Epilepsy & PCD Update:
May, 2008
We are looking forward to a busy summer and fall of data analysis. As we write this, exciting new experiments are underway to detect DNA sequence differences at places in the dog DNA where more that one different base is known to occur in different dogs. We call sequence differences polymorphisms. The particular polymorphisms we are working with are called SNPs (pronounced "snip") for single nucleotide polymorphism. Our experiments are being performed using the recently developed "SNP chips". This work is possible through generous funding from the Irish Wolfhound Studies, Inc and with statistical support from the Penn Genomics Frontiers Institute (PGFI). A core facility within PGFI is currently performing SNP chip analysis on 300 dogs, including nearly 100 Irish Wolfhounds in the epilepsy study, using the Affymetrix 127K SNP-chip.
So, what is a SNP chip, what are we looking for in the data, and where do we go from here? To make a SNP chip, MANY short synthetic DNA molecules (called oligonucleotides or "oligos"), representing alternative DNA sequences known to occur in dog DNA, are individually attached to a small piece of silicon glass (about the size of your thumbnail) in a precise gridded pattern. These oligos, attached on one end to the silicon chip, are free to selectively bind to pieces of a dog's DNA that perfectly match them. Based on the pattern of binding of the dog's DNA to the grid of different oligos, each dog's DNA sequence at the sites of DNA variation can be detected and recorded.
Once the data is collected, we will start the analysis, in which we will look for instances when affected dogs have the same DNA sequence and unaffected dogs show variability at the same SNP. If we find this type of association, we will have identified the region of the dog genome (genome means all of the DNA in a cell) that contains a gene that is associated with epilepsy. By analogy, let's imagine that the DNA in the dog genome is represented by Interstate 80, spanning the United States. If we find an association between a particular SNP and epilepsy, we will know which state the gene is in. Our next task will be to find out which exit to use in that state. If we can find the exit, we should be able to develop a genetic test that will detect dogs carrying a DNA sequence that puts them at risk for developing epilepsy.
So why are we going to be analyzing for several months? Because we will be able to look at more than 120,000 different SNPs, in almost 100 dogs (remember that each dog has two copies of every gene or SNP). That is more than 24 million pieces of data that must be analyzed in multiple different ways. The SNP technology and the types of statistical analysis that will work best for dogs have not yet been well established, so we will be charting new territory. This new technology is potentially very powerful, and will ultimately benefit the Irish Wolfhound and other dog breeds not only for the study of epilepsy, but for many other simple and complex diseases, such as PCD and lymphoma. (note: PCD samples are now being examined using the same technique.)
Margret Casal, Dr. med. vet., Ph.D., Dipl ECAR
Paula Henthorn, Ph.D., professor medical genetics
Reprint requests to:
Margret L. Casal Dr med. vet, PhD or Paula Henthorn, Ph.D., professor medical genetics
E-mail: iwstudies@comcast.net
