DNA Testing FAQs

 

Which are better, DNA tests or more traditional screening tests?

It would depend on the disease, but for a breeder’s purposes DNA tests are the “gold standard” because they tell us the dog’s genotype where other forms of testing only measure the phenotype.  Carriers cannot reliably be detected with any form of phenotype testing and late onset diseases may not become active until a dog is well into its breeding years.

All the other screening programs (hips, elbows, eye exams, etc.) are for phenotype and only tell us what the dog was on that particular day.  They don’t tell us if the dog is a carrier, nor do they tell us that this currently healthy dog could develop disease later.  The important information from these tests is who DIDN’T pass.  Unfortunately, this information that often isn’t available in the US though such results are more readily available Europe.

Which DNA and screening tests are really necessary?

It is impractical, both logically and financially, for every breeder to screen breeding animals for every possible hereditary ailment.  Screening programs should be developed based on what problems are most frequently seen in a breed, in a sub-population of that breed (geographic, variety or function divisions), or in a particular line or family.  You might test some of your dogs for a particular problem but not others because the problem is rare and it has occurred only in relatives of those few dogs.

Age of onset is an issue affecting certification.  Hereditary cataracts may not arise until old age, so eyes must be re-certified annually.  Iris Coloboma is apparent at birth, so puppy exams will detect it.  Hip dysplasia requires a single screening test later in life. DNA tests should be used where available in conjunction with traditional screening.  ASHGI has developed a testing and screening protocol for Aussies.  However, any dog offered at public stud should have the entire standard screening test and every DNA test currently available for the breed with the exception of those for which both if his parents tested clear.

DNA is in every cell in the body so why does it matter what kind of sample you send in?

While it’s true that all your dog’s cells (except red blood cells) have DNA, not every cell type is going to be useful for sample submission.  You wouldn’t want to submit a bone marrow sample, for an extreme example, unless it was medically necessary.  Bone marrow isn’t easy to get to and being the donor isn’t a pleasant experience.

For the most part, when you send in a DNA sample on your dog it will be for one of three things:  Research, disease screening, or DNA profiling/parentage verification.  The needs and design of a particular research project dictate what type of sample you submit, with the most likely types being whole blood, cheek swabs, or – occasionally – a tissue sample.  If you want to save DNA in hope that it might later prove useful for research, as with a Gene Bank, whole blood is the ideal sample.  DNA screening testing labs will specify the sample type—usually a cheek swab.  DNA profiling and parentage verification programs usually require either a cheek swab or a blood sample.

 If blood samples are so much better for DNA testing, how come so many places use cheek swabs instead?

For the same reason polyvalent vaccines are so common:  Consumer demand.  People prefer things to be as inexpensive and easy as possible.  Swabs are both.  Cheek swabs are easy to use, don’t require a vet.  They are simpler to ship, but they aren’t without their quality control issues due to human error (generally on the sample-collection end).

Could I buy a supply of cheek swabs, use a bunch on each dog, and then keep them or later use?

Depending on how long you stored the swabs and whether or not you froze them, they may or may not be usable.  After a week at room temperature the enzymes in the saliva can start degrading the DNA.  Two weeks at room temperature is about the max for processing a useful sample.  Freezing might extend the useful life of the sample, but is not recommended.  In addition, some labs want you to use swabs which they supply.  The best thing to do is swab a dog only when you can get the samples in the mail soon after.

 How fast can scientists make DNA tests?

It isn’t as simple as do study/make test.  Once a gene is identified it doesn’t take long to set up a testing program.  But it can take a very long time to find a gene.  At this point it is very likely that most of the simple (one gene) inherited diseases already have tests.  From here on out, science will be trying to tease apart things that involve multiple genes, gene regulatory factors, and environmental influences.  These complex puzzles will take longer to solve or may not be something they can make a simple test for.

If I test a puppy and it’s clear, do I really need to test my bitch or the other pups?

Yes, because one puppy’s result will only tell you a little bit about the genotypes of the parents and its littermates.  Your puppy can have any of three results from a test:  Two normal copies of the gene, one normal and one mutation, or two mutated copies.

The best procedure is to make sure your bitch is tested and that any stud you breed her to is tested.  Then you will know what might occur in the pups.  The only time you do not need to test is if both parents have tested normal/normal.  The best procedure is to test the parents and then, if necessary, test the puppies.

 Why isn’t there a push to eliminate the bad genes found with DNA tests?

In theory it is possible to completely eliminate an unwanted gene mutation in a single generation by ceasing to breed all individuals that carry it.  This assumes full compliance with the testing of all breeding animals, which isn’t likely to happen.  However, concerned individuals could make it a litmus test for their own programs.

BUT…..doing so can have unwanted side effects:

  • If the mutated version of the gene is very common (MDR1 or the HSF4 cataract mutation in Aussies) and all dogs that have it are eliminated, you will eliminate a major portion of the breed overnight.  The remaining dogs may may or may not have the traits you want and will certainly have genes for a few things that you don’t want.  Those things might prove to be far worse than the target of the purge and not have handy DNA screening tests.
  • If the condition is of minor health impact, as with yellow coat color, the zealous removal of all carrier individuals could eliminate otherwise valuable dogs.
  • If the condition is polygenic, the target gene is only part of the picture.  This is also true for risk factor genes like the HSF4 mutation I Aussies.  Eliminating all dogs that have it may reduce the incidence of the disease but is unlikely to eliminate it entirely.

The goal is not to produce affected puppies. DNA tests enable a breeder to do that, or at least considerably reduce the risk of doing so.  Carrying a defective gene version should be considered a fault and preference should be given to offspring that do not themselves have the mutation.  Over multiple generations one could phase out use of dogs with the mutation, thereby eliminating the unwanted gene while preserving good qualities and genetic diversity.  How long this would take would depend on the frequency of the gene in the breed population.  It will take a number of generations to work MDR1 out of Aussies because half of them have it at present (2013).

If we would equate genetic health issues to faults and treat them as such when making mating selections, we’d do much better in reducing their frequency.  Some health issues are severe faults (epilepsy, cancer) and others are minor (MDR1 or CEA).   All other things being equal, preference should be given to the dog that does not have this “fault.”  Another important thing to remember:  Every dog has some bad genes.  You are several steps ahead of the game on those you can test for.

 Are DNA test results reliable?

Yes.  They are far more reliable than the subjective screening programs we use for hips, eyes, etc.  The DNA tests reveal the actual genotype of the dog.  The best a subjective exam can offer is an educated opinion about the phenotype.   – what the dog is, not what it might carry.

Errors can occur with a DNA test, but labs have protocols to prevent mishandling of samples.  Almost all errors occur when the sample is collected and prepared for shipping.  It is important that you follow all instructions in detail to prevent contamination or mislabeling of samples.

Errors can occur with subjective exams, as well.  The screening is performed by experts and the information is usually correct, but as with all subjective evaluations there will sometimes be errors.

 Why don’t labs offer a bunch of different DNA tests for a package price?    

There are labs that do that outside the US.  Recent (2013) legal decisions in the US may clear the way for bundled tests there.  However, an informed consumer will review what is offered to make sure that he is getting multiple tests that apply to his breed.

Early on there was an organization that tried to do something along this line in the US with a one-size-fits-all-breeds approach.  They had only one test that was useful for Aussies.  For Aussies it would be useful to have at least, CEA, PRCD (PRA), HSF4, and MDR1.  Hereditary cobalamin malabsorbtion, canine multifocal retinopathy, cone degeneration, degenerative myelopathy, vonWillebrand’s Disease, and the form of neuronal ceroid lipofuscinosis found in Aussies would be nice additions.

The HSF4 cataract mutation is only a risk factor gene.  There are probably other genes that might cause cataracts.  Is a risk factor gene test really useful? 

Risk factor genes aren’t THE cause of disease, but are significant contributors.  There definitely are more genes out there that are involved with the development of cataracts, and probably some environmental factors that, in combination with certain genes, can lead to cataracts.  There are also cataracts that arise from purely environmental causes (injury, certain nutritional imbalances.)  The same can likely be said for the Aussie’s two inherited cancers, though risk factor genes have yet (2013) to be identified.

The simple one-gene dominant/recessive things have probably mostly been found at this point.  From here on out the answers science gives us are less likely to be black-and-white.  Knowing that there is a risk, and planning accordingly, is better than having no information at all or, worse, ignoring information that is available.

 Why don’t they do double-blind studies before they make DNA tests available to the public?

Double-blind studies are not applicable to DNA tests:  They are used to test drugs and some other medical treatments.  Some subjects in a double-blind study will get the treatment while others receive a placebo.  Those receiving the placebo are termed “controls.”  This helps control for the “placebo effect” that can occur when people think they (or their dogs!) are receiving something that will help them.  In a double-blind study, neither the patient nor the person administering the treatment knows what the patient is receiving, hence the name “double-blind.”  Animals aren’t prone to the placebo effect and if owner feedback is not part of the data study might use a single blind approach – where the person administering the treatment and/or recording results doesn’t know if it’s real or placebo.  This will minimize the effects of perceptual errors made by the people dealing with the animals.  If you really like an individual animal, you might want it to get better so might make biased assumptions about what you were observing.

Since DNA tests are used to determine genotype and sometimes to confirm a diagnosis, the placebo effect isn’t an issue.  Therefore there is no need to do a double-blind study on them before they are made commercially available.   However, the current techniques of DNA research do make use of “controls.”  Genome searches will be done on a set of dogs that have the disease under study and on another set of unrelated dogs who do not (the controls) in order to emphasize genetic differences between the two groups.

I got a DNA test done and then the dog was diagnosed with the disease.  How can that happen? 

Depending on which test it was, any of several things may have happened.  Some diseases (progressive retinal atrophy, neuronal ceroid lipofuscinosis) have several different genetic forms.  If you used the test for one and the dog has another it could appear that the test didn’t work when it actually did – for a different form of the disease.

If the diagnosis was based on exam findings, as it is with most eye diseases, it is possible that the exam diagnosis is incorrect.  CEA and PRA can both be misdiagnosed upon occasion.  In this case, it is the examiner who is in error.

Finally, if the DNA sample was not handled properly (i.e. mixed up with that of another dog) you might have an incorrect test result because what you got does not belong to your dog.

Can DNA be used to confirm a diagnosis? 

Yes.  If there is no definitive diagnostic test or diagnosis is based on observation, a DNA test can be used to confirm.  Among tests available for Aussies that this can be done with are any of the available eye disease tests, the hereditary cobalamin malabsorbtion test, and the degenerative myelopathy test.

My dog’s DNA test result was two mutations, but her sire is clear.  How could that happen?

First you need to re-test her to make sure the result is correct.  (Report the situation to the lab and they may not charge you for the second test.)  If the result comes back the same, you need to do parentage verification to make sure there wasn’t an error there.  (This isn’t necessarily anyone’s fault – sometimes another dog slips one by everyone.)  If the parentage checks out, then the sire better be tested again because he can’t have produced a double mutant offspring if he is really clear.    If the stud owner refuses, or the results come back the same again, something somewhere is out of order.

 What DNA tests are available for Aussies?

Currently (2013) Aussies can be tested for:

  •  Canine Multifocal Retinopathy (CMR) a form of retinal dysplasia
  • Cataracts
  • Coat Color – black/liver
  • Coat Color – dilute
  • Coat Color – merle
  • Coat Color – yellow
  • Collie Eye Anomaly (CEA)
  • Cone Degeneration (CD)
  • Degenerative Myelopathy (DM)
  • Hemophilia
  • Hereditary Cobalamin Malabsorbtion (HCM)
  • Hyperuricosuria (urate bladder stones)
  • Multi-Drug Resistance 1 (MDR1)
  • Neuronal Ceroid Lipofuscinosis (NCL)
  • Progressive Rod Cone Degeneration (PRCD – a form of Progressive Retinal Atrophy)
  • Von Willebrand’s Disease (VWD)

What gene does the Canine Multifocal Retinopathy (CMR) test examine?

Bestrophin 1 (BEST1), also called vitelliform macular dystrophy 2 (VMD2), is located on canine chromosome 18.

 Is this the only form of CMR?

There are two forms, CMR1 and CMR2, both arising from mutations in the BEST1 gene.  CMR2 is found only in the Coton de Tulear.  All other breeds, including the Aussie, should test for CMR1.  CMR is a form of retinal dysplasia sometimes featuring retinal folds and Aussies with CMR will be reported as having one or the other of these on eye exam reports.  There are also other types of retinal dysplasia but at this time none have been identified in the Aussie.

 What are the possible results from the CMR test?

Two normal copies of the gene – the dog does not have CMR

One copy of the mutation – the dog is a healthy carrier of CMR1

Two copies of the mutation – the dog is affected with CMR1

 What do these CMR test results mean for my dog?

Your dog will be affected only if it has two copies of the CMR1 mutation.  If your dog has an eye exam by a veterinary ophthalmologist the disease will be described as retinal folds or retinal dysplasia.  Most dogs with CMR have normal eyesight, however occasionally the disease will impact vision.

 How common is the CMR mutation in Aussies?

Unknown at this time (2013) because too few dogs have been tested.  However, eye exam results indicate that about 1% of Aussies are probably affected which means that approximately 18% are likely to be carriers (one copy.)

 What do these CMR test results mean in a breeding dog?

If the dog has two copies of the mutation and its vision is impaired, it should not be bred.  Dogs with two mutations and normal eyesight, as well as carriers (one mutation) should be bred to clear-tested dogs.

 What gene does the cataract test examine?

Heat shock transcription factor 4 (HSF4) on canine chromosome 5

 Is this the only form of cataracts?

No.  Cataracts can arise for many reasons, not all of them hereditary.  In addition there are multiple inherited cataracts.  The HSF4 gene has recessive mutations that cause cataracts in Staffordshire Bull Terriers, Boston Terries, French Bulldogs and other breeds.  Australian Shepherd have a dominant mutation that is a risk factor for cataracts.  In addition Aussies have at least one other inherited form of cataracts for which the gene(s) are not yet known.

 What are the possible results from the HSF4 cataract test?

One or two mutations put the dog at significantly increased risk (x17) for developing cataract.  Dogs that do not have the mutation will not develop cataracts related to HSF4.

 What do these HSF4 cataract test results mean for my dog?

70% of Aussies with cataracts have at least one copy of this mutation.  If your dog has it, it has 17 times the risk of developing cataracts at some point during its life as a dog that does not have this mutation.  Cataracts can arise anytime in life from early adulthood into old age, though most occur in young to mature adults.  Cataract progression varies widely, both in speed and extent.  Some dogs retain functional vision all their lives while others become blind.  However, many dogs with the mutation do not develop cataracts.

 How common is the HSF4 cataract mutation in Aussies?

This mutation is extremely common with about 25% of Aussies having at least one copy.  However, a much smaller number (about 4%) develop cataracts.

 What do the HSF4 cataract test results mean in a breeding dog?

Dogs with the mutation (one or two copies) and cataracts should not be bred.  Dogs with normal vision and the mutation (one or two copies) may be bred to mates that have tested clear.  Because cataracts are potentially blinding, preference should be given to clear-tested offspring for future breeding.

 What gene does the black/liver coat color test examine?

Tyrosinase related protein 1 (TYRP1) on canine chromosome 11.

 Is this the only way to inherit black or liver coat color?

Yes, though the action of other genes may at least partially mask the TYRP1 phenotypes. (Examples:  Merle or yellow.)

 What are the possible results from the black/liver coat color test?

One or two copies of the dominant version of the gene, the coat will be black.  Two copies of the recessive version of the gene, the coat will be liver (also called brown, chocolate, or red).

 What do these black/liver coat color test results mean for my dog?

In most cases you will know what color your dog is either by looking at its coat or the exposed skin (nose, eye rims, footpads, etc.) in the case where other genes, like the one that causes yellow, change the hair color.  The test can indicate whether a dog is a carrier for liver, generally referred to in Aussies as “red factored.”

 How common is the liver coat color version of the gene in Aussies?

Extremely common given that liver and liver merle are popular coat colors.

 What do the black/liver coat color test results mean in a breeding dog?

Testing can tell you whether your dog is “red factored” should you want to breed for liver or liver merle pups.

 What gene does the dilution test examine?

Melanophilan (MLPH) on canine chromosome 25.

 Is this the only form of dilution?

While the recessive version of MLPH produces dilute black (generally termed blue) or liver (variously Isabella, deadgrass, or fawn) in many breeds including Aussies, research in Aussies found that there are dilutes that do not have the recessive version of MLPH.

 What are the possible results from the dilution test?

One or two copies of the dominant version of the gene, the coat will be fully pigmented (black or liver).  Two copies of the recessive version of the gene, all sections of the coat that would have been black or liver will be dilute.

What do these dilution test results mean for my dog?

For Aussies they will confirm the phenotype you will already have observed in your dog but will also indicate whether it carries dilute.

 How common is the dilution mutation in Aussies?

Unknown.  There is no good data source, however dilute is the most common disqualifying coat color other than excess white markings.

 What do the dilution test results mean in a breeding dog?

If your dog is dilute (two copies of the mutation), the color is disqualifying and the dog should not be bred.  Carriers (one copy of the mutation) should be bred to clear-tested mates.

 What gene does the merle test examine?

Silver (SILV) on canine chromosome 10.

 Is this the only form of merle?

Yes.

 What are the possible results from the merle test?

There are three versions of the gene, the merle version, the cryptic version, and the recessive non-merle version in that order of dominance.  Dogs with two merle versions will be “double merles” and likely will have defects.  Dogs with one merle and either cryptic or non-merle will be “normal” merles (no defects).  Dogs with two copies of cryptic or one cryptic one non-merle will probably be cryptic merles – mostly solid color dogs with one or a few very small areas of merle.  Dogs with two non-merle versions will not be merle or cryptic.

 What do these merle test results mean for my dog?

They will confirm the phenotype you observe in the dog.  In rare cases a double merle may appear to be normal and the test would confirm its status.  Double merles typically have too much white for an Aussie, severe eye defects, and deafness.  Other color variations do not have associated health issues.

 How common is the merle mutation in Aussies?

Extremely.  The pattern is signature to the breed and highly popular.

 What do the merle test results mean in a breeding dog?

The test will identify the rare dog that appears to be a normal merle but is actually a double merle.  Merles should not be bred to other merles to avoid producing puppies with two copies of the gene and the associated defects.  The breeding of cryptic merles to merles does not appear to result in defects typical of “double merles.”

 What gene does the yellow coat color test examine?

Melanocortin receptor 1 (MC1r) on canine chromosome 5.

 Is this the only form of yellow?

Yes.  It is sometimes referred to as “lemon” or as sable, though true sable is caused by a different gene.  It is possible that a dog might be both sable and yellow without any notable difference in phenotype if it has a slick coat.  However, true sable is absent in purebred Aussies though sometimes people use that word to describe yellow.  Note:  Actual color of the dog can range from pale yellow to deep red-gold.

 What are the possible results from the yellow coat color test?

There are four versions of this gene.  In order of dominance:  Mask, grizzle, extension and yellow.  Mask with itself, grizzle, or yellow will put a mask on the dog’s face (color will be depend on the actions of other genes).  Mask and extension would either be black or liver, possibly dilute, and/or have a merle or brindle pattern all depending on other genes.  In a tan-pointed dog mask might obscure face markings.  Mask and yellow will be a yellow dog with a color and possibly patterned (depending) mask.  Grizzle is found in Salukis and Afghan Hounds, where it is called domino.  Two copies or one with either extension or yellow will result in the pattern.  Extension with itself or yellow could be almost any color depending on other genes.  Two copies of yellow makes a dog yellow.  None of these will have any effect on the presence or absence of white markings.   Aussies have two copies of extension.  They may have mask, never have grizzle and occasionally have yellow.

What do the yellow coat color test results mean for my dog?

For Aussies they will confirm the phenotype you will already have observed in your dog but will also indicate whether it carries yellow.

 How common is the yellow coat color version in Aussies?

Unknown, there is no good data source.  However, yellow is almost as common as dilute.

 How common is the mask version in Aussies?

Unknown, there is no good data source.  However, any tan-pointed Aussie with no markings on the face or only limited markings may have at least one copy of mask.

 What do the yellow coat color test results mean in a breeding dog?

If your dog is yellow (two copies of the mutation), the color is disqualifying and the dog should not be bred.  Carriers (one copy of the yellow version) should be bred to clear-tested mates.

 What gene does the Collie Eye Anomaly (CEA) test examine?

Non-homologous end-joining factor 1 (NHEJ1) on canine chromosome 37.

 Is this the only form of CEA?

Yes.  This test specifically identifies a mutation causing choroidal hypoplasia (or chorioretinal dysplasia), a retinal lesion found in all CEA-affected dogs.  More serious defects associated with the disease probably have other genetic causes but those do not develop without two copies of the CEA-CH version of NHEJ1 so it suffices for a screening DNA test.

What are the possible results from the CEA test?

A dog with two copies of the normal version will not have or produce CEA.  A dog with one normal and one mutated copy is a CEA carrier.  A dog with two mutated copies is affected.

 What do these CEA test results mean for my dog?

A dog with at least one copy of the normal version of the gene will not have CEA.  If the dog is affected (two copies of the mutation) it will have choroidal hypoplasia, but this defect rarely causes any visual deficit.  However, some dogs will also have optic nerve coloboma or retinal detachment, both of which can be blinding.

 How common is CEA in Aussies? 

Just under 1%.  Around 15% are probably carriers.

 What do the CEA test results mean in a breeding dog?

Affected dogs should not be bred.  Carriers should be bred only to clear-tested mates.

 What gene does the Cone Degeneration (CD) test examine?

Cyclic nucleotide gated channel beta 3 (CNGB3) on canine chromosome 29.

 Is this the only form of CD?

Yes.

 What are the possible results from the CD test?

Two dominant copies – normal.  One dominant one recessive – carrier.  Two recessive copies – affected.

 What do these CD test results mean for my dog?

Dogs with at least one dominant version of the gene will have normal vision.  Affected dogs (two recessive copies) will become day blind as puppies.

 How common is CD in Aussies?

Unknown, probably rare.

 What do the CD test results mean in a breeding dog?

Affected dogs, whether diagnosed upon eye exam or identified with the DNA test, should not be bred.  Carriers should be bred only to clear-tested mates.

 What gene does the Degenerative Myelopathy (DM) test examine?

Superoxide dismutase 1, soluble (SOD1) on canine chromosome 31.

 Is this the only form of DM?

Yes.

 What are the possible results from the DM test?

Two normal copies – clear, one normal one mutant – carrier, and two mutant – potentially affected.

 What do these DM test results mean for my dog?

If the dog has at least one normal copy of the gene it will not develop DM.   Dogs with two copies have are at risk of developing DM.

 How common is the DM mutation in Aussies?

Unknown at this time. (2013)  The test is relatively recent and too few Aussies have been tested to draw a conclusion.

 What do the DM test results mean in a breeding dog?

Clinically affected dogs should not be bred.  However, onset for this disease is late and dogs probably will be bred before it begins.  Since not every dog with two copies develops disease but those that do have a severe neurodegenerative disease.  Having two mutations should be treated as a severe fault and breeding of these individuals limited.  Carriers (one copy of the mutation) should be bred to clear-tested mates.

 What gene does the hemophilia test examine?

There are two forms of hemophilia: Hemophilia A, coagulation factor VIII (FVIII), and Hemophilia B, coagulation factor IX (FIX).  Both genes are on the canine X chromosome

 What are the possible results from the hemophilia tests?

Normal copies of the genes means the dog is clear.  Males with a copy of either mutation and females with two copies of either (A and A or B and B) will be affected.  Females with one copy of either  mutation will be carriers for the form that they carry.

 What do these hemophilia test results mean for my dog?

The hemophilias are severe blood-clotting disorders.  Males with a copy of either mutation will need special care and treatment.  Females are rarely affected because it requires that they have two copies of the  mutation for the same form, but if affected are at great risk of bleeding out during the first estrus cycle.  Female carriers are healthy.

 How common are the hemophilia mutations in Aussies?

Unknown but probably rare.

 What do the hemophilia test results mean in a breeding dog?

Affected dogs should not be bred.  Carrier females should be removed from breeding.  Dams and daughters of carrier females should be tested so their status is known.

 What gene does the hereditary cobalamin malabsorbtion (HCM) test examine?

Amnionless (AMN) on canine chromosome 8.

 Is this the only form of HCM?

No.  Border Collies have a form caused by a mutation of the Cubilin (CUBN) gene, but the AMN mutation is the only one identified in Aussies.

 What are the possible results from the HCM test?

Two dominant copies – normal, one dominant/one recessive – carrier, two recessive – affected.

 What do these HCM test results mean for my dog?

Only dogs with two copies of the recessive form of AMN will be ill, but the disease is potentially life-threatening unless treated life-long.  With treatment the dog is fine.

 How common is the HCM mutation in Aussies?

Unknown.  The disease is probably underdiagnosed because signs mimic those of a variety of common or well-recognized diseases.

 What do the HCM test results mean in a breeding dog?

Affected dogs should not be bred.  Carriers may be bred to clear-tested mates.

 What gene does the Hyperuricosuria (urate bladder stone) test examine?

Solute carrier family 2, member 9 (SLC2A9) on canine chromosome 3.

 Is this the only form of Hyperuricosuria?

Yes.

 What are the possible results from the Hyperuricosuria test?

Two dominant copies – normal, one dominant/one recessive – carrier, two recessive – affected.

 What do these Hyperuricosuria test results mean for my dog?

Only dogs with two copies of the recessive form of the gene will be ill.  Hyperuricosuria can be painful and sometimes requires surgery.  It can be treated.

 How common is the Hyperuricosuria mutation in Aussies?

About 1% of Aussies develop Hyperuricosuria, which means around 18% are carriers.

 What do the Hyperuricosuria test results mean in a breeding dog?

Affected dogs (two copies of the mutation) should not be bred.  Carriers may be bred to clear-tested mates.

 What gene does the Multi-Drug Reactivity 1 (MDR1) test examine?

ATB-binding cassette, subfamily B, member 1 (AABCB1), formerly called multi-drug resistance 1, on canine chromosome 19

 Is this the only form of MDR1?

Yes.

 What are the possible results from the MDR1 test?

This mutation is dominant, dogs with one or two copies are affected.  Dogs with two copies of the normal, recessive version will are not affected.

 What do these MDR1 test results mean for my dog?

A dog with one or two copies of the mutation is at risk for reacting to certain drugs depending on dosage; dogs with two mutations react at a lower dose than those with one.  Reactions can be fatal.

 How common is the MDR1 mutation in Aussies?

Half of Aussies have at least one copy of the mutation.

 What do the MDR1 test results mean in a breeding dog?

Dogs with the mutation may be bred, but it should be treated as a fault with two copies being a greater fault than one.  Dogs with the mutation should only be bred to clear-tested mates.

 What gene does the Neuronal Ceroid Lipofuscinosis (NCL) test examine?

Ceroid-lipofuscinosis, neuronal 6 (CLN6), canine chromosome 30.

 Is this the only form of NCL?

No.  There are several genetically distinct forms, however this is the only one identified in an Australian Shepherd to-date.

 What are the possible results from the NCL test?

Two normal – clear, one normal/one mutant – carrier, two mutant – affected.

 What do these NCL test results mean for my dog?

Affected dogs (two mutations) have a severe and ultimately fatal neurodegenerative disease.  Most dogs die by two years of age.

 How common is the NCL mutation in Aussies?

Extremely rare.

 What do the NCL test results mean in a breeding dog?

It is unlikely that an affected dog could be bred but if it can be, don’t.  Carriers should be bred to clear-tested mates.

 What gene does the progressive rod cone degeneration (PRCD) test examine?

Progressive rod-cone degeneration (PRCD), on canine chromosome 9

 Is this the only form of Progressive Retinal Atrophy?

No.  There are multiple genetically distinct forms of PRA of which PRCD is only one.  PRCD is the only form identified in Aussies at this time.  If an Aussie dog is diagnosed with PRA and is clear on this test it has another form of PRA and the PRCD test results should not be taken to mean the dog is clear of PRA; steps should be taken to determine which form it is (most have DNA tests.)

 What are the possible results from the prcd/PRA test?

Two copies of the normal form of the gene – clear; one normal/one mutant – carrier; two mutant – affected.

 What do these prcd/PRA test results mean for my dog?

If your dog has two copies of the mutation it will develop PRA and will eventually go blind.

 How common is the prcd/PRA mutation in Aussies?

Around 1%, which means approximately 18% are carriers.

 What do the prcd/PRA test results mean in a breeding dog?

Affected dogs should not be bred.  Carriers may be bred to clear-tested mates.

 What gene does the Von Willebrand’s Disease (VWD) test examine?

Von Willebrand factor (VWF) on canine chromosome 1.

There are at least 5 mutations associated with VWD in dogs, however specifics about what other gene(s) may be involved is not freely available probably because of patents filed by those who offer the tests.

Is this the only form of VWD?

There are three forms of the disease (Types I, II, and III).  There are tests available for all three.

What are the possible results from the VWD test?

For all tests and types of VWD, dogs are clear, carrier (one mutation), or affected (two mutations).

 What do these VWD test results mean for my dog?

Your dog will be affected only if it has two mutated copies of the gene.  Severity of disease will depend on which type it as.

 How common is the VWD mutation on Aussies?

Unknown but probably rare.

 What do these VWD test results mean in a breeding dog?

Affected dogs should not be bred.  Carriers may be bred to clear-tested mates.

 What is DNA parentage verification?

 It is the use of a set of DNA markers to establish that an individual is the offspring of a particular male and female by verifying that the offspring has a set of markers that reflect the potential contributions of markers from the two parents.  Example (deliberately simplified):  If the male had markers A-A, B-B, and C-C and the female had D-D, B-B, E-E, the offspring would have to be A-D, B-B, and C-E.  Any other combination would exclude it.

 Is it the same as DNA fingerprinting?

 The process used is the same.  A “DNA fingerprint” is a set of markers unique to that particular individual.  These sets are used in the parentage verification process.

 Can DNA testing be used to identify parents when the dog’s background isn’t known?

Theoretically, you might be able to identify a dog’s unknown parents this way but practically it may not be possible.  Both of the dog’s parents would have to be in a parentage verification registry (usually operated by studbook registries).  That registry would have to offer a service that would allow you to collect a sample from your unknown dog and submit it to them for comparison to dogs already in the registry.  Both the dog’s parents would have to be in the same registry.  (Different registries use different marker sets.)  If only one of the parents is in the registry they would not be able to match it to the unknown-background dog because there is no way to verify which marker came from a particular parent if the other parent’s set isn’t available.

Can DNA tell the offspring of two brothers apart?

Yes, provided the dam(s) have been profiled along with both males.  Full siblings will have different marker sets.  Labs deliberately choose enough markers, and markers with enough variation (multiple versions) so that even the closest relatives won’t have the same DNA profile.

How is DNA used to determine parentage on multi-sire litters?

Because each sire will have a different profile, even in the case where they are closely related) their profiles and that of the dam are compared to the profiles of each puppy in a multi-sire litter.  Results will indicate which pup was sired by which dog.  Multi-sire litters can maximize the production potential of a high-quality brood bitch.  However, you should make sure that the studbook registry the dogs are listed with allows it and, if they do, make sure you follow whatever rules apply to multi-sire litters.

How accurate is DNA parentage verification?

Far more accurate than blood typing ever was, which is why human paternity testing is now down with DNA and why DNA evidence is so frequently used in court cases.

Does it matter what organization you use for DNA parentage verification?

Any of the extant DNA parentage verification programs or even a private DNA lab can develop a DNA profile on your dog.  They can all verify parentage if the parents and offspring are all profiled.  However, it does matter where the dogs have been profiled.

Work done by direct arrangement with a private lab is useful only for your own purposes.  It will not be accepted by a registry’s program.  Studbook registries that have DNA parentage verification programs will only recognize dogs profiled through their own program.  This applies even if you pay the same lab they use to do the work.  Where dogs hold dual registrations it may be necessary to profile the dog with each registry’s program.

When owners submit samples directly to the lab how can we know somebody isn’t sending another dog’s sample?

Someone intent on cheating can just as easily present the wrong dog to a vet who is asked to collect the sample as send one in himself.  However, unlike using a dog of the same breed, color and gender for standard screening exams, pulling a switch in a DNA parentage verification program is going to backfire as soon as offspring of that dog are entered into the program.

If you send in Shep’s sample and say that it’s Oso’s, when you breed Oso and someone profiles one of his offspring it isn’t going to match.  You won’t be able to use Oso, ever, because his pups will never match “his” profile unless you always substitute Shep to do the actual breeding.  Likewise, Shep could never be used under his own name because he couldn’t be profiled or the ruse would be uncovered, and if you didn’t profile him all his puppies would come back as “Oso’s” so what’s the point?  If a registry requires that all breeding stock be profiled, falsification is impossible.

Can DNA profiling prove that two dogs are the trandparents of a third dog based on samples from these three alone?

If those three dogs are the only available relatives, the answer is no.  You don’t know what marker alleles either parent had, nor the other two grandparents.  Even if you have one grandparent from each side of the pedigree, you can’t confirm or exclude them with any degree of confidence because you don’t know what the other grandparents’ markers were.

Realizing that there could be instances when a parent’s DNA might not be available, ASCA did establish a rule (Registry rules section 2.2.3) whereby  a single unavailable parent’s profile can be determined with about 90% probability.  It requires that eight offspring of the unavailable dog be profiled, along with the mate or mates with which those offspring were produced.  The rule also allows for other combinations of closely related dogs to be used, so long as a 90% probability is achieved.

At best it requires testing a whole batch of dogs.  In the scenario you describe you’d need a lot more than just those two grandparents tested before you could prove parentage on your subject dog.

What are the advantages of DNA profiling?

For the breeder, it provides uncontestable proof that the litters he produced are by the stated parents.  For the registry it reveals registration errors and prevents fraud.

When errors are found, what happens?

That depends on the rules of that particular registry.  It is technically possible to correct some errors – as when another male breeds a bitch unbeknownst to the breeder.  Note:  mis-assigned parentage can happen through no fault or knowledge of the breeder if someone else allows the dog access to the bitch or when the dogs are particularly determined and clever.

Is it possible to prove two dogs are littermates with their DNA?

DNA can’t tell you whether dogs are littermates, but it can indicate whether they are full siblings.  However, without having the parents’ profiles you can’t be completely sure. If the dogs’ markers show very little difference it is an indication that they may be full siblings but it isn’t conclusive proof.

Can the DNA sent for parentage verification be saved and used for other things like health research?

Probably not.  The information generated by the ID/parentage verification process is not useful for disease research.  Registries usually use swabs or FTA cards for sample collection.  Swabs generally don’t hold enough material left to store and are discarded after use.  Even if DNA was left over, the “shelf life” of used swabs is limited.  At this point researchers rarely if ever use FTA cards, so what is left over there also isn’t helpful either.

In most cases, researchers want whole blood in EDTA (purple top) tubes.  If this kind of sample was used for parentage verification it could be useful if stored properly and there was a system in place to make them readily available to researchers.  I don’t know that this is the case with any of the extant parentage verification programs.

DNA banking programs, like that of OFA’s Canine Health Information Center (CHIC), which are known by researchers and have gathered large numbers of samples from many breeds along with associated health data are invaluable resources for health research.

Has DNA ever proven a crossbreed?

All the parentage verification process can do is just verify that the reputed parents are indeed the parents of the dog in question.

In laboratory conditions researchers have been able to identify the breeds of blind samples, but as yet there is no commercial test that reliably distinguishes purebreds from crossbreeds that look like purebreds.  In a breed like the Aussie which is of relatively recent development (mid-20th century) it might be difficult to determine with any certainty if a dog was purebred if the other breed was another “collie type” as all these breeds are related.