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July 20, 2020 – Dr. Kelly Diehl talks with Dr. Annette McCoy, an assistant professor of Equine Surgery at the University of Illinois Urbana-Champaign. The two discuss osteochondrosis, a significant health and welfare issue for horses. They also cover Dr. McCoy’s Morris Animal Foundation-funded study to try to identify genetic risk factors for development of the disease.

00:10 Dr. Kelly Diehl: Welcome to Fresh Scoop, Episode 23, Osteochondrosis in Horses: New Understanding of an Old Foe. I'm your host, Dr. Kelly Diehl, Morris Animal Foundation Senior Director of Science and Communication. And today we'll talk to Dr. Annette McCoy, a Morris Animal Foundation-funded researcher and geneticist. Dr. McCoy is an assistant professor of Equine Surgery at the University of Illinois Urbana-Champaign. Fresh Scoop is the monthly podcast of Morris Animal Foundation, one of the largest non-profit foundations in the world, dedicated to funding studies to find solutions to serious health threats to animals. And in each episode we'll feature one of the researchers we fund or one of our staff members, discussing their work in advancing animal health. Whether you are a practicing veterinarian, technician or student or just an animal loving science geek, Fresh Scoop is the podcast for you. You can learn more about us at

01:10 DD: So on to today's show. And today we welcome, as I mentioned, Dr. Annette McCoy. Since 2015, she has been an assistant professor in Equine Surgery at the University of Illinois College of Veterinary Medicine, where she splits her time between research, teaching and her clinical work as an equine surgeon. Dr. McCoy's research interests include investigating the underlying genetic factors that play a role in the development of orthopedic disease in horses, both developmental and degenerative. She also investigates the role of genetics in the development of gait. Clinical research interests include wound healing and gastrointestinal disease. Annette, thanks for joining us today.

01:49 Dr. Annette McCoy: Thanks for having me.

01:52 DD: So before we get into your work, we always ask everyone to tell us a little bit about yourself and your background, and what drew you to veterinary medicine.

02:02 DM: Sure. I was definitely one of those kids that decided at an early age that I wanted to be a veterinarian. I didn't have a strong, large animal background, but I knew that being well-rounded was really important for veterinarians and getting into vet school. So when I was an undergraduate, I went into Animal Science and I was always a horse person in terms of I liked riding and just being with them, but really in undergrad and vet school was when I really decided that horses were the way I wanted to take my career. So that sort of sent me off in that direction. And I was interested in surgery, and so the combination of those two things really added up to the clinical side of my interests. And I can also credit my undergraduate experience with my interest in genetics, because that is where I got started with that, was with a project in a dog genetics lab as an undergraduate, and that really sparked my interest in that field, and then happily I was able to come back to it as a PhD student.

03:10 DD: Great. And you just talked a little bit about this, but why did you decide to focus a lot of your research on orthopedic diseases in horses, and specifically taking a genetics lens when you look at those problems?

03:27 DM: Orthopedic disease is one of those things that affects everybody: All species, all disciplines, and so it's really a universal thing, and so I love the fact that the research that I do can really have lots of different applications. And so, from a clinical perspective as an equine surgeon I deal with orthopedic disease literally every day on the clinic floor. It's a huge problem in our patients, both the developmental diseases that we see in the foals and then also degenerative diseases that we see in our athletes and older horses of all types. And so it's really that universal problem that we don't have a lot of solutions for yet, despite lots of research. And so, the genetics angle really excites me because it really digs down into the underlying reasons why all this happens. And so, if we can understand those earliest steps, then that will help us as we develop new diagnostics and new therapeutics that can hopefully address the orthopedic issues that we see clinically on a daily basis.

04:39 DD: There are a lot of folks who are listening, and I would include me in this, who probably don't know a lot about horses in general. And you spoke to just now, a lot of your work as a surgeon is orthopedic diseases. Can you give us a broad picture of the frequency of orthopedic diseases in horses and some of the financial and quality of life costs of orthopedic disease?

05:09 DM: Yeah, absolutely. We know that lameness, which is typically related to orthopedic disease, is the most common cause for horses to not be able to perform their normal activity. And so it's a huge health issue in horses across breeds and across disciplines. The economic costs in dollars are hard to quantify, but because osteoarthritis in particular, which is quite common, is a degenerative progressive condition, this is not the type of thing where you do surgery and you fix it, or you give a medication and you fix it. This is a life-long management issue. And horses are often, especially if they are in a really high level athletic capacity, they often develop signs early in their life, and so the care of those patients continues throughout their entire life, and it can certainly shorten both their athletic career and their overall lifespan based on quality of life issues. So, in terms of what we see in foals, that can also affect their ability to go on and do whatever they were supposed to do with their life. So it really affects all segments and, as I said earlier, is probably the most common reason for presentation to a surgical or sports medicine service at a veterinary practice.

06:43 DD: Okay, thanks for that. Let's cone down a little bit, because I know a lot of your research has focused on osteochondrosis. So can you talk a little bit about that disease in horses? And if you want to talk about it in dogs too, just so people have some kind of idea, a comparative idea, that would be great.

07:04 DM: Sure, yeah. So when the skeleton forms in any animal, the bones actually start out as cartilage, and then as the animal develops that cartilage turns into bone. And at the end of long bones, so long ones are like the tibia or the humerus, so the long bones in the body, at the ends of those, of course, those turn into joints in the places where the two bones come together. And so the cap of those long bones is a special kind of cartilage that over time develops again into bone, and then the articular cartilage that covers the joint surface. And so in Osteochondrosis, there is what we call delayed ossification. So that process where the cartilage would normally turn into bone gets delayed for some reason. And there's lots of ideas and theories as to why this might happen, and we don't know 100% the exact molecular events, but we do think that disruptions in blood supply to that part of the bone probably play a pretty important role in the disease process itself.

08:17 DM: And so, under most circumstances, really in about 70% of cases, that delayed ossification, even though it's behind schedule, so to speak, goes on, does its thing, and you end up with a normally formed bone underneath a normal joint. But in the remainder of the cases, some sort of external force, it maybe trauma, it may be repeated trauma, sort of sub-clinical trauma, we're not talking about an accident, we're talking about the daily work that this foal is doing just walking around, you can get damage through that cartilage that was supposed to be bone but isn't. And so that can lead to a breaking off of a large chip or fragment into the joint, and so that's what people commonly will call osteochondrosis dissecans or OCD. OCD lesions in this context refer to those large fragments of bone and cartilage that have broken off from the ends of those joints.

09:27 DM: And it's really, again, it's a fairly universal disease. I study it in horses, it is common in dogs, it's common in pigs, it's common in people. And the interesting thing about this disease is that there's a lot of shared what we call predilection sites between species. So in horses, for example, the hock, which is the tarsus or the ankle, that's the equivalent, in a dog or human, is one of the predilection sites, and we also see that very commonly in people. In dogs, we see it more commonly in the elbow, for example, and that is also a common predilection location in pigs. So we think that there's probably a shared underlying cause for this disease across species, which makes it really interesting to investigate.

10:16 DD: So you mentioned, again, it's a pretty broad disease as far as the individuals it affects, but is there a breed predisposition in horses or not?

10:27 DM: Yeah, so if we look at the information that's out there looking at large populations of horses, we do notice that there are differences between breeds. So for example, I work primarily with Standardbred horses, and they are known to be predisposed to lesions in their hock, their tarsus. If you look at Thoroughbreds, they are much less likely to have hock lesions, they're more likely to have stifle lesions, so in their femorotibial joint or femoropatellar joint, whereas Quarter Horses actually seem to have a very low prevalence of this disease. And so one of the things that we're interested in from a genetics perspective is why would Standardbreds and Quarter Horses have a different frequency of disease, but then also why would Standardbreds and Thoroughbreds have the disease showing up in different locations? So that's one of the questions that we're trying to tease apart from the genetics perspective.

11:23 DD: And we'll talk a little bit more about this, but for those who are listening, and you can correct me because now I'm going to show my tiny bit of horse knowledge and having grown up near the Meadowlands in New Jersey, Standardbreds are for people who know, harness racing horses typically, so they're the gaited horses that you see versus the flat racing the Thoroughbreds do, and we'll get more to that, I think, because if you recall from our introduction everyone, this is something that Annette studies too, which is gait and the influence on this disease. So I'm going to ask you for a big heavy lift here, which is Annette's had several grants, and I'm going to put her on the spot in trying to summarize from a high level her grant portfolio with the Foundation.

12:16 DM: Yeah, so we've sort of been working in stages on this same big picture or big map of what we're trying to do. So the big idea of what we're trying to do is we're trying to identify genetic risk factors for development of disease. We know that genetics is not the whole story when it comes to osteochondrosis. We know that environmental factors play a role. And so when you have a disease like osteochondrosis where you have genetic factors and environmental factors, we call that a complex disease. And so, we also know that it's what we call a polygenic disease. That means that unlike something like, say, cystic fibrosis or sickle cell anemia, it's not one gene that causes this disease, it's the combined action of many genes working together. And so with that in mind, we have to take a very specific approach to discovering these risk factors, or these risk genes or risk alleles.

13:19 DM: And so that involves taking a large population of horses that have been what we call phenotyped, so they've been identified as either having the disease or not having the disease. So they're selected as cases or controls, affected or unaffected. And we look at them across their genome. So we get lots of information about their genetic code, and we look for differences between affected and unaffected animals, and those are our road map. Where there are differences, those are places that we're interested in looking at more closely. And so we kind of zoom in on those locations and then we start looking for more specific variants between the two groups. And so we're taking sort of the... I like to use a forest analogy, so the genome is like a forest and we're trying to find the tree, where our risk factor is, and then from the tree, now we've got to identify all the leaves on the tree. And then we've got to pick through the leaves to find the one leaf that's the most important, and then we move on to the next tree.

14:28 DM: So, in the first study that we did with Morris, we used... It's large, but in the scheme of genetic studies it's a relatively small population of horses. So a little bit under 200 horses were in that first study, and they were phenotyped and we did that coning down view, and we identified some regions of the genome that seemed to be associated with osteochondrosis in that population. And then we looked for new variants, so changes in the genetic code that had not been previously reported. And then we tested those in the same population and said, "Are they the same or are they different?" And when we found some that we thought were really interesting and that could be close to what we were looking for, then we went and looked at a different population of horses and we said, "Okay, our population says that these might be important. Let's go see if this other population says that they're important as well."

15:29 DM: And what we found was that although the specific markers were not shared between the two populations, the regions of the genome were shared between the two populations. So we know that we've found the right tree, per se, but we're still looking for the leaf. So our current project is now expanding this to from 200 horses to a 1000 horses. We're going from a relatively coarse mapping of the genome to a very fine mapping of the genome. So again, think about if you were trying to get from Kansas City to St. Louis, and you only had markers on your map every 50 miles, you might get lost in between if you didn't have something more specific. So we're going from a map that has markers every 50 miles to a map that has a marker every 50 feet, so to speak. So it's a much more fine map and it'll help us to dig down to the more specific locations that we're looking for.

16:38 DM: The other thing that we've added onto this is what we call gene expression or transcriptomics data. So, we know that the tissues that are really important in development of osteochondrosis are cartilage and bone, because that's what's in the joint. And so by looking at genes that are expressed in cartilage and bone, that can help us to narrow down our search as well. Because if we find a difference in between cases and controls, but it's in a gene that isn't expressed in those tissues, it's highly unlikely that that gene is involved in the disease. So we're using that, what we call tissue-specific gene expression, to help us narrow down our focus as well. And then in the last phase of the project, which we haven't done yet, this is the current project that we're working on, what we'll do is we'll take those alleles or variants that we think are most likely to be important, and we're going to go through that validation process again in a separate population. So we've started small and now we're getting big, and then we're going to focus down again.

17:50 DD: And I think you answered one of my other questions, which was looking at when you find a difference, how you figure out whether it is associated with the disease or not, and I think that was an interesting thought. I don't think of that very often about looking at what is expressed in the tissue, then. So I have a little tiny side bar here, and I'm going to put you on the spot for two terms that I hear all the time, and I think they're confusing, which is what we call a SNP and a GWAS. And I think they're bandied a lot about. People are hearing more about genetic analysis of viruses, for example, COVID and things like that, so can you explain what a SNP and a GWAS are?

18:41 DM: Yeah, absolutely. So SNP, or S-N-P, stands for Single Nucleotide Polymorphism. So your genetic code is made up of a series of 3 billion bases, and so those bases are A, G, C and T. And so your genetic code is just a very long series of letters, and each of those corresponds to a base and they are paired with each other and that makes up your DNA. So, my DNA and your DNA are different from each other in lots of places. So out of three billion base pairs, our DNA is probably different at at least three million of those base pairs, and that's between me and you, between you and the person you meet on the street. So that is the natural underlying variation that makes me, me and you, you and every person an individual, and it's the same for animals. Most of our species that we interact with, horses, dogs, etcetera, have about three billion base pairs and they vary from each other.

19:47 DM: So those variations, the most common one is at the single base pair level. So I have an A, you have a G. That is what we call a single nucleotide polymorphism. Polymorphism meaning "different" or "difference". So we can use those differences where I have an A and you have a G, and we can quantitate those. So we can say, "What percentage of the population has an A, what percentage of the population has a G?" And we call those allele frequencies; the A and the G are what we call alleles. They're different variations of that base pair at that specific location. And we scan for those across the entire genome.

20:30 DM: And so, every place where there's a difference, that's what we call a SNP. And so we use SNPs in our GWAS, which stands for genome-wide association study. Some people will also call it a GWAA, which is a genome-wide association analysis, but it's essentially the same thing. The idea here is it's just a statistical test. You have a large population of individuals that have been genotyped at lots of SNPs. So we know whether they have an A or a G or a C or a T at hundreds of thousands to millions of locations across the genome. And then we split those individuals into cases and controls or into... Maybe there's a, what we call, a continuous factor, like weight or height that we assign to those people. And then we simply run a statistical test and we say, "At which locations in the genome is there a difference in the allele frequency between our cases and our controls?"

21:33 DM: So let's say on average, 50% of individuals have an A and 50% of individuals have a G at this one location, but if instead 90% of cases and only 10% of controls have a G at that location, that's a significant difference that tells us that that may be important, that may be an important difference between those two individuals. Now, having said that, there are lots of reasons why there might be a difference and that difference may have nothing to do with the question that we're actually interested in. And so, that's where you have to be careful with GWAS, because it's just statistics, it doesn't mean anything by itself. You have to dig down to the actual biology behind it to find the stuff that makes sense in the context of the condition or disease or trait that you're looking at.

22:22 DD: Okay. And that, I think, ties back to what you said, which is finding the difference is just the beginning of really evaluating whether it's an important difference or not. So you find the difference first by screening lots of individuals, and then you start focusing down on the leaf to decide if that leaf really is... That difference means something, or the difference means you have blue eyes versus brown eyes.

22:51 DM: Exactly. Yeah, and that's actually, it's really applicable in my own research because... You said I look at gait and I look at osteochondrosis. I actually use the same population of horses to do both studies, so I have Standardbreds that are affected and unaffected with osteochondrosis, and they are pacers and trotters. So they have two phenotypes at a minimum that may make them different from each other. And so whether I'm asking a question about osteochondrosis or whether I'm asking a question about gait, I have to accept the fact that that specific difference that I'm looking at could be due to another reason why those two individuals are different and not the one that I'm looking for. So that's where, again... I think that there's been a lot of hype about, "Oh, this gene was associated with this trait." Well, that's true. But at that point, it's just correlation, it's not a causation. So we have to do more to show causation. And one of the really important steps in that is validation in an independent population, and that's where a lot of GWAS that's been published falls short.

24:00 DM: And that's not anything against GWAS. GWAS is an important tool in our toolbox for looking particularly at complex diseases, but just because you found it in one population doesn't mean it holds true in a second population, and that's where I think a lot of confusion about this approach comes in, is that it is completely valid to report a GWAS, and say, "This is what we found in this population." But the next step is looking at it in another population and seeing if it holds true. If it doesn't hold true, it doesn't mean it's wrong, it just means that it's not true in that second population, and then you have to figure out why that might be.

24:41 DD: Right. So, in all these studies you've been doing, has something surprised you that came out of your research that you were... You formulate a hypothesis and you're going to test it, but I think we all have ideas how things are going to come out at the other end. And did you find something that really was not what you were expecting?

25:04 DM: It's an interesting question because I actually live very much in a hypothesis-generating world when I do a lot of my genetic studies, and there's a huge debate in the scientific community about hypothesis-driven research versus hypothesis-generating research. And so, we actually go into these large genetic studies with a very open mind. We aren't expecting one particular response or one particular answer to pop out at us, we use the GWAS to generate ideas about where we need to go from a mechanistic perspective next. We call them agnostic approaches to science because we don't have any pre-conceived ideas. I did find it really interesting, and this is work that we've already published, when we went to validate the specific variants that we had found in our first population, when we went to validate them in the second population, the interesting thing about that second population is that they had already published a GWAS in that population.

26:19 DM: And we found that the markers that we tested, which I should say were not in either GWAS, they weren't in our GWAS, they weren't in their GWAS, they were novel ones that we had found. Through our identifying the leaves on the tree, right. They were more highly associated with disease in that validation population than their original GWAS results. And so, that really brought home the point that, as long as we're working with these very sparsely populated maps, so to speak, we may be missing something. And so the exciting thing moving forward is that now we have the tools that allow us to look on a much more fine scale, and that will hopefully help us to really move this project forward and not just this disease, but any complex disease should be advanced forward because of these advances in technology over the past few years.

27:24 DD: That's pretty interesting, and now I'm going to ask you to take a step back again. And how do you feel your findings can actually benefit horses with osteochondrosis or how we manage them?

27:39 DM: Yeah. So our long-term goal for this project and really for this whole series of projects is going to be the development of a risk assessment test. So it's not going to be a traditional genetics, genetic test, in the sense that you're not going to turn in the sample and say, "Yes, it's affected or No, it's not affected." The idea here would be to test a panel of genes and then tell you if the horse falls in a low, moderate or high risk category. And so, ways that that can then be used would be, for example, if you have a young horse that is in a high genetic risk category, you may change your management, to not push them nutritionally, for example, because we know that nutrition can play a role in disease onset. You may be more careful about how they're exercised, because we know that exercise over really rough, bad ground can play a role in lesion severity. So you can take that information and modify the management side of things, to help reduce the risk.

28:49 DM: And if you're on a breeding side of things, the heritability of this disease is somewhere in the 25 to 30% range, so again, this is not something that we're going to be able to get rid of by breeding. But for example, if you have a known high-risk mare, you may not want to breed her to a known high-risk stallion. You may choose to breed her to a low-risk stallion instead, because that should make the risk of the foals being affected lower. So we do know that there are familial predispositions to this disease and being able to categorize horses in risk categories should help to reduce that. We are not claiming that we're going to be able to get rid of this disease. It's unlikely because of its complexity, but we do want to be able to reduce the incidence of the disease with this type of risk assessment.

29:50 DD: So thinking about that, what's next for you, what are you looking at in the future, where you'd like to go with looking at this disease?

30:00 DM: Yeah, so right now we are really concentrating on getting that big, the bigger GWAS population, and we're pretty close to getting ready to run that on, again, a population of about 1000 horses. And so we're going to take that information. We just published a paper looking at that site-specific gene expression differences between cartilage and bone, and so we have that data. And so the next step from there, once we have all that raw data is to combine those two things and look at them as a network together. And then from there, we'll be going through with a fine-tooth comb and picking out probably about a 1000 variants, check in a validation population. So, unfortunately, the COVID situation has put us a little behind in terms of sample collection, we weren't able to make our usual sample collection trips to the spring, but hopefully, we're going to be able to get that validation population in place.

31:01 DM: And the really, I mean the really exciting part of this is going to be that validation piece, which will probably be in a couple of years that we're actually going to get to that piece. But that's the part that's going to be really exciting because if we can get down to a handful of genes, 20, 30 genes that are really predictive, that's going to take it to that next step of actually being able to put together a commercial test that people can use. And we have a similar test that we were able to put together for the gait side of the project, and so we're hoping that this is going to lead us down that road for osteochondrosis.

31:43 DD: So just to finish, what is the take home message for our listeners as far as what they should be aware of when it comes to osteochondrosis, whether they're a veterinarian or possibly a owner of a horse, as far as looking how they should manage it?

32:02 DM: Yeah. So the reality is, is that osteochondrosis is really common, and particularly if you are involved with Warmbloods, Standardbreds, Thoroughbreds to an extent, Quarter horses not so much. But those breeds that we know have a high prevalence of it, those young foals should be getting screened for this disease. And the reason for that is because we know that surgical removal of these fragments at a young age, so before these horses are put into training, really mitigates the negative effect of this disease in the vast majority of cases. Now, there are certain very severe cases that you really can't do anything about, but we do surgical removal of osteochondral lesions very routinely at surgical practices around the world. But it's really important to get that done earlier rather than later, so before you put them into training, because if you leave those fragments in there, unfortunately, even though the spots where these fragments form aren't weight-bearing themselves, the inflammation that gets caused by having a fragment in that joint can lead to arthritis down the road.

33:18 DM: And I have, unfortunately, been involved with removing osteochondrosis fragments from older horses that had really severe arthritis that were likely secondary to that condition. So, it is unfortunate that you have to go in and do surgery, but it really is an important thing to do. And then if you have a mare and stallion pairing that you know has thrown horses with osteochondrosis in the past, those kids should definitely be kept an extra close eye on and making sure that they're not being pushed nutritionally, making sure that they're getting appropriate micronutrients, we know is really important for osteochondrosis. So just being aware that you are doing all of the things to reduce your risk but recognizing that the risk still remains and that you need to be checking.

34:13 DD: Well, cool. Well, that sounds really interesting. And I think maybe, hopefully in a couple of years, we'll have, like you said, a genetic panel where you can look at risk factors. I think for those of us, I hate to admit how old I am, but when we go in now and they look, for example, for risk for heart disease, they have the whole bunch of questions they ask about your cholesterol and your family history, and they assign you a number. And it's the same for statins, which I'm on right now because of just the panel. So you're talking about it from a very specific genetic standpoint, but I'm thinking it sounds like the same thing, kind of a risk factor score that then you can manage these horses based on that.

35:00 DM: Exactly.

35:02 DD: Great. Well, Annette, thanks so much for coming today and joining us from all of our quarantine lands, and telling us about this issue, and I'm sure we'll be reading more from you on this topic in the future.

35:18 DM: Great. Thanks so much for having me, and we appreciate Morris' work and support more than I can express, so thank you.

35:27 DD: Great. Thanks. And that does it for this episode of Fresh Scoop. And once again, thanks to Dr. Annette McCoy for joining us. And again, thank you also, I'm going to give you a extra thank you for being on, and that's on our large animal, small animal. Or large animal advisory board, and you are the chairman this year, correct? Yeah, so she's got a lot on her plate that she's doing for Morris Animal Foundation, we really appreciate it. We'll be back with another episode next month, and we hope you'll find it just as informative. As we know, the science of animal health is ever-changing, and veterinarians need cutting edge research information to give their patients the best possible care, and that's why we're here.

36:10 DD: You can find us on iTunesSpotifyGoogle Play Music, and Stitcher. And if you liked today's episode, we'd sure appreciate it if you could take a moment to rate us because that will help others find our podcast. To learn more about Morris Animal Foundation's work, again go to There, you'll see just how we bridge science and resources to advance the health of animals. And you can follow us on FacebookTwitter, and Instagram. I'm Dr. Kelly Diehl and we'll talk soon.