Liquid Biopsy in Solid Tumors: Clinical Trial Design and Regulatory Guidance

By Gert Bluschke, MD-PhD, Associate Medical Director at Allucent

Advances in molecular diagnostics are revolutionizing cancer research and management, with methods, such as liquid biopsies and next-generation sequencing (NGS), gaining significance in the investigational and clinical practice setting. Increasing its presence in solid cancers, the minimally invasive approach aids in detecting and monitoring malignancies and can help guide treatment decisions. Circulating tumor DNA (ctDNA), in particular, has demonstrated clinical utility across various cancer types. Due to its advantages and role in state-of-the-art diagnostics of modern medicine, its role in the clinical trial setting and design needs to be evaluated.

Circulating tumor DNA is cell-free, plasma-derived tumor DNA that originates directly from tumors or circulating tumor cells, reflecting a partial or complete tumor genome. The quantity of ctDNA depends on tumor type, location, stage, tumor burden, and response to therapy. Detection methods for ctDNA include polymerase chain reaction-based approaches such as digital droplet polymerase chain reaction and next-generation sequencing (NGS) techniques.

Clinical Applications of Liquid Biopsy in Solid Tumors

While still evolving, liquid biopsy shows promise for early cancer detection through the analysis of ctDNA in peripheral blood. In January 2023, the FDA approved elacestrant together with the Guardant360 CDx companion diagnostic for ESR1 mutation detection in ctDNA from breast cancer. The TriOx test, developed in early 2025 using machine learning and deep whole-genome TET-Assisted Pyridine Borane Sequencing (TAPS), represents a significant advancement in this area. This innovative test analyzes multiple features of DNA across six cancer types with a reported 94.9% sensitivity and 88.8% specificity.

Detecting Minimal Residual Disease with Liquid Biopsy and ctDNA

One of the most promising applications of ctDNA is detecting molecular/minimal residual disease (MRD) following curative-intent treatment.

The GALAXY study, part of the CIRCULATE-Japan observational study, demonstrated that ctDNA-based MRD detection was highly prognostic of recurrence and mortality risk in patients with resectable colorectal cancer. Similarly, the BESPOKE CRC study showed that ctDNA-based MRD detection was highly prognostic of recurrence and predictive of benefit from adjuvant chemotherapy in patients with stage II/III colorectal cancer.

Monitoring Treatment Response with Liquid Biopsies for Solid Tumors

Circulating tumor DNA provides a real-time, non-invasive method to monitor tumor burden and treatment efficacy. The ease of obtaining liquid biopsies makes them useful for real-time monitoring of disease progression, as tumors evolve and may require different treatments based on genetic changes. ctDNA clearance has emerged as a potential surrogate endpoint for treatment efficacy.

Clinical Trial Design and Endpoints for Liquid Biopsy in Solid Tumors

Various trial designs incorporate ctDNA testing, such as:

• Randomized trials comparing ctDNA-guided treatment versus standard of care: These trials assess whether treatment decisions based on ctDNA status can improve outcomes compared to conventional approaches.
• Trials for ctDNA-positive patients: Some trials randomize ctDNA-positive patients between standard-of-care treatment and intensified regimens to determine if the latter improves outcomes.
• Trials for ctDNA-negative patients: Other trials aim to de-escalate therapy in ctDNA-negative patients to reduce unnecessary toxicity without compromising efficacy.

Primary endpoints in these trials typically include progression-free survival for adjuvant therapy, event-free survival for neoadjuvant therapy, or overall survival. However, there is growing interest in using ctDNA clearance as a surrogate endpoint to accelerate drug development.

Regulatory Guidance for Liquid Biopsy and ctDNA Testing

The FDA guidance on ctDNA in clinical trials released in November 2024 aims to standardize the use of ctDNA as a biomarker in clinical trials for early-stage, curative-intent solid tumors, aiming to accelerate drug development while emphasizing rigorous assay validation and regulatory alignment. This guidance helps sponsors incorporate ctDNA as a biomarker into early-stage solid tumor clinical trials and supports its use in seeking market approval for in vitro diagnostic assays. Our Regulatory Affairs consulting team supports oncology trials, including submissions aligned with FDA and EMA expectations for studies using ctDNA and liquid biopsy approaches.

The FDA has outlined four main uses for ctDNA as a biomarker in early-stage solid tumor clinical trials:

1. Patient selection based on molecular alterations: ctDNA could be used to identify patients with genetic alterations matched to the targeted investigative treatment and for biomarker-based stratification. However, additional tumor testing may be required for false negative results.
2. Patient enrichment by way of treatment optimization: ctDNA can detect MRD, identifying high-risk patients for recurrence and who are likely to benefit from adjuvant therapy escalation (or de-escalation for low-risk patients). For instance, the GALAXY study in colorectal carcinoma showed adjuvant chemotherapy reducing the recurrence risk in MRD-positive patients.
3. Measure of response: Monitoring ctDNA could be used to estimate antitumor activity and aid in determining duration of response and progression-free survival.
4. Early endpoints: ctDNA clearance could be particularly useful as an early endpoint in the early-stage, curative-intent setting.

For trial enrichment, ctDNA tests need to offer high sensitivity and negative predictive value if used to inform potential de-escalation of treatment, and high specificity and positive predictive value if used to support treatment escalation.

The FDA encourages collecting ctDNA data before and after drug treatment and tracking long-term outcome data to characterize the association between ctDNA clearance and overall survival. The agency also stresses that quantitative testing and the use of tests at multiple time points would be ideal.

The European Medicines Agency (EMA) has provided guidance on biomarker assays in anticancer drug development. Following the FDA’s earlier approval in January 2023, the Committee for Medicinal Products for Human Use (CHMP) of the EMA issued a positive opinion in July 2023 for elacestrant with a companion diagnostic for ESR1 mutation detection in ctDNA.

The European Society for Medical Oncology (ESMO) released guidelines that endorse liquid biopsies as a standard of care for genotyping and treatment selection for many patients with advanced cancer provided the limitations of the assays are considered.

For molecular testing of MRD in early-stage cancer patients, ESMO acknowledged that ctDNA has “high evidence of clinical validity” for predicting relapse but cannot yet be recommended in routine clinical practice due to a lack of clinical utility data.

Challenges and Future Directions for Liquid Biopsy for Solid Tumors

While ctDNA holds great promise, especially in early-stage solid tumors, its widespread adoption is still limited by a range of technical, procedural, and clinical challenges.  These must be addressed to enable consistent application in clinical trials and eventual integration into standard practice. Key barriers include:

• Lack of standardization across ctDNA assays and methodologies
• False negative results in some settings due to low assay sensitivity
• No universally accepted protocols for sample collection, handling, or analysis
• Uncertainty about optimal timing for sample collection and monitoring

Despite these limitations, the field is rapidly evolving — and several innovations could help overcome current barriers and expand ctDNA’s role in precision oncology:

• Use of ctDNA as a surrogate endpoint to support faster regulatory approval
• Application of machine learning algorithms to extract more predictive insights from genomic data (e.g., the TriOx test)
• Integration with other biomarkers and clinical data for a more comprehensive patient view

As new studies validate these approaches, ctDNA could play a broader role in trial design, treatment decisions, and personalized care pathways—particularly in the context of early-stage, curative-intent solid tumors.

Conclusion

Liquid biopsy, particularly ctDNA analysis, represents a significant advancement in cancer diagnostics and management. Its applications are rapidly evolving across multiple areas, including patient selection, MRD detection, treatment monitoring, and as potential surrogate endpoints in clinical trials. With supportive regulatory guidance from the FDA and EMA, and ongoing clinical validation, ctDNA testing is poised to become an integral component of cancer care, enabling more personalized and effective treatment approaches while minimizing patient discomfort. However, standardization of methodologies and further validation through well-designed clinical trials remain essential for realizing the full potential of this promising technology. Learn more about our oncology expertise and how we help sponsors efficiently design and execute studies in solid tumor indications.

For more on how targeted strategies are transforming oncology, read our Precision Oncology blog.