The breed testing process, including number of markers used, was discussed in the FAQs for the MuttMix project, a collaboration between Darwin’s Ark and IAABC:
“Our reference panel of dog breeds has information for about 200,000 markers in each dog, so these are the markers we currently use in our breeds test. Our technology, however, tests at least 1 million markers in each dog. For some dogs, we have information on all 2.4 billion nucleotides in their DNA. Over time, our breed calling algorithm will perform better and better as we change over to a reference panel that includes just as much information for each dog.”
For comparison, here’s Wisdom Panel’s summary of their process:
“Once your sample is received at our lab it is scanned into our system and assigned to a batch for testing. It then undergoes processing to extract the DNA from your dog’s cells, which is examined for the 1800+ markers that are used in the tests. The results of these markers are sent to a computer that evaluates them using a proprietary algorithm designed to consider all of the pedigree trees that are possible in the last three generations of your dog’s ancestry. Our computer algorithm uses samples from our extensive breed database to analyze these potential pedigrees and calculate which one is the best match.”
…and Embark’s summary of their process:
[link deleted, because it created a huge obnoxious Embark logo…lol…but, this is from the FAQs on their website]
“At the lab we extract your pup’s DNA and run it on our custom-built genetics chip, which is a proprietary DNA microarray with over 200,000 markers…Ultimately, we use several proprietary algorithms to build the story of your dog and his or her DNA one chromosomal segment at a time. If numbers are your thing, we test about 256 quadrillion (that’s 500 million times 500 million) different possible genetic ancestry combinations for your dog using the latest and greatest science.”
So, Darwin’s Ark’s breed testing process is different from both WP’s and Embark’s in that they’re using low-coverage sequencing, which does test many more markers, but their reference panel of purebred DNA is still in the process of being built up, simultaneous with the DNA testing of dogs they’re already doing. (Initially, their reference panel contained only whatever breed-specific DNA information was publically available, as alluded to above.) So, owners of dogs who’ve already received their initial breed test results will most likely see those results update over time, with an increasingly lower % of “Unknown” ancestry as the reference panel becomes more robust.
All three tests use algorithms to analyze each dog’s results for their chosen markers against the purebred dogs in their reference panel. Wisdom Panel’s and Embark’s algorithms also produce three-generation predicted “family trees” for each dog, whereas Darwin’s Ark reports their breed calls as a simple bar chart ordering the detected breeds from lowest to highest percentage of ancestry.
But probably the biggest difference is that Wisdom Panel and Embark are for-profit companies focused specifically on breed analysis (Embark does also publish some research based on their findings), whereas Darwin’s Ark is a “citizen science” study focused on the genetic bases of dog behavior, with breed analysis effectively being a side benefit of your dog’s being selected for one-or-another phase of the ongoing study. And participating is free (unless you choose to donate, as explained in the FAQs, under “About” at the top of this page).