Thanks to all those Stabyhoun owners who have released their EMBARK results to our project, we have been able to do further analysis. To date, we have analyzed 207 dogs with more still coming!
What analysis tools have we used? First, all the data from the .csv files is compiled into an Excel spreadsheet that contains all the pedigreed Stabys or a separate one for the non-pedigreed look-alikes. To compile this takes some time, as the dog’s full information is not always included in the emails we receive. We need the ZooEasy Registration No., the registered name, the call name, height, weight, and whether the dog is clear or a carrier of cerebral dysfunction as this test is not currently available on the EMBARK mutation list. This is because the University of Utrecht has not yet published their paper on the identification of the mutation so scientists can review it for accuracy. Findings must have “peer review” before they are considered true.
Then we download the raw data in the zip folder for each dog. PLINK command-line program is then utilized to combine those individual files into groups to be studied down to the SNP level. With this tool, we can measure the degree of ”Heterozygosity” per SNP and per individual and per group and measure frequency of different alleles in the markers tested.
Tools such as TASSEL, and CRAN-R (Comprehensive R Archive Network) have enabled us to get a marker based matrix of genomic similarities among individual dogs. A similar matrix can be done from pedigree data, but that method treats siblings as “identical” when in fact they can have a very different mix of alleles. We also can put the relationships into a dendrogram or a scattergram plot to visualize the relationships.
What else can we learn?