Genetic Diversity Test for Akitas
  • lwrothlwroth
    Posts: 161
    The Vet Genetics Lab at UC Davis will shortly be offering a genetic diversity test for Akitas, Japanese and American, so breeders have the best chance of increasing diversity in their breedings and especially increasing the number of different alleles in the MHC region of the genome, which moderates the immune system. I think this is the best chance we've had of trying to decrease the amount of autoimmune problems in Akitas. In the research phase, the test will be $50 with a few free tests available; the regular test will be $100. The test is now available for Poodles and Italian Greyhounds; the write-up for the Poodle test will explain more about what the test and its certificate will show: https://www.vgl.ucdavis.edu/services/dog/GeneticDiversityInStandardPoodles.php

    If you have any questions, I can try to find answers for you
  • aykayk
    Posts: 1979
    Is there a way to get results based on just the JA population (UKC-registered JA) versus a combined AA+JA population?

    And if UC Davis doesn't offer this segregation service, will they provide raw data so a fancier could compile their own database?
  • lwrothlwroth
    Posts: 161
    I don't think they'll separate them but many of the JAs will come from other countries so won't be UKC registered. I'll ask your questions, though. The allele range for each dog would be for an individual dog and wouldn't matter whether it's JA or AA or blend.
    Post edited by lwroth at 2015-05-15 16:19:48
  • lwrothlwroth
    Posts: 161
    Until I get an answer, I can say the purpose of the test is to choose breeding partners that give the best chance of an efficient immune system. Here's a very good article that explains the importance of that:

    http://www.ashgi.org/home-page/genetics-info/immune-mediated-diseases/the-rising-storm-what-breeders-need-to-know

    If you looked at the certificates issued with the test, there's a bell curve of diversity; the relative positions of two (or more) JAs on the curve wouldn't change. If you look for a breeding partner with more genetic diversity between two JAs, compare their certificates to see their relative positions. Those positions wouldn't change if JAs were separated out. To use the allele chart on the certificates, look for dogs with more alleles or different ones. That again won't change if JAs are separated out.
    Post edited by lwroth at 2015-05-15 16:20:55
  • lwrothlwroth
    Posts: 161


    Sorry, forgot to get article in above.
  • lwrothlwroth
    Posts: 161
    If you want to have a JA database, post the certificates online. For a more private one, remove the identifier (reg number, I think) and have one person in charge of it.
  • aykayk
    Posts: 1979
    Actually, the bell curve or relatedness would change if just a subpopulation, the JA, are being calculated. It's why UC Davis also mentions in the original link,

    "This data will be updated as more dogs are tested, so allele and DLA haplotype frequencies may change to a limited extent over time." Conversely, it will change when results are deleted if you were to remove the AA.

  • lwrothlwroth
    Posts: 161
    Why wd that change the relative positions of two dogs? Also, they've looked at Akita alleles in several projects already so not a big chance of many new alleles.

    I can ask if, when they have a good number of samples, well past the research stage, if they could separate JAs or UKC JAs. Would JACA or ?? pay for the extra work if they could do it?
  • aykayk
    Posts: 1979
    I'll give a simplified example that demonstrates how things would change if the sample population is different.

    Say for one loci there are 4 alleles.

    In a previous research paper where they blended AA and JA results, they found 100, 200, 300, and 400 for alleles. Say in equal parts.

    But if they had not blended the AA and JA, the distribution would reveal something else.

    ie. in the AA
    100 = 49% of the population
    200 = 49 % of the population
    300 = 1% of the population
    400 = 1% of the population

    in the JA,
    100 = 1% of the population
    200 = 1 % of the population
    300 = 49% of the population
    400 = 49% of the population.


    If a dog is located in a country where the breeds are split, you * should* get two different diversity ratings. An AA with allele of 300 would be very valuable with respect to the rest of the AA population. A JA with an allele of 300 would not be very diverse with respect to the rest of the JA population. But compared against the blended bell curve, you wouldn't know where you stand.



    With respect to who would do the statistics of the JA population, it can be calculated outside of UC Davis. As long as the raw data is provided (ie. dog's registration # which can be cross-checked against breed and DNA results), a volunteer can do the calculations. Calculations are not propriertary.


    Post edited by ayk at 2015-05-15 16:56:03
  • lwrothlwroth
    Posts: 161
    I don't know if they'd provide the raw data. How does what you wrote affect comparing one dog to another?
  • aykayk
    Posts: 1979
    Under your blended bellcurve, a AA that has the rarer alleles 300/400 is of the same worth as a dog that has the overly represented alleles of 100/200.

    This blended scheme doesn't give a direction on how to proceed in order to preserve the rarer alleles. The population of rarer alleles can easily disappear through genetic drift - which is bad.
    Post edited by ayk at 2015-05-15 17:10:10
  • lwrothlwroth
    Posts: 161
    I don't see how the bellcurve affects the listing of the alleles. If the important thing to you is to preserve particular alleles, wouldn't you look at the listing of alleles and pick two dogs that had those rarer alleles? I'll wait til I get an answer from VGL; it feels like we're talking about "apples and oranges."

    Poodle people, who have a much more organized approach to health than Akita people, have a great slideshow that explains more about the test in regard to their breed, but a lot of it is general useful information: http://poodlesdegrenier.com/geneticspresentation
  • aykayk
    Posts: 1979
    Chapter 3 of the poodle slides states how the IR value is calculated.


    "The IR Value takes into consideration not only how many pairs of genes a dog has that are the same or different, but also how common those genes are, and how many different possible genes have been found at that locus in all dogs."
  • *JackBurton**JackBurton*
    Posts: 1369
    If this really is the best chance at reducing the risk of autoimmune issues then the group running this needs to be willing to separate the Akita by breed. It's easy just take a pedigree and see if it falls under one of these three conditions:

    (a) all ancestors in a three-generation pedigree are registered with the Japanese Kennel Club and/or Akita Inu Hozonkai(AKIHO) as a Japanese Akita or trace all their ancestry back to such dogs OR (b) all ancestors in a three-generation pedigree were registered as a Japanese Akita within a registry created by an FCI Kennel Club since their recognition in October 1998 , the Kennel Club (UK) since 2006, the United Kennel Club since 2012, OR (c) it has a three-generation pedigree which is a combination of the above, provided all eight great-grandparents are either as specified in (a) or (b).

    Sure some data would be off as blends would not follow under these criteria and thus would land as American Akita. Of course the few blends that are registered as Akita Inu would throw it off the other way(example would be the one you helped export to Finland). But over all this would encourage US JA owners to participate.

    Ann, thank you for explaining all of this. I have a hard time wrapping my head around all of this and your replies hell put them into context. I find the idea of genetic tests to be a appealing but I struggle with the analysis part.



    www.akita-inu.com
    www.Japanese-Akitas.com
    pedigrees.akita-inu.com
  • PoetikDragonPoetikDragon
    Posts: 2875
    Why does it matter to separate the two breeds? The same reason breed matters at all in the testing. If breed wasn't relevant, then it wouldn't be limited to Akitas, or Poodles, or Greyhiunds, etc.
    「怪獣荘秋田犬」Kaiju Kennels Japanese Akita and Hokkaido, Claire Matthews
    http://www.facebook.com/PoetikDragon
    http://www.facebook.com/KaijuKennels
    http://www.kaijukennels.com
  • lwrothlwroth
    Posts: 161
    I won't write more about the test here. It's there if you want to use it; they won't be separating, looking at pedigrees, giving out raw data. Both types/breeds were one historically and still are in the AKC, so looking at both would show which haplotypes were lost in each. If you read the descriptions, two types of Poodles were tested under Poodle and show in different AKC classes; European IGs were different enough from US IGs to be almost another breed. That didn't invalidate the test. JAs have one of the highest rates of autoimmune diseases and this test is the best way now to try to get a better functioning immune system. If you want a UKC JA test, you can set it up and pay for it yourselves. If you're referring to me above, I didn't help anyone export a dog to Finland.
  • aykayk
    Posts: 1979
    I don't think you fully understand how you'll be wrecking the potential good that this research could give by not acknowledging that the AA and JA are currently separate populations.

    I do understand that you are coming from the AKC Akita outlook and there is a remote possibility that someone may import a JA and register it as AA, but that is a tiny trickle compare to the majority who would stay within their own types/breeds. I understand that you're convinced that people will change and in hindsight appreciate your pro-blend work, but for me, I'd rather educate people on diversity within the separated breeds. I see that as more international and more apt to encourage participation.
  • rikumomrikumom
    Posts: 438
    Until I get an answer, I can say the purpose of the test is to choose breeding partners that give the best chance of an efficient immune system.


    As an AKIHO member I will only be breeding to AKIHO member owned JA. AA and tweenies are outside the the breeding partners allowed for us anyways. So if it's no breed split, there is no incentive for me to participate.
    Post edited by rikumom at 2015-05-16 16:33:14
  • Sorry to butt in but I think this needs to be said. The way you split the breed shouldn't be an issue here. This isn't a matter of American vs Japanese but one of breeding populations. 99 times out of 100 you won't find an AKC registered Akita being bred to an Akiho Akita. For the most parts they are separate and the gene pools don't mix. This will ruin the study if you include dogs from two different breeding populations and then draw conclusions for one population on a mixed set of data as it won't apply to either and is therefor, worthless.
    Don't misunderstand I'm not saying "they are two different breeds and need to be separated" I'm trying to be objective. If you consider them different, that's wonderful and many think so to. If you consider them the same, that's fantastic and many agree with you. But you can't draw conclusions for inaccurate data and that will happen here if you aren't careful. If AAs that aren't regularly being bred to JAs are included and you draw conclusions for JAs then the conclusions are inherently incorrect as they aren't an accurate representation. If JAs that aren't regularly being bred to AAs are included and you draw conclusions for AAs then the conclusions are inherently incorrect as they aren't an accurate representation. If a dog from Japan Akiho registered and by all accounts is a JA is being bred to an AKC fullblodded american regularly and it's pups are entering the gene pool, and you want to drew conclusions for the American gene pool, include it! That dog is an important part of the study and contributes to the population your drawing conclusions from. Otherwise the populations need to be separated for the good of BOTH!
    At the end of the day the health of the dogs is all that matters and politics or preferences shouldn't end this study as it will be priceless to the health of this breed, no matter how you divide it.
    image
  • lwrothlwroth
    Posts: 161
    I wasn't going to reply more but Dr Pedersen had a response to what ayk wrote. He says,

    "I have no idea what the concern is about. Without actually testing a number of American
    and Japanese Akitas, this is all just theoretical. The two breeds may be
    very different, or at the extreme, exactly the same. Perhaps this person
    should study the Standard Poodle, Italian Greyhound and Alaskan Klee Kai
    links on the VGL website. The Standard Poodle is genetically diverse but
    diversity is out of balance. Also, there is no difference in Standard
    Poodles across the world. The IGs are also diverse, but out of balance.
    Interestingly, the European and USA dogs are genetically distinct, almost
    to the point of being two different breeds. Are the Akitas like IGs? The
    AKK are another story, because they started with a few founders and they
    seriously lack genetic diversity. Are Akitas like AKK? This should give
    her a better idea of what is being tested and how genetic diversity is
    determined. What do these breeders have to lose by having their dogs
    tested? They will be given all of the information on each dog and if they
    want to study the information on their own, that is ok. At the least, they
    will have some good background information to make sense of their data."

    As I said, JACA/UKC JA people will have the results on each individual dog entered, identified by registration number. These data can be collected and studied for just these JAs. rikumom doesn't understand the principle of the test; it has nothing to do with what she thinks it's about. ayk, I don't understand what you mean: you can educate people about diversity within a breed even if I don't mind blends.

    I dislike the paranoia I've encountered in this forum. I have no "agenda" other than wanting healthier Akitas of any breed/type. I've been interested and involved in Akita health since 1990, shortly after I got my first Akita. I've been interested in genetic diversity since my veterinarian introduced me to Dr Pedersen in 1995. I've contributed to and taken part in many Akita health-related studies but gradually came to see research for gene tests for diseases and research for disease cures as band-aid approaches. I'd rather see emphasis on genetic diversity for the future of this breed (or any breed). I see a growing turning away from the purebred concept: "A closed stud book puts an expiration date on a breed." Just because my outlook may seem extreme, it doesn't mean there's no value in the test. I wish I could explain it better.

    I'd just like to see an end to the suffering of dogs with autoimmune diseases and the suffering of their owners. I've had 25 or so Akitas and none have had autoimmune diseases, probably because they were almost all rescues from "backyard breeders" with more genetic diversity than inbred show dogs.
    Post edited by lwroth at 2015-05-16 18:17:08
  • PoetikDragonPoetikDragon
    Posts: 2875
    The study is for a breed of dog, to learn something about that breed. Including dogs of another breed muddies the data and makes the study useless. You wouldn't include a Husky in the AKK study (same root stock - and only ~25 years apart instead of 60). Including non-AAs in a study about AAs is exactly the same.
    「怪獣荘秋田犬」Kaiju Kennels Japanese Akita and Hokkaido, Claire Matthews
    http://www.facebook.com/PoetikDragon
    http://www.facebook.com/KaijuKennels
    http://www.kaijukennels.com
    Post edited by PoetikDragon at 2015-05-17 13:25:39
  • *JackBurton**JackBurton*
    Posts: 1369
    The goal for the is to help combat Autoimmune disorders right? So if splitting the samples leads to more participation how on earth could someone be against that?







    www.akita-inu.com
    www.Japanese-Akitas.com
    pedigrees.akita-inu.com
  • tim3308tim3308
    Posts: 71
    Very informative and interesting discussion. The linked slide show was great and helped me get my head around all the conflicts that cross one's mind like when reading A. Akita books by authors such as Andrews, Killilea (especially), Bouyet, etc... lots of pro line-breeding and setting "type" advocation, which flies in the face of the dog's smell test shown in the slides fascinatingly directly linked to pheromones (human subjects have performed the same way w/ women smelling sweaty t-shirts of unseen males, they prefer scents out of their own gene code as more "pleasant" smells) - all sex related stuff as most of life evolved into opposite partner sex for reproduction for... well, for better "armed" offspring to fight disease, parasites, etc. Suffice to say, very mixed messages when reading about beloved Akita breeding (uhh "inbreeding").

    So, am I wrong to guess that JA's likely have less genetic diversity the AA's? After all, as I reread parts of "Dog Man", Morie Sawataish was breeding AA looking dogs the vast majority of his life (one could loosely argue the breed look of AA has been around at least 200 years, granted along w/ other versions of "Akita" - floppy eared etc,). The less stout and leggy, very oriental eye and thick coat but limited acceptable colors and markings of the modern JA, according him, didn't really get started until the 80's and 90's. Ironically (to me anyway), he accused the look of being the latest Akita taste in Japan(and predicted that too would change as well, as fashion does? Morie had seen a lot of changes after all), not a sentimental recapturing of the "pure" Japanese dogs of his distant historic youth.
    Tim Jessell
    http://timjessell.com
    Kuma 7yr/m/Shiba, Miko 6yr/f/Shiba, Saki 5 yr/f/Klee Kai/Shiba, Kaiju 1 year/m/A Akita
  • lwrothlwroth
    Posts: 161
    Dogs are now being chosen for free participation in UC Davis's Vet Genetics Lab Genetic Diversity Test. Pedigree research from the database in Akita Inu Pedigree is being used to try to find as unrelated Japanese Akitas as possible. Preliminary work with samples from American Akitas shows the breed to be much more inbred that was thought. For directions on how to participate, see http://www.akita-unleashed.info/2015/07/08/diversity-test-for-akitas/
  • T_DogT_Dog
    Posts: 331
    I am wondering if a DNA test could even tell the difference between a JA and an AA? I am not sure if DNA test are accurate enough to recognize the difference under the scope. But I do see how mixing the two populations might mess the accuracy of the test. But I don't claim to know anything about this. I think when I was reading about the AKC DNA test that they require before you breed. They can't tell the precise breed. Just that it it's 75% or above in matching DNA that it's likely a purebred, and UKC says they go off of the pedigree of reciprocal registries. Because DNA is not accurate enough. I might be all mixed up Cuz I am kinda new to this.
  • Yes, it can, and has in the past.
    「怪獣荘秋田犬」Kaiju Kennels Japanese Akita and Hokkaido, Claire Matthews
    http://www.facebook.com/PoetikDragon
    http://www.facebook.com/KaijuKennels
    http://www.kaijukennels.com
  • Saw this in a FB group I'm in and was wondering if someone could explain the results in layman terms? https://www.vgl.ucdavis.edu/services/dog/GeneticDiversityInAkitas.php
    Post edited by akitarise at 2015-11-14 08:25:26
  • @akitarise
    AA, JA and blend were tested. The point of the test was to tell how closely related the Akitas tested were to each other (not exactly that but that's the basic idea/ genetic diversity). Dogs were labeled as either JA, AA, or blend. The number of dogs tested is small so only general results could be made. Two panels testing 33 and 58 different genetic factors were done, the results were basically the same even though the number of factors tested to see a difference was changed.

    They found that the JA has alleles (genetic information that lead to real life physical traits) that the AA does not have and that the AA has alleles the JA does not have. This means that they each have unique genetic information the other does not have. Blends in this study shared more genetic similarities with AAs than JAs.

    If any one else has anything else to add or clarify feel free, I'm not an expert by any means:)!
    image
    Post edited by Vulpesvulpes89 at 2015-11-14 09:54:40
  • @Vulpesvulpes89 Seems pretty good.

    I will add that since most blends are not actually 1/2 but many are 1/4 or 1/8 JA (and 3/4 or 7/8 AA) it makes sense that they favored the AA genetics.
    「怪獣荘秋田犬」Kaiju Kennels Japanese Akita and Hokkaido, Claire Matthews
    http://www.facebook.com/PoetikDragon
    http://www.facebook.com/KaijuKennels
    http://www.kaijukennels.com
  • Thank you Vulpesvulpes89.
  • lwrothlwroth
    Posts: 161
    The VGL test results are basically the alleles in the panel that *your* dog has, so you can choose breeding partners or puppies to keep for breeding with the most diversity, including diversity in the region associated with immunity--all other factors like health, temperament, etc, being considered of course. The test is now $50 until 200 dogs have been tested and still free for Akitas of any type with autoimmune disease. Over 200 kits have been ordered, but the price will be $50 probably for another month. After that the test will be $100. This is the same price as the Optimal Selection Wisdom Panel, where MARS has paired with My Dog DNA in Finland; but the VGL test gives a "look under the hood," which Optimal Selection doesn't. There is more material on the test in the FB group Akita Genetic Diversity Test (by VGL/DAVIS).
  • lwrothlwroth
    Posts: 161
    As you can see from the VGL test page for Akitas and other material, the dogs have been compared in three groups: JAs, AAs, and Blends/Unregistered. This matters only for the listing of rare and common alleles in a type: it doesn't matter at all for the individual alleles--these are tested with the same panel for all breeds.

    Quoting from someone above:
    "The study is for a breed of dog, to learn something about that breed. Including dogs of another breed muddies the data and makes the study useless. You wouldn't include a Husky in the AKK study (same root stock - and only ~25 years apart instead of 60). Including non-AAs in a study about AAs is exactly the same."

    I asked Shayne at VGL to comment on the misunderstanding:

    "If the comment is in regards to including JAs in the study, it's not true, and actually, I would say that the comment about Husky and AKK is not true either. It depends upon what you're doing and how you do it, of course. We are looking at allele frequency based statistics that, yes, could be muddied by inclusion of JAs in an AA study. However, these dogs have all been classified as JA or AA and we have looked at how they cluster based on genetic distance. It is clear that they form two quite separate clusters, and so on our data page of allele frequencies, you will see that we break them out, JA, AA, blend. As well, the results that are being sent out are tuned specifically for JA, AA, and blend. We really are handling this like three separate breeds.

    "Additionally, testing dogs of other breeds or varieties adds context to the data. If we had only studied one small population, we would have no basis for saying that diversity is limited or just how limited it is. Behind all of this work is our study of the village dogs which have the most diversity, but also the ability to compare breeds is useful to get a sense of where they stand. For example, we are just about to put data out on Havanese. They have quite a bit of diversity, comparable to Mini Poodles.

    "That said, the point of doing this work is to improve the health of the dogs. Limited diversity from inbreeding will lead to increased genetic disease. This test provides a tool to manage the diversity that remains and to evaluate potential outcrossing. To some extent this can be done using just the marker report which is the same test for all breeds. The statistics and DLA haplotypes make it more powerful and able to identify rare types that could be lost otherwise."

    So far, Akitas are the most inbred of the breeds studied and have the most AI problems, and JAs are more inbred than AAs.

  • lwrothlwroth
    Posts: 161
    Quoting from vulpesvulpes89:
    "They found that the JA has alleles (genetic information that lead to real life physical traits) that the AA does not have and that the AA has alleles the JA does not have. This means that they each have unique genetic information the other does not have. Blends in this study shared more genetic similarities with AAs than JAs."

    The alleles in the panel are not connected to any physical traits in any of the breeds. The blends will reflect whatever their makeup is; I know there are at least 3 blends in the study, belonging to friends, who are 7/8 JA and 1/8 AA. As/if more blends are tested, the genetic similarities may change.

    A number of certificates are shared on the FB Group; people can post them there if they want.
    Post edited by lwroth at 2015-12-17 16:00:41
  • zoomiazoomia
    Posts: 16
    I did it out of curiosity; my results are posted in the FB group if anyone wants to see them. I can upload them here if there's enough interest.
  • KitagrlKitagrl
    Posts: 48
    It's been awhile since I have been over here! I just got this test done on my Akita because he was just diagnosed with VKH. :-( I got the results but have no idea what they mean! It doesn't matter because his parents are both retired anyway. I just did it to help.
    American Akitas:
    "Kota" Male 5-12-12
    "Kyra" Female 1-12-15
    Post edited by Kitagrl at 2016-04-28 23:32:18
  • aykayk
    Posts: 1979
    Could you post his results here?

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

In this Discussion