Dr. Cori Cross (Host): This is Transformational Pediatrics with Children's Mercy, Kansas City. I'm your host, Dr. Cori Cross. Today, we are discussing a truly exciting topic, optical genome mapping. Children's Mercy, Kansas City is the first pediatric hospital in the United States to clinically launch optical genome mapping, an advanced digitalized technology that enhances the detection of genetic abnormalities.

 Today, we will be speaking with the Assistant Director of the Cytogenetic Laboratory at Children's Mercy, Kansas City, Dr. John Herriges. Dr. Herriges will be discussing what optical genome mapping means for pediatrics and how it will change pediatric patient care in the future. Dr. Herriges, thank you for being here with us today.

Dr. John Herriges: Thanks for having me.

Host: So, Children's Mercy Kansas City is the first pediatric hospital in the U.S. to use optical genome mapping. How is this type of genome mapping different and more advanced than other more traditional testing?

Dr. John Herriges: So, I think what optical genome mapping really brings to the table is the ability for us to look at structural rearrangements within the genome at a resolution of a gene and at a genome-wide scale. So right now, traditional testing that we use in our cytogenetics lab are chromosome analysis, so karyotyping, which is the banding of chromosomes, it's low resolution and FISH analysis. FISH analysis is very targeted and you only look for what you set out to look for. And there's a lot of things you can miss in doing that. Chromosomes are very coarse, so they don't give us high resolution. So, optical genome mapping really provides us the opportunity to, identify novel gene fusions that could impact cancer treatment, therapy, or ends to identify novel rearrangements within the constitutional germline realm that will give patients diagnoses.

Host: So when you say when you do FISH, you have to know what you're basically FISHing for, right? And that you go in looking for that. Are you saying that with optical genome mapping, you don't have to be specific in what you're looking for? You're getting a broader picture of everything, but more crisp than you would with the coarse way that you were doing the full chromosome?

Dr. John Herriges: Exactly. So right now, the WHO for leukemias, they define different leukemias based on different genetic rearrangements or fusions. And so, we will target those fusions with FISH probes to identify the most common rearrangements. But it's not possible for us to target everything. So, there are certain things that might slip through the cracks, just because it's just not practical to FISH everyone for every different gene fusion that's out there.

So, what optical genome mapping does is it gets around that and it will just blindly look for everything, like every different type of rearrangement. So, we had cases in our validation where we weren't looking for a specific type of rearrangement, but we found it. And we were able to confirm it with FISH, and FISH had missed it previously just because we hadn't FISHed for that. So, the biggest thing that this brings to the table is that it will allow us to identify novel rearrangements within pediatric cancer patients that will allow us to, hopefully, have a better outcome through change in therapy.

Host: So, is it possible then you'll actually find rearrangements? So right now, like say we're looking at a particular type of cancer, we know that there are certain things genetically that can lead to that, but we might not know all the combinations. Are you saying that you're now able to find other combinations that we didn't even know existed before?

Dr. John Herriges: Exactly. So, there are certain genes that we know are rearranged, and they have multiple different partners when they have rearrangements. And those partner genes can impact therapy. So, for example, like a KMT2A rearrangement in a pediatric ALL patient. If it has one partner, that can be associated with a better prognosis than if has a different partner. And that will change therapy decisions. So, because there are so many different partner genes with KMT2A, we can't FISH for all of them, and we will just say that this is a KMT2A-rearranged ALL patient. And OGM will basically allow us to identify those partner genes which will impact therapy decisions.

Host: That's amazing. So, walk us through a little bit of OGM or optical genome mapping. How does the testing take place? What's the validation process?

Dr. John Herriges: Optical genome mapping is done on high-molecular weight DNA. It's really, really large strands of DNA that are labeled at this six-base pair hexagon. These long strands of DNA after they're labeled, they're run through these nanochannels that are imaged, and then these images are compiled into sort of a map for your patient that is compared against a reference genome, a normal individual. And using this, we can tell whether or not there's a gene that's deleted or a gene that's rearranged.

So, for our validation, we reviewed 65 cases that had been tested using traditional techniques. These were all blindly analyzed. And these were 65 abnormal cases. And then additionally, we looked at a number of normal cases as well, just to make sure that we weren't having any false positives. These cases that we picked had some classic cytogenetic abnormalities, such as aneuploidies, which are gains of chromosomes or losses of whole chromosomes; segmental copy number variants, which is deletions or duplications of genes; translocations and fusions. Classic example is a BCR-ABL translocation, 9;22 translocation, that leads to that fusion, that is seen in ALL and CML complex events like chromothripsis or just catastrophic events within the genome that lead to different fusions, as well as we tried to put in a number of rearrangements that we felt would challenge the OGM platform, such as IGH rearrangements, T-cell receptor rearrangements, that are known to be sort of challenging regions for the OGM platform.

So, all of these cases that we analyzed were analyzed blind, meaning that we didn't know what the abnormality was going to be for each of these cases. They were all compared to traditional testing methodologies, chromosomes, FISH, and array. And we looked at basically all the results that had been reported in traditional testing methodologies and compared the results of OGM to those. And there were 465 total calls using traditional testing methodologies. Of those, 446 were confirmed by OGM.

 Importantly, none of the missed calls would have impacted tumor classification or therapy. And even though we were not really setting out as part of the validation to identify novel, rearrangements, we did identify two cases as part of our validation that had these novel rearrangements that we didn't know about prior to the validation starting. And we were able to confirm that they were in fact true rearrangements, using the traditional testing methodologies. And these were both examples of rearrangements basically that we didn't think to look for because they were rare. And we were able to find them using OGM.

Host: So when you use OGM, you draw a patient's blood, right?

Dr. John Herriges: So yeah, blood or bone marrow.

Host: And the optical has nothing to do with the eye. It's that you're visualizing it directly. Correct?

Dr. John Herriges: Yeah, it has nothing to do with the eye.

Host: So, you draw the patient's blood or bone marrow, and you obviously run the OGM. How long does it take to get these results comparatively to the older way of doing it?

Dr. John Herriges: So, it takes roughly the same amount of time to get all of the results. So traditionally, we would be running FISH chromosomes in array on all of these patients. If we just run OGM, we can get all of the results in the same amount of time as those testing methodologies.

Host: What impact do you hope that these capabilities or OGM has on your patient population?

Dr. John Herriges: My hope from the cancer side of things is that patients won't slip through the cracks, we will be able to identify these novel fusions that could impact therapy. For example, in ALL patients, the activation of tyrosine kinase pathway through fusions can be targeted with tyrosine kinase inhibitors. So, the hope is that, if we identify a novel fusion that should lead to activation of a tyrosine kinase pathway, that we would know that, and we would be able to provide that information to the oncologist, the providers that are going to be treating this patient, and they would then be able to make informed decisions about whether or not that type of therapy would be warranted in this patient.

Host: I would assume that it's sort of almost like a secular process too. So as you're learning about different fusions, and then you're seeing and following these patients through their treatments, you may learn more about how these fusions react to different treatments, and then be able to get that knowledge and bring it forward. Because at first, it sounds like we didn't actually know all these fusions were either possible or we weren't able to track them as well. So, it seemed like now we'll have more information to actually track and then maybe learn more from that as well.

Dr. John Herriges: Oh, 100%. And I think it's going to be sort of like a snowball effect. It might have less impact initially. But as we understand more and more about these novel fusions, it will have more impact going forward in terms of how we treat these patients. And I think, one of the big things that I'm going to try to be pushing for is to publish more of these cases so that it can get out into the literature, so that more people can understand that there are these novel fusions out there. And they may be rare, but if you were looking across the entire country, it's going to affect a not small number of individuals. And collectively, the hope is that it would be, in fact, more patients.

Host: No, that makes perfect sense. As we wrap up, what do you see as the future or what's next for optical genome mapping in Children's Mercy, Kansas City?

Dr. John Herriges: The next big step is going to be to use this on solid tumors. So right now, we are primarily using this on leukemias because the DNA isolation procedure is a little challenging, and we've gotten that down at this point for the leukemia samples, the bloods and bone marrows. Solid tumors are a little bit more challenging, and our hope is that we will soon be able to get those isolations down and be able to utilize this technology in solid tumors, because gene fusions are also a critical part of tumor genesis within solid tumors.

Host: Oh, absolutely. Well, Dr. Herriges, thank you so much for joining us today and sharing your expertise. This was groundbreaking technology and science, and it was just really interesting to learn about. So, thank you.

Dr. John Herriges: Thanks for having me.

Host: To learn more about Children's Mercy Kansas City, to get connected with one of our providers, or to refer a patient, please visit childrensmercy.org. That's childrensmercy.org. That concludes this episode of Transformational Pediatrics with Children's Mercy Kansas City. If you found this podcast helpful, please share it on your social channels and be sure to check out the entire podcast library for other topics that might be of interest to you.

Please remember to subscribe, rate, and review this podcast and all other Children's Mercy podcasts. I'm your host, Dr. Cori Cross. Thank you for listening.