Liquid biopsy analysis has revolutionized cancer research, presenting a novel, noninvasive approach for detecting key mutations and monitoring disease status. While developed largely in the field of hematological oncology, liquid biopsy holds great promise for monitoring changes in solid tumors. Assessments of circulating tumor DNA (ctDNA) in bodily fluids have demonstrated great promise for research evaluating cancer prognosis, progression, and relapse while reducing the burden of costly and invasive procedures for patients.
Highly sensitive molecular tools, such as next-generation sequencing (NGS) and Droplet Digital PCR (ddPCR) technology, have enabled researchers to precisely characterize low-abundance biomarkers in liquid biopsy samples. While most of this work has focused on molecular response monitoring and assessment of treatment efficacy, the utility of ctDNA analysis extends far beyond these applications. With the power of ultrasensitive tools, researchers can characterize drug resistance mechanisms, gain deeper insights into intra- and inter-tumor heterogeneity, and accelerate progress in our understanding and treatment of cancer.
Reimagining Possibilities in ctDNA Testing
Commonly used platforms such as quantitative PCR (qPCR) have inherent limitations, reducing investigators’ ability to glean valuable information from ctDNA samples. Because ctDNA analytes are often highly fragmented, low in abundance, and found within a complex milieu of other biological components, they typically fall below the limit of detection for qPCR. However, advanced molecular techniques such as NGS and ddPCR technology have empowered researchers to access the wealth of insights offered by ctDNA analysis.
The unique capabilities of these methods make them suitable for particular applications in ctDNA testing. NGS can be used to conduct broad screening for hundreds to thousands of mutations within a tissue sample, generating a extensive genetic picture of a tumor. Using ddPCR assays, researchers can achieve efficient, ultrasensitive, and absolute quantification of target nucleic acids within a sample while avoiding the bioinformatic burden associated with NGS testing. The high sensitivity of ddPCR technology also enables robust and precise detection of subtle changes in low abundance ctDNA biomarkers. These capabilities, in tandem with its fast turnaround time and low cost, position ddPCR technology as an ideal method for serial sample analysis. But the utility of ultrasensitive ctDNA analysis is not limited to assessing molecular tumor response or detecting minimal residual disease (MRD)— a growing number of scientists are leveraging these techniques to open new doors in precision oncology research.
Expanding Applications of Sensitive ctDNA Analysis
Reducing Time to Treatment for Advanced Cancers
The wait times associated with molecular assessment of tissue biopsies can have a detrimental impact on a patient’s time to treatment and, in turn, their overall outcome, especially in cases of advanced cancer. Several studies have investigated the efficacy of a “plasma-first” diagnostic approach to treatment initiation in suspected cases of advanced lung cancer. While tumor biopsy is ultimately necessary to diagnose and characterize cancers, this work demonstrates the potential value that ctDNA molecular profiling has compared to tissue biopsy alone. This highlights the potential of rapidly providing critical information for more timely decision making.
Guiding Precision Treatment Selection
The development of cancer treatments personalized to target specific molecular pathways driving tumor growth has made a significant impact on clinical outcomes. Although molecular testing of tissue samples is still the gold standard for characterizing relevant genetic alterations, ctDNA analysis is an increasingly common alternative or complementary approach. Plasma-based ctDNA testing with ddPCR assays or other sensitive molecular tools can help investigators identify key mutations that one day may be used to guide targeted therapy selection.
Understanding Mechanisms of Drug Resistance
Characterizing specific drug resistance markers can be an invaluable tool in informing therapeutic selection after first-line treatment in patients with advanced cancer. ctDNA-based methods have proven useful in identifying markers of resistance, leading to the adoption of liquid biopsy in certain investigational settings. Recent studies have explored the use of ctDNA analysis to assess resistance-associated mutations and guide treatment selection in patients with EGFR mutant non-small cell lung cancer and in metastatic colorectal cancer. The positive findings of these and other studies highlight the potential of ctDNA analysis as a complementary molecular approach to characterizing drug resistance markers and guiding treatment selection.
Forging Ahead in Precision Oncology Research
Advanced molecular tools have expanded the capabilities of liquid biopsy analysis beyond simple cancer detection and monitoring. With increased accuracy and precision, tools like NGS and ddPCR technology have enabled investigators to leverage ctDNA molecular profiling for precise detection of drug resistance markers and advancing research into tumor response to therapies. By harnessing the full potential of these ultrasensitive tools, researchers are continuing to conduct studies that can drive improvements in diagnosing, characterizing, and treating cancer.
To explore the full suite of ddPCR assays available for liquid biopsy applications, visit bio-rad.com/ddPCR-oncology.