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HGTD This Week: What is a SNP-chip? FCI Podcast talks about genomic chip technology


Aimee Llewellyn-Zaidi

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The 9 November FCI (Fédération Cynologique Internationale) podcast, hosted by Attila Márton, featured Dr Sára Sándor, who gave an excellent description of what a genomic chip is and how it assesses a dog's DNA to identify genetic variants (mutations) - taking some of the mystery out of a technology that many may know the name of, but few could describe!

 
Canine genetic testing technology has changed rapidly since the first DNA tests were offered to dog breeders and owners in the late 1990's. STRs were the standard for many tests, and in some cases are still used today, before SNPs based testing became more useful and economical. Across commercial genetic test providers and some research groups, the utilization of SNP-chip or genomic chip technology has made capturing a wealth of genetic information across the whole of a dog's genome possible, and the industry standard. 

In the FCI Podcast (9 November 2021), Dr Sándor talked about some of challenges and limitations of this data, including breeding implications. The talk highlighted familiar challenges in genetic testing, such as what to do with dogs who have something other than clear/normal test results for inherited diseases. Dr Sándor raised several good points about the importance of understanding the disease impact on the dog, and how removing the dog from breeding could negatively impact the genetic diversity of the breed. She also acknowledged that there are certainly some rare cases, usually affecting individual dogs or specific inherited diseases that do not have simple modes of inheritance, where dogs that carry one of the undesirable variants could have some degree of disease impact (e.g. incomplete penetrance, multivariate, or complex). 

global-screening-array illumina.jpg

What was missing, in my opinion, was "Big Picture" thinking on health - where breeders must remember that the most common and serious problems facing a breed do not now and may never have a genetic test.  The Big Picture should also be applied more specifically to genetic testing, with more discussion on the realities that face dog breeders making decisions based on multiple genetic test results. As we are more able to identify variants associated with disease risk or undesirable traits, then it will be even more apparent that all dogs (and all mammals and plants, etc.) carry a mixture of genetic risks and benefits and that there simply isn't a dog that is completely without all genetic risk. There are already many breeds where there are dozens of genetic tests associated with disease risks, that a breeder must consider in balance with the risks to the individual dog, and any potential offspring. Breeding from only "clear" tested dogs is not only going to be impossible, but undesirable. DNA test results are one factor in breeding, and knowing the genetic risks gives options to breeders to match dogs that balance each other. The overwhelming majority of genetic tests available are single-gene, with a simple recessive inheritance. Meaning in most cases, as long as one of the parents is free of the mutation, there will be no genetically affected offspring.
When you consider that there are also many attributes and health risks to consider that do not have a genetic test, and are unlikely to, then it becomes even more apparent that the solution to over-all good breeding is going to be a "Big Picture" approach. 

Overall, I encourage you to listen or watch the podcast. It was very informative and interesting, as well as an excellent overview of genomic chip technology. 

YouTube premiere: https://youtu.be/5YJp0UVK-CM

 

A small selection of IPFD's "Big Picture" resources:

Get a GRIHP! A Globally Relevant Integrated Health Profile (GRIHP) describes the Big Picture of health on (all) conditions that are of interest within a breed and is intended to inform owners, breeders, and those counseling them. 

The Big Picture, on genetic diversity blog offers additional links to information and resources

International Actions. These articles link to many international projects supporting canine welfare, health, and breeding, as well as other human-dog interactions. 

 

Photo of an Illumina chip, via illumina.com

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    The contents of this blog are for informational purposes only and represent the opinion of the author(s), and not that of the International Partnership for Dogs (IPFD). This is not intended to be a substitute for professional, expert or veterinarian advice, diagnosis, or treatment. We do not recommend or endorse any specific tests, providers, products, procedures, opinions, or other information that may be mentioned on, or linked to from this blog.

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