Have you ever wondered how scientists unlock the secrets of our DNA to diagnose and treat our myeloma? Today, we're diving into three powerful tools used in modern medicine to look at our genetic blueprint: karyotyping, FISH testing, and the cutting-edge next generation sequencing, or NGS. While they all help detect changes in our genes, they do it in very different ways. So how exactly does NGS stand apart from the others, and why is it transforming the way we understand cancer? Let's explore the fascinating differences.
How does next generation sequencing differ from karyotyping and FISH testing? So when it comes to evaluating the genetics for myeloma patients, remember that we're not looking at the genetics that you inherited from your parents or share with siblings or passed on to your children. We're looking at the genetic changes in the myeloma cells themselves. And for the most part, nowadays we have three main types of genetic testing. One is called karyotyping. And again, just so that we have a kind of shared lexicon, when we're looking at karyotyping, we're looking at 20 cells. And then you kind of crack them open like eggs and spread out the chromosomes. Here we're looking—we know we have two pairs of 23 chromosomes and then sex chromosomes: XX for women, XY for men. And this is just looking at 20 cells for any main translocation. That's where two chromosomes swap material, deletions where part of the chromosome is deleted, or additions where there's extra material on that chromosome. And this actually just looks at, again, 20 cells. So it's not that fine-tuned. And it doesn't look for anything specific for myeloma. It just looks for any changes.
Then there's FISH. FISH stands for Fluorescent In Situ Hybridization. And we kind of jokingly say we're going fishing for abnormalities in the myeloma cells. Here we look at 200 to 400 cells typically. And in general we have panels, meaning if we think you have myeloma, we're going to send the myeloma FISH panel which looks for specific additions, deletions, and translocations that we know have meaning in myeloma, either in terms of prognosis—some of these you do better, some you do worse—or therapeutics. For example, we know that if you have an 11;14 translocation, drugs like Venetoclax may work very well for your disease.
More recently, we began to use another sequencing technique that we call NGS, or next generation sequencing. And here we look at these large panels of genes to see which ones are turned on, which ones are turned off, which ones are overexpressed. This gives us a lot of information across a variety of things. One, it looks for some abnormalities we know have direct impact on myeloma. Secondarily, we look for something called CHIP mutations. That stands for clonal hematopoiesis of indeterminate potential. Much like MGUS can be a precursor to myeloma, CHIP can be a precursor to other disorders like myelodysplastic syndrome. So this gives us some insight about what therapies may have higher risks for causing secondary cancers.
The other thing we can use NGS for is that it turns out there are a number of what we call actionable mutations, meaning there's some genetic abnormalities that are more common in other cancers that have drugs that are already approved to target them, which we can now use in myeloma. For example, there's something called a BRAF mutation, which is in over 95% of melanoma. And there are many drugs approved. It turns out that about 10 to 20% of myeloma will have this type of abnormality as well. So sometimes when we have fewer standard therapies and we find these actionable mutations, we can actually take drugs designed to treat other cancers and use them to treat patients with myeloma.
To learn more about BRAF, KRAS, NRAS, CHIP, and actionable mutations, watch the lessons on these topics in HealthTree’s Chromosomal and Gene Abnormalities course.
How long have karyotyping, FISH testing, and next generation sequencing been used to evaluate myeloma? We've been doing karyotyping for a really, really long time, for many decades. Karyotyping is looking at the chromosomes of the cancer cell and trying to identify abnormalities in the chromosomes. We're talking about mutations—but big mutations—where a huge chunk of DNA is lost, for example, a deletion, an insertion, or a translocation. These are called structural abnormalities of the chromosomes. So that we've been doing for a long time. More recently, we started doing FISH. FISH is fluorescence in situ hybridization. This is a more sophisticated way of approaching this where we say, well, we know what the specific alterations are in myeloma that are associated with high risk, for example. So let's go looking specifically with probes and get a yes/no answer: is this abnormality present or not.
Now we're getting to the next generation of doing this type of profiling, where we're going deeper at a gene level. When you lose a big chunk of your DNA, you're losing many genes at a time. But what happens if that's not the situation, but there's just some change that happens at a gene level? Maybe that gene alone is the one that's no longer active, or it's hyperactive. You can only detect this by doing next generation sequencing studies, usually from a bone marrow aspirate.
Is next generation sequencing a standard of care test in myeloma? NGS, or next generation sequencing, is kind of right at that cusp of standard of care. There are many centers that now routinely involve NGS testing on the bone marrow, but a lot of centers are not quite there yet. So I think we're on the verge of this becoming a standard of care, but it's not going to be sent for everyone, every time.
We learned in a previous HealthTree University lesson that next generation sequencing technologies offer three main approaches for DNA sequencing: whole genome sequencing, whole exome sequencing, and targeted gene panels. Targeted gene panels are what is primarily used in myeloma. To learn more about these three approaches, watch the “What is Next Generation Sequencing” lesson in this course.
Can you explain what genes are examined when a next generation sequencing test is performed? There are a bunch of commercial third parties that tend to run it. Two of the more common ones are Foundation Medicine and NeoGenomics. Each of them have their different panels. They can have an “all-haem panel,” which looks at abnormalities we tend to see in blood disorders. We can have myeloma or lymphoma specific panels. There is some variance between them about which thousand genes each one looks at. But some of the more common ones that we know have meaning are usually included in all of the panels.
Are the next generation sequencing panels used in myeloma fixed or evolving? Because there is no clear indication to do this in myeloma, most of them don't have a specific myeloma panel. They have a panel that they use for other cancers that they can adapt or tailor to a patient with myeloma. And that is ever-evolving. As more data comes in, we may find that a gene might actually have some significance in myeloma. Let's say, for example, the BCMA gene. Many novel treatments in myeloma are BCMA-directed therapies. So what does it mean if a patient has a mutation in the BCMA gene? Maybe that makes them more likely to respond to a BCMA treatment, or less likely. That has certain implications, and we have to start looking at that. As we produce more research that makes its way to the clinic, it will become more widely available.
To better understand the laboratory technologies used to analyze genetic abnormalities in myeloma and assess your risk status, watch the other videos in HealthTree University’s Cytogenetic Testing in Myeloma course. If you found this video helpful, consider giving us a like and subscribing to HealthTree University.