DNA Testing is rapidly growing among breeders, giving them increasingly detailed information to manage and improve the genetic health, diversity, and physical traits of their breeding lines. Given the importance of these test results to the health of not only each dog but also that of future generations of dogs, we believe it’s critical to provide transparency into Embark’s testing methodology and detail how our results are so accurate. Stringent quality control ensures >99% accuracy for mutation tests and 99% for most linkage-based tests.
Embark’s innovative testing platform is a customized SNP Microarray developed in partnership with Cornell University College of Veterinary Medicine using the latest research-grade canine genotyping platform. This platform enables the hundreds of genetic health and traits test results provided in Embark’s products, while also creating research-ready data for use by canine health organizations and scientists. The core of our platform has now been used to test hundreds of thousands of dogs at Embark, and over a hundred thousand more by scientists at university laboratories throughout the world.
“We chose to use a custom SNP microarray platform to provide the highest possible accuracy of results and enable us to have the greatest potential to make future genetic discoveries.” – Adam Boyko, Chief Science Officer and Professor of Canine Genomics at Cornell University College of Veterinary Medicine
In this article, we provide an overview of SNP microarray technology and a summary of Embark’s rigorous quality control standards. This information is provided as part of our commitment to maintaining the highest possible standards for accuracy and reliability of test results, and as part of our mission to work collaboratively across the canine health community to research and address important health conditions facing dogs today.
SNP Microarray Technology – How it Works
Embark uses microarrays to test each sample of dog DNA that we receive. Microarrays are microscope slides (often called “chips”) that contain hundreds of thousands of tiny beads called probes, where each probe is individually designed to assess the genotype at a specific location, or locus, in the dog’s genome. An individual probe may be relevant to health conditions, physical traits, and other genetic aspects of interest.
Microarray probes primarily identify “single nucleotide polymorphisms”, also called “SNPs” (pronounced “snips”). These are places where a single base pair (letter) of DNA is mutated to another letter. A few probes also target “Indel” polymorphisms where one or more letters are deleted or inserted in the sequence. There are millions of known polymorphisms in dogs, and the 230,000+ polymorphisms Embark tests for include nearly all of the known genetic variants impacting health and traits as well as markers throughout the genome for computing inbreeding, relatedness and ancestry, as well as power research and discovery.
Because of the extremely high accuracy of SNP microarray testing, this method has become the go-to standard for DNA testing. It has been used to test tens of millions of people over the past 15 years by leading direct-to-consumer human DNA tests, and the method has been given FDA approval for testing of dozens of human genetic conditions. These “SNP chips” have also been integral in thousands of research studies, and led to countless new discoveries not just in human medicine, but also in animal and agricultural studies.
The hundreds of thousands of probes available on a microarray enables geneticists to comprehensively assess the canine genome with a single DNA sample. As Embark’s research scientists identify new genetic tests for health conditions and physical traits, they design new probes that are added to the microarray. In this way, Embark is able to continually expand the number of tests available to customers through its products.
Highly Accurate and Reliable Results
As a genetic testing platform, microarrays are extremely accurate. The accuracy of individual probes on Embark’s platform is over 99.9%, and each health condition is tested using at least 3 (and up to 8 ) separate probes. This redundancy gives us over a 99.99% genotyping accuracy for each health condition
As Embark has grown, we’ve developed processes for the rare occasions where the results of the probes testing the same gene do not match. Embark’s quality control process requires that a secondary analysis be conducted by two independent geneticists to determine what nucleotide is present at the locus in question. The conclusions of both geneticists must agree in order for a result to be provided to the customer.
Embark’s usage of SNP microarrays exceeds industry quality control standards by also checking the breed, sex, and relatives of every sample to ensure DNA samples are correctly labeled and unique identity is recorded. Among other reasons for quality control purposes, this also helps fraud prevention by making it impossible for the same dog to be tested multiple times without Embark knowing. (Note: many non-microarray testing methods do not have this same ability for quality control, and thus errors due to the wrong dog being tested – whether by mistake or on purpose – cannot be detected).
Please note: For a detailed explanation of why SNP microarray testing platforms are so accurate, including technical information about the science and technology utilized, we recommend this excellent video summary by The University of British Columbia, this in-depth explanation by Bitesize Bio, this reference guide from Illumina about their SNP chip, and Embark’s previous blog post that compares microarrays to other testing methods.
Beyond Testing Methods – The Highest Standards for Laboratory Facilities and Quality Control
Embark’s processing laboratory is ISO and CLIA certified. These are the highest ratings available for commercial laboratories processing DNA samples, and are the same ratings attained by human DNA testing companies. We have worked hard to bring automation and redundancy to canine genetic testing to make it more accurate than ever before. Every sample is uniquely barcoded and handled by robots in the laboratory to ensure samples are never misidentified or mixed up, which minimizes the risk of human error contaminating samples or affecting results.
For additional quality control, many breeders and registries wish to use a veterinary verification process to confirm samples were collected from specific dogs, which often includes the veterinarian certifying microchips being added to the dog. Embark facilitates this added quality control with our Veterinary Verification forms. Please see this article explaining the process.
Linkage Test Capabilities Expand Scope of Testing
The vast majority of Embark genetic results are mutation tests where probes are designed to determine the genotype of the exact disease-causing mutation. However, in cases where it is difficult to identify the exact gene causing a condition, scientists may be able find sections of DNA that are usually inherited alongside the unknown gene, and perform a linkage test, inferring the presence or absence of a mutation of interest by examining the genetic variation surrounding it. Embark’s linkage tests are typically 98% predictive of genotype, and linkage tests are identified in results for full transparency to our customers when this method is used on a particular test. For two examples of linkage tests currently offered by Embark, see this article about POMC and this article about IVDD.
Our Innovations Offer Unprecedented Potential
At Embark, we’re proud of our world-class canine DNA testing service and are committed to continually raising the industry standard. We’re on a mission to provide breeders, and all dog owners, with the high level of accuracy they need to optimize their breeding programs, manage the lifetime care of their dogs, and improve the health of future generations of dogs. Embark employs research scientists, veterinarians, and geneticists to address the important issues facing dogs today, with a mission to improve the long term health of dogs. See the many research discoveries already made by Embark and learn about our various projects underway here.