Woof! Dog Genome Assembled

Manwe's Herald writes "The first draft of the dog genome sequence has been deposited into free public databases for use by biomedical and veterinary researchers around the globe, the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), announced today."

Comments

Open Source Pets

[spector30]

Who would have known they would Open Source this stuff. I'm surprised someone didn't get a patent so you'd have to pay a royalty for every breath your dog takes.

Re:Open Source Pets

[SB9876]

Actually, the vast majority of gemone sequences are in the public domain in whole or part. Even many of the proprietary genomes ended up being made availabe to the public after a year or two.

Open source is not a new idea for the academic sciences - they've been operating on that principle for a couple hundred years now.

Genealogy of a Mutt

[crow]

So how soon will I be able to take a DNA sample from my dog and find out what combination of breeds she is?

Re:Genealogy of a Mutt

[Otter]

IIRC, the primary sequence was from a boxer and they did additional sequencing in 10 other breeds, including a greyhound and a Pomeranian (forget what else) plus coyotes and wolves. Celera, meanwhile, sequenced Craig Venter's poodle.

Much of the point of looking at dogs is to understand the differences between breeds, like why collies are born knowing how to herd sheep while Shih-Tzus are completely stupid all their lives. So, to the degree that your dog is related to breeds they've looked at, you can get started as soon as they clean the data enough to post it to dbSNP.

Re:Genealogy of a Mutt

[Anonymous Coward]

By the way, kudos for a thoughtful question about biology instead of a witless comment about open sourcing dogs...

Re:Genealogy of a Mutt

[SB9876]

The issue of Science a few weeks back had a bg article devoted to the dog genome completion. They also reported results from initial studies that showed the relationships between various dog breeds. It turns out (as suspected) that dogs were domesticated in Asia as asian breeds are the most different from other domesticated breeds and most similar to wolves. They did an evolutionary tree for the rest of the dog breeds but the cladistics are still being worked out so most of the other breeds are still in a bit of limbo. They expect to work out the relationships of those breeds over time.

This study was significant because it was the first to be able to unambiguously identify dog DNA by breed reliably. Previous attempts using smaller numbers of SNPs tended to be very innacurate.

The biggest result of the dog genome is for human medicine. Geneticists have been pushing for dog genomes (they're already working on a second dog breed genome) for years. Purebreed dogs are a geneticists dream. Each breed has distintive features as well as characteristic diseases such as arthritis, nerve degeneration and cardiovascular disease. Purebreed dogs are also basically giant inbred families with meticulous documentation about their lineage. Having dog genomes actually has a great deal of potential to revolutionize human medicine as a result.

Re:Genealogy of a Mutt

[Forbman]

As long as they didn't sequence a cocker spaniel...

Oh, fun lets DNA mark our pets.

[kabocox]

Forget tracking people. We need to elimate all those strays. This is the first step toward tracking all those pets. After we have all the pets marked, then we can remove all the unmarked ones. Let's just hope our removal system just removes that species and not us as well.

Re:Oh, fun lets DNA mark our pets.

[I_Love_Pocky!]

Sounds like a mark and sweep garbage collector algorithm.

In case of slashdotting....

[Hex4def6]

Heres the text in case of a slashdotting;

ATCTATCTC
TYGACTATA
ATCTATCTA
TGATCTACG
TGAT CTACG ...

Please try to keep posts on topic.
Try to reply to other people's comments instead of starting new threads.
Read other people's messages before posting your own to avoid simply duplicating what has already been said.
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Problems regarding accounts or comment posting should be sent to CowboyNeal.

Re:In case of slashdotting....

[PateraSilk]

ATCTATCTC TYGACTATA ATCTATCTA TGATCTACG TGATCTACG ...

This must be one of those new dogs with six nucleotides.

What does "Y" pair with?

Re:In case of slashdotting....

[gstoddart]

I for one welcome our new "dogs with six-nucleotides" overlords. =)

And geeks everywhere rejoyce...

[stefanlasiewski]

And open source geeks everywhere begin compiling their own version of Dog.

Re:And geeks everywhere rejoyce...

[dnahelix]

And the GREEKS are creating a pile of dogs, too.

Re:And geeks everywhere rejoyce...

[Poeir]

Ha, I'm compiling mine backwards.

This means big changes in the world of dogs

[Kanpai]

Dog liscences will now be under the GPL. Breeds will be reffered to from this point forward as Distros. Microsoft will build a grossly ineffiecent one, but will show everyone how it looks really pretty and doesn't bite, and everyone will buy that dog instead of decent dogs.

I wonder how long it is before a joint effort by animal rights owners and fanatical christians start complaining about whether man understanding this much of Dog is morally right.

Somebody

[Marxist Hacker 42]

Tell NASA: now they can have cloned dogs to go with their robotic cats.

Massive number of chromosomes

[RobertB-DC]

I had heard that the biggest problem with either sequencing the dog's DNA or cloning a dog (the Missyplicity project) was the comparatively large number of chromosomes. In fact, a National Geographic article titled "Wolf to Woof" (tiny excerpt available here) notes the dog's 78 chromosomes (compared with our measly 46) as one of the reasons you can group a Great Dane and a Pomeranian as part of the same species.

I'm a cat person, myself. Cats, being contrary by nature, allowed themselves to be cloned, but then came out looking completely different because coat color and pattern is determined after conception.

Re:Massive number of chromosomes

[bcrowell]

Specifically, they found:

• on chromosome 37: bringing home dead things.
• on chromosome 16: sniffing other dogs' butts
• on chromosome 19: rolling in the mud
• on chromosome 62: peeing on fire hydrants
• on chromosome 77: chasing cyclists and mail carriers
• on chromosome 44: jerking your leg when you get your belly scratched

And in case any of this seems like irrelevant ivory-tower stuff, it has some very real applications, e.g., they may be able to modify the human genome to remove some of these same behaviors from the males of our own species.

Just One Step Closer To Chocobos!

[Wandering Wombat]

The vehicle of the future! Back on topic, just because we can sequence genomes, how does this help to edit them for various purposes?

Re:Just One Step Closer To Chocobos!

[eurleif]

Editing isn't hard, it's the compiling that'll get you.

Re:Open Source Pets. What sort of license?

[julie-h]

I wonder if Mother Earth uses GPL. If, where do I submit the changes?=)

I see a SCO case coming

[julie-h]

I don't know Open Source pets. Vets are pretty expensive as it is, and I don't think I can afford a monthly SCO lawsuit on top of that.

Is allergy relief in sight?

[boredman]

Oh, I wish I could have a dog. I love 'em. The only problem is that I'm horribly allergic to them. I break out in hives, my throat closes up, the works.

I hope we will eventually be able isolate the allergen, find the sequence that codes for it (assuming it is a protein), and alter it such that it doesn't adversely affect the dog's health and keeps people like me from having horrible reactions to them.

Re:Is allergy relief in sight?

[amide_one]

Not to sound unsympathetic, but why should dogs be changed (genetically modified, presumably) for the sake of your sinuses? Especially when the protein(s) that bother different people might be completely different?

I'd rather hope for the protein to be identified, as you said, and then for some sort of medicine created that specifically binds to that protein and blocks your immune response. Repeat for cats, plants, whatever else people are allergic to, you've got a nice allergy spray that really really works.

Re:Is allergy relief in sight?

[boredman]

Good point. That works, too. Either way, having the dog genome mapped out will help in this endeavor.

Re:Is allergy relief in sight?

[Anonymous Coward]

I wish people wouldn't grow up in sterile environments. Raised by soccer moms with floors disinfected by Mr. Clean, you westerners have the most allergies. In countries where children grow up exposed to allergens, bacteria, viruses and other 'dirt', allergies are much more rare. If you grow up on a farm, you chances of having an allergy are less than 1%. However, if you grow up in a sterile urban home, full of chemical pollutants, you are liable to get at least one. An allergy is the result of an 'untrained' immune system overreacting to a benign threat(pollen, dust, fruit juices). If the immune system is exposed to real threats at an early age, it adapts, balances itself out and is able to differentiate between harmless pollen and harmful bacteria.

Stop blaming the dogs and start blaming this 'progress' which reduced everyone(including me) to cube-dwelling keyboard monkeys living in sterilized blocks of plastic with information fed to us through a cathode-ray tube.

Re:Is allergy relief in sight?

[Fratz]

Mind you I saw this on TV - who knows if it's true or ethical or what. But there's a crossbreed called a Labradoodle (Labrador / Poodle mix) that is a "designer breed" for people with allergies. Poodles don't shed, apparently, and, well, people like Labradors better. Google it and see what you can find.

Re:Is allergy relief in sight?

[imnoteddy]

There is already are breeds for people with alergies. on this web page:

Among the hypoallergenic breeds to choose from: the Standard Poodle, Giant Schnauzer, Afghan Hound, Irish Water Spaniel, Komondor, Miniature Poodle, Standard Schnauzer, Portuguese Water Dog, Puli, Soft-coated Wheaten Terrier, Kerry Blue and Bedlington Terriers, Toy Poodle, Miniature Schnauzer, Bichon Frise, Mexican Hairless and Chinese Crested Dog.

"Hypoallergenic" is the fancy way to say "doesn't affect people with allergies".

meh

[AragornSonOfArathorn]

meh, I won't be impressed until they harness this technology to create a real-life Catdog!

Degeneracies, IUPAC codes, etc.

[dexter riley]

To generate the sequence, all the chromosomes were cut into fragments, cloned, then sequenced. Dogs have two copies of each chromosome (and either an XX or XY pair). The DNA sequence of a region of one chromosome may be different than same region of the other chromosome. In this example, one sequence had a cytosine at that position, while the other sequence had a thymine. To make it easier to decsribe that difference, or polymorphism, the International Union of Pure and Applied Chemistry (IUPAC) created a nomenclature for describing degenerate sequences. The symbol Y represents either a C or a T at that position. To answer your question, Y (C or T) pairs with R (G or A).

A full listing of IUPAC codes may be found here.

Re:Degeneracies, IUPAC codes, etc.

[PateraSilk]

Whaddaya know. I thought I was snarking on a typo. Cool. Thanks for the correction.

Re:Degeneracies, IUPAC codes, etc.

[Anonymous Coward]

Perhaps more importantly, you failed it.

Even more disturbing...

[Anonymous Coward]

is that the image for the poster child of the project was disproportionately scaled from 1024x1536 to 145x160.

Lets hope they didn't do the same with the dog genome.

But will this allow Poodles to fly?

[jebiester]

From "The Vidiot from UHF"...

Ola! And welcome to Raul's Wild Kingdom! Today, we're teaching poodles how to fly! Are you ready Fifi? Are psyched? Here we gooooooo..... (Throws poodle out of window)

yipe yipe yipe yipe yipe yipe *thump*

You know, sometimes it takes 'em a leetle longer to get it right.

More or Fewer Experiments on Dogs?

[bill_mcgonigle]

So will this lead to more or fewer medical experiments on dogs? Having the genes could answer alot of questions but it could also make the dogs more desirable test candidates.

I don't know if it's still true, but at one time vivisection of dogs was common practice in medical and dental schools in the United States so students could "see how organs worked."

I admit it, I have a soft spot for other social mammals of a certain brain size. I can understand lower primates as an unfortunate necessity for human safety, but dogs? The same creatures who are poisoned by chocolate, coffee, tylenol and onions? Heck, I've lived on similar diets.

Here's a random website about vivisection - I can't vouch for whether they're OK or PETA-style whackos:

Help The Dogs

Re:More or Fewer Experiments on Dogs?

[Bowling Moses]

I personally doubt that having (another) dog genome out there will increase the use of dogs in medical experiments. In the West, dogs are pretty much universally regarded as pets so it makes research on them very unpopular--eg your website. Also, we have much better animals for research--rat and mouse, both of which have had their genomes sequenced IIRC. They take up less space, reproduce and mature much more rapidly, are less expensive to feed, multiple different inbred strains are available (much moreso than for dogs) which increases experimental repeatability and are "vermin" which make research on them much less prone to provoke animal rights activists and the general public to condemn the animal experiments. That and somebody's got to kill the animals and it's a no-brainer that it is physically and psychologically easier for a (Western) lab tech to kill a rat than kill a dog. The only advantage that dogs might have over rats or mice is that they are bigger so dissection or the extraction of some compound might be easier. One advantage, lots of disadvantages.

Re:More or Fewer Experiments on Dogs?

[Dave21212]

somebody's got to kill the animals and it's a no-brainer that it is physically and psychologically easier for a (Western) lab tech to kill a rat than kill a dog.

Actually, I've heard that there is a movement to stop using rats...

Major research universities and labratories have started to use lawyers instead of rats for their experiments. There are three reasons why they are favoring lawyers over rats.

1. There are more lawyers than rats.
2. They find that lab technicians do not become as emotionally attached to the lawyers.
3. There are just some things you cannot get a rat to do.

Finally...

[ThoRoNic]

Finally I can have my chairdog, and move arround the office while having a massage.

MS Dog

[Anonymous Coward]

Microsoft Dog will be shipped with every kennel you buy, regardless of whether you want it or not. It will bloat exponentially after several weeks use, requiring either to reinstall the dog or get a kennel extension. The dog will be constantly ill from viruses and may keel over with a blue face for no reason whatsoever.

great !

[dario_moreno]

now, with genetic engineering, we can create dogs of arbitrary size, color, aspect, and abilities. Oh, wait...

research

[cybergrunt69]

I think it's kinda odd that the article notes that the fruit fly is so close in structure to the human... Maybe they will be using bugs for further testing instead of the dogs - at least the animal protection groups won't get so upset about that.

Also, I'm not sure how exactly this genome assembly was conducted, but maybe the people doing the research could benefit from using Stanford University's Folding@Home program (or at least the distributed computing idea behind it) to do additional testing in this field. Recent article from /.