Can Doggie DNA Tests Decode Your Mutt’s Makeup? [Discover Magazine]

The Crux

Can Doggie DNA Tests Decode Your Mutt’s Makeup?
By Gemma Tarlach | November 25, 2014 9:00 am

Photo by Ernie Mastroianni/Discover
Mixed breed. Mongrel. Roadside setter. A something-something. Dogs of uncertain provenance get called a lot of things. When the animal arrives at a shelter, staff usually can make only an educated guess about the dog’s parentage.
Most of the dogs at my local animal control are assessed as “pit mixes” upon arrival — including the three I’ve adopted over the past 2 years. But a pit bull isn’t a breed: it’s just a type of dog characterized by a short coat, muscular frame and broad, oversized head.
All three of my dogs clearly — at least to my eyes — showed signs of specific breeds somewhere in their heritage: Tall and snow white Pullo looks like the breed standard for an American Bulldog. Tyche’s body is svelte like a boxer’s and inky black like some Labs. And lanky, long-limbed Waldo sometimes bays like a hound, especially when treeing squirrels.
Guessing my dogs’ breeds was a fun parlor game, but I wanted more definitive answers. So I turned to science. And, well, let’s just say it’s a good thing I didn’t place any bets on what was in my dogs’ family trees.

Finding Fido’s Family Tree
Consumer-targeted dog breed identification testing has been around for about a decade, with Wisdom Panel 2.0, owned by Mars Veterinary, as the dominant player on the American market.
Wisdom Panel looks at 321 genetic markers in your dog’s DNA to create a unique profile. That profile is fed into a program that assigns each ancestor from three generations — parent, grandparent and great-grandparent — into the best fit among more than 200 breeds in the Wisdom Panel database.
The doggie DNA test works differently than human ancestry tests, which typically trace both Y-chromosome DNA and maternally-inherited mitochondrial DNA back several generations. Instead, Wisdom Panel looks across the entire genome, not just on the sex chromosomes.
Wisdom Panel, like human ancestry tests, is more for the curious than for owners whose dogs are facing serious health problems. Medical DNA testing for dogs is much more focused and hunts for typically single-gene mutations that cause disease.
Urs Giger, a leading veterinary clinician and researcher, heads PennGen, at the University of Pennsylvania’s School of Veterinary Medicine in Philadelphia. He says that though Wisdom Panel is less focused, it still has some medical value. “Wisdom Panel’s purpose is to identify the breed or breed composite, which can be quite helpful information,” says Giger. Knowing your dog’s breeds can help your veterinarian tailor the treatment for a number of conditions, such as anemia, which may have different, breed-specific causes.

On the Path to Wisdom
I read up on some of the research that led to testing for breed, like Wisdom Panel does, and wandered around the test’s consumer-friendly site, which is loaded with easily digested information, including the basics of the test explained in a video that even a kid could understand.
I decided I was ready to see what science had to say about my pups. I ordered the Wisdom Panel kits online for about $80 each (without mentioning my media affiliation).
Collecting each the DNA with swabs that resembled tiny toilet brushes — two for each dog — was a snap. Placing the swabs one at a time between cheek and gum, I counted to 20 and then popped them into the kit’s little holder to air-dry for a few minutes before sliding them into plastic sleeves to reduce risk of contamination.
I then activated each test online, a two-minute process that assigns a unique specimen number to each dog’s sample. I affixed the labels, closed up the kits and, the following morning, handed them over to my postal carrier. It was all easier than our average trip to the vet.
Who’s Your Daddy, Bitch?
Tyche’s report arrived first. Although she’s lean like a well-conditioned boxer, her head is classic American Staffordshire Terrier, the breed most commonly associated with “pit bull type” dogs. Perhaps not surprisingly, Wisdom Panel declared she was 50 percent American Staffordshire. Each of her parents was the offspring of a purebred AmStaffie, as fans call them, and a mysterious “mixed breed” parent.
I flipped a few pages past her shadowy family tree to a page called “Mixed Breed Signatures.” The five breeds Wisdom Panel identified as being most likely somewhere in the mix, so to speak, were, in descending order of probability, Standard Schnauzer, Curly-Coated Retriever, Great Dane, Irish Terrier and Saint Bernard.

Saint Bernard?
I saw nothing of any of those breeds in the black, blockheaded dog beside me on the couch, sniffing the report in hopes that it might be edible.
The next report to arrive belonged to Pullo, who everyone I knew had guessed was an American Bulldog. Bigger than an AmStaffie, with the snow white coat common to American Bulldogs, I was sure Pullo would be close to purebred.
And he was — just not purebred American Bulldog.
Wisdom Panel found he was 75 percent purebred AmStaffie — apparently, one great-grandparent ruined his otherwise snow-white ancestry. So…what was that bastard interloper?

Again I turned to the Mixed Breed Signatures page. While no other breed had crossed Wisdom Panel’s “detection threshold” — the line in the data that gives the lab enough confidence to include the dog as a definite ancestor — the breed closest was a Smooth Fox Terrier.

According to the American Kennel Club breed standard, the Smooth Fox Terrier should not be more than 18 pounds. Pullo weighs in at 70.
The next four breed signatures potentially in his background were the Golden Retriever, Bull Terrier, Staffordshire Bull Terrier and Great Pyrenees, none of which I saw in the sleek-coated, big-boned doofus snoring in my lap.
Where in the World are Waldo’s Roots?
Then came the DNA detective work for Waldo, the most recent addition to the pack. I’d been fostering him over the summer, but no one wanted to adopt the big, dopey dog that I affectionately nicknamed Lurch. So I kept him.
Waldo has floppy ears shaped like perfect equilateral triangles and feet too big for his lanky body, which continues to grow. And grow. He topped 80 pounds a few days ago and shows no signs of slowing. Shelter staff told me they suspected he was part Great Dane. But his huge, baying bark and obsession with treeing squirrels suggested some kind of hound to me.
Eagerly, I downloaded his report.
Wisdom Panel found that Waldo was nearly half AmStaffie. The rest of his makeup was a mix of breeds (none of them hounds), but two signatures were strong enough to pass the detection threshold: boxer and Entlebucher Mountain Dog.

For anyone unfamiliar with an Entlebucher Mountain Dog (as if!), it’s the smallest of four regional herding dogs in the Swiss Alps, collectively called Sennenhunden. I looked up the breed standard and saw a compact, tri-colored dog with an all-business, very un-Lurch-like expression. It’s a rare breed, not exactly common to Milwaukee’s mean streets.
What was going on here? Was Wisdom Panel wrong?
I wanted answers, so I called Wisdom Panel’s veterinary geneticist, Angela Hughes.
Don’t Judge a Book (or a Dog) by its Cover
Hughes spends a lot of her time helping dog owners understand the test’s results, and is willing to admit the test sometimes barks up the wrong tree.
“I’m sorry, but that Entlebucher Mountain Dog is a false positive,” she said.
Having had a few days to ponder the reports by then, I felt a little disappointed. I’d already concocted a romantic, sepia-tinted backstory for Waldo’s great-grandparent, perhaps brought to Wisconsin by Swiss immigrants to wrangle a few of the plentiful ruminants of America’s Dairyland, then, one day, seduced by an urbanite boxer passing through town, running off to the bright lights and big city of Milwaukee.
“The Entlebucher is a rare breed with a strong signature. The computer could be fixating on one or two chromosomes,” Hughes explained, digging deeper into Waldo’s report, looking at breed signatures that popped up as possible ancestors but below the detection threshold. She decided that the Mastiff, suggested in his Mixed Breed Signature, was more likely to be in his background because it appeared on many of the lineage trees the computer builds as it processes a dog’s unique profile.
Hughes also had an explanation for why Tyche and Pullo’s results threw me for a loop. Wisdom Panel looks for genetic markers that don’t affect gene expression, she explained. The genetic markers aren’t dictating a dog’s behavior or appearance, and they’re not causing disease. Instead, they’re the product of random mutations that form a pattern over time in a single breed, just sitting quietly in the background of the dog genome.
By focusing on those “non-coding” markers, Wisdom Panel reduces the chances of a false positive — that’s how the company can claim an accuracy rate of 90 percent. It’s also how, Hughes says, owners can be surprised by their pets’ Wisdom Panel results.
“As humans we fixate on one trait,” said Hughes. “People think, for example, that bigger dogs with merle (a mottled coat pattern) are Catahoula, smaller merle dogs are Australian shepherds. But there’s a single gene for merle and it’s dominant — it could be from 20 generations ago, and everything from Schnauzers to Great Danes has it. We need to move beyond the single trait. It’s like seeing someone with blue eyes and saying ‘Oh, you must be from Sweden.’”

Trait-Baiting
Everything Hughes said made sense to me as a science journalist, but as someone who has spent a lot of time peeling Waldo off trees in futile pursuit of squirrels, I clung to the idea of him having some large hound in his background.
Following up via email a few days later with Hughes, I asked for a better idea which specific marker might have caused all the Entlebucher confusion. Her reply answered my question by providing greater insight into the overall test:
The computer is making in the neighborhood of 7 million statistical calculations matching Waldo’s data to our database and what I see is a very distilled version of that analysis (otherwise it would take me days or months to wade through the data of a single dog). So I don’t have that degree of granularity available to look at and be able to tell you that it is making a match say on chromosome A at position D. What I can tell you is that some breeds (especially the rarer ones) have a genetic signature/pattern that is very “tight” – e.g. not a lot variation in certain areas – and so if a mixed breed dog happens to have a similar pattern or signature by chance (through genetic recombination and mutations), it can come up as a false positive match to that breed … I will tell you that the Entlebucher is not one I commonly see as a false positive (or a true positive for that matter!) so Waldo is definitely unique that way.
Oh, Waldo is unique, all right. Lurch is special, as are Tyche and Pullo, and any dog loved by its forever family. But, if the Wisdom Panel test told me only what I already knew for certain — that American Staffordshire terriers pop up in all three dogs’ background — was it a waste of money?
“I think it’s amazing that even the one breed was deciphered by 320 or so different markers,” says PennGen’s Giger, whose lab has no affiliation with Wisdom Panel. “The answer is so complex.”
Hughes notes that knowing the high percentage of AmStaffie in my dogs can also help me be vigilant about certain conditions, such as skin cancer, that they are more likely to get, regardless of what other breeds contributed to their DNA.
It’s also possible, note both Giger and Hughes, to run a much more precise breed identification DNA test, but it would cost thousands of dollars, well beyond what most dog owners would be willing or able to spend.
Giger theorizes that Wisdom Panel may be less helpful to owners of dogs — like pit bull types — that are the product of backyard breeders, who operate outside of AKC-registered bloodlines and often introduce other breeds to their stock in hopes of capturing a specific trait such as size, coat color or even regional aesthetics.
“One would have to moderate enthusiasm for the test results of a more locally generated dog,” Giger says tactfully.
I’m glad I gave Wisdom Panel a shot, even if my rambunctious but good-natured dogs are definitely of the locally-generated variety. It gave me a better understanding of the science that goes into breed identification — though I can’t help but note the shelter assessment (which Wisdom Panel says in its FAQ is generally only 25 percent accurate) nailed a three-out-of-three for my pups.
“In the big picture, people want a label,” says Karen Sparapani, executive director of Milwaukee Area Domestic Animal Control Commission (MADACC), where I adopted my dogs. “Some people were calling [the pit mixes] boxer-black lab mixes, or terrier mixes. But I decided it’s in the dog’s best interest to call it what it looks like. So, you know, if it looks like a duck, call it a duck.”

[ My intention with my blog is to simply collect articles of interest to me for purposes of future reference. I do my best to indicate who has actually composed the articles. NONE of the articles have been written by me. – Louis Sheehan ]

Posted but not written by: Lou Sheehan

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