Replies to This Discussion

Permalink Reply by John Wolff on January 26, 2009 at 2:17pm

Thanks, really interesting (I'm a lab tech in a medical genetics lab). My bosses will be interested; probably know all about this already. Neurologists.
ALS was I think one of the earlier genetic diseases gene-mapped and identified. That raised eyebrows because the gene involved, superoxide dismutase (SOD), is "just" a "housekeeping" gene present and conserved in practically all living things; the SOD enzyme decomposes and thus detoxifies superoxide, a free radical that's otherwise free to do chemical mischief in a cell. Apparently the motor neurons are very sensitive to this sort of damage over time. It's usually dominant, meaning that if only one of the your two SOD genes is broken, that can cause Lou Gehrig's Disease. One good gene is not enough.

I'll bet your post is slightly inaccurate: I'd guess the same GENE is responsible for both ALS and DM, but ANY mutation that damages that gene will cause these diseases. When one mutation descended from one founder is responsible for most cases of a genetic disease (I think Cystic Fibrosis is like this), it's really easy to make a cheap, quick, simple PCR* test for it. Otherwise, you have to sequence the DNA of the entire gene, looking for an unkown mutation, a big job that still doesn't necessarily find all the mutations. But in purebred dogs, most of the familial DM cases could well be an inbred mutation descended from a single founder, and that might make a cheap and simple PCR test possible.
But a lot of times, these diseases are "sporadic": a new mutation, out of the blue, not something inherited that can be bred out.

Our canine friends help us in so many unexpected ways.

*PCR = "Polymerase Chain Reaction"; for genetics, this is about as important as the invention of fire.

Permalink Reply by Wendt Worth Corgi's on January 26, 2009 at 2:22pm

Thank you for your comment but will have to admit..alittle above my head or below the feet. *giggles* Let me ask you this..if we go ahead and do the testing for DM and even if we test clear this isn't a guarantee that this couldn't happen in an offspring?

Permalink Reply by John Wolff on January 28, 2009 at 3:56pm

I am AMAZED at what I've found out about this. The state of the art has gone far beyond my wildest fantasies. I've been slipping. Affymetrix has a SNP array for the whole canine genome!? Who needs science fiction when they do stuff like this?

Yes, there is a FREE genetic test for DM:
http://www.caninegeneticdiseases.net/DM/ancmntDM.htm
http://www.caninegeneticdiseases.net/DM/resrchDM.htm

It's a missense mutation that changes amino acid#40 from glutamate to lysine in the SOD1 gene (same gene that causes ALS in humans). 96 of 100 affected DM dogs tested positive for this one mutation, which means most DM in dogs comes from 1 single founder in their ancestry, making it much easier to test for since you know what to look for.

DM is recessive in dogs, with incomplete penetrance: heterozygotes (carriers) do not develope disease, only homozygotes (both copies mutated) develope DM -- but not ALL of them do.

So if you don't breed carriers, this mutation can be bred out of the population.

If you breed two dogs that test "clear" (two copies of the normal gene) their offspring won't get DM from THIS mutation, the major cause of DM. But remember that 4% of affected dogs that did not test positive for this mutation? That suggests there are other, much rarer mutations, either in this gene or other unknown genes, that can also cause DM. This test wouldn't catch them. But this test will avoid the greatest risk. Wow.

Permalink Reply by John Wolff on February 21, 2009 at 8:43pm

I got the PNAS paper on DM/ALS. Here’s an update.

The mutation involved is a G-to-A change in the SOD1 gene. It changes 1 amino acid in the SOD protein. But to say this causes DM is an oversimplification; better to call it a “risk factor”. Here’s what they found in PWCs:

Basically, all 50 PWCs affected with DM were AA., but a LOT of unaffected PWCs are AA, too. So the AA genotype is necessary, but not sufficient, for the disease.*

Here are the numbers for their 67 UNAFFECTED control PWCs:
AA 44 66% at risk
AG 14 21% carriers
GG 9 13% clear

A form: 76% of the gene pool (wow)
G form: 24% of the gene pool

So if I’ve got it right, and their controls are representative of the entire PWC population, 2/3 of Pems are at risk for DM! Clearly, this A form is recessive with rather low “penetrance”; necessary but not sufficient. I think they sorta goofed, because about half of their healthy controls were well under 7 years of age, too young for symptoms to show. Some of these young “unaffected” AA controls might develop DM later. The stats are too much for my poor little brain, and I’ll trust the statisticians and their computers, but these numbers don’t look like as strong a connection as I would have expected.

If breeders scrupulously breed only dogs clear for the DM “A” form, they have only about 13% of the PWC population to choose from!

So there’s more to the story. I’ll bet there are two, not one, genotypes necessary for DM, and the next thing they'll look for is a “modifier”gene that affected AAs have but unaffected AAs don’t. Maybe there’ll be a test for this additional gene someday.

If I've got this right, there's little point in having your Pem tested for DM unless you're a breeder. Chances are 2/3 it'll tell you that your Pem is at risk: 150% of the overall incidence in Pems. That's not saying much.

Also, it’s not truly recessive. Microscopic examination of spinal cord tissue from AG dogs showed some of the same changes seen in AA dogs, but not as much; presumably, dogs don’t live long enough for clinical DM symptoms to appear in the AG carriers.

If I got it right, this G-to-A mutation must be descended from a single founder ancestral to Pembrokes, Boxers, German Shepherds, Rhodesian Ridgebacks, and Chesapeake Bay Retrievers. Looks like a highly inbred situation.

*Among 537 dogs of all 5 breeds, they found 4 AGs and 4 GGs diagnosed with DM by the “least stringent” criteria, without confirmation by microscopic spinal cord examination. These were probably misdiagnoses (they call them “phenocopies”), symptoms that look a lot like DM but are probably caused by something else. So even if a dog is clear for DM, there are other things to worry about, like rarer diseases and back injuries.

SOD mutations cause ALS, Lou Gehrig’s Disease, in humans. SOD is “SuperOxide Dismutase”. Oxygen is toxic largely because of the superoxide form, a nasty corrosive free radical that makes chemical mischief. SOD detoxifies this. You’d think that ALS/DM results from the loss of this function, but no. Mice with both SOD genes removed develop normally(!). They think these mutations in SOD cause a “toxic gain-of-function”, perhaps making these proteins clump into aggregates that kill nerve cells somehow. Spinal cord sections from both AA and AG dogs show tiny granules that stain with anti-SOD antibodies. Other ills of the flesh like Alzheimer’s show similar granules of different proteins.

Here’s a link to the PNAS paper, something only a biology major could love, but if you’re into both biology and dog breeding:
DM in dogs PNAS 2009 Coates et al.
The scientists seem excited about this, hoping to learn more about our homologous affliction from our canine friends.

The technology is stunning. Affymetrix has markers for the whole dog genome on chips. To do a Genome-Wide-Association (GWA), you just soak these chips in a few micrograms of a dog’s DNA, feed it into the machine, and the computers spit out the numbers. Who needs science fiction? I graduated in 1974, and if anybody’d told me they’d be doing stuff like this someday, I’d have asked them where they got that good stuff they were smoking.

Permalink Reply by John Wolff on February 22, 2009 at 1:04am

If I read the paper correctly, this G-to-A missense mutation (and the haplotype that includes it) is the same in all 5 breeds (PWC, GSD, Boxers, RR, CBR), indicating that it's all the same, from a single founder presumably. Originally, it was called "German Shepherd Dog Myelopathy".
I'm so amazed by the numbers that I wonder if I'm reading it right, but Table 1 says that in their control group of 67 unaffected PWCs, 44 were AA at-risk, 14 were AG carriers, 9 were GG clear. 66% of this unaffected control group was AA, at risk! The incidence in the general PWC population is... what? I thought it was well under 1%. So the penetrance must be low.
They tested 120 dogs from breeds in which DM is rarely diagnosed:
AA 0
AG 5
GG 115 so the A allele is very rare in other breeds

I think it's wonderful that they're offering the test for free. It'll take awhile, but this A allele can be bred out of the population. I'm just wondering if it's linked to something desirable nearby that breeders have selected FOR...? and DM has gone along for the ride?

One thing I got out of this paper is: how much we can learn from dogs! Human gene mapping is really tough because our litters are so small and our generation time so long. There is such a wealth of pedigree info on canines. But they have the same genes we do, so...

Permalink Reply by John Wolff on February 22, 2009 at 11:59pm

The test is free only for dogs over 10 y.o.? That seems odd -- self-defeating, even. I'd think the best use of this test is for breeders. Even if you breed a carrier to a clear dog, the pups shouldn't get DM and you're reducing the prevalence of the "A" allele. But if the "Fluffy" test is $58, it can't be that expensive....

But I'll bet more of this story will be coming out in years ahead. If 66% of PWC are at risk , but less than 1% are getting DM, there's got to be some other gene involved here (I can hardly believe that many PWC are homozygous for this A allele, but that's their control group if I got it right).

And that's where canine genomics can make such a great contribution to human genomics. Human litters are so small, and our generation times so long, that gene mapping is a nightmare. With dogs, there is such a wealth of pedigree information.

Permalink Reply by John Wolff on February 27, 2009 at 1:57am

My last 2 cents' worth:
What surprised me was that 66% of their control group is homozygous for the A allele, at-risk, and only 13% of it was clear [these numbers may not be representative of the Pem population, but shouldn't be too far off.]
They had 50 affected AA corgis and 44 unaffected AA corgis; why can't their computers pick out something that all these affected dogs have and the unaffected ones don't (i.e., a modifier gene necessary for DM)? I'll bet that's the next step. They'd have to throw out half their unaffected controls because they were younger than the age-of-onset. Just look at old, unaffected dogs for controls. Their GWA (Genome-Wide Association) did show weaker scores on chromosomes CFA6,18, 20, and 35 (SOD1 is on CFA31). Maybe another culprit is lurking in one of those places. Stay tuned.

If their control group is representative of the whole Pem population, ~20% are carriers and only ~13% are clear. Not many clears to work with. But if you breed clears to carriers, half the pups should be clear, none affected, and you can still reduce the A gene.

This is pure speculation, but... why so many AA Pems? Random accident, or human selection? I wonder if there might be some valuable corgi gene tightly linked to this DM locus, so we've inadvertently selected for the DM "A" allele, too? That would make it a lot harder to get rid of -- breeding only GG clears, we'd lose some baby with the bathwater -- we'd have to find a crossover between DM A and this hypothetical valuable gene, and separate the two. So watch for what happens when people start breeding GG clears to GG clears, and see if there are unpleasant surprises.