Pancreatic cancer cells with blue nuclei forming a sphere surrounded by red membranes in a lab setting. [Credit: National Cancer Institute]
The promise of molecular testing approaches
Over the years, increasingly complex molecular testing approaches have gained favor in the field by shedding more light on the mechanisms underlying the onset of cancer and its progression. Currently, two technologies used in tandem are providing greater insight into how to conquer cancer than ever before: next-generation sequencing (NGS) and Droplet Digital PCR (ddPCR) technology. But why does this pair of technologies, in particular, give scientists such an edge when optimizing cancer therapy?
When treating cancer, oncology researchers and clinicians need different types of information at different stages of the process. Sometimes, they need to explore a tumor’s genetic landscape in a broad, unbiased fashion; other times, they need to track specific known mutations, or biomarkers, with high precision and accuracy. NGS and ddPCR together meet these different needs.
NGS has been an invaluable tool in oncology for profiling a tumor’s biomarkers to enable drug discovery and preclinical testing. However, cancer research is increasingly focused on tumor response to treatment. Therefore, scientists are now utilizing liquid biopsy to monitor changes in ctDNA levels. This inexpensive, noninvasive technique uses a molecular method to assess blood, urine, or other fluid samples for a biomarker or biomarkers. While NGS and ddPCR are both highly sensitive technologies for analyzing liquid biopsy, their unique strengths make these techniques ideal in certain circumstances. Where NGS may be called for when searching for numerous or unknown mutations, ddPCR is the premier solution for rapid, economic and ultra-sensitive ctDNA analysis. Used together, these technologies offer great potential for improving the cancer patient journey.
Drug discovery & development
Oncology researchers constantly seek more effective ways to treat cancer, fueling ongoing drug discovery and biomarker research. In their work, scientists use NGS’s massive parallel sequencing capabilities to uncover biomarkers such as DNA mutations, RNA expression patterns, and epigenetic abnormalities related to a type of cancer. They then evaluate how different drug candidates affect levels of these target biomarkers in tumor cells, evaluating them by ultrasensitive methods such as ddPCR, looking for candidates that cause levels to diminish. Additionally, researchers may leverage NGS to identify mutations that promote resistance to specific therapies. With this information, they can find drugs that may bypass drug resistance.
Based on the target biomarkers and positive drug candidates identified, researchers can anticipate treatments that will maximize safety and efficacy. Finally, if drug candidates succeed in clinical trials, patients may receive them in a clinical setting.
The cancer patient journey
From cancer diagnosis onward, the patient’s journey may occur over a long period of time, but every step is incredibly time-sensitive. Most cancers require a combination of treatments, including surgery, radiation therapy, chemotherapy, immunotherapy, targeted therapy, or hormone therapy, and these may be administered simultaneously or in sequence. Oncologists need cutting-edge tools that provide rich, detailed information to track biomarkers to help them better understand which therapeutics they should administer, at which time points, and for how long.
After cancer diagnosis, clinicians may use NGS-based diagnostics to assess if a biopsied tumor carries druggable biomarker targets. While performing tissue biopsies to profile tumors often provides valuable information, this approach can be invasive, can only offer a single snapshot of a tumor’s status, and cannot account for heterogeneity within a tumor. Moreover, since timing is critical throughout the treatment process, it is advantageous to assess tumor status as rapidly as possible during neoadjuvant therapy to assess drug efficacy, analyze the remaining tumor burden immediately after curative procedures to evaluate treatment response and conduct long-term monitoring to catch potential tumor recurrence as early as possible.
While these kinds of repetitive testing are not amenable to tissue biopsy, each of these areas represents groundbreaking fields of intensive research in which liquid biopsy methodologies offer an ideal way to track genetic biomarkers. NGS and ddPCR technology stand at the forefront of this research, backed by thousands of publications documenting their utility.
Balancing liquid biopsy approaches
When using NGS or ddPCR technology to conduct a liquid biopsy, each approach brings something different to the table, and therefore, each will be better suited to specific situations. In some cases, a scientist may want to perform a liquid biopsy over the course of treatment, looking at the biomarker landscape and how it may change over time, for example, to decipher the mechanism of newly developed drug resistance. NGS offers an unparalleled way to broadly evaluate thousands of mutations in a single instrument run. That said, NGS analysis can be highly complex, so it requires biostatistics expertise and can take days or weeks for results to become available. Furthermore, NGS reagents are expensive, and lab-to-lab results often vary.
Other situations call for routine monitoring, where a researcher may perform liquid biopsies at intervals to get a sense of how critical biomarker levels change in real time. Such monitoring may be valuable over the course of treatment to track response or once a tumor has gone into remission to monitor for recurrence. In this case, ddPCR technology is ideal for the task. Although a ddPCR assay is limited to about a dozen biomarkers per well, it can provide same-day results, ultra-high sensitivity and unmatched precision at a relatively low cost.
Given their complementary capabilities, both technologies will undoubtedly continue to generate critical insights as oncology research progresses—particularly research focused on circulating tumor DNA (ctDNA) analysis. Together, they can provide a rich source of timely information about a tumor that keeps pace with the urgent nature of the cancer treatment process.
How liquid biopsy may shape future treatment
Overall, both NGS and ddPCR technologies are tools with immense potential, as evidenced by the thousands of oncology-focused research publications that have used them to great effect. By fine-tuning how to balance the large volume of biomarker data generated by NGS with the rapid, cost-effective, and ultra-sensitive capabilities of ddPCR technology, clinical research will begin to establish new practices to facilitate a higher quality of care, providing future patients with a better chance of overcoming their disease.
Jeremiah McDole is oncology segment, manager at Bio-Rad Laboratories.
Filed Under: Drug Discovery and Development, Genomics/Proteomics, Oncology
