Genetic Tests: Beyond the Basics

The mode of inheritance of a particular disease is important to understand in order to interpret test results.  The majority of DNA–based tests are for autosomal (not sex-linked) recessive disorders.  If a disease is inherited as autosomal recessive, then the animal must have two copies of the mutant allele (version of the gene) to have the disease (genotype: d/d).  If the animal only has one copy of the disease allele and the other copy is normal the animal will appear normal (genotype: d/N).  Animals that have one normal allele and one mutant allele are called carriers.  Identification of these animals is important to a breeding program since they appear completely normal but can produce affected offspring.  If two carriers are bred to each other 25% of the offspring will be affected with the disease (d/N X d/N results in 25% d/d, 50% d/N, and 25% N/N- see Table 1).

Table 1: Simple recessive disease

d= disease allele
N = the normal allele 

Table 2: Genotype - disease correlation simple recessive

Breeders can utilize the DNA tests to identify carriers and avoid breeding them to each other.  The simple recessive mode of inheritance underlies the majority of DNA based tests available to date; however, there are notable exceptions and, in the near future, more exceptions are likely to be made available to breeders.  This article will focus on understanding these exceptions.

Some diseases are not inherited in a simple manner.  Some are caused by mutations in multiple genes or a combination of gene and environment interaction while other disease may have unidentified complexity.  This does not imply that there is not an underlying genetic component that can be tested and used for breeding but the relationship of genotype to disease is not as straightforward as in the example above.  To understand these more complicated aspects, let’s first consider some variations on our original simple autosomal recessive mode of inheritance.   There are still two copies of every gene in every dog so, from the testing standpoint, the results reported will be the same.  The difference lies in the fact that not all d/d animals will get the disease.  This can occur for many different reasons and those reasons may be labeled differently by geneticists. 

The first reason that there might not be a one to one relationship between the genotype and the disease state is reduced penetrance.  The term reduced penetrance just means that rather than 100% of the d/d animals getting the disease less than 100% will develop it.  If a disease is reported to have reduced penetrance, then the amount should be reported - even if it is just an estimate.  For example, a reduced penetrance of 85% means that 85% of the d/d animals will get the disease.  A penetrance of 5% means that only 5% of the d/d animals will get the disease.   One key point about a disease with reduced penetrance is that an animal that has the d/d genotype may be clinically normal and therefore might have been used for breeding with the assumption that the animal was either a carrier or even clear.  Therefore in cases where a genetic disease has reduced penetrance, a DNA test is useful to identify carriers (d/N), normal animals (N/N) and normal animals with the disease genotype (d/d) prior to breeding. 

Table 2: Genotype - disease correlation for a disease with 20% penetrance

The second reason that not all d/d animals will get the disease is if the gene is a susceptibility gene.  In this case, it could be dominant or recessive but it confers susceptibility to disease.  The DNA test interpretation requires knowing what percentage of animals with the susceptibility allele will get the disease.  This is called the relative risk.  Animals with two copies of the risk allele may be more likely to get the disease than animals with one copy of the risk allele.  The inheritance and ratios will be the same as in table 1 but the genotype- disease correlation will be different.  An example of a susceptibility gene with moderate risk is shown in Table 3.

Table 3: Genotype - disease correlation for a disease with a moderate relative risk

Both of the previous examples can be confounded by phenocopys or molecular heterogeneity.  A phenocopy is a disease state caused by an environmental factor and molecular heterogeneity means that there is more than one genetic cause of the same disease.  The DNA based tests are ONLY testing for the specific gene and allele that they have been designed for - not every possible cause of the same disease.   

There are some general principals of DNA based genetic tests that researchers can use to evaluate their potential disease causing mutations.   Within the breed where the test was developed, are all affected animals explained by mutation (heterogeneity)?  This percentage should be as close to 100% as possible.  What percentage of unaffected animals have the mutation (penetrance or risk)? This percentage should be as close to 0% as possible.  As these two percentages fall away from the ideal the test becomes more and more suspect and less useful as a tool to decrease the incidence of diseased puppies.

One last confounding factor is the use of linked marker tests where the disease mutation is unknown but a marker nearby is used to reflect the state of the actual mutation.  There are error rates associated with these types of tests because sometimes the marker does not reflect the actual disease allele.  Linked marker tests can be used within families to determine disease states but there can be problems using them in unrelated individuals.  The reason that linked marker tests or haplotype tests would be used is the long period of time it can take researchers to find a causative mutation.  In the meantime, in order to assist breeders, a test will sometimes be offered that may be imperfect.

While this may all seem very complicated, the good news is that tests are available that can help breeders decrease the risk of producing affected dogs.  However, caution should be used in aggressively selecting against mutant alleles which have low penetrance or low risk for the disease state when the mutant allelles are common throughout the breed. This could result in a reduced gene pool and reduced genetic heterozygosity leading to other potential health risks.