Reply To: Change in Results

[kathleen morrill]

Hi Kristen & Bre Anne,

The primary reason for breed results changing were changes to the algorithm we used. A couple other aspects of constructing the new breed reference panel might further explain the new results for Dexter & Dexter:

First, the individual 12 dogs sampled for each breed have changed. Previously, we used publicly available array data for these breeds, for which the genetic data is sparser (~200,000 locations on the DNA) than the data we gain through sequencing (millions of markers). Wherever possible, we substituted in dogs of the same breed that had deeper sequence data available.

Second, the number of genetic markers has increased. When we were limited by the publicly available genotyping data, we previously examined under 200,000 markers for breed ancestry. Now, we have identified over 600,000 informative markers that help distinguish between 101 breeds.

When I take a closer look at Kristen’s Dexter and the old results, I do see that the most confident breed portions came from JRT and ACD (followed by Wire Fox Terrier). I suspect that the non-JRT Terriers — including the current 2% Yorkshire Terrier call — are misidentified portions of Jack Russell Terrier. The Jack Russell Terrier is an especially challenging breed for both the old and new algorithm, because, as a breed, JRTs are exceptionally genetically diverse!

For Bre Anne’s Dexter, these results were certainly affected by the substitutions in the panel. Golden Retriever is a breed with a ton of deep-sequenced data available, so we were able to prioritize representing more diversity within the Golden Retriever breed panel.

Please let me know if I can clarify more with the new results!

Best,

Kathleen