1. Epilepsy in Australian Shepherd Dogs Mentor: Ned Patterson DVM, PhD, DACVIM Katie Minor Valeria Rivera Genetics Lab- James Mickelson

2. Big Picture Looking for genes that cause Epilepsy in Australian Shepherd dogs. First find associations of SNPs with the disorder Epilepsy is a brain disorder of abnormal brain electrical signals that cause seizures Idiopathic Epilepsy involves recurrent seizures in which no underlying abnormality can be identified (Patterson et al. 2003)

3. Scientific Landscape Genetics Know the molecular cause of the disorder It is being treated without knowing what causes it Prevent the transmission of the disorder by selective breeding Compare to human genome Serve as a naturally occurring model for further epilepsy research for people Medicinal Develop new drugs based on specific genetic mutations ( ion channels, others)

4. Facts Epilepsy affects 1% of the human population and 4% of dogs 3 million Americans per year 200,000 new cases per year 50 million people globally Studies identified mutations in ion channels for IE in people. None of the known genes that cause epilepsy in humans are responsible for epilepsy in 4 dog breeds (Ekenstedt et al. 2011) One of the new research is… A SNP is a Single Nucleotide Polymorphism, a difference in base pairs when a single nucleotide is altered Every pair of chromosomes contain 2 alleles TT, CT, CC

5. SNP

6. Dog Seizure Video

7. Previous Work The Lab team performed previous research (whole genome association analysis) in which they established that there is a possibility of one or two genes that cause epilepsy. These genes are likely to be at specific locations on chromosome 1, 19 or both. This was determined by testing 170,000 SNPs on a SNP chip between 19 affected dogs and 21 unaffected dogs (40 dogs total).

8. Whole Genome Association WGA is a technique that examines the genome of different individuals searching for differences among them DNA samples are placed on a glass slide that detects all the 170,000 canine SNPs SNPs that travel together as crossing over occurs are in what is called Linkage Disequilibrium Common ancestors in population bottlenecks Recessive traits get concentrated in dog breeding due to common ancestors A study using 5 distinct breeds showed that popular breeds have shorter LD needing more markers for WGA (Sutter et al. 2004)

9. SNPs and Allele frequencies

10. How we got the SNPs? Noticed associations of SNPs between affected and not affected dogs after WGA Chi2 (a statistical test analysis between observed and expected results) determined if the association occurred by chance or if it is likely to be a real association The lower the P value, less the possibility of chance P value less than .05 is consider statistically significant -log10X makes easier to graph SNPs that are more likely to occur (the SNP with a P value close to zero will otherwise show no difference) New scale Higher than 1.3 is equivalent to a P value lower than .05

12. Cont. In chromosome 19, the SNP showed statistically significant association (a distinct pattern) with epilepsy There is one SNP every on average every 14,000bp in a total of 2.4 billion bp. Also, there is a gene on chromosome 1 called DOK6 near one of the associated markers of interest, the area where the SNP is located. One of the objectives is to sequence DOK6 to see if there is any difference in bp between dogs affected and dogs not affected. DOK6 has 8 exons There are some other 5 or more genes near the marker that might be sequenced later on.

13. Recognition Site for Sau3AI When the individual has the SNP TGATC, The RE will recognize the SNP (C) and cuts. If he nucleotide sequence is TGATT (SNP T). The RE will not cut in this site It recognizes nucleotide C that is associated with epilepsy, and cut the DNA there. CFA1 5’…T G A TC ...3' 3'... G C T A G^...5'

14. CFA19 5'…G C A T C (N)5^...3' 3'…C G T A G (N)9^...5' Recognizes the SNP G (associated with epilepsy ) and cuts there. The enzyme won’t cut when the sequence is ACATC. Heterozygotes (GA) will have 3 bands in which one allele the enzyme cuts and in the other one remains uncut. Recognition Site for BsmI

15. Hypothesis There is a gene causing epilepsy in Australian shepherd near the dog SNP marker BICF2G630711334 (CFA1) and/or near BICF2G63036912 (CFA19)

16. An overview of the planed protocol Test a marker on chromosome 19 on 80 additional dogs. Test a marker on chromosome 1 near DOK6 on 80 additional dogs. Compare genotypes of additional dogs, dogs with epilepsy and dogs without it . Use restriction enzymes that cut DNA around the marker, either C (CFA1) or G (CFA19)

17. Cont. Use primers that encompass the 8 exons that make DOK6 to amplify all 8 exons. Sequence DOK6 in affected and unaffected dogs; compare to each other compare it with Tasha’s. Search for a difference in bp that cause a mutation that leads to a protein change and probably causes epilepsy.

18. Current Status Currently in the middle of genotyping the 80 additional dogs for both SNPs Chi square analysis of the results To see if the association present is real (confirmed) or by chance

19. Data CFA19 Digest 385bp 216bp 169bp GG AG AA

20. Data Sequencing Results DOK6: Exon 2-8 good sequence Exon 1 Still working on it. Compared the sequence with Tasha, no difference in the coding area

21. Acknowledgements Dr. Ned Patterson Katie Minor LSSURP Colin Campbell

22. Thank you!