Steps Involved to Develop the test

Initially, our partner laboratory, extracted DNA from a buccal sample (mouth swab) for the AncestryByDNA™ and/or EuroDNA™ 1.0 and 2.0 tests to determine the sequence of an individual's DNA at a large number of different positions. The buccal sample contained thousands of cells, and each of these cells contains DNA. Though all humans are 99.9% identical at the level of our DNA sequence, there are certain regions of each chromosome that are different from person to person. These regions (which are also found in canines), are called genetic markers or Single Nucleotide Polymorphisms (SNPs), and it so happens that some small fraction of these SNPs is also different among the world’s continental population groups. These types of markers are best termed Ancestry Informative Markers (AIMs) and they constitute less than 5% of our genetic material, which is related to the very recent common origin of a species. The positions in a human's DNA which we have sequenced are those we discovered that are different in this way, and they are spread across all of our chromosomes. That is why it is called a “genomics” test – it is a survey of all of our genetic material, which is known as a “genome.” In other words, we have sequenced markers from chromosome pairs 1-22, the autosomes.

Each individual's DNA is derived from both their mother and father, and theirs was derived from their mothers and fathers, and theirs from their parents and so on. Humans have 23 pairs of chromosomes. Other animals have more or less (for example, canines have 40 pairs of chromosomes, 38 pairs of autosomes [Reimann et al]). Your maternal copy of chromosome 1 could have been passed through your mother from your maternal grandmother OR your maternal grandfather, but which one you received was randomly determined at conception (you could not have received both). Most of the time this chromosome 1 copy that you receive from your mother is actually a chimeric chromosome that includes parts from your grandfather and your grandmother and other ancestors. Recombination is the process by which these chimeric chromosomes are created and as such occurs at least once on each chromosome every time a new sperm or egg cell is made. Although blending does not occur at the level of the gene (the unit of trait expression), human (and canine) chromosomes are mixed together and the genomes contain segments of DNA from all of the individual's ancestors, male plus female.

By measuring a human's (or dog's) ancestral proportions using a genomics method, we are actually measuring the average population affiliations of many thousands of ancestors. Since random processes (recombination and independent assortment) determine the mixings and pairings each individual harbors, two siblings from a set of parents may have different sets of chromosome pairs, and therefore different ancestral proportions even though they were the product of the same male + female union. The same processes occur in canine DNA.

Doggie DNAPrint - The Test

As described above, our partner laboratory has established itself as a pioneer in the development of innovative consumer genomics testing products. Many of our consumer testing products, such as the AncestrybyDNA™ 2.5, EuroDNA™ 1.0 and EuroDNA™ 2.0 were enabled by the recent completion of the sequencing phase of the Human Genome Project. These products now allow customers to measure their genomic ancestry admixture, or BioGeographical Ancestry – the genetic component to “race” or “ethnicity”. For example, with AncestrybyDNA™ 2.5 one customer may register as 90% Indo-European, 10% sub-Saharan African admixture and another may register with 100% East Asian genomic ancestry.

Thus, the human genome sequence provides test developers with a database of genetic markers from which an admixture panel can be constructed and then validated. Until recently, it has not been possible to make similar measurements for species other than homo sapiens because genome sequence drafts have not been available. As stated above however, this is now changed and we are applying the technology to evaluation of canine DNA.

As a result of the release of the canine data, and our partners internal research and development efforts, DNA Worldwide is pleased to offer Doggie DNAPrint to the general public. Doggie DNAPrint 1.0 is a genetic test for the assessment of dog ancestry and breed data from each dog's own DNA.

Customers who order Doggie DNAPrint 1.0 receive a DNA collection kit. The saliva/cheek swab from this kit is used to collect a specimen from inside the dog's mouth, it is allowed to air-dry and upon return to DNA Worldwide, we extract DNA from the swab and sequence the specimen at 204 specially selected Canine SNPs (CanAIMs) as described for our human testing. The SNPs we target with Doggie DNAPrint 1.0 were selected from the Canine Genome SNP database based on their information content for dog ancestry and breed.

Doggie DNAPrint 1.0 - Breed Data

Scientists at UC Berkeley and Seattle's Fred Hutchinson Cancer Research Center are the pioneers in dog genome research and have carried out analyses of various breeds using large SNP panels (called “chips”) as well as with sets of other polymorphisms called microsatellites. For example, in 2004 Parker et al. sequenced 75 SNP and 96 microsatellite loci in 85 dog breeds and showed that modern dog breeds are distinct genetic units and that breed can be accurately determined from canine DNA. Looking back relatively far in the dog family tree, Parker et al. noted that there appear to be 4 main dog breed types:

1. The wolf-like (yellow in the K=4 part of Figure 1)
2. The Herders (green in the K=4 part of Figure 1)
3. The Hunters (red in the K=4 part of Figure 1), and
4. The Mastiff (blue in the K=4 part of Figure 1)

Figure 1 below shows some of their data (Figure 3 of Parker et al., 2004), where dog breeds are clustered based on their affinity with the founders or parental dog populations for each of these 3 ancestral groups. Dog breeds such as the Akita, Chow Chow and Siberian Husky fall into the Wolf-Like group, Collies, Greyhounds, Borzoi etc. fall into the Herder group, Beagles, Pointers and Terriers (etc.) fall into the Hunter group and Bulldogs, Mastiffs, Boxers (etc.) fall into the Mastiff group. You will note that, due to the history of their origins, each breed is characterized by a unique ratio of admixture among these families.

Parker et al., 2004, showed that it is possible to use these same markers they described in a more complex analysis and look more recently in time along the dog family tree to unambiguously distinguish each breed. These scientists developed this technology for disease mapping research. Because the dog and human genomes are similar, comparison of canine and human genomes may provide extensive understanding of the origins and mechanisms for those human diseases shared by dogs. This particular technology however is not well suited for routine dog breed testing by lay-customers because it is relatively expensive, and because academic institutions that developed it are not in the business of consumer genetic testing. This particular panel of dog markers is expensive because microsatellites require a cumbersome and expensive method called capillary electrophoresis for reading. Reading SNPs on the other hand is relatively inexpensive and is a technology we use daily at DNA Worldwide.

More recently, a US company has developed DNA chips containing large numbers of dog SNPs (two types, one with 26,000 SNPs and another with 125,000 SNPs). These chips would provide the highest possible quality data for breed admixture assessment, but are very expensive. As with the microsatellite based panel of dog markers discussed above, these chips were developed not for lay-customers but for medical researchers and for the academic research community; price is less of a concern than for the typical consumer.

The costs would also be high for a company developing a chip-based dog breed testing service. Any company developing a dog-breed assay needs to build a database in order to interpret their results, and as the cost of these chips is high, chip-based databases are prohibitively expensive to build. The result of this is that, while considered the ultimate in dog breed testing, the cost of this type of analysis would put the testing out of reach for all but the wealthiest of customers.

Doggie DNAPrint database - 10 basic elements (canaims)

Recognizing the need for an affordable, mass-production dog breed genomics test, scientists at our partner laboratory scoured the dog genome database and selected 204 especially informative SNPs or CanAIMs. This small number of SNPs can be read efficiently with high-throughput instrumentation and so the cost to DNA worldiwde, and hence the customer, is fairly low and within reach of many dog owners. We use these SNPs with a Bayesian algorithm and a reference set of dogs to infer your dog's breed or breed admixture with respect to 10 basic elements of dog genetic ancestry.

Figure 2 below shows our current database with Doggie DNA Print and an example of a test sample which may represent the dog of a given customer.

Each dog is shown as a column of colors, and the colors indicate the % of ancestry for each type of dog ancestry. We can call these elements of dog ancestry by colors, numbers or we could give them names though the names would be arbitrary.

Breaking the dog family tree into 10 basic elements of ancestry, and describing the elements by their colors in this analysis, we can see that the;

• Wolf-like dogs such as the Husky share extensive “blue” and “red” ancestry.
• Pug dogs share mostly “peach”
  
• Collies share “gold” type ancestry.
• Border Collies show some “gold”, like Collies, but also some “yellow” like Beagles.
• Note that the Beagles share extensive “light blue” ancestry in common with Bassett Hounds.

Have you ever wondered why your beagle looks like a hound? Beagles come in 2 types, one of which has been traditionally used for hunting. This type bears a striking resemblance to hounds, with elongate snouts. The sharing of “light blue” ancestry with Doggie DNAPrint shown in Figure 2 below suggest that this resemblance is due to shared recent ancestry, rather than coincidence.

Schnauzers show mainly “grey” ancestry and the Mastiffs such as Bulldogs, and English Bulldogs show predominantly “light green” ancestry. Though German Shepherds belong mainly to the Mastiff family (according to Parker et al., 2004), Doggie DNA resolves between them and other Mastiffs and those we have tested register mainly with “purple” ancestry.

The dog at the far right of Figure 2 (“mutt”) may represent a customer's dog – a dog of unknown ancestry for example. This dog is actually a mixture of unknown breeds. Its ancestry admixture is different from any of the other pure-breeds in this analysis, though is most similar to the Jack Russell and Parsons Russell Terriers so we would infer that one of its parents may very well have been a Terrier. This line of logic illustrates how we can infer breed or breed admixture. With Doggie DNAPrint we provide two snapshots of your dog's ancestry:

1. admixture percentages with respect to the 10 basic elements of dog ancestry, which will be unique for each dog, but characteristic of breed.
2. through comparison with our database of dogs, we can infer the most likely breed or breed sets to which the dogs parents belonged.

In our example "mutt", we can recognize that the dog has its own unique mixture of dog ancestries, but its mixture is most similar to the Terriers and Havanese. It is not exactly the same as any of these however, so we would infer that the mutt is possibly a mixture of one or more of these breeds, and possibly another breed not represented in our current database. For example, the dog could also be a mix of one of these with a Shiba Inu or Lhasa Apso/Lhasa Apso Mix dogs.

We are gradually building the DoggieDNAPrint®1.0 database and it may seem that later customers would benefit more from the added information than early customers. However, we give full access to our database to all customers online so as the database grows, you can repeat your search. To access our database please click here.