HGTD This Week, 15 July 2020: One Disease, 20 Causes? It's All in the Name

The Harmonization of Genetic Testing for Dogs (HGTD) project work includes harmonizing genetic test information across many different boundaries. That can be as simple as adding consistency to nomenclature from around the world, or as challenging as cataloging test information and research from dozens of different international sources. With so much variation in how tests are developed, and how they are released to the public, a big part of my work is ensuring that phene names we publish on HGTD are consistent, accurate, and representative of whatever genetic test a person is seeking out. 

In most cases, a test name refers to a recognized clinical disease. In essence, 1 phene + 1 breed = 1 test name. However, many tests are relevant to more than one breed, because many breeds share ancestors at some point. Even more often, test names (because remember, they’re based on the clinical disease) are very similar or even the same, within the same breed. Confused yet?

A perfect example of this is the disease Progressive Retinal Atrophy (PRA). Progressive retinal atrophy refers to the clinical description (symptoms, essentially) of what is actually a group of inherited retinal diseases. During the progression of the disease, the retina of the eye atrophies (degenerates) over time, eventually leading to complete blindness. The main differences between the various PRAs being the age of disease onset, and how quickly the disease progresses. 

There are currently 20+ different forms of PRA on HGTD – which can be breed-specific, relevant for a few breeds, or more than one form of PRA applying to the same breed. 15 years ago, there was only one “PRA” test! As 20+ new mutations causing PRA where discovered over many years, the naming of the PRAs in a distinctive and unique way became more challenging. 

Researchers had a variety of ways of naming, as there is currently no international phene naming standard. Generally, they started falling into a few categories:

Breed-focused, e.g. PRA “Italian Greyhound”

Inheritance-focused, e.g. PRA “X-linked”

Varietal, e.g. PRA “Type B” 

Mutation, e.g. PRA “rcd-4”. 

When you start getting more than a few similar test names it can be easy to lose confidence which test name represents a specific gene and mutation. There is a very real risk of selecting the wrong test for a specific mutation. HGTD tackles this confusion in a few ways, and it is one of the advantages in using a resource that catalogues all phenes.

Using HGTD, you can see the genetic tests that are breed-specific when searching by breed, but you can also double-check yourself using a number of different referencing points:
-    The OMIA number
-    Gene and mutation(s) associated with the test name
-    Synonyms/related terms
-    Clinical descriptions
-    Breed-specific publications 
-    Researched breeds references

For most dog owners and veterinary clinicians, the clinical descriptions, breed-specific publications and researched breeds references are particularly useful. This is an ideal way to ensure that the breed or breeds you’re interested in not only have this test available to them, but that there is some research and relevance associated with that specific test and specific breed. Researchers, genetic advisors, and clinicians will find benefit in cross-referencing with the OMIA number, and/or double-checking that the specific mutation in the specific gene is associated with the phene/disease test that they are interested in. 

HGTD tries to provide a bit of a confidence short-cut through our development of Breed Relevance Ratings (BRR). Still a work in progress, BRRs are a good way of indicating the relevance of a specific test for a specific breed/type. These can help take some of the guess-work out of what tests might be important for your dog, and/or how the results should be considered as part of breeding strategies. 

When in doubt about which phene you are trying to find a test for, using the generic phenes search provides you with centralized information to guide you, and help you to make accurate and informed choices. 
 

photo with thanks to Lum3n via Pexels.com