Liquid Biopsy and NGS: Teaming Up to Take Cancer Apart
Liquid biopsy is generating a lot of interest among the laboratory and clinician communities as a technique that enables research into tumor evolution. But, how is its use impacting the work of those in the lab, and how might it fit into the pathology lab in the future? We consider the pathologist’s and oncologist’s perspectives.
The Pathologist's View
What is your background and what kinds of tests does your lab perform?
I'm a molecular biologist by training. In my lab, we perform ~20,000 tests annually, of which 7–8 percent are molecular tests for cancer – occasionally comprehensive gene panels, but mainly single biomarker tests to predict therapeutic response. We usually look at KRAS, NRAS and sometimes BRAF in colorectal cancer; EGFR, ALK and sometimes BRAF in lung cancer; BRAF and sometimes KIT in melanoma; KIT and PDGFRA for gastrointestinal stromal tumors; and JAK mutations, chromosomal translocations and other alterations in hematological malignancies. At present, we only see liquid biopsy samples when tissue samples are not available, but that's changing, and I expect to see lots of liquid biopsy samples very soon.
How useful is the liquid biopsy technique?
The main advantage is speed. Using liquid biopsy samples, you can analyze the tumor molecular profile without the need for other techniques, so it helps you provide results for research in a shorter amount of time. You don't need any unusual equipment, so it's easy to incorporate it into the normal workflow. Liquid biopsy is also very useful when you're trying to understand the effect of therapy on a research sample. For example, lung tumors often relapse after EGFR tyrosine kinase inhibitor (TKI) treatment, and usually have an EGFR T790M mutation. Treatment exists for this mutation profile, but first you have to show that T790M is present. As tissue biopsy usually isn't feasible in these cases, liquid biopsy can serve as a powerful tool to advance thinking.
What are the advantages of the liquid biopsy–NGS combination?
We're still in the early clinical research phase, but we've found it to be a robust technique. Since implementing it, we've been collecting liquid biopsy samples at specific time points and analyzing them by next generation sequencing (NGS). Research shows that NGS techniques are able to detect mutations both in the expected genes and also in many other cancer-associated genes in the panel – p53 for instance. Furthermore, the mutation abundance in liquid biopsy samples correlates well with the tumor burden measured by clinicians in their research. It’s a sensitive technique too. Concordance studies with ~500 tumor samples in our laboratory have shown over 95 percent sensitivity in detecting mutants in the primary tumor. You can increase or decrease sensitivity by reaction optimization; we can call variants of frequency ~0.1 percent in a wild type background, which is good. Again, it's easy to fit liquid biopsy-NGS into a standard laboratory workflow, which is a big plus.
For a single biomarker, like T790M, PCR methods are still useful; however, as more resistance-associated alterations are identified, we'll need to detect multiple mutations at once. The need for multiplex techniques such as NGS will grow, and techniques optimized for liquid biopsy – like the Oncomine Lung cfDNA Assay (see Figure 1 and Table 1) – will have a place in clinical research.
Where will liquid biopsy fit in the laboratory of the future?
I think it may become a routine procedure in three main applications:
- Liquid biopsy research is well-suited to better understanding how a tumor changes after initial treatment. This understanding may, in the future, help us to select second-line therapy.
- As a replacement to tissue biopsies, particularly where speed is important and in situations where tissue biopsies are difficult
- To study tumor evolution during treatment and to use research findings to inform anticipatory second- or third-line therapy according to the molecular evolution of residual disease.
Going forward, molecular biologists, pathologists and oncologists must work closely toclinically contextualize liquid biopsy-NGS data, and thus to avoid drowning in a sea of genetic and molecular information.
The Oncologist's Perspective
How useful is the liquid biopsy technique from your perspective?
In liquid biopsy sample analysis, we are starting to see an important improvement: obtaining the samples is less invasive and less expensive compared with tissue biopsy samples.
In the future, the real outcome of this advantage may be that liquid biopsy sample analysis is accessible for more tumor types, at more pathology labs. These outcomes may be most clear for analyses where tissue samples are often not available.
Figure 1. Overview of the Oncomine Lung cfDNA Assay.
Table 1. Variants called from Horizon cfDNA Multiplex Reference Set. All eight mutant hotspots were called at 0.1%.
What are the advantages of the liquid biopsy–NGS combination?
Tumors are highly heterogeneous, and every tumor that responds to targeted treatment eventually will become resistant. We can observe in research that each mutation may offer the potential for therapeutic intervention. Single mutation techniques, however, will not provide you with the information that you need to follow the molecular evolution of the tumor; techniques like NGS will be essential to the generation of a comprehensive molecular portrait of the tumor. Today, a liquid biopsy-NGS combination enables research to build understanding of tumor evolution. In the future, this understanding may guide therapeutic options.
Advancements in liquid biopsy-NGS are adding to our understanding of tumor resistance. As new targets are detected, we can imagine a future without chemotherapy. Ten years ago we wouldn't have believed that this was possible.
Liquid biopsy-NGS still requires further research and validation, however; circulating tumor DNA can come from many sites, whereas tissue biopsies samples are localized; they portray the situation in a small piece of tumor. Nevertheless, we find that liquid biopsy-NGS data are often confirmed by other techniques.
How do you see it being used in the future?
I believe that liquid biopsy-NGS research is starting a new era of personalized medicine for cancer. It enables a better understanding of tumor heterogeneity, and it’s improving the field of oncology. However, we need external assessments to confirm that our results are reliable and may be useful for guiding treatment in the future. There's still a lot of work to do before this approach is routine in the clinic.
Also, we'll need to get better at managing information. The complexity of liquid biopsy-NGS tumor heterogeneity data may be difficult for medical oncologists to handle, so pathologists must contribute to the professional interaction and help us – oncologists and others – to interpret the data. If pathologists don’t take on this proactive role, it will be difficult for us to transfer the growing number of benefits of these new discoveries to cancer therapy.
Nicola Normanno is Director of the Cell Biology and Biotherapy Unit, INT=Fondazione Pascale, Department of Research, Naples, Italy.
Jose Machado is Director of the Genetic Diagnosis Laboratory, Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, Portugal.
