Liquid biopsies are an emerging area of research, particularly in the context of cancer. These blood draws collect tumor DNA that has been shed from the primary tumor and is now found in the bloodstream. While there are many ways to analyze circulating tumor DNA (ctDNA), the choice depends on one’s research objectives and the information one already has. Two ideal methods are next-generation sequencing (NGS) and digital polymerase chain reaction (dPCR). These methods each have their own strengths, and while some scientists may prefer one or the other, there’s a case to be made that they’re better together.
Circulating tumor DNA generally presents relatively small quantities of highly fragmented tumor-derived DNA. NGS can successfully read that DNA, providing comprehensive detection of mutations. The breadth of information that NGS can induce, whether via whole-genome or targeted sequencing, translates into the ability to detect mutations far beyond those predicted or expected in a given cancer. This includes “passenger” mutations that are not part of the cancer’s mode of action but may provide a way to track cancer progression or target treatments. Targeted NGS panels are particularly well suited to detecting known, cancer-related somatic mutations, fusion genes and copy number variations (CNVs). While whole-genome NGS can be expensive, and take a relatively long time to generate results, targeted NGS approaches offer simpler, automated workflows that save time and can reduce the complexity of analysis.
Another often-used platform for liquid biopsy analysis is dPCR. dPCR works by partitioning a nucleic acid sample into thousands of parallel PCR reactions that are each read separately and then combined into a single calculation, generating very accurate readings of DNA amounts. Like PCR, it functions based on the primers it is given, meaning it is difficult to use for broad, exploratory measurements and is better suited for analyzing a small number of known markers or mutations. However, dPCR generates precise values for those markers, more so than other methods, and at a lower cost than qPCR or NGS. It is not sensitive to changes in overall circulating DNA level in the same way that alternative techniques are, and provides absolute quantification rather than ratios or relative amounts.
Because of these differences, it is incorrect to suggest that one method is simply better than another. Each can be an ideal solution under different circumstances, but they most often work better as complements to one another. For cancers that have very well-defined and consistent genetic markers, diagnosis can follow a simple dPCR test, but others may require the breadth of a complete NGS panel to properly understand and identify potentially actionable alterations. Once NGS has provided this broad, exploratory view, precise dPCR measurements can be used for follow up or serial monitoring over time, saving resources and effort. Also, dPCR is ideal for validating NGS results from the same sample, and may be used in the future for tracking resistance levels to therapies whose resistance alleles are well characterized. Perhaps most excitingly, dPCR can be used to turn markers discovered via NGS into monitoring tools for future use, combining the two techniques into a single protective whole.
Thermo Fisher Scientific offers numerous liquid biopsy assays, including Oncomine cell free nucleic acid and DNA assays and the TaqMan liquid biopsy dPCR assays. For more information about Thermo Fisher Liquid Biopsy solutions including sample preparation options as well as NGS and dPCR assays and instruments, click here.