A 'Supermutt' Reveals His Secret Identity – Treehugger

Russell McLendon / Treehugger
The best way to get a dog, in general, is to rescue one. That often means adopting a mutt, the joys of which are too numerous to list. Yet many mutts also come with hazy origins, potentially hiding breed-related needs, quirks or health risks in their DNA.
Five years ago, I wrote about two dog DNA tests I bought for my rescue mutt, Otis. The results were interesting and entertaining, if a little light on practical value. I took them with a grain of salt, but I was glad to get at least some small insight.
As I mentioned at the time, commercial dog-DNA testing was still fairly new in 2012. I'd wanted to eventually write a follow-up to that blog post, and then a Texas-based startup called Embark contacted me about reviewing its new test.
My previous post featured tests sold by BioPet Vet and Wisdom Panel, but I'm not re-reviewing them here. BioPet Vet is no longer on the market, and although Wisdom Panel has a newer version, I was reluctant to pay again for a test that may only be slightly different from what Otis already took. And frankly, I might not have tried Embark yet if they hadn't sent me a free test. I do think it's a good deal in hindsight — yes, even at $200 — but as I'll explain below, it depends what you're looking for.
First, let me briefly introduce Otis. We adopted him from the shelter in 2010 as a months-old "husky mix." We saw little reason to doubt that at the time, since he was a puppy and already had some hints of huskiness like a bushy, curly tail.
We also didn't really care about the exact breed makeup. Our curiosity grew as Otis aged, though, since this alleged husky stayed pretty small. Given how much exercise a husky would need compared with many other breeds, we decided to dig deeper.
I won't dwell on those earlier results, but suffice to say they didn't exactly match. Neither test reported any husky heritage, and the only breed listed by both was pug. BioPet Vet also listed Pekingese, beagle and bulldog, while Wisdom Panel had a more detailed family tree that included Australian cattle dog, chow chow and corgi.
Then, a few months ago, Embark contacted me on Twitter to ask if I'd be interested in trying out their test on Otis. I said I was, so they sent me a free kit.
Embark was founded by two brothers, Ryan and Adam Boyko, who grew up with rescue dogs. Ryan is a computer scientist, and Adam is a biomedical science professor at Cornell University, where he focuses on the genomic study of dogs. They founded Embark in 2015, and launched its first product in May 2016.
"One thing we found in our research is that lots of people wanted to have their dog take part in the studies," Adam Boyko tells MNN. "Because they thought it was cool and they wanted to contribute to the research, but also because they wanted to know about their own personal dog. As we did more and more, we started brainstorming and came up with the idea of doing cutting-edge research DNA testing for people's dogs, which is very different from the one-off DNA testing. That way is smaller and cheaper, but less comprehensive and doesn't push the science forward at all."
Embark is a commercial product, but it arose from a scientific quest: identifying genetic markers for diseases in dogs, which could ultimately benefit both canine and human health. And by crowd-sourcing DNA from mutts to reveal their breed mix, Embark can satisfy its customers’ curiosity while also collecting health data en masse. It’s similar to the “recreational genomics” model of 23andMe, but for dogs.
"We're in it to make dogs healthier," Boyko says, "and a nice addition to that is we're able to look at things like ancestry."
When the Embark kit came in the mail, it outlined a familiar process: Swab cheek cells — and inevitably slobber — from Otis’ mouth, secure the swab in a container, ship it off to be analyzed. (The kit offers more detailed instructions, which you can see in this video.) Unlike the earlier tests, I was also told to create an account online.
It was a few weeks before the results were ready. When they finally arrived, I didn't just receive a single document by snail mail or email — I logged into my Embark account and found myself immersed in colorfully presented information.
With this account, I can check back over time as research reveals new insights relevant to Otis. Embark will also let me know when new features and results are available. And in the meantime, there’s a public link for sharing Otis’ results. Embark offers separate privacy settings for breed, health and trait data, but I just made all of Otis’ info public. (Sorry, buddy!) You can see his full Embark profile here.
Here's the initial breed breakdown. It includes some overlap with Wisdom Panel, namely pug, chow and Australian cattle dog. The highest percentage, though, goes to "supermutt," which is Embark's way of acknowledging genetic ambiguity:
Aside from 'supermutt,' the top breed results for Otis are lab, pug and chow.
"Some dogs descend from other dogs that were themselves mixed breed," Embark's website explains about the supermutt label. "These other dogs can give small contributions to the ancestry of your dog, so small that they are no longer recognizable as any one particular breed."
Still, as you can see above, there were enough clues to identify three possible members of the supermutt portion: basset hound, Boston terrier and coonhound. "Looking back through the last three generations, we can see it's not a full great-grandparent," Boyko says, "but we definitely see markers from a breed, so we put that in there." Most dogs only have a small percentage of supermutt, he adds.
Like Wisdom Panel, Embark also mapped out a family tree with more detail about Otis' supermutt roots. It's not his only possible parentage, but Embark says "our algorithms predict this is the most likely family tree to explain Otis' breed mix."
A possible family tree for Otis, courtesy of Embark.
Despite the obvious differences, this family tree does have surprising similarities with the one from Wisdom Panel. Not only do both include pug and chow in Otis' ancestry, for example, but both feature a pug mix and a chow mix as likely grandparents. Australian cattle dog also appears on both, albeit as a full grandparent in Wisdom Panel and only part of one great-grandparent in Embark.
It could just be the power of suggestion, but I can see hints of all these breeds in Otis. He has the tail, torso and appetite of a pug, the athleticism of a retriever or a boxer, and maybe even a little of a chow's independence. And given the way he herds me around the house at meal time or walk time, I certainly don't doubt the cattle dog.
The keys to a test like Embark are genetic markers, which can reveal the genetic basis of inherited traits ranging from hair color to health risks. Researchers use a tool called a DNA microarray to find genetic variations among individuals, including single-nucleotide polymorphisms (SNPs, pronounced “snips”).
Early breed tests relied on just 30 or 40 markers, making them pointless for many dogs, but they've grown more accurate lately. Wisdom Panel is now up to nearly 2,000 markers, while Embark uses more than 200,000 based on its own in-house research. "To my knowledge, we don't use any of the same markers," Boyko says, adding that the companies' algorithms are also "totally different."
But quantity of markers isn't everything, notes Urs Giger, head of the clinical program in veterinary genetics at the University of Pennsylvania. A test's accuracy is "very dependent on how many dogs they have tested to establish the algorithm to get to the right answers," he says. "Furthermore, when people say they're using 2,000 or 200,000 SNPs, the question is how many of those SNPs are really informative for differentiating between one or other breed, disease traits and so on?"
Embark and Wisdom Panel aren't perfect, but according to Tufts University clinical genetics professor Jerold Bell, their research elevates them above most U.S. rivals. "I would stick with these two companies for their reliability," he says, "and their ability to answer questions and investigate further into questions about their test results."
Exploring the heritage of a mutt like Otis may be interesting, but to many veterinarians, dog DNA testing has a far more valuable role to play.
"I think animal health is more important than telling breed and ancestry," says Giger, whose lab has done hereditary-disease testing in dogs for 25 years. Bell agrees, since knowing a dog has a certain genetic marker "could allow for preventative measures that minimize or eliminate the occurrence of disease." Testing for breed and ancestry, on the other hand, strikes him as "more of a novelty for the owner."
Yet despite high accuracy, Giger says disease testing was much narrower and pricier until recently. "It is very exciting to have these SNP chip samples be analyzed, and be available in a rather inexpensive way for not only one disease test, but multiple disease tests as well as breed composition and ancestry for the same price."
Health results are a selling point for Embark, and since my older tests didn’t delve into health, I was intrigued to see that part of Otis’ profile. (Wisdom Panel 2.0 is still breed-only, but newer versions do test for a small number of disease mutations. For more than that, you’d need the company’s veterinary or breeder tests.)
Like the rest of his report, the health section is brimming with info. As the summary below makes clear, though, Otis' results were about as positive as possible:
A screenshot of Otis' health overview from Embark.
Embark currently tests for about 160 hereditary diseases, and Otis tested clear across the board. That’s not uncommon, Boyko explains, noting about half of dogs they’ve tested so far get this result, and about a third are carriers for a few diseases.
While this is welcome news about Otis, it still isn’t conclusive. “No dog and no person is genetically perfect,” Giger says. “Every dog can have some deleterious mutations that may result in some individuals having some disease presentation.” Otis is prone to cancerous mast cell tumors, several of which had to be surgically removed in the last few years. Embark doesn’t yet have enough data to test for that, but they’re working on it — and more clues from dogs like Otis should help.
"Mast cell tumors are an active area of research," Boyko says. "We've collected hundreds and hundreds of mast cell tumor cases, also controls, and we're hoping that through health surveys at Embark, we'll get more mast cell cases with genetic information. And with larger sample sizes, I think we'll start to identify that."
"So be sure to fill out the health survey for Otis," he adds. (I did.) "That was one of the main reasons we wanted to build Embark, because we use it to identify markers for all kinds of things. As an academic, there's really no good way to get a research grant that's going to pay for testing thousands and thousands of dogs."
Yet as with human DNA tests, health results carry a risk of misinterpretation. Having a marker for a disease doesn't necessarily mean a dog will get sick, for instance, and some mutations that sicken a certain breed "may actually cause a different presentation in another breed," Giger says. "They may cause disease in one breed, and cause no disease or milder disease manifestation in another." (So, in that sense, a mutt's breed mix could be more than just a matter of curiosity.)
To reduce the risk of confusion, Embark avoids giving medical advice, provides online resources to put results in perspective, and encourages customers to consult a vet. Genetic counseling is a key part of genetic testing, Giger says, although both he and Bell note that some vets may not be well-versed enough to offer such assistance.
Otis' results offer a few other interesting stats, too, like predicted adult weight (49 pounds), genetic age (57 human years) and "wolfiness" (0.6 percent):
"Wolfiness Score is based on hundreds of markers across the genome where dogs (or almost all of them) are the same, but wolves tend to be different," Embark explains. "These markers are thought to be related to 'domestication gene sweeps' where early dogs were selected for some trait." Most pet dogs now have wolfiness scores of 1 percent or less, but some "especially unique individuals" hit 5 percent or higher.
Predicted weight is one of the few results I can fact-check, and it's spot-on. That could be a lucky guess, but Boyko says these estimates aren't as loose as you might think.
"By looking at body size and other factors, we can actually convert a dog's calendar age to a human-equivalent age to see where in the life cycle that dog is," he says. "And from a geneticist's standpoint, there's so much you can predict from their DNA, much more so than in people. There are a few genes that code for body size, so we look at the 18 different genes and based on that, can predict what the dog's size should be with 80 to 90 percent accuracy. That's much higher than in humans."
Why is body size easier to predict in dogs? "Because of the way we've bred dogs," Boyko explains. "Just a few genes are driving the vast majority of that difference, whereas with people, there are lots of small variants across the genome."
Still, despite the many differences between dog and human DNA, Boyko says Embark's big data could offer broad genetic insights relevant to both species.
"You may have dogs that have a genetic marker but never develop the genetic disease, so is there a compensatory mutation somewhere in their genomes that's preventing them from getting that disease?" he says. "That's big for human health, too, because humans can get some of the same diseases dogs do. Next to humans, dogs have more known genetic diseases than any other animal — and of the genetic diseases that dogs have, almost all have analogous human disorders."
I still haven't covered all the info Embark revealed about Otis. There are two sections on ancestry, for example, depicting both his maternal and paternal lineage. There's a list of mutations for traits like coat color, facial markings, snout length and shedding, among others. There's a color-coded map of breed mix by chromosome. And a section of his profile is also populated with photos of other dogs "that have one or more breed percentages similar to Otis," with links to those dogs' Embark profiles.
Eventually, Boyko says, Embark could even help reconnect dogs with their littermates — assuming they all have Embark profiles. "Something like a relative finder is certainly something you can do with genetic technology," he says. "That's actually something we're working on, but we haven't rolled it out yet."
There are also more health and trait results in development, he adds, "as well as other things we can't predict because the research hasn't been done yet."
Embark is meant to be a long-term relationship, updating its results and services over time much like 23andMe does for humans. It costs $200, which is more than Wisdom Panel's comparable consumer tests, but it also gives more detail in return.
Whichever DNA test you choose, you're taking part in what Bell sees as the personalized future of health care, both canine and human. "The ability to test for multiple disease genes in a panel test is very important," he says, "and as such panel tests evolve (as with humans), they will become an important part of the health history and medical management of the dog."
Otis, meanwhile, is blissfully oblivious. As I pore over reports about his genetic markers for coat color and snout length, he's snoring loudly from the sofa.
It's kind of weird to know so much about Otis' DNA, especially since he doesn't even know what DNA is. Yet I'm glad to have all this insight — both because it might eventually benefit dog health in general, and because it has already helped remind me how lucky I am to know this strange creature sleeping on my couch.
There was an error. Please try again.
Thank you for signing up.

source