Molecular Testing Options in Colorectal Cancer

A pathologist explains how she chooses between a variety of molecular testing technology options in colorectal cancer.

Andrea Cercek, MD: In terms of technology, you mentioned Sanger sequencing initially, now we do next-generation sequencing. What do you use? Do you use next-generation sequencing, IHC [immunohistochemistry]? What are the best options for us in colorectal cancer?

Jaclyn Hechtman, MD: It’s dependent on multiple factors. It’s what’s available, and what your timeline is, sometimes a really fast answer is desired, and based on how much tissue you have, and the quality of tissue. Going down the list of some of these biomarkers, for KRAS, NRAS, and BRAF mutations, we are always doing sequencing. Whether it’s next-generation sequencing or Sanger sequencing, we’re sequencing the DNA to determine a point mutation status. For microsatellite instability [MSI], we extract the DNA. It’s a DNA-based test again, we can do it by next-generation sequencing, or we can do it with PCR [polymerase chain reaction]-based tests that are a little simpler. Sometimes instead of, or in addition to, microsatellite instability testing, we test for mismatch repair [MMR] deficiency, and those are IHC markers. There are 4, and this is commonly done. The sensitivity and specificity of MMR IHC is very good, but nothing’s perfect, and because of that, we sometimes do MSI status plus MMR IHC because it’s such an important biomarker to determine eligibility for new checkpoint inhibitors, as well as screening for Lynch syndrome in patients with colon cancer.

For NTRK gene fusions, we can do IHC as a screen, so we have an NTRK IHC. But in a lot of the newer, more broad next-generation sequencing assays, we find the majority of NTRK gene fusions, even if we’re looking at just the DNA, but the RNA ones are even more sensitive. So there are RNA next-generation sequencing assays for fusions. And then when we get to HER2 amplification, it’s a little different. These can be detected by next-generation sequencing provided we have good enough tumor purity. But if a quick answer is desired, we have low tumor purity, or if we have very little tissue in total, like a small biopsy, then we have other methodologies. IHC is one methodology, and often when IHC is equivocal, meaning the staining is of moderate intensity, we reflex to fluorescent in situ hybridization [FISH]. IHC and FISH are these piecemeal assays that only detect 1 thing, but they’re faster, so each assay has its advantages and disadvantages.

Andrea Cercek, MD: That’s the key point, in general, for community oncologists where you’re sitting in front of a patient with metastatic colorectal cancer, you want as many answers as possible with the test to determine the next steps in treatment. So next-generation sequencing really provides us with MSI information, RAS information, and HER2 amplification. As you said, it’s not perfect. The issue with that is it takes some time to get those results. But something like mismatch repair deficiency to offer potentially immunotherapy for a patient who’s mismatch repair deficient, or for genetic screening for Lynch syndrome is a very quick turnaround, and can help guide first-line therapies. It’s as you said exactly, a little dependent on what we’re looking for and what the timing of things is. But certainly, the most comprehensive I would say is next-generation sequencing, which really should be done on all patients at some point, preferably at the beginning, at the time of diagnosis.

Transcript edited for clarity.

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