July 2018 – PBGVCA Health Committee Reference Center

Genetic Testing and Genetic Counseling in Pet and Breeding Animals

by Jerold S. Bell, DVM, Tufts University School of Veterinary Medicine Jerold.Bell@tufts.edu

Genetic testing and genetic counseling are not just for breeding animals. They include; testing for the bleeding disorder von Willebrand’s disease before performing surgery on susceptible breeds, altering diets for pets that are prone to developing bladder stones or crystals, and switching from rapid growth puppy food to lower calorie foods in young, large breed dogs, so that joint tissues can develop at a more uniform rate.

The hallmark of genetic disease is the ability to predict disease before its onset. This allows the possibility of medical or surgical intervention in order to prevent later suffering. Knowledge of breed-related genetic disease and the tests that are available permit early diagnosis and treatment.

Breeders and veterinarians have been utilizing genetic tests since the beginning of domestic animal breeding. Most genetic tests measure the phenotype of an animal, or what you can see. These include radiographs, blood values, eye examinations, skin biopsies, urinalysis for crystals or metabolites, observations on structure or behavior, and ausculting for heart murmurs. Most tests of the phenotype only identify affected individuals, and not carriers. These may, or may not directly relate to the genotype, or the genes regulating the defect.

A test of the genotype is one that assesses the DNA of the animal. These tests can be run at any age, regardless of the age of onset of the disorder. Utilizing polymerase chain reaction (PCR) technology, affected, carrier, and normal individuals can be identified. As the majority of genetic disorders are recessive or have a major recessive component, the identification of carriers is important for effective management.

As additional DNA tests are developed for disorders, the role of genetic counseling becomes more important. Without these tests, the number of individuals that can be identified as carriers is low, even though many may be suspect due to having affected relatives. Breeds have closed gene pools; in other words, the diversity of genes in a given breed is fixed. The number of individuals removed from consideration for breeding based on concerns regarding a specific genetic disease is usually low. While this has slowed the management of genetic disease, it has also prevented genetic drift and diversity problems for pure breeds.

History has shown that breeders can be successful in reducing breed-wide genetic disease through testing and making informed breeding choices. However, there are also examples of breeds that have actually experienced more problems as a result of unwarranted culling and restriction of their gene pools. These problems include: reducing the incidence of one disease and increasing the incidence of another by repeated use of males known to be clear of the gene that causes the first condition, creating bottlenecks and diminishing diversity by eliminating all carriers of a gene from the

breeding pool, instead of breeding and replacing them, and concentrating on the presence or absence of a single gene and not the quality of the whole animal.

DNA tests have to be developed specifically for each breed (or group of related breeds that share an ancestral mutation). There are two different types of tests of the genotype; direct gene tests and linkage-based tests. Direct gene tests check for a specific mutation in a defective gene. The animal either carries the defective gene, or does not.

Linkage-based DNA tests can be developed even if the defective gene causing a disorder has not been identified. Genome research has identified thousands of genetic markers, or “marker-DNA” that are spread across the chromosomes of the species. A linked-marker is a piece of DNA that lies close to the defective gene on a chromosome.

Breeders can use linkage-based genetic tests the same way direct genetic tests are used. The only difference is that you are not directly testing for the defective gene, only an associated marker; so false-positive and false-negative test results can occur.

A genetic crossover between paired chromosomes mixes the genes that an individual receives from its sire and dam. This occurs on a regular basis during the formation of eggs and sperm. As a defective gene and the linked marker are different areas of DNA that lie close together on a chromosome, it is possible that a genetic crossover can occur between them. This would separate the marker from the defective gene and create false positive (testing for the marker without the defective gene), or false negative (testing as normal, but having the defective gene) results. Depending on the relative distance between the marker and the defective gene on the chromosome, researchers can predict the frequency of false results for a linkage-based test; for example: 1 in 100.

If an individual’s linkage-based test for the defective gene is producing false-positive or false-negative results, all of its descendants that inherit this portion of the chromosome will also have false test results. This has been documented with families of Bedlington Terriers tested for the autosomal recessive copper toxicosis gene.

It is obvious that direct gene tests are better than linkage-based tests. However, a test with 90% or 95% confidence is better than no test at all. As genomic research progresses, researchers can identify the defective genes responsible for disorders, and can develop direct gene tests to replace linkage-based tests. The defective gene for copper toxicosis in the Bedlington Terrier has now been identified, and a direct gene test is now possible.

Based on the mode of inheritance of a disorder, and the availability of genotypic or phenotypic genetic tests, breeding management recommendations can be used to prevent or reduce the frequency of carrier or affected offspring. See the article “Breeding Strategies for the Management of Genetic Disorders” in the proceedings for specific recommendations.
Once a genetic test is developed, it allows breeders to positively determine if an individual is a carrier of a defective gene. The typical response of a breeder on finding that their animal is a carrier is to remove it from a breeding program. If a majority of breeders do this, it puts the breed’s gene pool through a genetic bottleneck that can significantly limit the diversity of the breed. The goal of genetic testing is to allow the superior genes of a breeding individual to be propagated, even if the animal is a carrier. One defective gene that can be identified through a genetic test, out of tens of thousands of genes is not a reason to stop breeding. If an owner would breed an individual if it tested normal for a genetic disease, then a carrier result should not change that decision.

Owners of carrier animals who are of breeding quality in other health, temperament, performance and conformation aspects should be bred to normal testing mates. This prevents the production of affected offspring. The breeder should be counseled to test the offspring prior to placement; to determine whether a pet or breeding home is appropriate. The goal is to replace the carrier parent with a quality, normal testing offspring that carries on the lineage of the breeding program.

If the only quality offspring is also a carrier, then breeders can use that offspring to replace the original carrier. The breeder has improved the quality of the breeding stock, even though the defective gene remains in the next generation. The health of the breed does depend on diminishing the carrier frequency and not increasing it. Breeders should therefore limit the number of carrier-testing offspring placed in breeding homes. It is important to carry on lines. A test that should be used to help maintain breed diversity should not result in limiting it.

By breeding and not selecting against carriers, breeders are selecting for a carrier frequency of fifty-percent; higher than most breed averages. Each breeder must assess the frequency of the defective gene in their own breeding stock and determine their own rate of progress. As each breeder reduces the number of carrier breeding stock, the frequency of the defective gene for the breed will decrease.

We know that most individuals carry some unfavorable recessive genes. The more genetic tests that are developed, the greater chance there is of identifying an undesirable gene. Remember, however, that an animal is not a single gene, an eye, a hip, or a heart. Each individual carries tens of thousands of genes, and each is a part of the breed’s gene pool. When considering a mating, breeders must consider all aspects – such as health issues, conformation, temperament and performance – and weigh the pros and cons.

Without tests, the management of genetic disease involves breeding higher-risk animals to lower-risk animals. Occasionally, a breeding male is determined to not carry a defective gene for which there is no carrier test. The tendency is for everyone to breed to this male, as a guarantee against the disorder. Any major shift in the breeding choices to a limited number of males will restrict genetic diversity, and increase the possibility of propagating additional undetected defective recessive genes in a breeding population. Such genes have become widespread even in populous breeds due to prolific breeding of popular sires.

Breeders are the custodians of their breed’s past and future. “Above all, do no harm” is a primary oath of all medical professionals. Genetic tests are powerful tools, and their use can cause significant positive or negative changes. Breeders should be counseled on how to utilize test results for the best interests of the breed.

This article can be reproduced with the permission of the author. Jerold.Bell@tufts.edu

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Breeding Strategies for the Management of Genetic Disorders

Jerold S Bell DVM, Clinical Associate Professor of Genetics, Tufts Cummings School of Veterinary Medicine

With each new generation of dogs, breeders ask, “How can I continue my line and improve it?” Aside from selecting for conformation, behavior and ability, breeders must consider how they are going to reduce the incidence of whichever genetic disorders are present in their breed. There are no answers that will fit every situation. There are, however, guidelines you can follow to preserve breeding lines and genetic diversity while reducing the risk of producing dogs that carry defective genes, or are affected with genetic defects.

Autosomal Recessive Disorders
In the case of a simple autosomal recessive disorder for which a test for carriers is available, the recommendation is to test your breeding- quality stock, and breed carriers to normal-testing dogs. The aim is to replace the carrier breeding- animal with a normal-testing offspring that equals or exceeds it in quality. You don’t want to diminish breed diversity by eliminating quality dogs from the gene pool because they are carriers. As each breeder tests and replaces carrier dogs with normal-testing dogs, the problem for the breed as a whole diminishes.

For some disorders there are tests known as linkage-based carrier tests, which can generate a small percentage of false positive and negative results. When using these tests to make breeding decisions, it’s advisable to first determine whether the results correlate with the test results and known genotypes of relatives.

When dealing with a simple autosomal recessive disorder for which no carrier test exists, breeders must assess whether each individual dog in their breeding program is at high risk of being a carrier. This requires knowledge of the carrier or affected status of close relatives in the pedigree. An open health registry that is supported by the parent club makes it easier for breeders to objectively assess these matters. By determining the average carrier-risk for the breeding population, breeders can select matings that have a projected risk which is lower than the breed average.

If breeding a dog that is at high risk of being a carrier, the best advice is to breed to a dog that has a low risk. This will significantly diminish the likelihood that affected dogs will be produced, and can reduce by up to half the risk that there will be carriers among the offspring. Using relative-risk assessment as a tool, breeders should replace higher-risk breeding dogs with lower-risk offspring that are equal to or better than their parents in quality. Relative-risk assessment allows for the continuation of lines that might otherwise be abandoned due to high carrier risk.

Breeding a dog only once and replacing it with an offspring allows breeders to improve their chances of moving away from defective genes and also limits the dissemination of defective genes. When dealing with disorders for which carriers cannot be identified, the number of offspring placed in breeding homes should be kept to a minimum.

Autosomal Dominant Disorders
Autosomal dominant genetic disorders are usually easy to manage. Each affected dog has at least one affected parent, but it can be expected that half of the offspring of an affected dog will be free of the defective gene. With disorders that cause death or discomfort, the recommendation is to not breed affected dogs. To produce the next generation of a line, a normal full sibling of an affected dog can be used, or the parent that is normal can be used.

A problem with some autosomal dominant disorders is incomplete penetrance. In other words, some dogs with the defective gene may not show the disorder. Roughly half their offspring, however, may be affected. If a genetic test is available, this is not a problem. Otherwise, relative-risk assessment can identify which dogs are at risk of carrying incompletely penetrant dominant genes.

Sex-Linked Disorders
For sex-linked (also known as x-linked) recessive defective genes for which carrier tests exist, breeders should follow the same “breed and replace” recommendations as are outlined above in the discussion of autosomal recessive disorders. If there is no test, the defective gene can be traced through the pedigree. If a male is affected, he would have received the defective gene from his carrier mother. All of his daughters will be carriers, but none of his sons. By using relative- risk assessment to breed him to a female that is at low risk of being a carrier, you can prevent affected offspring, and select a quality son for replacement.

There are rare instances in which a female is affected with a sex-linked disorder. In such cases, she would have received the defective gene from both parents; specifically, an affected father and a mother who is either a carrier or is affected herself. If an affected female is bred, all the sons will be affected, and all the daughters would be carriers, so affected females clearly should not be bred. A normal male that is a littermate to an affected female, however, would be able to carry on the line without propagating the defective gene.

Sex-linked dominant disorders are managed the same way as autosomal dominant disorders are. The difference is that affected males will always produce all affected daughters.

Polygenic disorders
Polygenic disorders are those caused by more than one pair of genes. Most polygenic disorders have no tests for carriers, but they do have phenotypic tests that can identify affected dogs.With polygenic disorders, a number of genes must combine to cross a threshold and produce an affected dog. These are known as liability genes. In identifying a dog’s liability for carrying defective genes for a polygenic disorder, the breadth of the pedigree (that is, consideration of all siblings of individuals in the pedigree) is more important than the depth of the pedigree (consideration only of parent-offspring relationships.) A clinically normal dog from a litter that had one or no individuals affected with hip dysplasia (which is a polygenic disorder) is expected to carry a lower amount of liability genes than a dog with a greater number of affected littermates. This is why it is important to screen both pet and breeding dogs from your litters for polygenic disorders. Information on the siblings of the parents of potential breeding dogs provides additional data on which to base your breeding decisions.

Genetic disorders without a known mode of inheritance should be managed in the same way as polygenic disorders. If there are multiple generations of normalcy in the breadth of the pedigree, then you can have some confidence that there are less liability genes being carried. If a dog is diagnosed with a genetic disorder, it can be replaced with a normal sibling or parent and bred to a mate whose risk of having liability genes is low. Replace the higher-risk parent with a lower-risk offspring that equals or exceeds it in other aspects, and repeat the process.

Genetic tests are extremely useful tools to help manage genetic disorders. Even when there is no test, or a known mode of inheritance, much can still be done to reduce the incidence of affected and carrier animals. The use of these guidelines can assist breeders in making objective breeding decisions for genetic-disease management, while continuing their breeding lines.

This article can be reproduced with the permission of the author. Jerold.Bell@tufts.edu

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Exploring the Mysteries of Liver Shunts

By Jerold S Bell, DVM, Tufts University School of Veterinary Medicine
(This article originally appeared in the “Healthy Dog” section of the April, 2005 AKC Gazette)

Five out of every 1,000 dogs in the general population are born with an inherited liver shunt. This condition, also called a porto-systemic shunt (PSS), is an abnormal blood vessel that bypasses the liver. The portal vein carries blood drainage from the gastrointestinal system. This blood contains nutrients, but also the waste products from digestion. Because of these waste products, the portal blood is kept separate from the rest of the (systemic) blood supply, and sent to the liver for processing.

A major portion of the waste product from protein digestion is ammonia. The liver metabolizes ammonia into urea, which is then sent to the systemic circulation through the vena cava (the major vein in the body). The kidneys filter the urea into the urine for disposal.

A porto-systemic shunt bypasses the liver, placing the portal blood into the vena cava instead. The high level of unprocessed blood ammonia and waste products can affect the brain, causing drooling, mental dullness, and seizures. This condition, called hepatic encephalopathy, can worsen after a high-protein meal. Because of the lifelong effect of waste products on all cells in the body, affected dogs can be stunted in size.

A liver shunt can be diagnosed by measuring elevated blood bile acid and ammonia levels. Most affected dogs showing clinical signs of hepatic encephalopathy can be diagnosed through a single (non-fasted) blood level. Pre-breeding screening for subclinically or mildly affected dogs requires paired, fasted, and post-meal values to make a diagnosis.

The type of liver shunt varies between affected dogs. The shunt may be a single large blood vessel, or may involve many small vessels. It can run along the outside of the liver, or be totally encased in the body of the liver. Large shunts can be diagnosed by an experienced ultrasonographer, or through a surgical contrast radiograph called a portogram. Some dogs have a disorder called hepatic microvascular dysplasia (HMD), in which the defective vessels connecting systemic and portal circulations are not large enough to be identified by ultrasound. Because of this, the definitive diagnosis for the condition requires blood measurements.

Treatment
The best way to treat a young dog with a liver shunt is through surgery. This is possible if the shunt is a large blood vessel, either inside or outside the liver. A surgeon narrows the shunt, so that a majority of the portal blood will now enter the liver. The shunt cannot be completely closed, or the liver – which because of the shunt is not accustomed to receive a high volume of portal blood – will swell and back up. This can cause fluid to build up in the abdomen (ascites), and cause liver failure. By narrowing the shunt, most affected dogs will go on to live normal lives.

If the liver shunt is microvascular, or if surgery is not a possibility, medical management may reverse the signs of hepatic encephalopathy. One third of affected dogs do well with medical management, living an average of seven years. Diets with high levels of crude protein should be avoided. Depending on the extent of clinical signs, dogs should be fed either a senior diet, or a special prescription diet. A medication called lactulose will bind to ammonia in the intestines. This prevents ammonia from being absorbed into the portal circulation, so it is eliminated in the stool. Certain antibiotics will also reduce the amount of ammonia producing bacteria in the intestines.

Breed Prevalence
Thirty-three breeds are significantly more likely to have a liver shunt than the general dog population. The breeds with the highest risk include: the Havanese, Yorkshire Terrier, Maltese, Dandie Dinmont Terrier, Pug, Miniature Schnauzer, Standard Schnauzer, Shih Tzu, Bernese Mountain Dog, and Bichon Frise. The majority are small-sized breeds, but the condition is also seen in large breeds, such as the Irish Wolfhound, Scottish Deerhound, and Old English Sheepdog.

Dr. Karen Tobias, a surgeon at the University of Tennessee College of Veterinary Medicine, has been performing epidemiological studies on congenital canine liver shunts. She has found that the incidence of liver shunts in Yorkshire Terriers has increased more than 11 times over the past 20 years. On average, approximately three percent of all Yorkshire Terriers have a porto-systemic shunt. The genes causing liver shunts in the breed are old and widespread, as inbreeding does not significantly increase the incidence of the disorder.

Tobias has found that mating two (surgically corrected) affected Yorkshire Terriers produced normal offspring – which eliminates simple autosomal recessive as the mode of inheritance. Tobias has also found that if two Cairn Terriers with microvascular shunts are bred together, they can also produce affected offspring with single, large liver shunts. This finding suggests than liver shunts can show variable expressivity, and that the single vessel and microvascular shunts may be caused by the same genes.

Genetic studies into liver shunts in Yorkshire Terriers, Cairn Terriers, Irish Wolfhounds, and Maltese have all proven a hereditary basis. It appears to be autosomal, as there is an equal ratio between affected male and female dogs. It is probable that the condition is polygenic, or controlled by more than one gene pair.

Tobias recommends testing fasting and post-feeding bile acids and blood ammonia levels on all prospective breeding stock, and to refrain from breeding dogs with elevated levels. This will eliminate phenotypically affected dogs from breeding. There is an increased risk for phenotypically normal siblings and first-degree relatives of affected dogs to be carriers of liver shunt liability genes. Therefore, breadth of pedigree normality (normal- testing littermates) is important in selecting breeding stock.

For permission to reproduce this article, please contact Dr. Bell: jerold.bell@tufts.edu

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Managing Polygenic Disease: Canine Hip Dysplasia as an Example by Jerold S. Bell, DVM

Jerold S Bell, DVM
Cummings School of Veterinary Medicine at Tufts University, N. Grafton, MA

Polygenic disorders have been difficult for breeders to control. Examples are hip dysplasia, congenital heart defects, and epilepsy. Controlling polygenically inherited disorders involves; 1) identifying traits that more closely represent genes being selected against, 2) the standardization of nuisance factors (such as environment) that can limit your selective pressure against the genes and 3) selecting for breadth of pedigree as well as depth of pedigree.

Hip dysplasia is a classic example of a polygenically controlled hereditary disease. Due to genetically controlled defects in anatomy and/or joint laxity, affected dogs can become lame, and eventually crippled due to secondary osteoarthritis. The genetic test used to control hip dysplasia is the pelvic radiograph (x-ray).

To control polygenic disorders, they must be considered as threshold traits. A number of genes must combine to cross a threshold producing an affected individual. Genes that combine in an additive manner are considered quantitative genes. If we theoretically state that five quantitative genes contributing to hip dysplasia can produce a dysplastic dog, then dogs receiving less than five genes from their parents would have normal hips. If phenotypically normal parents produce affected offspring, both should be considered to carry a genetic load that combined to cause the disorder.

Many polygenic disorders have a major recessive or dominant trigger gene that must be present to produce an affected individual. Genes that act in a dominant or recessive manner are considered qualitative genes. If qualitative genes play a role in hip dysplasia, then it is possible that dogs with more than the threshold of quantitative genes could be phenotypically normal if they do not carry a qualitative trigger gene. They would pass on a high liability for dysplasia through their contributing high numbers of the additive genes.

A trigger gene in one breed or family may be different from the gene in others. Consequently, if a test for a trigger gene is developed in one breed or family, it may not provide useful information for all breeds or families. Molecular genetic research to identify major qualitative disease causing genes can allow better control of polygenic disorders such as hip dysplasia, epilepsy, and cataracts.

Breeders must break down hip phenotypes into traits that more directly represent the genes that control them.

One reason we have not had great progress with hip dysplasia control is that it is being treated as a single gene disease, with a test for carriers. There is no excellent hip gene, although that is what most breeders are selecting for. In polygenic disorders, the phenotype of the individual does not directly represent its genotype. Breeders must break down affected phenotypes into traits that more directly represent the genes that control them. These include clinical signs of lameness (especially during the critical period of bony ossification between six and eighteen months of age), palpable laxity under anesthesia, deep acetabula, rounded femoral heads, the absence of remodeling, deeply seated hips on an extended leg view, and radiographic distractibility.

We know that the environment has a role in the expression of hip dysplasia. Overnutrition and excessive environmental trauma during the critical growth periods prior to skeletal maturation will promote later dysplastic development. While limiting these environmental stresses is prudent in pet dogs, it is recommended that breeders do not overly protect or overly stress prospective breeding dog’s development. You do not want to mask the expression of dysplasia causing genes in breeding stock. Breeders should evaluate prospective breeding dogs raised under fairly uniform conditions, which neither promote, nor overly protect against hip dysplasia.

The genetic cause of hip dysplasia between these two dogs is different.

All dogs do not have hip dysplasia due to the same gene combinations. A dog with laxity and subluxation but normal anatomy has hip dysplasia caused by different genes than a dog with no subluxation but malformed sockets. Selection against the components of the syndrome may provide better control. If a quality dog is to be bred, but has shallow hip sockets, it should be bred to a dog with deep hip sockets. Two dogs with fair hips can be bred together and produce much worse hips if they share detrimental traits, or could improve on each other if they compliment each other’s good traits. You need to select for enough genes influencing normal development, to get above the threshold where dysplasia develops. Not all of these aspects will insure a genetically normal dog, but the chances increase with the more that are present.

Phenotypic Tests for Hip Dysplasia Control

The Orthopedic Foundation for Animals (OFA) has a longstanding hip dysplasia registry to attempt to control the disorder based on an extended-hip radiograph. OFA ratings are based on hip joint conformation (anatomy), joint laxity, and remodeling (arthritic changes). The Institute for Genetic Disease Control (GDC) also maintains a registry for hip dysplasia based on the extended leg view.

The PennHip method of evaluating hip status is based on a measurement of joint laxity different from that recorded on the extended leg radiograph. The PennHip method utilizes a radiograph taken while applying a uniform force on the hips of an anesthetized dog to measure the maximum distractibility of the hips. By computing a breed average of distractibility, and selecting for tighter hips than the breed average, it is believed that the incidence of hip dysplasia should decrease over time.

There are pros and cons to both the OFA and PennHip radiographic methods of hip dysplasia control. The OFA radiograph documents anatomical abnormalities (shallow sockets, early bony changes), but only natural laxity in a hip extended view. The PennHip radiograph documents maximum distractibility, but many dogs with a high distraction index do not develop hip dysplasia. It is shown that both techniques have false positive and false negative results. For both methods, radiographic findings at an early age are highly correlated to dysplasia at a later age. OFA does not give permanent certification until two years of age, but offers preliminary evaluations at any age.

While PennHip identifies maximal laxity, and OFA identifies hip conformation, neither radiographic method accounts for the breadth of pedigree. For selective pressure against hip dysplasia, these tests must be used in conjunction with knowledge of the hip status of the littermates.

Selection for Breadth vs. Depth of Pedigree

Another reason for diminished progress against hip dysplasia and other polygenic disorders is that breeders have been selecting for generations of phenotypically normal parents and grandparents (depth of pedigree). In polygenic disorders the phenotype of the full brothers and sisters more directly represent the range of genes present in the breeding individual. In other words, the breadth of the pedigree is as important, if not more important than the depth of the pedigree in polygenic disease control. If a dog with normal hips comes from a litter with a high incidence of hip dysplasia, you would expect it to carry a higher than normal genetic load of genes for hip dysplasia. By selecting for breadth of phenotypically normal littermates of breeding dogs, and of parents of breeding dogs, all breeds should realize a decrease in hip dysplasia. In addition, the offspring of breeding dogs should be monitored to see which are passing the disorder with higher frequency.

This article can be reprinted with the permission of the author: jerold.bell@tufts.edu

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