Next-Generation Sequencing in Precision Oncology: Detecting Minimal Residual Disease

Like most diseases, cancer does not have a one-treatment-cures-all solution. Patients with the same type of cancer can respond very differently to the same treatment, or respond differently over time, necessitating more personalized treatment plans. The development of next-generation sequencing (NGS) has made the sequencing of patient tissues or tumors a realistic option and has allowed for the rapid development of personalized cancer treatments. Clinicians can now know the genetic contributions of their patients’ diseases and select the best treatments based on their individual needs. This has been especially important in oncology, where mutations drive the formation of cancer cells and tumors.

By determining the mutations that are causing a patient’s tumor, clinicians can better diagnose and treat that specific tumor using targeted therapies. After treatment, the identification of surviving cancer cells, or minimal residual disease (MRD), greatly impacts patient prognosis. However, MRD can escape current experimental methods until relapse is well underway.¹ Therefore, a more sensitive method to find MRD is being developed using NGS to research the presence of circulating tumor DNA (ctDNA) from a blood sample.

How is NGS used to detect MRD?

Detecting MRD using NGS depends on uncovering cancer cell markers in cell-free DNA (cfDNA). When cancer cells die, they release DNA into the bloodstream. By collecting all the cfDNA in a blood sample, the sample can be analyzed for cancer cell markers to determine if there are still cancer cells present in a patient. NGS allows for a broad characterization of tumor-specific markers that are present in all or most cancer cells. There are currently two major ways that MRD is discovered: tumor-informed and tumor-naïve. For tumor-informed, markers specific to the patient’s tumor are identified with an initial broad genomic profiling test (for example, whole-exome sequencing or a large pan-cancer sequencing test). While DNA mutations are most commonly used, epigenetic changes such as methylation can also be used.

For tumor-naïve, a panel of common markers is used; while it is more practical to have a universal test, cancer is such a diverse disease that it is likely to be insufficient for many patients. The mutations that are revealed occur at a low frequency and in a small amount of cfDNA, therefore a larger number of markers are required to identify ctDNA. While digital PCR is helpful in situations where mutant copies are available, being able to look at a larger number of markers is also helpful, and that is where NGS shines. NGS allows you to look at more markers in addition to non-sequence markers (e.g., methylation and fragmentation patterns).

By identifying cancer cell markers within cfDNA, clinicians can see if what they are doing is working and adjust treatment accordingly. If ctDNA is still present, the prognosis for the patient is much worse, and adjuvant treatment can be considered.¹ If the patient is cancer free, the clinician can then back off some of the harsher therapies. Though it is not yet a standard practice, the potential of NGS to identify MRD holds the power to provide clinicians with valuable information about how their patients may be responding to treatment and help inform future medical plans.

What are the challenges of NGS for MRD detection?

While detecting MRD using NGS provides care-driving information to clinicians, there are several challenges facing its implementation, such as the physical limitations of sequencing cfDNA in a blood sample. There is a small amount of DNA available, of which only a small portion may be derived from cancer cells, making efficiency a crucial consideration. To be successful, library preparation must be highly efficient, and the sequencing needs to cover the markers as evenly as possible. The sequences also need to be sequenced deeply – which cannot be achieved when looking at the whole genome. To sequence the markers at a greater depth, hybrid capture probes can be used to enrich the markers and sequence the target sequences with greater frequency. In addition to the challenge of sequencing these low abundance markers, the challenges of performing clinical lab tests apply to using NGS for MRD. Time is of the essence for patients; therefore this assay must be able to provide data on the tumor rapidly. This can be especially challenging for the tumor-informed approach, where a patient-specific test will need to be designed and manufactured as quickly as possible. Lastly high-volume clinical trials are required to demonstrate the clinical utility of MRD detection.

NGS developments: Using MRD to detect solid tumors

Using NGS to detect MRD is a relatively new and quickly developing method. An important new development is the ability to look at ctDNA from solid tumors, which affect the majority of cancer patients. Traditionally, MRD has been a method used to monitor blood cancers, but technical improvements in efficiency and error correction have allowed for the evolution of this method for solid tumors. As the sensitivity and accuracy of assays using new markers such as methylation and fragmentation patterns improve, future advances could have a huge impact on the use of NGS to identify ctDNA in symptom-free patients for early cancer detection. The principles are very similar to finding MRD and there is potential promise for using a similar method to screen patients for cancer.

Detecting MRD using NGS is an emerging technique that can help clinicians potentially uncover cancer relapse sooner than existing methods. By sequencing the cfDNA present in the circulation, dozens of markers – including epigenetic and fragmentation patterns – can be analyzed at once to determine the presence of lingering tumor cells after treatment. Using this rapidly evolving method, clinicians can improve patient care by tailoring treatment to better meet their patients’ needs.

References

1.  Moding EJ, Nabet BY, Alizadeh AA, Diehn M. Detecting liquid remnants of solid tumors: circulating tumor DNA minimal residual disease. Cancer Discov. 2021;11(12):2968-2986. doi: 10.1158/2159-8290.CD-21-0634

About the author:

Mirna Jarosz, PhD, is director of global market development and applications at Integrated DNA Technologies.

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