Armamentarium of Biomarker Testing Strategies in Cancer Care


Expert perspectives on the wide array of biomarker testing modalities available to patients receiving treatment for cancer.


Samuel K. Caughron, MD, FCAP: Several types of testing can be used to identify actionable alterations in solid tumors. These are going to include, for example, polymerase chain reaction [PCR] or real-time PCR, which is a variant of PCR. Next-generation sequencing, which we’ll go into a little more depth about, is the ultimate multiplexed modality. But next-generation sequencing is, in some ways, so complex that it’s not 1 methodology. There are 2 major platforms. Each has an interpretive software component or informatics pipeline that goes with the bench chemistry to yield the final results.

When we talk about PCR, we’re talking about traditional amplification. The benefit of PCR is that it probably remains 1 of the most sensitive and easily adapted technologies. This is all flavors of PCR…. Next-generation sequencing is the newer approach. Next-generation sequencing is going to be quite a bit more expensive. It’s going to require more expertise within the laboratory, so it’s not going to be as ubiquitous. Next-generation sequencing is the platform is the technology behind the platforms that have launched, including several highly visible commercial labs that everyone is familiar with. Next-generation sequencing does require a little more material to do the initial testing. However, with next-generation sequencing, you can get many more results because of the massive, paralleled testing that goes on with it. At the end of the day, next-generation sequencing is going to be the most common method used when you’re looking for multiple biomarkers.

Also, because of the inherent way next-generation sequencing is performed, and the bioinformatics pipeline that’s used to interpret the data that comes out of the analyzer, next-generation sequencing can be used to find small mutations—point mutations, small insertion deletions—as well as larger abnormalities, such as gene amplification and gene rearrangement fusions. A third methodology that you could probably include when we talk about testing solid tumors would be fluorescence in situ hybridization [FISH].

FISH is commonly used today for HER2 [human epidermal growth factor receptor 2] testing. FISH cannot identify those small mutations within the DNA. It looks for larger events, such as translocations deletions, duplications, amplifications, or those types of events. The benefit to FISH is that you can know by looking through the microscope, when you interpret it, that you’re indeed analyzing tumor cells. One downside to FISH—there are probably multiple downsides to FISH because it’s 1 of the older methodologies—is that you’re not going to see this analytic sensitivity that’s in situations where you don’t have many tumor cells. The ability to analyze them is a little more restricted. All the different methodologies are going to have different pros and cons.

Timothy J. Pluard, MD:Let me shift a little. Sujith, you talked about both tissue biopsies and liquid biopsies. I’m curious about what each of you think the role is. Obviously, in situations where we don’t have accessible tissue, liquid biopsies play an important role. But is there a role for doing both tissue and liquid biopsies? If so, should they be done concurrently? Do you think they should be done sequentially? There can be additive information because a tissue biopsy is sampling only 1 location, whereas a liquid biopsy is giving you the sum of all the sites where there may be disease. Sujith, share your thoughts on that.

Sujith R. Kalmadi, MD: In colon cancer, there’s not much treatment I can add onto frontline standard treatment with chemotherapy plus bevacizumab or something like that. It doesn’t really make a difference. Tissue procurement is easy because typically it’s in the liver, and I can get a big liver biopsy very easily. In colon cancer, I don’t send circulating tumor DNA. I send just a tissue testing [to the lab], and I don’t do them. If I can’t get it, then I may sequentially send it.

On the other hand, in lung cancer, it’s critical to know if a patient has an EGFR or ALK mutation—which has very relevant frontline treatment—so I send off both of them when I see the patient. Invariably, we wait for the results to come back before we start treatment. That’s because if we don’t start a tyrosine kinase inhibitor [TKI] for EGFR mutation in lung cancer, and if you start them on immunotherapy and subsequently put them on EGFR TKI, the risk of pneumonitis is exponentially increased. Because of that risk,we’d rather put them on a TKI before we put them on immunotherapy.

In lung cancer, I send both so I have all the information available. Typically, there’s a time lag. For circulating tumor DNA, I get my results back within 7 days. For a tissue sample, it may take 2 weeks, sometimes up to 3 weeks. If I have the first information from a circulating tumor DNA and PD-L1 testing done on an IHC [immunohistochemistry] platform, which typically takes 2 to 3 days, that gives me enough information to start my frontline lung cancer treatment. I won’t wait for the tissue results to come back. Obviously, there’s the chance of having not enough specimen, which is the dreaded report we get from them. Then we have to do a second biopsy. I don’t have to worry too much about that. That’s what I do in lung cancer, in sharp contrast with colon cancer.

Transcript edited for clarity.

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