I sent my dog's DNA to three different DNA testing
companies and the results all came back a little different.
Let's talk about why.
This video is sponsored by Datacamp.
We're going to be talking about analyzing genetic data today.
And that's all done with bioinformatics.
In grad school, I used Python and R all the time.
But when I got there, I didn't even
know how to use the terminal.
So I learned it via lot of Google and help from friends.
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This is Penny.
We adopted her in May of 2020.
And she is just an absolute sweetheart.
Her favorite things in the world are naps and chicken
and more naps, especially naps in the sunshine.
She is the sweetest dog we could ever have hoped for.
She is so sweet and all she wants to do is snuggle.
And we love her so much, so much.
We got her from her rescue.
And they told us that she was a chihuahua/corgi mix.
And chihuahua I can see, but corgi, not so much.
So I sent her DNA off it to get some doggie DNA ancestry
testing done.
And I want to be clear, we would love her just the same
if the results came back and said
that she was happy chihuahua had Loch Ness Monster.
But I am a geneticist and I couldn't resist.
So I also didn't just send her DNA to one company.
I sent it to three.
You can get down or over here.
OK, you sit your butt right there?
You can sit your butt right there.
The way each company analyzes the DNA is a little different.
And to understand why, we've got to talk
a bit about the structure of DNA and why there really isn't such
a thing as a chihuahua gene.
A chihuahua, a golden retriever, and a German shepherd
are all dogs.
Even though they all look super different, genetically,
they are 99.9% identical.
And this makes sense.
They are mostly the same.
They pretty much all have limbs and brains and ears
and fur and tails and toe beans and "boopable" snoots.
So they all have genes for making those different parts.
And usually, it's not just one gene that makes up a trait,
but many.
There isn't just one eye color gene,
but many genes that all contribute to eye color.
And each of those genes can come in different versions
or alleles.
For example, there are a number of genes
involved in coat length.
And it's not that there is a gene for short hair
and a gene for long hair, but rather, different versions
of a hair length gene that can predispose your dog
to having short or long hair.
And the difference between these versions
is usually really small.
For example, there's a position in a gene
called FGF5, where a Tbase is associated
with having long hair.
And a C-base is associated with having short hair.
And remember, that like you, dogs
have two copies of every gene, one from each parent.
So dogs that have a TT at that position, typically
have long fur.
And dogs with a CC or CT typically have short fur.
So you can look at that position in your dog's DNA
and make a prediction about what their traits will be.
So when we think about the whole dog genome, 99.9% of it
is the same.
But it's studded with these small locations
that differ between dogs.
Some of them are SNPs, Single Nucleotide Polymorphisms.
And others are indels, short insertions
or deletions of a few bases.
And there are also small regions of repeats
that can vary between dogs.
But most of the DNA is exactly the same.
And really, it's just about 0.1% of the locations
in the 2.8 billion base pairs long genome
that give us all of the different kinds of dogs
in the world.
So back to the tests.
If 99.9% of the DNA between dogs is the same,
you don't really need to look at that 99.9% of the DNA
to learn something about your dog.
And the dog genome is over 2.8 billion base pairs long.
So it can be time consuming and expensive to look at parts
that aren't going to tell you much.
So two of the companies, Embark and Wisdom Panel
just look at that other 0.1%.
They do this using something called a microarray.
This is a chip covered in tiny pieces of DNA
that match to those 0.1% of locations,
about 100,000 to 200,000 locations
depending on the company.
So if you add a dog DNA sample to this chip
and see what binds, you can tell if your dog has an A, T, C,
or G at each of these specified locations.
On the other hand, Darwin's Dogs that
does whole genome sequencing.
This means that they read every single base pair of your dog's
DNA on a DNA sequencer.
This captures those many little regions of variation.
But it also allows them to look for new unidentified locations
of interest as they sequence more and more dogs
and learn more about the dog genome.
So how can this tell me if Penny is a chihuahua or a corgi
or an Alaskan malamute?
As you can maybe already guess, since I told you
that dogs are mostly genetically the same,
there aren't chihuahua genes or husky genes or terrier genes.
But there are variants or a alleles of those genes
and many genetic markers along the genome that
show up in some breeds more than others.
There are also patterns of markers
that show up more in one breed than another.
So before they can analyze our pet's DNA,
these companies look at the DNA of lots and lots of dogs.
And they figure out which SNPs or alleles or patterns
show up more in one breed than another.
So they look at all the chihuahuas together
and they say, OK, they're most likely to have DNA that looks
like this.
Then they do the same thing for the Huskies and the Dalmatians
and the German shepherds and the terriers and on and on.
Then when they sequence your dog,
they can compare the patterns of DNA in your dog's DNA
to the types of dogs in their reference panel
and say, OK, at this location, Penny's DNA
looks most like the DNA found in a chihuahua.
And at this location, it looks most like the DNA
found in a terrier.
And they do this for the whole genome
and they calculate percentages.
So how did Penny's DNA look?
OK, we're going to view Penny's--
oh, I was wrong.
37% chihuahua, 25% Cocker Spaniel,
14% American Staffordshire terrier, interesting.
Well, now we get to see what the other two come back as.
Oh, they sent us a video.
Interesting.
So as I suspected, the results aren't the same.
And I can't wait to get the third one back.
That's going to be fun.
And according to Darwin's Dogs, Penny
is 22.9% Cocker Spaniel, 20% chihuahua,
and a whole bunch of you know, other mixes.
So all three of Penny's ancestry reports
came back and said that her major components
were a chihuahua and a Cocker Spaniel, which was surprising.
But then, all of the other percentages
were pretty different.
Two of them had American Staffordshire terrier.
One of them had poodle and Pomeranian.
And there was dachshund and pit bull.
So the main components of her results were all the same.
But they weren't identical.
And why not?
They all sequence the same DNA.
It's because each company is using a different reference
population.
Imagine that the company only sequenced
two types of dogs, Dalmatians and German shepherds.
When I sent in Penny's sample, they
would have only had those two types of dogs to compare it to.
And so they would match her DNA to the closest breed possible,
or tell me that they couldn't find a good match.
If they then added chihuahuas to their reference panel, now,
they would have a much better match
and be able to update her percentages
with much more confidence.
So because no company has sequenced every single dog
in the world, they have to rely on trying
to build the best, most diverse reference panel possible.
But each company's panel is going to be a little different.
So they might have slightly different results
when trying to assign breeds to sections of Penny's DNA.
And as the reference panel grows and they sequence
more and more dogs, their confidence in their matches
will get even better.
That's why you might get an update on your dog's breed mix.
It's not because your dog's DNA has changed.
But rather, because the reference panel
it's being compared to has changed.
And if you've had direct-to-consumer testing
like 23andMe or Ancestry DNA done,
you might be wondering if the same thing is true for us
humans too.
And the answer is, yeah.
You might get updated ancestry percentages every now and then.
And it's not because your DNA has changed,
but because the reference panel has changed.
And the pattern matching works in the same way too.
My DNA test came back that I was 45% French and 25% Lithuanian.
But that's not because there are French genes
and Lithuanian genes.
It just means that 45% of the markers in my DNA
looked most like the pattern of markers
found in people with long family histories in France.
And 25% looked most like the pattern of markers in people
with the long family histories in Lithuania.
And again, these markers make up a tiny, tiny fraction
of the genome.
You and me are 99.9% identical at the DNA level,
just like Penny and Pandora and Java are.
This isn't a review of these companies.
I'm not ranking them.
I think they all did a good job.
If you want to test your dog's DNA
to find out what breeds it is, you really
only need to do it once.
And it's kind of just your preference
on what options or other features these services
offer that will make you choose one or the other.
Come on up.
We got to say thank you.
Come here.
Yeah, good girl.
OK, good girl.
Thank you to Datacamp for sponsoring this video.
And thank you to you for watching.
As always, a huge shout out to my Patreon patrons,
who help me to make all kinds of different videos
about genetics.
And also, a huge thank you to everybody on Twitter
who sent in pictures of your pups
that I could use in this video.
I mean, I know people like sharing pictures of their dogs.
But I can't tell you how much joy
there is in just getting a notification
list full of dog photos.
I loved it, even if Penny didn't.
And as always, remember to go forth and do science.
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