 Hi everybody, so thank you so much for coming. So for the row people sitting behind me, you do not get to fill this out until you've heard me speak, so put your punch of pencils down there, all right? So how many how many people in the audience have dogs? Or yeah, so good. This is a this is a great dog-friendly audience because we're going to be talking today about dogs and a couple of different aspects. We're going to talk about health as well as morphology, you know, why dogs are different shapes and how all that data sort of comes together to inform us about about human health and human biology as well. So we'll leave some time at the end. We'll have lots of time for questions. So this is the closest ancestor to the dog. Who knows what we're looking at here? What kind of wolf? Gray wolf, right, of course. So dogs were believed to have domesticated from gray wolves. The latest data suggests maybe around 13,000 years ago. So evolutionarily, that's really a that's a drop in the bucket. I mean, that's not very long ago at all. And so one of the things we're always sort of thinking about and pondering about when we look at our pets wandering around our houses, you know, it's whatever they're doing caused by genes that are embedded in this wolf genome, or or is this something new that's come up during the process of domestication. And that's one of the things that we go back to and we ask ourselves over and over and over as we look at all of our friends. So how many of you recognize your dog breed up there? All right, there's got to be some golden retriever owners. I'm betting there's probably some schnauzer owners. Right? Maybe maybe some hound owners, you know, a Weimar owner owner or two. So these are a small number of the 175 breeds of dog that are recognized by the American Kennel Club. And the American Kennel Club is the largest registering body of dogs in the United States today, but they are not by any means the only registering body. There's a United Kennel Club and and several other Kennel Clubs as well. And there are Kennel Clubs actually all over the world that an aggregate recognized 493 different dog breeds today. 493 different dog breeds today. And those dog breeds show an extraordinary amount of variation. Right? So we would say that there's probably three things you need to keep in mind as we're going to talk about dogs for the next 45 minutes or so. It's important to remember that even though all of these guys look very very different, they have a different body size, different coat colors, different head shapes, different leg lengths. All dog breeds are members of the same species. So they all have the same karyotype or the same chromosomal organization. They all have the same genome organization. And they could be crossed to produce for loft spring. Now clubs like the American Kennel Club don't really encourage you to cross dogs from from one breed to the next. And as a matter of fact to be for instance a registered golden retriever, your parents had to be AKC registered golden retrievers and your grandparents in turn had to be AKC registered golden retrievers. So one of the reasons people like me study dog breeds is because each one represents sort of a closed population. So if you think about human populations that are isolated, you know, people who live in Finland or Iceland or people who have lived on islands for many many generations or the Bedouin pedigrees, geneticists like to study those kinds of populations because there isn't a lot of admixture from the outside. They really have sort of a set number of different alleles at each genetic loci and that makes the problem of setting complex traits like diabetes and cancer and epilepsy actually an awful lot easier. The only problem in human genetics is that there's a limited number of such isolated populations, whereas in the dog world we have 493 of them. And so we actually in my lab have been working hard to get DNA samples from each one of those 493 breeds. We have a great relationship with the American Kennel Club. We don't breed any dogs. We don't keep any dogs in Kennels, but if you go to a dog show or an obedience trial or a specialty or an agility trial anywhere here in the Tri-State area, you're probably going to find someone from my lab there taking cheek swabs or handing out kits or collecting blood samples. And we've now got a set of 50,000 DNA samples in my laboratory. So that's pretty impressive, huh? So when we look at these dog breeds, we really see extremes of a variation and one of the things that makes a breed a breed is that that variation breeds true. So if you cross one golden retriever to another golden retriever, the puppies are all going to pretty much look the same. And there's some nice examples up here for you. You know, if you cross one Dalmatian to another, they're all pretty much going to look the same. Across one box or to another, they're all pretty much going to look the same. And the American Kennel Club is really strict about the things that are important and that define each breed. And it's different for different breeds. For some breeds it's their coat color. For some it's how tall they are. For some it's how long their legs are. For some it's the shape of their face, how far apart their eyes are, whether their ears are perked or whether they're down. And when a dog goes into a dog show, those are all the things that the judges are actually grading them on. So because breeders have been breeding for those traits for years and years and years and years, those are the things that in my lab we're trying to find the genes that control them. And in doing so, we're sort of getting a vocabulary of growth regulation that we really can't get from studying worms and flies and mice and rats and all those other traditional model organism systems. Now I really like this picture and don't worry if you can't read the writing here. But what we've done is we took a thousand DNA samples from dogs representing 85 different breeds. So we took about 12 different dogs from each breed and we tested their genome at 100,000 different positions. And we were looking at the variation in the A's and those T's and C's and G's that you're always hearing about. And then we fed it all into a computer program and we said tell us how all the dog breeds relate one to another. And that's what this wheel, and you can really follow the color coding in the round, is telling you so well. So if you look at your upper right, you see there the red, and you see all the Spaniels, the American Cocker Spaniel, the English Cocker Spaniel, the English Springer Spaniel, the Cavalier King Charles Spaniel, the Irish Water Spaniel, the Brittany Spaniel, and so on. And if you look over down at about four o'clock, you'll see the sort of Bull Mastiff type dogs, the Miniaturbal Terror, the French Bull Dog, the Bull Dog, the Boxer, and so on. Now we have this hanging in my lab, and we use this every single day as we're developing a hypothesis. So if I'm going to study something like epilepsy, and I've got a whole bunch of samples from English Springer Spaniels, those are the red up there at about two o'clock, then I can actually probably go out and get DNA from affected American Cocker Spaniels and Irish Water Spaniels and Cavalier King Charles Spaniels that are also affected. And I can probably be correct when I hypothesize that they all got the disease because they carry a mutation in the same gene. And that's because they all share a common set of founders. That's why they're all colored in red. And when I study epilepsy in the Mastiff-like breeds, well, they probably have a mutation in a different gene, but when I look at the Mastiff and the Bull Mastiff and the Bull Dog and the Boxer and the French Bull Dog, again, they're all colored in kind of that teal color, they probably got the disease because, again, they share a mutation in the same gene and they likely got it from a founder. So how long ago did this founder live? Well, how long ago do you think most dog breeds were developed? You know, domestication occurred about 13,000 years ago. How long do you think most dog breeds have been in existence? Any guesses? Pretty close, about 300 years. So most dog breeds were developed in Europe. Most were developed by fanciers during the Victorian times. So most of them have only been around, really, for 200, 300 years. So, again, evolutionarily, we're not even talking about a drop in the bucket. We're talking about, you know, a perspiration drop in the bucket. I mean, as tiny as you can really get. So we can make these kinds of hypothesis when it comes to morphology or when it comes to disease susceptibility and we're usually right. And the other thing is that the genes that we end up finding by studying dogs usually turn out to be important for the same things in humans. It's just that, gosh, it's a lot easier to go to my freezer of 50,000 dog DNA samples and pick out a few related breeds and look up their health records and find out what they've got and what they don't have and correspond with their owners and start studying a pool of affected and a pool of unaffected dogs in order to find a disease gene of interest. Okay, so this is actually one of my favorite dog pictures. So this is a Harlequin Great Dane. It's skeletally among the largest of the dog breeds and down here is a little chihuahua which is skeletally among the smallest of the dog breeds. Now, we've been studying dog morphology for several years in my lab and we've published papers describing genes that control body size and leg length and skull shape and fur. And we rely on samples from these extremes in the population in order to do studies on things like body size. Again, remember, both of these guys are members of the same species and they could be crossed. These two guys here to produce fertile, if singularly unattractive, but nevertheless fertile offspring. And you might want to give a little thought as to who would be the male, who would be the female. All right, so what do we have over here? Okay, so this is again a chihuahua. This is Zeus. I have to put this picture in. Zeus actually holds the 2013 Guinness Book of World Record as the tallest dog. So he is 44 inches at the withers or the shoulders. This is not Photoshop. This is actually how tall Zeus really is. And so we've been collecting samples from dogs at these extremes as well as everything in the middle in order to find genes that are responsible for this dramatic, dramatic difference in body size that exists within this one species. And I can tell you from a couple of papers that we've published that there are about a half a dozen genes that account for most of that size variation. And so I didn't put their names up, but if you're interested I can tell you there the insulin-like growth factor one gene. There are a couple genes on the X chromosome. There's the insulin growth factor receptor, SMAD2, HMGA2, STC2, growth hormone receptor. And so some of these may sound familiar to you because they've been shown in studies of mice to be important in controlling mouse body size. The only thing is you don't learn a lot from studying mice in this case because you don't find mice that differ in size by 40-fold, right? I mean wouldn't that be truly frightening? I mean if you did, right? But of course we do find that in dogs. So we've spent a lot of time identifying the genes and the mutations that account for variation in body size. And we just published this and I know it's kind of complicated, but I wanted to show it to you because I'm actually really excited about the implications of this study. So if you look on the left, you see a bunch of bricks that are either yellow or red. And I know it's probably hard to read on the bottom, but on the bottom is the name of each one of these genes one at a time, growth hormone, IGF1, so on until we get to IGF1. And you don't have to worry about, you know, really which gene is which. Going along the vertical are the weight in pounds of different dog breeds that we've assayed. And then what the red and the yellow is telling you is that in each one of these genes there's two possible alleles or there's two possible mutations or variants that can occur. One is an ancient variant that we find in wolves and one is a new variant that's only been on the planet for a few hundred years and we only ever see it in domestic dogs. Now the yellow is the ancient variant that we find in wolves and red is the new variant that we've only ever seen in dogs. Now what's really striking is if we look at really little dogs that weigh like zero to five pounds all the way across you see red telling us that those dogs have the new variant the one that we only see in dogs at every single one of these genes. But as dogs get bigger and bigger and bigger that drops off till it's basically all mustard yellow and so all those big dogs are big because they carry the DNA variant that came from the ancient wolf. So that's kind of cool. So we took that data and we said how how predictive is it you know if I if I actually take what the data is predicting versus what I really see in a panel of 500 dogs how good is the predictive value of my half a dozen genes and that's what this line over here on your right is telling you. And the fact that you get a pretty good line from all of those data points is telling you that just those six genes if we could assay them and every single puppy that was born would actually have great predictive value for what the final size of the dog is going to be we'd be right to about 82 percent. So think about this this means that you could go to the pound you could get a puppy you can get a cheek swab you could get an assay that these six genes and you would know what the final size of that puppy is going to be pretty close to accurate to about 82 percent accurate. So that's really amazing six genes just six genes control that much variation. Now one of the things about this study is that it actually only holds true for dogs that weigh up to 90 pounds. And if you think about the giant breeds the Great Danes the Newfoundlands the St. Bernard's these six genes only have about five percent predictive value. So there's probably lots of genes responsible for giantism in dogs that I actually haven't found yet. And that's one of the things that my lab is in the process of doing so that we can extend this line and make it bigger and bigger and bigger until we can actually understand all the genes controlling that full range of body size going all the way up to you know 180 200 pounds. Now as we've begun to publish more and more of this data people have gotten really excited and they've kind of picked out different things that they want to study or that breeders would like to try and breed for. So I have people in my lab studying leg length and studying skull shape others are continuing to study body size some are even studying performance. And we built a big data set based on a thousand different dogs from 85 breeds and we also included 500 wild cane and silk coyotes wolves from all over all over the world and and we we tested their DNA at a thousand different points in the genome and we've made that DNA publicly available without any restrictions without any patents to anyone who wants it so you know we really encourage other people to to try and and think about these problems as well. Now I like this particular story this is one that was led by Heidi Parker and she was a graduate student in my lab and then she went on to be a postdoc and then she went on to be a staff scientist and she's been with me for 15 years and I actually don't think she's ever going to leave. So Heidi has been really interested in short-legged dogs and there's about 20 such breeds they're called chondratus plastic they have a ratio of height to body length less than zero so they sort of have a normal head and and a normally proportioned body but then they have these very short and thick legs. In the dog world we would say their structure is well boned or heavy and their forelimbs like you can see on that basset hound are often sort of bowed or a little bit curved out. So Heidi came to me one day and she said I want to try and find the genes responsible for this trait across these 20 breeds and I said well you know this could be a really hard problem it could be that they all share a common mutation but these breeds were developed for different purposes some are developed to be to go down rabbit holes some are fox hunters some are companions some are radders so I said I'm not so sure they're all going to have the same mutation in the same gene and she said well I think this is a really interesting problem I'm going to try it anyway and she's not being totally unbiased here because you see that doxin in that basset hound those are actually her dogs yeah and so you know when you come to my lab and you work people are often motivated by things that they have in their own dogs and and you know some of my graduate students are top show have top show dogs or top dogs in the agility ring so it's not I've actually had mushers come and be graduate students in my lab so again motivated by trying to understand the underlying genetics so Heidi went after the gene for chondrodysplasia now I know this is looks like just a bunch of lines to you but what you're looking at here in the alternating gray and black each one represents a different dog chromosome and dogs have 38 chromosomes and we also included the x but we didn't put in the y because we figured there was nothing important on the y anyway and then what we're doing is we're comparing cases who are chondrodysplastic to what we call control which are all the other breeds that are not chondrodysplastic and we're looking at at a hundred thousand different points in the genome and we're saying is there a chromosome that has a data point that's significantly different between cases and controls and you can see this is very significantly different here on canine chromosome 11 and and for those of you have calculated p values the p value here is 10 to the negative 102 so 0.000000 put 102 O's and then a 1 and that's how statistically significant so this is hugely statistically significant so we decided to to follow up on this and the way we did it is we look for something that evolutionary biologists call a selective sweep so what's a selective sweep well when you have a selective sweep you assume as I've told you before that there's a ancestral mutation that occurred many many generations ago in this case before dogs were divided up into lots of different breeds and then dog breeders breed and they breed and they select for different things and and and there's a lot of scrambling of chromosomes but the mutation stays because they're always still selecting for that one trait in our case chondrodysplasia and so now when we look at modern-day dogs their chromosome may look nothing like the ancient chromosome except for where the mutation is and in the space right around the mutation and so we look for that region of commonality and when we find a region of commonality across a group of breeds who have a trait then we know the mutation has to be somewhere in there and that turns out to be exactly the the case here so this is an old-fashioned gel and I put it up because I think probably some of you in college had a had a chance in science classes to run a gel a gel simply separates dna based on its size the controlled dogs are things like gray hounds and boxers and cocker spaniels and if you look at the top you don't really see anything of the gel but when you look at the case dogs and these are of course are the basset hounds and the doxons and the pecanese you see a bright yellow a bright white band and that's telling you that all of these cases have some extra dna that's responsible for this trait that's not present in in the group of controls so right away we know that what our mutation is it's not a single base pair change and it's not a loss of dna all these chondratus plastic breeds have acquired extra dna and in fact they've acquired an extra copy of a gene called fibroblast growth factor four now they didn't acquire any of the regulatory machinery that tells it when to turn on or when to turn off but they acquired the full sequence of the gene and so actually the genes around it they sort of parasitize the regulatory machinery from genes around this this what we call a retro gene and that's telling it to be expressed and fetal condorcise and you know what that's doing that's closing the growth plates prematurely so the legs never elongate as long as they should this gene is expressed the growth plate closes and the leg can't elongate to its full and natural length and every single one of those 20 breeds I showed you has exactly that gene including this which is the corgi breed so this was really exciting and and we were able to publish this in science not because the editors of science care about corgis although I think they should but because this was sort of a new way to screw up the genome that had never really been described before in mammals and the other thing is we of course know that there are humans who suffer from from forms of of what we historically call dwarfism but it's really chondrodysplasia and and we don't always know what's causing that so now this gene goes into into that lexicon into that vocabulary is something that we need to think about when we look at those so this is a really neat example just by studying a phenotype that dog breeders have been breeding for for a couple hundred years in a bunch of healthy dogs using DNA from my freezer we've been able to figure out a whole new mechanism for screwing up the genome and we've been able to add a gene to the medical genetics vocabulary that turns out to to then become very important so this to us is is really a huge success so we've gone on to to do that in several other ways and and I'm going to give you one more example of morphology and I'll give you one example on disease and then we'll we'll have some time for questions in the end what are these absolutely these are all skulls from dogs and these are pictures we took down here at the Smithsonian turns out they have a lot of skulls in the back room right and and these are all different dog breeds and they differ in both shape and what else and size exactly so when Jeff shone back joined my lab he said I want to find the genes to control this I want to understand the genetics of the skull shape and size in dogs and I said well I don't know this sounds like a really hard problem but Jeff had one of these giant lean burger dogs with a big round kind of fluffy face and so you know this is what he wanted to do and so that's what we did now the first problem we had was we don't know how to how you quantitate a skull right I mean counter this plastic is easy the dogs either have it or they don't have it and body size is easy you measure them or you weigh them how do you actually quantitate a skull it turns out to be a hard problem but we solved it and and what we do is we have something called a microscribe digitizer and we touch each skull at 51 different landmarks and that sends data to a computer and then in the end the computer takes a 51 data pieces and it draws a three-dimensional picture of what that particular skull looks like so here I'm showing you top and bottom and side views of a particular dog's skull and everywhere there's a red or a blue number that's one of those data points that we've we've gotten so the the palette can be long or short that's the roof of your mouth for a dog that has a long or a short snout that angle and picture c between the rostrum and the in the nose that can be you know pretty much a ski slope or it can be at a right angle like it is in a newfoundland we would say they have a roman nose or a very high forehead and there's variation actually in every one of these traits now we've actually been fortunate to travel around the world we've measured about a thousand skulls from 161 different breeds and people always ask me where do you go to do this and we go to lots of museums and certainly the Smithsonian is the first place we went um but we've been to museums and universities all over the country and actually all over the world um the university in and Switzerland actually has something like 2000 canine skulls um that we're about halfway through measuring now but i have to i have to admit there are a group of people in the united states that have a lot of skulls in their basement and i don't know why but they do and they all call me and they say you know i got a bunch of dog skulls why don't you come down and measure and this is alex one of the people in my lab and she's measuring the dog skulls this is a gentleman in california who called us to fly out and go down to his basement and measure all the skulls and you can see he has all kinds of animal skulls we really don't know why we don't ask those questions we just measure the dog skulls and and get out of there but yeah there's a lot of these people in america they all want to friend me in facebook it's a whole it's a whole culture thing so anyway but but um these people have been very generous with their collection so we've actually gotten a lot of data from skulls where we could verify the breed and we could verify um the the age okay so this is this is in some way sort of a tragic slide so um this is really what motivated jeff to begin this this project so in the left hand column are a set of human conditions that that are really different kinds of craniofacial abnormalities and i know not you're not familiar with most of those words but they describe different um abnormalities that that we see unfortunately in in humans often associated um with particular syndromes and and next to them are breeds where the where the breeders are actually trying to breed that in as part of the breed standard and and really one of the the examples that i i i use and this is not something that the american kennel club is doing this is not an akc breed but this dog shown here is a pashon navarro um and and the breed standard includes having this deep cleft that goes all the way from the outside of the snout um all the way down into the roof of the mouth so you know this is not something that american breeders are are advocating but you know it is something that you know we see and so we want to try and find those genes because we think that'll help us understand something about cleft lip and cleft palate and we're actually interested in in all of these um craniofacial features so the one that we've been doing the most work with is called brachycephaly and that means having a very pushed in face so if you think about your saturday morning cartoons those of you that are old enough and some you know something happens and you know the face just kind of accordions in like kind of like that right and and so that's the kind of appearance you see in the pug or the kind of course so and that's very different than what you see in the afghan and the bolteria which have very elongated noses and that's referred to as a dolcosaphalic benotype so a long nose versus that very pushed in um base so we've been going um after these kinds of genes and we do the exact same experiment over and over we comb the genome and we look for evidence of a selective sweep and that's what the data actually looks like so um these are our base pair positions along canine chromosome 30 and you see a certain level of chatter and then when you get right here you can see this big dip and that's telling us that there's a selective sweep there that that's a place where there's a lot of homogeneity something breeders have been selecting on for years and years and years and years so they don't know that there's a gene under there they don't know what the gene is they've been selecting on um but we're going to find it and we're going to tell them what it is okay so um here are a set of of 12 dog breeds that my lab has now sequenced um we've sequenced these breeds uh pretty deeply so we've got a pretty good genomic sequence and we picked these breeds for lots and lots of reasons um we have lots of different studies going on and and there's another actually 40 dog breeds that that we and others have sequenced as well um but these are the first 12 and and partly we picked them because if you think about going very brachycephalic to very dolicocephalic you have a really nice continuum so we will be able to use this data to try and figure out what's underneath that little v that statistical blip that the breeders have been selecting on over and over by comparing the brachy and the dolicocephalic dogs now you've heard a lot about the genome project and usually people talk about the human genome project when i hear about the genome project i think about the canine genome project because that's what's really important to me so i know this again looks like a a checker board but um each one of the rows is giving us information about the sequence variation we saw in those 12 dog breeds so we started out with 190,000 base pairs and 2000 possible variants and then we started filtering and filtering we got it down to 85,000 variants and 48 variants and in the end when we applied the sequence of all those other breeds we were able to find the single base pair in the single gene that turns out to be important and it's how canine chromosome 30 contributes to that facial phenotype so the gene is called bone morphogenesis protein 3 kind of makes sense it's a bone morphogenesis protein and it is a single base pair change the change is one amino acid phenylalanine to lucy one amino acid now when jeff came to me with that data i said gosh you know i believe you but in order to publish this we're you know we're gonna have to have more proof and so jeff did lots of statistical studies and they all looked really really good and we wrote it up and i said you know it's pretty good but i i think we're just gonna need just a little a little bit more proof to get it into one of the fancy journals and jeff said well okay i can knock that gene out in zebrafish and i can make a pugnose fish and i said you're gonna make a pugnose zebrafish and he said i'm gonna make you a pugnose zebrafish and so there's a technique he used and he knocked that gene out and that is exactly what jeff made so let's let's forget the top row for a second i'll come back to that but if you look where it says e f and g that's a zebrafish you know several about 48 hours after the embryo was fertilized and it it didn't get injected with the stuff that knocked out the gene and then the blue is the the cartilage from the top of the jaw the top jaw and the the g is the bottom jaw and now the other two are examples of fish that did get injected with what we call morpholinos and they knock that gene out um and and you can see that the jaw is gone especially that bottom jaw look there's almost no blue staining in j and m and and even the top jaw is pretty screwed up as well so in essence jeff made me up pugnose zebrafish and indeed in doing so demonstrated that by knocking out just that one gene we're able to dramatically affect the jaw structure and so this gene in fact does turn out to to be important in one particular type of human cranial facial abnormality so this is another example of of how you know we started with with healthy dogs long-lived dogs but they had a particular phenotype that sort of pushed in face and and we've been finding the genes responsible for that and there's not just one it turns out there's actually several and in aggregate they are responsible for the dramatic difference between being being breaky cephalic with a pushed in nose or dolico cephalic with that elongated nose and we can prove we're right by going to some of these model organism like zebrafish which are these sort of little tiny fish um that that people use in the lab sometimes okay so those are examples of of how my lab has been studying morphology and and right about this point in time someone usually says to me well you know that's great but gosh dogs have an awful lot of diseases do you do actually directly study any of those diseases as well and if you do are they telling us something about human disease and the answer to both those questions is a resounding yes so here are the top 10 genetic diseases in dogs and what do you notice is number one right about one in how many humans will get cancer in their lifetime anybody about one in four people will get cancer some kind of cancer at some point in their life they may not die of it but they'll get it and about one in three dogs will get cancer in their lifetime as well how many of you have had a dog or a cat who got cancer yeah right so um in my lab we do in fact study several different types of of cancer now this is one of my favorite dog pictures ever it was actually sent to me by a very well known and very generous dog breeder and she breeds what are these standard poodles right these are standard poodles so about four years ago we started getting phone calls from people who own standard poodles telling us that the dogs were getting a particular kind of cancer and it's called squamous cell carcinoma and oddly it was occurring in the toes and sadly the way the veterinarians have to treat it is they actually have to remove the toes and so that's horrible for the dogs it's horrible for the owners if the dog is a show dog it won't be after that and people obviously don't want to read to those dogs after after that and so this is really a big deal for this community but what was so interesting about this is they said you know we only ever see the disease in black standard poodles and we never see it in white standard poodles and so we've now looked at hundreds of standard poodles and we see it in black and brown very very very very dark gray but we don't see it in the white or the cream or or the apricot dogs so we thought well you know there's a lot of selection for coke color in standard poodles maybe they've been inadvertently selecting for a cancer gene as well and that in fact turns out to be the case now let me just tell you that we study lots of kinds of cancer in my lab but in fact across the world dog geneticists study lots of kind of cancer so um those of you who have long limb breeds like Scottish deer hounds or Irish wolf hounds probably worry about osteosarcoma we see tons of bladder cancer and scotties and westies and shelters and we actually have a paper we're writing about that now that comes again from sequencing tumors the DNA from tumors that we find in those dogs if you've got a bernie's mountain dog a super wonderful dog breed that's really increasing in popularity or a flat coda retriever one in four one in six of those dogs will get um lignin histiocytosis or or histiocytic sarcoma stomach cancer we see in the belgian sheepdog the belgian chevron as well as in the chow chow universally lethal dogs don't survive it and the idea here is we study these in dogs because the breed structure as i told you at the beginning simplifies the overall problem we'll see shared genetics among affected dogs and it'll be distinct from what we see of healthy dogs of the same or remembering the wheel very related um dog breeds so this is a picture of squamous cell carcinoma you can see that the toe is sort of blown out it's the most common nail bed cancer in dogs if you are a giant schnauzer your chances of getting this are 22 fold higher than the average mixed breed dog walking down the street if you are a breard your chances are 10 fold higher than the average mixed breed dog walking down the street and if you're a standard poodle they're about six fold higher although standard poodles are where we see most of this because they're the most popular of those three breeds and again in the cases of standard poodles we only see it in the black dogs not in the white for really complicated reasons in in the breard we actually see it in black as well as white dogs and we figured out why that is it's actually a a very very complicated genetic story but let me tell you a little bit about standard poodles so we again combed the genome with our hundred thousand points of variation um and we found a signal on canine chromosome 15 it wasn't as strong as what we saw when we were looking at those morphologic traits because breeders haven't been trying to breed cancer into dogs the way they're trying to breed you know short legs or large body size um but nevertheless um it's there and it's and it's in a lot of dogs I think this is the the last of the the data slides that I'll show you um and so what what we did is we we found a region on canine chromosome 15 it was about a million base pairs long we sequenced it and lots of affected and unaffected dogs and everywhere that there was a possible mutation there is a triangle and then we defined a region um that you know maybe if we were a liberal in our thinking was about five hundred thousand bases in size and if we're conservative in our thinking it's about eight hundred thousand bases in size and what's cool is there's only one gene in that region and that gene is called kit ligand and we knew instantly that we had found the right gene because it's a gene that's important in coat color but it's also a gene that's been shown to be important in cancer so we did a lot of work that took about three years and we in fact um found the mutation and in this case we again found sort of a new and interesting way that the genome gets screwed up so it turns out that the mutation is again extra dna it's not a deletion it's a it's an insertion of about five thousand bases and it can be present one two three four five or six times and the more times it's present the more these green proteins bind and the more these green proteins bind the more they ramp up production of this gene kit ligand and the higher you ramp up production of this the greater the chances are that you're going to get the cancer so if you're a dog who has this insert present on both of your chromosomes four or more times boy your chance of getting cancer are really really high if you have it maybe four times on one chromosome three on the other it's sort of moderate but four is really the threshold if both of your chromosomes have it repeated three times or two times or one dime or any combination thereof no chance you're going to get cancer no chance and we've looked at hundreds and hundreds of dogs and we've never even found one so this is one of these sort of threshold deals where you have to get kit ligand ramped up to a certain point in order for it to go ahead and cause the cancer so it makes it hard to develop a genetic predictive test but people are in the process of doing that we found out why white standard poodles didn't get this it isn't because they didn't carry the mutation the four four genotype they didn't they do indeed have chromosomes where where this insert is present multiple times but they have a compensatory mutation on another gene called mc1r and it completely knocks us out so it's a case where they have a bad mutation but they have a good mutation and good triumphs over evil in this case and so they never ever get this even though they carry the bad genotype so it's an important lesson because just looking for the presence of absence of the bad genotype isn't really totally predictive you also have to look for the presence or absence of the compensatory mutation and all the white standard poodles have it none of the black standard poodles have it and so that explains the the difference in in what we observed in in coat color so i'm going to stop there we have about 15 minutes to ask questions or 12 minutes or so i hope i've showed you that dogs are a really fun system for looking at both simple and complex traits including susceptibility to cancer which is of course a very complex trait when we study morphology in dogs we learn things that are important about development of all mammals and that includes humans as well for both canine and human health these studies of cancer become very very important and there are labs really at vet schools as well as at non vet schools that are studying every conceivable kind of cancer as well as all the other common human diseases epilepsy diabetes heart disease you know whatever you got including morphologic traits you don't like like baldness or obesity or things like that those there are labs all over the world that are studying those things as well many of these studies are long-term some are short term there are a number of disease genes that we've been able to find the mutation for we've been able to develop a genetic test and breeders are now using those genetic tests to make really good decisions to to to produce healthier more long-lived dogs so you don't see kidney cancer in the german shepherd anymore and and we've been able to wipe out collieye anomaly which is a degenerative disease of collies and border collies and a number of herding breeds as as well as several several other diseases and this has all been done in collaboration with breeders and owners and veterinarians actually all all over the world samples are always needed so if any of you have a really interesting dog breed i gave this talk yesterday and a man came up to me afterwards and said i have a sheba enu if you want dna from that yes we do want dna if you've got an interesting dog breed um we love your labs we love your golden retrievers we love your german shepherds but we probably have enough dna on those um but the more esoteric breeds we're still always collecting um more dna from and you know great progress um can be made um but you know it is necessary to to get the dna samples and allow us the the time to do our work so for the breeders in the audience i know many of you have contributed samples and you wonder how long it's going to take well sometimes it's a year sometimes it's going to be five or six years because some of these problems um end up being simple some of them end up being very complex but our goal is always to to make available to you some sort of a diagnostic test so i'm going to go ahead and and stop there um and allow you to turn up maybe turn up the lights turn up the lights um and i'll go ahead and and take questions okay this this slide how do we find out what how do we find out the disease risk so what we did is we got dna from a lot of poodles who had the disease and a lot of poodles who didn't have the disease and and then we sequenced it to see how many times this was reiterated um and how many times this particular five point base pair unit was repeated and we actually knew from looking at the human genome we knew exactly what these five thousand base pairs do we knew that this protein binds to them and when it does it ramps up production of of kit ligand so we can do statistics looking at dogs who have two copies three copies four copies five copies and we can look at them at 10 years 11 years 12 years 13 years 14 years and see who does and doesn't have cancer and from that we can figure out what the risk is for a dog who has three copies or four copies or five copies and four is really the cutoff if if both of your chromosomes have three copies or two copies or one copy we've looked at hundreds of dogs and not a one of those dogs has this kind of cancer but as soon as one chromosome gets four counts has the the repeat repeated four times then we we start to see the incidence of cancer creeping up and the more you have the higher it gets okay and and there are you know formal statistical tests that we can apply to that and if if you're interested if you're sort of got a statistical mind come see me afterwards and I'll I'll give you the paper and the tests that we use okay other questions yeah sure so the question was is epilepsy indeed prominent in dogs and yes we see it in lots and lots of dog breeds and have we found genes we we've been part of one study that identified one gene published it with a group in Belgium several years ago in science but lots of other people are looking at this problem because you know not only is it an important problem in humans it's a big deal in dogs I mean if your dog has epilepsy I mean that is a lifelong problem that you as a pet owner have to to deal with and and certainly those dogs don't show and and people don't you know put them in the breeding pool if they know and so some of those genes have been found not all of them have been found and there are some breeds where it's a much worse problem than it is in other breeds so that's one of the areas where we see some of the most active and intense work yeah you had a question okay I probably won't know the answer but go ahead oh yeah sure I do because I picked the breed for the reference genome so he asked me what breed of breeds make up the dog reference genome so it's one breed and it's one single dog so in in 2001 I had the chance to to pick the dog that was going to be sequenced and you know truthfully what I did is I probably looked at a hundred different dogs of all breeds and I picked the most inbred dog I could and the reason for that is the way genomes are sequenced is not from the top of chromosome one to the bottom of chromosome 38 what they do is they cut the DNA up into a zillion little pieces and then they sequence it all randomly and then they have a computer put it back together so if what you got from mom is really different than what you got from dad it's a harder computational problem if what you got from mom and dad it's pretty similar it's a much simpler computational problem so I tested a hundred dogs at a hundred places in their genome and there was one dog that was easily the most inbred it was a boxer and it was from New York state and and as luck would have it it was actually owned by a veterinarian so when I went to him and I explained that his dog was the lucky winner I mean he actually understood that this was really important he provided us with an awful lot of DNA and he understood that you know when the dog it was a pet you know like all of our dogs are um that when the the dog died that we you know we would like to get some samples from that dog because it was in fact going to be the reference genome and his only request was that I not divulge his name which I've never done or his location which I've never done so he was great he was fantastic but it was a boxer and her and it was a she almost all the reference genomes except maybe human are she because then we get good data on the X chromosome so is have we found a gene linked to fur loss in in breeds like the the Yorkie so I haven't looked at that there are breeds like the Chinese Crested or the Mexican Hairless there are breeds that have very little fur except for some tops at the top of their head and down by their toes and those genes have in fact been found but those dogs that's part of the breed standard that's how they're they're they're supposed to look when a dog blows all of its fur I mean and that's an anomalous sort of thing I'm sure there are people looking at it I'm not one of them and I'm not aware of a paper but I could certainly tell you wearing the literature to look for it yeah sure yeah so the question is what are the the healthiest breeds and it's a little bit of a trick question and the reason is because within every breed there are lines that are really healthy the breeders are very savvy they've gotten dogs from multiple places in the the world that are members of that breed or multiple places in the United States that are members of that breed and they've worked really hard to to maintain the hybrid vigor of that breed and there are other breeders you know who have read a lot of closely related individuals one to another and their lines may look good but they have a lot of health problems so there's there's no one right answer I mean you can look on the internet and and you know they'll certainly give you those that kind of information and they'll say things like well you see a lot of cancer in in boxers or in golden retrievers or you see a lot of copper toxicosis in the bedlington terrier you know there's different diseases that tend to predominate in different breeds there are some situations where where disease is so predominant like copper toxicosis was in the bedlington terrier before the gene was found that I think that was a fair comment you know there are other cases where I think you just have to really search I mean I wouldn't be hesitant to own a golden retriever or you know a german shepherder or any of these other really popular breeds I would just work really hard to to talk to people the breeder would sold to and find dogs that lived a really long a really long life in general small dogs live longer for sure the terriers the toy dogs in general they do live longer and dogs that have a working job like border collies boy some of those live 17 18 years my border collie lived to be 13 years so breeds where there's a working lineage I mean they have to be healthy to work those tend to to be pretty long-lived the really big breeds tend to have more heart difficulties and problems St. Bernard's and you know some of these giant breeds where they just almost been bred to be too big for their heart you know they they rarely live beyond the age of 10 or 11 because they almost always go from for heart problems so you always tell people that you know pick the breed you want pick the breed that matches your family there's all kinds of tests on the internet to help you do that I mean but then work with you know really look around and take your time to find a healthy and reliable breeder yeah no so yeah the question she asks is are breeds that are more related to wolf healthier I guess I would say no and you know in part because things that maybe look more wolf-ish you know like the Malamute or the Husky I mean you know there there were clearly multiple domestication events that occurred in multiple places in in the world and and you know by and large truly it's the small dogs that are the healthiest and and really do live the longest and so I wouldn't necessarily say those are you know among the healthiest so you know Adam Malamute that lived to be like 15 or 16 so you know again dogs that have a working function but this was bought from a line of dogs that you know were involved in mushing and so that's you know those are going to be healthy dogs so wouldn't necessarily say that other questions yeah do mixed breeds do better than purebreds you know everybody thinks that they're going to and I have so many people come up to me it's have bought a labradoodle or you know they have all these weird cool names um and they said you know and so hybrid bigger you know I'm my dog's going to live to be 22 and um then they're shocked when they don't and and the reason is because you know if the if the parent breeds or the parent lines were themselves not healthy particularly if they were not healthy because they had the same disease or the same mutation you haven't it doesn't do any good right and so um you know golden retrievers you know they get a bad reputation for having a lot of inherited disease I think there are some lines of golden retrievers that are wonderful out there but there are also some lines that really do have a lot of disease and because they're so good with families they're involved in an awful lot of these crosses um and and um you know you could say that of lots and lots of other breeds so you know in general what what I like about purebred dogs is you sort of know what you're getting you know most poodles I know live long long long long long periods of time they're an awesome breed in all three sizes um they have a reputation and the breed club are being very vigilant being very careful and so I don't necessarily think that's that's really the best choice yeah so so so the question is you know removing mutations does that happen widely so it isn't really removing mutations in in in the sense of how that language is used but it's really about breeding it out so breeding a carrier not to another carrier but to a healthy dog and when I talk to breed clubs I tell them first thing don't throw all the carriers out of the breeding pool because they're contributing so many good things that you're going to just end up with something else you didn't have a problem in before but but take your carrier and breed them to a non-carrier the carry get at the progeny tested breed carriers to non-carriers and gradually breed it out and we've seen examples where where a small breed has thrown out all the carriers and they have a disease it's really prevalent and then suddenly they have three other diseases um that crop up is recessive the american cattle club has just been wonderful I mean they they ask us to come to all their meetings and their and their specialty events and and their trials and we are inundated with invitations to come and give talks about exactly these kinds of issues um and labs like mine often make the data available without patenting it sometimes it is patented but often without patenting it just so the test can get out there and people can start using it and breeders are some of the smartest geneticists in the world they absolutely because it's their livelihood they want to breed healthier more long-lived dogs and if they're the first off the block with a reputation for using genomics to breed healthier more long-lived dogs people love that people love that um and so I have found that this I mean I have 50,000 DNA samples in my freezer and I can think of one incidence where I asked for a DNA sample and I was turned down no no there isn't right so so the question um that was asked was is there a is there a push in the dog world to you know mix dogs of different breeds um to to try and figure out what's going on with the genetics of of some of these traits I just put this up because it's my favorite picture in the slide show um and the answer to that is no first of all we don't breed or keep any dogs so we're not going to do that um and in the purebred dog world um you know people you know the the convention is you breed dogs of one breed only to members of the same breed um and that's just not the convention in that community you know to to take a dog that may be a popular sire and breed him to a bunch of other breeds to figure out what's going on that's just not what what what has done so it really isn't and you know I'm not in the management of the american kennel club so it's not really for me to say but okay one more can I take one more question all right one more question sure so I have I take 100,000 data points and I have 50,000 DNA samples from dogs in my freezer um I have my lab has very few mixed breed dogs almost all of those are from purebred dogs they're not all american kennel club recognized breeds you know some of them are odd you know european or asian breeds they're not all akc breeds but they are pure breeds they're not mixed breeds but there are other labs that have focused their studies on mixed breed so there's one at cornell who specializes in village dogs and he's traveled all over mexico south america africa to the outskirts of town on the garbage dumps and and he and his team sample hundreds and hundreds and hundreds of mixed breed dogs and that's you know his thing so you know you kind of can't do everything and so that's been you know where my focus has been but there there are certainly people doing that all right I'm going to let you go there's lots to see out in the museum um and I'll be around for questions and thank you all for your attention