analysis, particularly, next-generation sequencing, restricts its accessibility. Future trials should focus on cost-effective approaches to ensure sustainability and efficient resource allocation.

The Role of ctDNA for Diagnosis and Histological Prediction in Early Stage Non-Small-Cell Lung Cancer: A Narrative Review

Background: Circulating tumor DNA (ctDNA) may be released from neoplastic cells into biological fluids through apoptosis, necrosis, or active release. In patients with non-small-cell lung cancer (NSCLC), ctDNA analysis is being introduced in clinical practice only for advanced disease management. Nevertheless, an interesting and promising field of application is the analysis of ctDNA in the management of early stage non-small-cell lung cancer, both for evaluation before treatment, such as diagnosis and screening, and for prediction of histology or pathological features. Methods: A thorough review of the literature published between 2000 and 2024 was performed on PubMed, utilizing the advanced search feature to narrow down titles and abstracts containing the following keywords: ctDNA, early stage, and NSCLC. A total of 20 studies that met all inclusion criteria were chosen for this review. Results: In this review, we summarize the increasing evidence suggesting that ctDNA has potential clinical applications in the management of patients with early stage NSCLC. ctDNA levels in early stage cancers are very low, posing many technical challenges in improving the detection rate and sensitivity, especially in clinical practice, if it is to be implemented for early detection. Presently, the main limitation of ctDNA experimental and clinical studies, especially in early stage settings, is the lack of definitive standardization and consensus regarding methodology, the absence of systematically validated analyses, and the lack of adoption of sensitive approaches. Conclusions: Possible applications of this analyte open up new fields of diagnosis, treatment, and follow up, which are less invasive and more precise than other approaches currently in use, especially in early stage NSCLC patients.

Liquid biopsy for guiding breast cancer immunotherapy

Liquid biopsy is a laboratory test used to detect and analyze circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and other tumor-derived components, in a blood sample. In the context of breast cancer (BC), liquid biopsies hold significant promise for guiding the use of immune checkpoint inhibitors and immune-based combinations, offering real-time insights into tumor dynamics, treatment response, and resistance mechanisms. This review explores the role of liquid biopsy in BC immunotherapy, focusing on its applications, benefits, issues, and current and future research directions.

The prospects and limitations of liquid biopsy utilization for clinical practice in Taiwan

Objective

Liquid biopsy is a promising, non-invasive diagnostic tool for cancer, offering rapid and cost-effective genomic analysis. It provides a less invasive alternative to traditional tissue biopsies, with potential benefits in monitoring disease progression and detecting minimal residual disease (MRD). However, its clinical integration faces challenges, including utility assessment and workflow adaptation. This study evaluates the value of liquid biopsy in Taiwan from a clinical physician's perspective.

Methods

A survey was conducted with 16 physicians specializing in thoracic medicine and hematologic oncology. Participants responded to a 5-point Likert scale to evaluate the timing of liquid biopsy adoption, willingness to incorporate it into clinical practice, and agreement on its role in managing specific clinical conditions.

Results

Forty percent of physicians preferred liquid biopsy when tissue samples were unavailable. The inclusion of liquid biopsy under National Health Insurance (NHI) was a key factor in its adoption. Hematologic oncologists showed a stronger preference for liquid biopsy, particularly for MRD testing, compared to their counterparts in thoracic medicine (hematologic oncology vs. thoracic medicine: 4.2 ± 0.83 vs. 3.1 ± 0.60; p value = 0.01). Younger physicians valued turnaround time, while senior physicians prioritized test brand, with a focus on report speed.

Conclusion

Physicians are generally less inclined to replace tissue biopsies with liquid biopsy, but hematologic oncologists show more flexibility. Test brand plays a role in physician decision-making, and the inclusion of liquid biopsy under NHI coverage is vital for its broader adoption in Taiwan.

Clinical Utility of Combined Tissue and Plasma Next-Generation Sequencing in Patients With Advanced, Treatment-Naïve NSCLC

Introduction

Tissue and plasma-based next-generation sequencing (NGS) have complementary roles in patients with advanced NSCLC. Nevertheless, whether there is any added clinical value in combining both methods in the treatment of naïve patients remains unclear.

Methods

We retrospectively collected clinical and genomic data from 275 patients with treatment-naïve advanced NSCLC who had undergone plasma-based NGS at diagnosis in our institution. We analyzed patient data in two separate cohorts, each assessed with a different plasma-based NGS method: cohort 1 (n = 127, Guardant360), and cohort 2 (n = 148, FoundationACT/FoundationOne Liquid CDx). Ninety-five patients (75%) in cohort 1 and 108 patients (73%) in cohort 2 underwent concurrent amplicon-based tissue NGS testing locally.

Results

Forty-three patients in cohort 1 (34%) and 49 patients in cohort 2 (33%) harbored European Society for Medical Oncology Scale for Clinical Actionability of Molecular Targets (ESCAT) I or II targetable driver alterations. The addition of orthogonal biopsy (tissue to liquid, or liquid to tissue) offered no relevant clinical value in cases with ESCAT I or II targetable drivers already detected by one method. In contrast, adding orthogonal biopsy incremented the detection of ESCAT I or II targetable drivers not only in cases with uninformative testing (undetectable circulating tumor DNA, unavailable/inadequate tissue) but also in about 5% of the patients with seemingly informative but driver undetected molecular results. The prevalence of ESCAT I or II targetable drivers in plasma was significantly higher in patients with adenocarcinoma, 20 pack-year or less smoking history, and abdominal metastases.

Conclusions

Our study suggests that the addition of sequential orthogonal biopsy should be considered whenever an ESCAT I or II targetable driver has not been detected by the initial method, including cases with seemingly informative molecular analysis.

Establishing a Common Lexicon for Circulating Tumor DNA Analysis and Molecular Residual Disease: Insights From the BLOODPAC Consortium

The use of a liquid biopsy to assess molecular residual disease (MRD) of solid tumors holds significant promise for improving outcomes for patients with cancer. Liquid biopsies are a minimally invasive approach for the identification of circulating tumor biomarkers through a simple blood sample. Assays capable of detecting MRD through analysis of circulating tumor DNA (ctDNA) are rapidly evolving for clinical study applications and therapeutic interventions. To address these opportunities, BLOODPAC-a multi-disciplinary consortium representing stakeholders from public, industry, academia, and regulatory agencies-formulated a lexicon that provides a shared framework and clear definitions using liquid biopsies for solid tumor MRD with an emphasis on ctDNA detection. The terms in the lexicon are categorized under general MRD, ctDNA testing methodologies, reporting results, and acquisition timepoints, including examples of current and potential clinical use cases for MRD tests. The overall goal is to provide a unified language and approaches to solid tumor MRD to advance applications of these technologies, allow data aggregation to strengthen future evidence, and facilitate regulatory approvals, leading to the use of liquid biopsy as an early endpoint in clinical trials. We believe that a common set of terminology and methods for solid tumor MRD can improve understanding and appropriate use of testing, accelerate clinical development, and improve outcomes for cancer patients.

Cell-free tumor DNA analysis in advanced or metastatic breast cancer patients: mutation frequencies, testing intention, and clinical impact

Background

Circulating cell-free tumor DNA (ctDNA) provides a non-invasive approach for assessing somatic alterations. The German PRAEGNANT registry study aims to explore molecular biomarkers and investigate their integration into clinical practice. In this context, ctDNA testing was included to understand the motivations of clinicians to initiate testing, to identify somatic alterations, and to assess the clinical impact of the results obtained.

Methods

Patients with advanced/metastatic breast cancer were prospectively enrolled in the Prospective Academic Translational Research Network for the Optimization of Oncological Health Care Quality in the Adjuvant and Advanced/Metastatic Setting (PRAEGNANT study; NCT02338167). The FDA-approved and CE-marked GUARDANT360 CDx test was used to assess somatic alterations. A ctDNA-analysis report was provided to the treating physician along with a questionnaire about the intent for testing and the clinical implications of test results.

Results

ctDNA from 49 patients was analyzed prospectively: 37 (76%) had at least one somatic alteration in the analyzed geneset; 14 patients (29%) harbored alterations in TP53, 12 (24%) in PIK3CA, and 6 (12%) in ESR1. Somatic mutations in BRCA1 or BRCA2 were detected in 3 (6%) and 4 (8%) patients, respectively, and 59% of patients had hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer. Questionnaires regarding test intentions and clinical impact were completed for 48 (98%) patients. These showed that ctDNA testing influenced treatment decisions for 35% of patients.

Discussion

The high prevalence of somatic alterations in TP53, PIK3CA, ESR1, and BRCA1/2 genes, identified by ctDNA genotyping, highlights their potential as biomarkers for targeted therapies. Detection of specific mutations affected treatment decisions, such as eligibility for alpelisib, and might further facilitate treatment with e.g. elacestrant or capiversatib in future treatment lines.

New systemic treatment paradigms in advanced biliary tract cancer and variations in patient access across Europe

In recent years, treatment options for patients with advanced biliary tract cancer (BTC) have increased significantly due to the positive results from phase 2/3 clinical trials of immune checkpoint inhibitors, combined with chemotherapy, and molecularly targeted agents. These advances have led to the need for molecular testing to identify actionable alterations and patients amenable to targeted therapies. However, these improvements have brought with them many questions and challenges, including the identification of resistance mechanisms and therapeutic sequences. In this Series paper we aim to provide an overview of the current systemic treatment options for patients with BTC, highlighting disparities in access to innovative treatments and molecular testing across European countries, which lead to inequalities in the possibilities of treating patients with advanced BTC. We also discuss how ongoing European collaborative projects, such as the COST Action Precision-BTC-Network CA22125, supported by COST (European Cooperation in Science and Technology), linked to the European Network for the Study of Cholangiocarcinoma (ENSCCA), can help overcome these disparities and improve the current scenario.

Complications, Costs, and Health Care Resource Use with Tissue Biopsy Followed by Liquid Biopsy Versus Tissue Re-biopsy in Patients With Newly Diagnosed Metastatic Nonsmall-cell Lung Cancer

OBJECTIVES

We compared complications, costs, and health care resource utilization (HCRU) of patients with newly diagnosed metastatic nonsmall-cell lung cancer (mNSCLC) who had a tissue biopsy followed by either liquid biopsy (TFLB) (identified with a novel algorithm) or tissue re-biopsy (TRB).

METHODS

This claims-based retrospective analysis included commercial and Medicare Advantage members in the Optum Research Database with mNSCLC (January 2017 to June 2021) and ≥2 tissue biopsy claims (7 to 90 d apart) (TRB) or ≥1 tissue and ≥1 liquid biopsy claim within 90 days (TFLB). Patients in the TFLB group were matched 1:1 to patients in the TRB group using propensity score matching. Surgical biopsy-related complications and complication-related and all-cause medical costs and HCRU during the 6-month follow-up were compared.

RESULTS

Both groups had 235 patients post-match. During the follow-up, the surgical biopsy-related complication rate was lower in the TFLB group than the TRB group (65.1% [153/235] vs. 84.7% [199/235], P <0.001). Mean complication-related medical costs were significantly lower with TFLB ($8494 vs. $19,741, P <0.001) during the follow-up; mean (SD) duration of complication-related inpatient stays was significantly lower with TFLB (3.5 [7.0] vs. 6.6 [13.3] d, P =0.002). Mean all-cause medical costs were not significantly different between the groups; the TFLB group had fewer all-cause inpatient stays, inpatient days, and outpatient visits.

CONCLUSIONS

Multiple tissue biopsy procedures may be associated with significantly higher biopsy complication rates, higher complication-related medical costs, and longer complication-related inpatient stays than TFLB. All-cause medical costs were similar between groups.

Circulating tumour DNA in early stage and locally advanced NSCLC: ready for clinical implementation?

Circulating tumour DNA (ctDNA) can be released by cancer cells into biological fluids through apoptosis, necrosis or active release. In patients with non-small-cell lung cancer (NSCLC), ctDNA levels correlate with clinical and pathological factors, including histology, tumour size and proliferative status. Currently, ctDNA analysis is recommended for molecular profiling in patients with advanced-stage NSCLC. In this Review, we summarize the increasing evidence suggesting that ctDNA has potential clinical applications in the management of patients with early stage and locally advanced NSCLC. In those with early stage NSCLC, detection of ctDNA before and/or after surgery is associated with a greater risk of disease recurrence. Longitudinal monitoring after surgery can further increase the prognostic value of ctDNA testing and enables detection of disease recurrence earlier than the assessment of clinical or radiological progression. In patients with locally advanced NSCLC, the detection of ctDNA after chemoradiotherapy is also associated with a greater risk of disease progression. Owing to the limited number of patients enrolled and the different technologies used for ctDNA testing in most of the clinical studies performed thus far, their results are not sufficient to currently support the routine clinical use of ctDNA monitoring in patients with early stage or locally advanced NSCLC. Therefore, we discuss the need for interventional studies to provide evidence for implementing ctDNA testing in this setting.

Current Status of Staging and Restaging Malignant Pleural Mesothelioma

Malignant pleural mesothelioma (MPM) is the most frequent aggressive tumor affecting the pleura, accounting for over 38,000 deaths worldwide. It originates from the mesothelial cells and is mostly associated to asbestos exposure. Depending on the extent of the disease, the management of MPM varies from surgical intervention to a combination of systemic chemotherapy, immunotherapy, and radiation therapy. Major International scientific societies provide continuous updates on proper management of the disease, including recommendations on the optimal imaging algorithms, which are crucial for determining effective treatment options and optimizing clinical outcomes. However, despite the continuous efforts to improve patients' prognosis, median overall survival remains poor, ranging from 8 to 14 months. And even in case of initial response to treatment, local or distant recurrences represent almost a certainty, requiring appropriate imaging for the assessment of tumor sites. The aim of the present article is to illustrate the current status of imaging for staging and restaging of MPM, not forgetting most recent novelties in the diagnostic work-up of the disease.

Drug Resistance in Late-Stage Epidermal Growth Factor Receptor (EGFR)-Mutant Non-Small Cell Lung Cancer Patients After First-Line Treatment with Tyrosine Kinase Inhibitors

The development of tyrosine kinase inhibitors (TKIs) for late-stage epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) represented a drastic change in the treatment of late-stage lung cancer. Drug resistance develops after a certain period of first-line TKI treatment, which has led to decades of changing treatment guidelines for EGFR-mutant NSCLC. This study discussed the potential mechanisms of drug resistance against first-line TKI treatment and potential successive treatment strategies. Next-generation sequencing (NGS) may play a role in the evaluation of drug resistance in first-line TKI treatment. Emerging combination regimens and ongoing trials were discussed. Potential future strategies for treatment and for the management of drug resistance were proposed in this study.

Enhanced detection of actionable mutations in NSCLC through pleural effusion cell-free DNA sequencing: A prospective study

BACKGROUND

Inadequate tumour samples often hinder molecular testing in non-small cell lung cancer (NSCLC). Plasma-based cell-free DNA (cfDNA) sequencing has shown promise in bypassing these tissue limitations. Nevertheless, pleural effusion (PE) samples may offer a richer cfDNA source for mutation detection in patients with malignant PE.

METHODS

This prospective study enrolled newly diagnosed advanced NSCLC patients with malignant PE. PE samples were collected for cfDNA NGS analysis. Meanwhile, PE cell pellet RNA was extracted for reverse transcription polymerase chain reaction (RT-PCR) for clinically relevant actionable mutations and then confirmed by Sanger sequencing. The concordance between PE cell pellet RT-PCR and PE cfDNA NGS analyses was analysed.

RESULTS

Fifty patients were enrolled. The median age was 68.5 years, and the female-to-male ratio was 29:21. Most patients (74 %) were non-smokers. Notably, 45/50 patients (90 %) had actionable mutations, including EGFR exon 19 deletions (24 %), EGFR L858R mutations (36 %), HER2 exon20 insertions (10 %), ROS1 rearrangements (4 %), EGFR exon20 insertions (2 %), ALK rearrangements (4 %), RET rearrangements (2 %), KRAS G12C mutations (2 %), and CD74-NRG1 fusions (2 %). Among the 50 enrolled patients, actionable mutations were detected in 44 (88 %) by PE cfDNA NGS, 39 (78 %) by PE cell pellet Sanger sequencing, and 33 (66 %) by clinical tissue genetic testing (P = 0.031). The detection of actionable mutations from PE cfDNA NGS remained consistently high across M1a to M1c stages.

CONCLUSIONS

PE cfDNA genotyping has clinical applicability for NSCLC patients and can serve as an additional source for molecular testing. Incorporating PE NGS cfDNA analysis into genetic testing enhances diagnostic yield and aids in identifying actionable mutations in clinical practice.

Homologous recombination deficiency (HRD) testing landscape: clinical applications and technical validation for routine diagnostics

The use of poly(ADP-ribose) polymerase inhibitors (PARPi) revolutionized the treatment of BRCA-mutated cancers. Identifying patients exhibiting homologous recombination deficiency (HRD) has been proved useful to predict PARPi efficacy. However, obtaining HRD status remains an arduous task due to its evolution over the time. This causes HRD status to become obsolete when obtained from genomic scars, rendering PARPi ineffective for these patients. Only two HRD tests are currently FDA-approved, both based on genomic scars detection and BRCA mutations testing. Nevertheless, new technologies for obtaining an increasingly reliable HRD status continue to evolve. Application of these tests in clinical practice is an additional challenge due to the need for lower costs and shorter time to results delay.In this review, we describe the currently available methods for HRD testing, including the methodologies and corresponding tests for assessing HRD status, and discuss the clinical routine application of these tests and their technical validation.

Polymerase Chain Reaction Chips for Biomarker Discovery and Validation in Drug Development

Polymerase chain reaction (PCR) chips are advanced, microfluidic platforms that have revolutionized biomarker discovery and validation because of their high sensitivity, specificity, and throughput levels. These chips miniaturize traditional PCR processes for the speed and precision of nucleic acid biomarker detection relevant to advancing drug development. Biomarkers, which are useful in helping to explain disease mechanisms, patient stratification, and therapeutic monitoring, are hard to identify and validate due to the complexity of biological systems and the limitations of traditional techniques. The challenges to which PCR chips respond include high-throughput capabilities coupled with real-time quantitative analysis, enabling researchers to identify novel biomarkers with greater accuracy and reproducibility. More recent design improvements of PCR chips have further expanded their functionality to also include digital and multiplex PCR technologies. Digital PCR chips are ideal for quantifying rare biomarkers, which is essential in oncology and infectious disease research. In contrast, multiplex PCR chips enable simultaneous analysis of multiple targets, therefore simplifying biomarker validation. Furthermore, single-cell PCR chips have made it possible to detect biomarkers at unprecedented resolution, hence revealing heterogeneity within cell populations. PCR chips are transforming drug development, enabling target identification, patient stratification, and therapeutic efficacy assessment. They play a major role in the development of companion diagnostics and, therefore, pave the way for personalized medicine, ensuring that the right patient receives the right treatment. While this tremendously promising technology has exhibited many challenges regarding its scalability, integration with other omics technologies, and conformity with regulatory requirements, many still prevail. Future breakthroughs in chip manufacturing, the integration of artificial intelligence, and multi-omics applications will further expand PCR chip capabilities. PCR chips will not only be important for the acceleration of drug discovery and development but also in raising the bar in improving patient outcomes and, hence, global health care as these technologies continue to mature.

Advancements in non-invasive diagnosis of gastric cancer

Gastric cancer (GC), a multifaceted and highly aggressive malignancy, represents challenging healthcare burdens globally, with a high incidence and mortality rate. Although endoscopy, combined with histological examination, is the gold standard for GC diagnosis, its high cost, invasiveness, and specialized requirements hinder widespread use for screening. With the emergence of innovative technologies such as advanced imaging, liquid biopsy, and breath tests, the landscape of GC diagnosis is poised for radical transformation, becoming more accessible, less invasive, and more efficient. As the non-invasive diagnostic techniques continue to advance and undergo rigorous clinical validation, they hold the promise of significantly impacting patient outcomes, ultimately leading to better treatment results and improved quality of life for patients with GC.

Molecular testing of lung cancer in Australia: consensus best practice recommendations from the Royal College of Pathologists of Australasia in collaboration with the Thoracic Oncology Group of Australasia

Molecular testing plays a critical role in guiding optimal treatment decisions for lung cancer patients across a variety of clinical settings. While guidelines for biomarker testing exist in other jurisdictions, to date no best practice guidelines have been developed for the Australian setting. To address this need, the Royal College of Pathologists of Australasia collaborated with the Thoracic Oncology Group of Australasia to identify state-based pathologists, oncologists and consumer representatives to develop consensus best practice recommendations. Sixteen recommendations were established encompassing appropriate biomarkers, lung cancer subtype, tumour stage, specimen types, assay selection and quality assurance protocols that can inform and standardise best practice in molecular testing of lung cancer. These multidisciplinary evidence-based recommendations are designed to standardise and enhance molecular testing practices for lung cancers and should help ensure laboratories provide high-quality molecular testing of lung cancer for all Australians, including those from regional or remote communities.

A scoping review of factors influencing the implementation of liquid biopsy for cancer care

BACKGROUND

Liquid biopsy (LB) offers a promising, minimally invasive alternative to traditional tissue biopsies in cancer care, enabling real-time monitoring and personalized treatment. Despite its potential, the routine implementation of LB in clinical practice faces significant challenges. This scoping review examines the barriers and facilitators influencing the implementation of liquid biopsies into standard cancer care.

METHODS

Four academic databases (PubMed, Scopus, Embase, and Web of Science) were systematically searched without language restrictions. We included peer-reviewed articles that were published between January 2019 and March 2024 that focused on the implementation of LB in cancer care or described barriers and facilitators to its implementation. Data relevant to the review objective, including key article characteristics; barriers and facilitators of implementation; and recommendations for advancement or optimisation; were extracted and analysed using thematic and visual network analyses.

RESULTS

The majority of the included articles were narrative review articles (84%), with most from China (24.2%) and the United States (20%). Thematic analysis identified four main categories and their associated barriers and facilitators to the implementation of LB in cancer care: (1) Laboratory and personnel requirements; (2) Disease specificity; (3) Biomarker-based liquid biopsy; and (4) Policy and regulation. The majority of barriers identified were concentrated in the pre-analytical phase, highlighting the lack of standardization in LB technologies and outcomes.

CONCLUSIONS

Through a thematic analysis of the barriers and facilitators to LB implementation, we present an integrated tool designed to encourage the standardization of testing methods for clinical practice guidelines in the field.

Advances in liquid biopsy: From exploration to practical application

Liquid biopsy has received tremendous attention as a non-invasive approach for detecting and tracking cancer. Here, we discuss the latest work on circulating tumor DNA and circulating tumor cells with respect to clinical applications, including cancer screening, early detection of relapse, real-time monitoring of therapeutic efficacy, and detection of therapeutic targets and resistance mechanisms.

Plasma ctDNA kinetics as a predictor of systemic therapy response for advanced non-small cell lung cancer: a systematic review and meta-analysis

BACKGROUND

Predicting early treatment response in advanced non-small cell lung cancer (NSCLC) is challenging. Longitudinal monitoring of circulating tumor DNA (ctDNA) can track tumor response to treatments like immune checkpoint blockade (ICB) and correlate with outcomes. This meta-analysis evaluated whether ctDNA clearance or decrease is associated with improved survival across various settings in NSCLC.

METHODS

A systematic review of MEDLINE, EMBASE, and Cochrane databases (up to April 2024) identified studies evaluating the impact of ctDNA kinetics on survival outcomes in non-curative NSCLC settings. Pooled hazard ratios (HR) for progression-free survival (PFS) and overall survival (OS) were calculated using a random effects model.

RESULTS

We included 32 studies with 3047 NSCLC patients receiving systemic therapies such as targeted therapy (TT), ICB, and chemotherapy. Meta-analysis of 31 studies showed that ctDNA decrease/clearance was linked to improved PFS (HR: 0.32 [0.26, 0.40], I² = 63%, P < .01). Subgroup analysis indicated strong PFS benefits from ctDNA clearance (HR: 0.27 [0.20, 0.36]). Similar improvements were seen across patients undergoing targeted therapy (HR: 0.34) and ICB (HR: 0.33). Analysis of 25 studies revealed a significant association between ctDNA reduction and better OS (HR: 0.31 [0.23, 0.42], I² = 47%, P < .01). Subgroup findings were consistent for both TT (HR: 0.41) and ICB (HR: 0.32). Sensitivity analysis demonstrated that ctDNA clearance/decrease was consistently associated with improved PFS across study designs and ctDNA analysis methods. There was no significant variation in hazard ratios for PFS based on NSCLC subtypes, smoking status, or sex.

CONCLUSION

Plasma ctDNA kinetics was associated with improved survival outcomes in patients diagnosed with advanced NSCLC undergoing treatment with TT and ICB.

Extensive molecular profiling of KRAS wild-type as compared to KRAS mutated pancreatic ductal adenocarcinoma on 318 patients

PURPOSE

Molecular profiling is increasingly implemented to guide treatment of advanced pancreatic ductal adenocarcinoma (PDAC), especially when for clinical trials enrollment. This study aimed to describe actionable alterations detected in KRAS mutated (KRASm) versus KRAS wild-type (KRASwt) PDAC, the latter group being considered enriched in molecular alterations.

METHODS

This prospective monocentric study included patients with locally advanced or metastatic PDAC who underwent next-generation sequencing (NGS) on liquid biopsy and/or tissue samples between 2015 and 2023, as part of the BIP academic study (NCT02534649). Actionable alterations were classified using the ESCAT (ESMO Scale for Clinical Actionability of molecular Targets).

RESULTS

A total of 378 patients with a PDAC underwent NGS: 73 on tissue samples, 162 on liquid biopsies, and 143 on both tissue and liquid. Liquid biopsies had a 59.3 % performance (181 informative samples out of 305). Among 318 informative NGS samples, 273 (86 %) were KRASm, and 45 (14 %) were KRASwt. Median overall survival (OS) was 19.35 in KRASwt patients and 16.89 months for KRASm patients (HR 0.67, 95 %CI (0.49-0.90), p = 0.02). ESCAT alterations were found in 15.7 % of total population, with 31.1 % in KRASwt tumors and 13.2 % in KRASm tumors. BRCA1/2 mutations were identified in 7.5 % of the population, and one NTRK fusion was found in a KRASwt PDAC. The molecular tumor board considered 71 patients (22.3 %) eligible for early-phase trials, with 14 treated with matched therapy.

CONCLUSION

Although actionable mutations were more frequent in KRASwt tumors, 13.2 % of KRASm PDAC harbored ESCAT alterations, emphasizing the importance of molecular profiling regardless of KRAS status.

Analytical and Clinical Validation of the Plasma-Based Guardant360 CDx Test for Assessing HER2 (ERBB2) Mutation Status in Patients with Non-Small-Cell Lung Cancer for Treatment with Trastuzumab Deruxtecan in DESTINY-Lung01/02

This study demonstrates the analytical and clinical validity of the approved (United States and Japan) plasma-based Guardant360 companion diagnostic (CDx) test for selecting patients with human epidermal growth factor receptor 2 (HER2 [ERBB2])-mutated (HER2m) non-small-cell lung cancer (NSCLC) for trastuzumab deruxtecan (T-DXd) treatment. Concordance between the Guardant360 CDx test and the plasma-based AVENIO ctDNA Expanded Kit Assay (AVENIO), as well as the tissue-based clinical trial assays (CTAs) was investigated. Clinical utility was assessed by comparing T-DXd clinical efficacy results of patients in DESTINY-Lung01/02 who tested positive for HER2 mutations using the Guardant360 CDx test to benchmark efficacy results from DESTINY-Lung01/02. Finally, concordance between the Guardant360 CDx test and the tissue-based Oncomine Dx Target (ODxT) test was explored. High concordance was observed between the Guardant360 CDx test versus AVENIO [positive percent agreement (PPA), 98.8%; negative percent agreement (NPA), 91.5%] and CTAs (DESTINY-Lung01 Cohort 2-PPA, 91.0%; NPA, 100%; DESTINY-Lung02 arm 1-PPA, 86.0%; NPA, 100%). Confirmed objective response rates were similar in patients with HER2m NSCLC identified by the Guardant360 CDx test and by CTAs. There was a high level of agreement between the Guardant360 CDx test and the ODxT test. The Guardant360 CDx test demonstrated analytical and clinical validity for identifying patients with HER2m NSCLC for T-DXd therapy; results support plasma-based testing when tissue-based testing is not feasible.

Clinical use of circulating tumor DNA analysis in patients with lymphoma

The analysis of circulating tumor DNA (ctDNA) in liquid biopsy specimens has an established role for the detection of predictive molecular alterations and acquired resistance mutations in several tumors. The low-invasiveness of this approach allows for repeated sampling and dynamic monitoring of disease evolution. Originating from the entire body tumor bulk, plasma-derived ctDNA reflects intra- and interlesional genetic heterogeneity. In the management of lymphoma patients, ctDNA quantification at various timepoints of the patient's clinical history is emerging as a complementary tool that may improve risk stratification, assessment of treatment response and early relapse detection during follow-up, most prominently in patients with diffuse large B-cell lymphoma or classic Hodgkin lymphoma. While liquid biopsies have not yet entered standard-of-care treatment protocols in these settings, several trials have provided evidence that at least a subset of lymphoma patients may benefit from the introduction of liquid biopsies into daily clinical care. In parallel, continuous technological developments have enabled highly sensitive ctDNA assessment methods, which span from locus-specific techniques identifying single hotspot mutations, to sequencing panels and genome-wide approaches that explore broader genetic and epigenetic alterations. Here, we provide an overview of current methods and ongoing technical developments for ctDNA evaluation. We also summarize the most important data from a selection of clinical studies that have explored the clinical use of ctDNA in several lymphoma entities.

Lessons (to be) learned from liquid biopsies: assessment of circulating cells and cell-free DNA in cancer and pregnancy-acquired microchimerism

Tumors constantly shed cancer cells that are considered the mediators of metastasis via the blood stream. Analysis of circulating cells and circulating cell-free DNA (cfDNA) in liquid biopsies, mostly taken from peripheral blood, have emerged as powerful biomarkers in oncology, as they enable the detection of genomic aberrations. Similarly, liquid biopsies taken from pregnant women serve as prenatal screening test for an abnormal number of chromosomes in the fetus, e.g., via the analysis of microchimeric fetal cells and cfDNA circulating in maternal blood. Liquid biopsies are minimally invasive and, consequently, associated with reduced risks for the patients. However, different challenges arise in oncology and pregnancy-acquired liquid biopsies with regard to the analyte concentration and biological (background) noise among other factors. In this review, we highlight the unique biological properties of circulating tumor cells (CTC), summarize the various techniques that have been developed for the enrichment, detection and analysis of CTCs as well as for analysis of genetic and epigenetic aberrations in cfDNA and highlight the range of possible clinical applications. Lastly, the potential, but also the challenges of liquid biopsies in oncology as well as their translational value for the analysis of pregnancy-acquired microchimerism are discussed.

Clinical Validation of Local Versus Commercial Genomic Testing in Cancer: A Comparison of Tissue and Plasma Concordance

Genomic sequencing of tumours improves patient outcomes through implementation of precision oncology. At present, genomic testing is mainly confined to research settings, with samples sent to biopharmaceutical companies for analysis. The ever-expanding catalogue approved of targeted therapies has created an urgent unmet need for local genomic testing facilities, to enable upscaling of testing. Here, we compare the outcomes of local (IonTorrent™) and commercial (Foundation Medicine) genomic testing collected from 30 cancer patients in from plasma and tissue samples. Overall concordance was high in both tissue (98%) and plasma (94.2%). Variants identified by both platforms had a strong correlation in variant allele frequencies (VAF%): plasma: r = 0.99 p < 0.0001, tissue: r = 0.91 p < 0.0001. However, numerous low VAF% variants resulted in low positive percentage agreement (tissue 78.8% plasma 16.1%) and positive predictive values (tissue 56.3% plasma 71.4%). Local sequencing demonstrated higher fidelity in detecting fusions but low fidelity in detecting indels. Overall, this study supports the use of local genomic testing for routine molecular diagnostics but highlights outstanding issues before widespread implementation. Processing of variants detected at low VAF% and the limit of detection of assays needs to be addressed. Construction of gene panels requires careful consideration, including incorporation of markers of genomic instability.

What the Clinician Needs to Know About Laboratory Analyses of Circulating Tumor DNA

Liquid biopsies offer the possibility to evaluate cancer patients using noninvasive approaches. Circulating cell-free DNA (ccfDNA) is 1 of the most used and promising sources. Detecting tumor DNA among ccfDNA (ctDNA) can be used for early cancer detection, treatment response assessment, prognosis, and predictive evaluations. Providing analyses that can increase the quality of patient treatment is very much a joint effort between laboratory scientists and clinicians. With its use approaching clinical practice, it is important for clinicians to be familiar with the basic concepts and analyses behind ctDNA results in a similar way as laboratory scientists should have knowledge of the clinical needs to provide relevant analyses. In this Perspective, we describe the whole process of ctDNA analyses, from the preanalytical standards to reporting/analyzing results, and highlight some important factors that need to be addressed in the process of implementing them to clinical practice.

Optimizing therapeutic approaches for HR+/HER2- advanced breast cancer: clinical perspectives on biomarkers and treatment strategies post-CDK4/6 inhibitor progression

This review offers an expert perspective on biomarkers, CDK4/6 inhibitor efficacy, and therapeutic approaches for managing hormone receptor-positive (HR+), human epidermal growth factor receptor-negative (HER2-) advanced breast cancer (ABC), particularly after CDK4/6 inhibitor progression. Key trials have demonstrated that combining CDK4/6 inhibitors with endocrine therapy (ET) significantly improves progression-free survival (PFS), with median durations ranging from 14.8 to 26.7 months, and overall survival (OS), with median durations reaching up to 53.7 months. Actionable biomarkers, such as PIK3CA and ESR1 mutations, have emerged as pivotal tools to guide second-line treatment decisions, enabling the use of targeted therapies like alpelisib and elacestrant and emphasizing the important role of biomarkers in guiding the selection of therapy. This overview aims to provide clinicians with a practical and up-to-date framework to inform treatment decisions and improve patient care in the context of this challenging disease. Additionally, we review emerging biomarkers and novel treatment strategies to address this difficult clinical landscape.

A Comprehensive Approach to Neoadjuvant Treatment of Locally Advanced Rectal Cancer

At the end of the past century, the introduction of Total Mesorectal Excision (TME), preceded by either short-course radiotherapy (SCRT) or chemoradiation (CRT), established the new standard of care for locally advanced rectal cancer (LARC). Recently, significant advancements were achieved for both dMMR/MSI and pMMR/MSS LARC patients. For the 2-3% of dMMR/MSI LARCs, ablative immunotherapy emerged as a curative approach, offering the possibility of avoiding chemotherapy (CT), radiotherapy, and surgery altogether. In pMMR/MSS LARCs, the intensification of preoperative treatments with Total Neoadjuvant Treatment (TNT) afforded three outcomes: (a) a reduction of distant metastases, positively impacting on survival endpoints, (b) a significant increase of complete clinical response (cCR) rate, paving the way for non-operative management (NOM), and (c) the selective omission of radiotherapy following induction CT. The choice of the most appropriate therapeutic strategy can only be made through the shared decision-making process between physician and patient based on risk stratification and patient preferences.

Homologous recombination deficiency in ovarian cancer: Global expert consensus on testing and a comparison of companion diagnostics

BACKGROUND

Poly (ADP ribose) polymerase inhibitors (PARPis) are a treatment option for patients with advanced high-grade serous or endometrioid ovarian carcinoma (OC). Recent guidelines have clarified how homologous recombination deficiency (HRD) may influence treatment decision-making in this setting. As a result, numerous companion diagnostic assays (CDx) have been developed to identify HRD. However, the optimal HRD testing strategy is an area of debate. Moreover, recently published clinical and translational data may impact how HRD status may be used to identify patients likely to benefit from PARPi use. We aimed to extensively compare available HRD CDx and establish a worldwide expert consensus on HRD testing in primary and recurrent OC.

METHODS

A group of 99 global experts from 31 different countries was formed. Using a modified Delphi process, the experts aimed to establish consensus statements based on a systematic literature search and CDx information sought from investigators, companies and/or publications.

RESULTS

Technical information, including analytical and clinical validation, were obtained from 14 of 15 available HRD CDx (7 academic; 7 commercial). Consensus was reached on 36 statements encompassing the following topics: 1) the predictive impact of HRD status on PARPi use in primary and recurrent OC; 2) analytical and clinical validation requirements of HRD CDx; 3) resource-stratified HRD testing; and 4) how future CDx may include additional approaches to help address unmet testing needs.

CONCLUSION

This manuscript provides detailed information on currently available HRD CDx and up-to-date guidance from global experts on HRD testing in patients with primary and recurrent OC.

High-throughput methylation sequencing reveals novel biomarkers for the early detection of renal cell carcinoma

PURPOSE

Renal cell carcinoma (RCC) is a common malignancy, with patients frequently diagnosed at an advanced stage due to the absence of sufficiently sensitive detection technologies, significantly compromising patient survival and quality of life. Advances in cell-free DNA (cfDNA) methylation profiling using liquid biopsies offer a promising non-invasive diagnostic option, but robust biomarkers for early detection are current not available. This study aimed to identify methylation biomarkers for RCC and establish a DNA methylation signature-based prognostic model for this disease.

METHODS

High-throughput methylation sequencing was performed on peripheral blood samples obtained from 49 primarily Stage I RCC patients and 44 healthy controls. Comparative analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression methods were employed to identify RCC methylation signatures.Subsequently, methylation markers-based diagnostic and prognostic models for RCC were independently trained and validated using random forest and Cox regression methodologies, respectively.

RESULTS

Comparative analysis revealed 864 differentially methylated CpG islands (DMCGIs), 96.3% of which were hypermethylated. Using a training set from The Cancer Genome Atlas (TCGA) dataset of 443 early-stage RCC tumors and matched normal tissues, we applied LASSO regression and identified 23 methylation signatures. We then constructed a random forest-based diagnostic model for early-stage RCC and validated the model using two independent datasets: a TCGA set of 460 RCC tumors and controls, and a blood sample set from our study of 15 RCC cases and 29 healthy controls. For Stage I RCC tissue, the model showed excellent discrimination (AUC-ROC: 0.999, sensitivity: 98.5%, specificity: 100%). Blood sample validation also yielded commendable results (AUC-ROC: 0.852, sensitivity: 73.9%, specificity: 89.7%). Further analysis using Cox regression identified 7 of the 23 DMCGIs as prognostic markers for RCC, allowing the development of a prognostic model with strong predictive power for 1-, 3-, and 5-year survival (AUC-ROC > 0.7).

CONCLUSIONS

Our findings highlight the critical role of hypermethylation in RCC etiology and progression, and present these identified biomarkers as promising candidates for diagnostic and prognostic applications.

The Current Role of Circulating Tumor DNA in the Management of Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is projected to be the second leading cause of cancer-related death by 2030. Early identification is rare, with a 5-year overall survival (OS) of less than 10%. Advances in the understanding of PDAC tumor biology are needed to improve these outcomes. Circulating tumor DNA (ctDNA) represents a promising novel biomarker in the identification and management of PDAC. Drawn from peripheral blood and analyzed using a variety of techniques, the detection of ctDNA in PDAC has been associated with shorter OS, minimal residual disease presence, and shorter recurrence-free survival. The use of ctDNA has also been examined as an indicator of therapeutic resistance, susceptibility to targeted therapy, and therapeutic response. While promising, ctDNA analysis is limited by its low rates of detection in some settings and lack of predictive ability in others. Many studies examining the utility of ctDNA for the management of PDAC have been relatively small retrospective cohort studies. The current findings will need to be validated by incorporation of ctDNA analysis into cancer registries and larger prospective studies. Given the current, rapid evolution in the field, it is possible that with time, ctDNA will be more routinely incorporated into the clinical management of PDAC.

Liquid Biopsy and Challenge of Assay Heterogeneity for Minimal Residual Disease Assessment in Colon Cancer Treatment

This review provides a comprehensive overview of the evolving role of minimal residual disease (MRD) for patients with Colon Cancer (CC). Currently, the standard of care for patients with non-metastatic CC is adjuvant chemotherapy (ACT) for all patients with stage III and high-risk stage II CC following surgical intervention. Despite a 5-20% improvement in long-term survival outcomes, this approach also results in a significant proportion of patients receiving ACT without any therapeutic benefit and being unnecessarily exposed to the risks of secondary side effects. This underscores an unmet clinical need for more precise stratification to distinguish patients who necessitate ACT from those who can be treated with surgery alone. By employing liquid biopsy, it is possible to discern MRD enabling the categorization of patients as MRD-positive or MRD-negative, potentially revolutionizing the management of ACT. This review aimed to examine the heterogeneity of methodologies currently available for MRD detection, encompassing the state-of-the-art technologies, their respective advantages, limitations, and the technological challenges and multi-omic approaches that can be utilized to enhance assay performance. Furthermore, a discussion was held regarding the clinical trials that employ an MRD assay focusing on the heterogeneity of the assays used. These differences in methodology, target selection, and performance risk producing inconsistent results that may not solely reflect biological/clinical differences but may be the consequence of the preferential use of particular products in studies conducted in different countries. Standardization and harmonization of MRD assays will be crucial to ensure the liquid revolution delivers reliable and clinically actionable outcomes for patients.

Rotavirus-Inspired Nanointerface Engineered Biosensors for All-in-One Cancer Diagnosis

Ultrasensitive and population-scale cancer screening technologies are critical to reducing cancer mortality. However, the current qRT-PCR falls short in high-throughput screening of multiple cancers. Here, a rotavirus-inspired multicancer diagnosis system (RMDS) is developed via nanointerface engineering. RMDS employs Y-shaped DNA (YDNA) probes to encircle the graphene quantum dots (GQDs) for nanointerface modification. The biotransduction mechanisms at the nanointerface are systematically investigated. RMDS greatly enhances the transduction efficiency of biological analytes by optimizing the probe density and configuration. RMDS realizes ultrasensitive detection of the lung cancer KARS G12D mutation with a limit of detection (LoD) of 5.7 aM and the breast cancer-related AKT2 gene (LoD: 3.0 aM). The multiple chambers enable simultaneous diagnosis of multiple cancers and determination of cancer progression. Clinical validation shows RMDS can be a practical solution, which could complement or replace qRT-PCR and become the next-generation all-in-one tool for large-scale population cancer screening.