What are haplotypes and how does Embark determine them?

We stand on the shoulders of genomic giants

Canine genomicists have put an incredible amount of work into describing haplotypes (patterns of DNA sequences) in the domestic dog and its related species. Haplotypes and their relatedness across the canid species have been published in peer-reviewed articles and publicly available datasets. Embark has built upon these with our own data to produce one of the most comprehensive haplotype databases in the world.

But first, what is a haplotype?

A haplotype is a generic term for a single copy of a dog’s diploid genotype (haploid = 1 copy, diploid = 2 copies). Dogs will have 2 copies of their autosomes (non-sex chromosome), so parent 1's copy and parent 2's copy are each inherited as a single unit referred to as a haplotype. 

How are they determined?

Due to the way dog breeds have been generated, each dog breed has its own set of unique haplotypes. We use these breed-specific haplotypes to determine the percentage of breeds present in your dog.

Mitochondrial DNA (mtDNA) and Y chromosome haplotypes can also be used to trace maternal and paternal lineage. Mitochondrial DNA is inherited solely from the mother and passed on to sons and daughters, whereas the Y chromosome is inherited solely from the father and is passed on to only sons. 

You may have noticed that we also categorize your dog's mtDNA and Y haplotypes by haplogroups, simply groups of related haplotypes. Just like a genus is a group of species that originated from a common ancestor, we can determine if haplotypes have originated from an ancestral sequence.