Increasing Widespread Accessibility of Molecular Testing for Oncology Research

Advancements in cancer diagnostics and monitoring have revolutionized the way we understand and treat this complex disease. The advent of molecular technologies for analyzing nucleic acids has made it possible to detect, analyze and monitor cancer more precisely and sensitively than ever before. Furthermore, it has made noninvasive liquid biopsy techniques an increasingly viable alternative to more taxing methods such as imaging or tissue biopsy. By analyzing circulating tumor DNA (ctDNA) and maintaining the highest vigilance for minimal residual disease (MRD), cancer researchers can gain key information to help them better predict relapse, assess treatment response, inform candidate selection for clinical trials, and more.

However, some advanced molecular technologies remain out of reach for smaller laboratories or clinical research institutions. With limited budgets and more niche in-house expertise, it can sometimes be difficult to justify the purchase of a next-generation sequencing (NGS) instrument and the associated reagents, consumables and software. Fortunately, droplet digital PCR (ddPCR) technology presents a more accessible option that can be used for multiple molecular applications that are continuing to drive oncology research toward a brighter future.

Why bring molecular testing in-house?

Bringing molecular analysis technology in-house – rather than relying on external contract testing services – offers several advantages to research institutions of all sizes. By utilizing their own equipment, researchers can ensure that samples are being handled in accordance with their specific protocols, reducing the risk of errors or inconsistencies. Additionally, in-house analysis often allows for faster data turnaround times, enabling researchers to make more informed decisions and move their research forward more quickly. By building up their own molecular testing capabilities, research institutions can gain a deeper understanding of the technology and its applications, potentially leading to the development of new research methods and techniques. Finally, keeping samples within a research institution allows for greater privacy and security of patient samples and data, which may be particularly important for researchers dealing with sensitive information.

Defining roles for each molecular technology

NGS and ddPCR technology each offer unique strengths for cancer monitoring research, and their roles are often complementary. Given that tumor mutation profiles can differ significantly from one patient to another, it is crucial to conduct a broad sequencing analysis to characterize the tumor before engaging in molecular monitoring. NGS technology is especially suited for identifying mutations and biomarkers in this initial characterization process. However, while NGS can detect a wide range of mutations, it may not be sensitive enough to detect low levels of ctDNA or MRD, which are critical for gaining insights into treatment efficacy and early signs of relapse.

In contrast, ddPCR technology can detect these low levels of ctDNA or MRD with high precision, making it an ideal tool for monitoring treatment response and detecting early signs of relapse. Furthermore, it offers a simpler workflow to streamline repeated sample characterization for ongoing monitoring. When used in combination with NGS, ddPCR technology can provide a more complete picture of tumor progression and how it is responding to treatment, allowing researchers to make more informed decisions and assessments. Since ddPCR assays are more likely to be used serially whereas sequencing is more likely to be a single, up-front investment, it may make more sense for institutions with limited resources to bring ddPCR technology in-house and rely on external partners for sequencing.

ddPCR technology is accessible for many organizations

Multiple features of ddPCR technology contribute to the ease with which it can be brought in-house. Most importantly for researchers or institutions with budget constraints, ddPCR technology can be more cost-effective over time than NGS. While NGS requires significant investment in equipment, reagents and bioinformatics resources, ddPCR technology requires a lower investment in the long term. This makes it more accessible to smaller research institutions with limited budgets. Furthermore, because ddPCR technology offers absolute quantification with simple data readouts, it does not require the extensive bioinformatics analysis that NGS does. This also saves time and money, as well as reducing the need for specialized data expertise.

Another advantage of ddPCR technology is its ease of use. The instrument is relatively simple to operate and requires minimal training. Sample preparation is straightforward, and after researchers load the samples, the instrument takes care of generating droplets before running the PCR reaction and analyzing the results to produce data automatically. This ease of use means that researchers with limited expertise can easily incorporate ddPCR into their research workflows, allowing them to answer new research questions that were previously out of reach. Furthermore, the simple workflow and straightforward, high-quality data reduce the chances of user error, making it less likely that experiments need to be repeated. Overall, this efficient technology can conserve time and resources.

When considering an investment holistically for an institution, it is also worth noting that ddPCR technology is highly versatile. It can be used for a variety of applications, including detecting mutations, copy number variations, and rare alleles in a range of sample types.

In summary, ddPCR technology is an attractive option for smaller research institutions with limited budgets and personnel. With ddPCR technology, these institutions can easily bring molecular monitoring in-house, allowing them to answer new research questions and contribute to the growing body of knowledge about cancer biology and treatment.

Examples of ddPCR oncology workflows in action

Numerous studies have demonstrated that ddPCR technology can accurately detect ctDNA and MRD in liquid biopsy samples and predict the response to treatment and overall survival. In 2018, researchers developed a multiplex ddPCR assay to simultaneously detect multiple KIT mutations in ctDNA during a course of tyrosine kinase inhibitor treatment in gastrointestinal cancer patients. Their study demonstrated the high sensitivity and specificity of the assay, with an easy, cost-effective workflow and short turnaround time.¹ Similarly, a study in 2021 used ddPCR assays to monitor changes in ctDNA levels in response to immune checkpoint inhibitors for lung cancer treatment. Researchers were able to accurately predict treatment outcomes and relapse risk in patients.² The results of the studies suggested that these assays and others like them may be especially useful for ongoing treatment response monitoring for oncology.

Another group leveraged the paired workflow of NGS and ddPCR molecular testing. They sequenced mutations within individual tumors to select multiple biomarkers for MRD testing, then switched to ddPCR assays for each ctDNA biomarker to follow changes over time. The study found that the presence of MRD post-surgery – when detected with ultra-sensitive assays – was a good predictor of early relapse.³

Other clinical studies have also demonstrated the effectiveness of ddPCR assays in ctDNA and MRD monitoring in various types of cancer, including lung cancer, breast cancer and prostate cancer. These studies show how molecular testing using ddPCR assays is already bringing greater precision, sensitivity and insight to oncology research.

Improving cancer research for everyone

ddPCR technology is highly effective for ctDNA and MRD monitoring in cancer samples. Its ability to detect low levels of DNA mutations with high accuracy and reproducibility makes it an invaluable tool in research that monitors the progression of the disease, assesses treatment efficacy and predicts the likelihood of recurrence. Furthermore, its ease of use, affordability and minimal training requirements make it accessible to a wide range of laboratories, regardless of their size or resources.

As more and more studies continue to demonstrate the effectiveness of ddPCR technology in ctDNA and MRD monitoring, it is likely that its use will become increasingly widespread in clinical research. Ultimately, this could lead to more personalized and effective treatments for cancer patients and improved outcomes for those living with this devastating disease.

About the author:

Jeremiah McDole, PhD, is marketing oncology segment manager for Bio-Rad.

References

1. Boonstra PA, Ter Elst A, Tibbesma M, et al. A single digital droplet PCR assay to detect multiple KIT exon 11 mutations in tumor and plasma from patients with gastrointestinal stromal tumors. Oncotarget. 2018;9(17):13870-13883. doi: 10.18632/oncotarget.24493
2. Van Der Leest P, Hiddinga B, Miedema A, et al. Circulating tumor DNA as a biomarker for monitoring early treatment responses of patients with advanced lung adenocarcinoma receiving immune checkpoint inhibitors. Mol Oncol. 2021;15(11):2910-2922. doi: 10.1002/1878-0261.13090
3. Tarazona N, Gimeno-Valiente F, Gambardella V, et al. Targeted next-generation sequencing of circulating-tumor DNA for tracking minimal residual disease in localized colon cancer. Ann Oncol. 2019;30(11):1804-1812. doi: 10.1093/annonc/mdz390