Thursday, June 27, 2013

My dogs' evolutionary history. Part 3: Inside scoop and why

Recall that we ordered DNA testing kits for our mutts. First we made predictions, then we revealed the results. Today I want to tell a bit more of the story...
Remember that time a doctor used a vibrator on my hips because I had a cyst on my knee? I was all into it "for science." It was an opportunistic science sting operation. There was totally gum on my shoe. There was all kinds of pseudoscience that day.

Anyway, I was all psyched up for that sort of Dateline-style, hidden camera intrigue when I called up Mars Veterinary, the people who do the analysis for Wisdom Panel doggie DNA kits, last Friday afternoon. I was all psyched up because, as Kevin said, I needed, "to make sure they're not defrauding people."

Me? I do? Little old me?

That sounds about right. I mean, just because I can see all the educational potential here doesn't mean I should be endorsing it without understanding it better. And while I'm understanding it better shouldn't I make sure they're not entirely full of s--t?

But I already know they're not full of s--t because they gave us results for both Elroy and Murphy that made sense. They didn't report crazy results and there are lots of ways they could have... there are 200 breeds on that list, most of which do not look like our dogs or like they've wafted their DNA anywhere near our dogs.

So, they can't be completely fraudulent. Whew. Okay then, less of a burden on me for this interview. But wait. Could it be maybe a little more nuanced, this hypothetical fleecing? After all, they're the ones who saw my blog and reached out to me to have an interview--isn't that a little big brothery? And, after all, their website doesn't tell us what their methods are, not really, not for those of us who have ever operated a PCR machine or run a gel. And they don't tell us what these markers are in our dogs' reports that led them to make the reports. I'm used to having too much information, even, because of 23andMe.

Anyway, there were all kinds of reasons to be professional when I called up the veterinary geneticist. But after she answered my first question so well, I pretty much lost all professionalism and drooled all over her, albeit through the phone.

Here's what I learned. Please bear with me... I didn't take direct quotes because (a) that's hard to do without a hands-free headset (or fancy recording software I don't have because I never needed), and (b) I got a wee bit excited and flailed my arms most of the conversation. 

All questions and answers are my paraphrasing.

Question: Are you using a chip or what? How are you genotyping?
Answer: A chip like 23andMe's isn't cost effective. Yes, there's a chip but it's not specific to the test. They use a sequenom platform. It's PCR markers combined into panels.  They run those PCRs for 321 markers, broken up into several panels, optimized so that they don't interfere with each other clearly and don't have to change primers. They use nested PCR for segmenting around the mutation and then to get the exact SNP they throw the DNA in a mass spec to find the particular A, T, C or G mutation. Each has a different weight, so each can be identified. 

Question: Do you get both alleles from that?
Answer: Yes. They don’t sequence in both directions but they sequence both chromosomes.

Question:  Are those 321 markers for visible or perceptible phenotypes? 
Answer: No. None are visible phenotype. They're ancestry markers/SNPs.

Question:  Have you found any dogs that have none, not one, of those breed markers?
Answer: No. And we don't expect to. But it's not completely out of the question given the spectral nature of variation over space and time. 

Question: How did you validate your mixed breeds family tree methods? Do you have mixed dogs with known parents and grandparents and type them all in the family?
Answer: The pure breed tests validate so well already. And also, yes, they do validate with mixed dogs with known heritage but not many. The methods are built out of Ostrander's research with 85 breeds, 5 dogs from each and 96 microsatellites. She licensed the patent exclusively to WisdomPanel. 

Question: How do your mixed breed reports compare to how people guess based on external cues? Aren't people already good at guessing their mutts ancestries?
Answer: Actually they're not. Ancestry DNA testing is much better. People aren't that good at guessing mutt ancestry based on phenotype, as far as the few studies suggest. (There's one by Victoria Voith that I want to check out and there's one by Levy on pitbulls specifically.)

We chatted for much longer than that and she shared all kinds of interesting information about genetics for dogs' visible traits and also lots about their reproduction which I'm keen to learn about. But that right there's all the relevant information regarding our doggie DNA testing experience that I got during the 30 minute phone call. She was completely open with me about everything which is why I'm kicking myself that I forgot to ask why they require the dog's weight when you submit its cheek swabs. I have a hunch, however, that it's got something to do with validating their mixed breed body size estimates given how many people use WisdomPanel on shelter puppies that will be better adopted if their projected size is known. 

So the question remains... If you don't have a puppy or don't care what it will grow up to look like or be like, why do Wisdom Panel? 

The promotional video on the homepage sums up why many people might do it: 

I wasn’t sure what my dog was made up of...Pretty sure she wasn’t just a [breed name]...I wanted to know so I could tell people when they ask me 'what kind is she?'

This is fascinating.

Why do we care where our dogs come from or what kind they are? Same reason we care the same things about humans and ourselves. And it all boils down to the fundamentals of the field of anthropology... and it's complicated.

And finally, why have I titled all three of these posts "my dogs' evolutionary history"? 
Because evolutionary history is a synonym for family history and for ancestry. And vice versa, all around. And, clearly, I'm trying to make a point about that.

When you type "evolution" into the Wisdom Panel website search, this is what you get:

But that's not going to stop me from using this to teach evolution. I've decided that Wisdom Panel will be a good alternative for students who aren't interested in doing 23andMe in my anthropology courses, so I'm going for it.

Dogs, humans, what's the difference?  A lot and not.


Anne Buchanan said...

Thanks for this, Holly. I'd love to have been able to hear a recording of this conversation -- two passionate scientists talking about a subject they love!

Holly Dunsworth said...

Given our recent posts, the MT is becoming the DT :)

Anne Buchanan said...

It's the CM.*

*Cat's meow.

Holly Dunsworth said...

It really is. I tried to find a catmaid and this is what came up: picture of catmaid