Monday, 7 November 2011

Exciting Exciting NEWS. SNP Arrays to commence

Today I have received confirmation that there has been sufficient donations received by the Centre for Equine Health (UC Davis) (CEH) combined with a small grant, that the first stage of the Genome Wide Association Study (GWAS) is ready to start at the Bannasch Laboratory.
This is such exciting news that we have progressed so far, so quickly.
From the researchers at Bannasch Lab I received this today:

"We are still interested in donations for the 2nd stage of the project (either SNP genotyping additional samples or sequencing a candidate gene/region).
I am waiting on 9 more unaffected distantly related control samples to come in this week and then we plan to send out the DNA. We should have the results before the holidays and some preliminary information by the end of the year."

The next stage of the project requires $5000.

The research group has no idea who has donated money via CEH for this work to commence so promptly, but we thank you from the bottom of our collective hearts.

For those of you who wish to know more and to understand what is about to happen

The whole process involves looking for areas on a gene (or genes) which are different from what the reference genotype shows.   There are breed differences so that it why the genome of non-related ponies are needed to compare the genes of the affected ponies too.  In other words there can be specific genes which are not on the reference (library copy) of the horse genome, but which are in fact totally normal in another breed.

Because we already know what the problem is at a functional level, then the genes influencing lipid metabolism in hoof (keratin) structure is a an area for possible candidate gene(s) or a region within one of the keratin coding genes.

Here is a link which explains GWAS in detail.  It is actually talking about the use in people but the principles are exactly the same for any species.

The genome analysis is performed on an Illumina and for our ponies uses a 75K SNP chip.   That means that 75 thousand single nucleopeptides (the building blocks of our genes) are checked for each pony.
Illumina technology.   The SNPs from our ponies will also get compared to the reference Horse Genome which is logged in Genbank

After the all the pony's genomes have been mapped then comes the statistical work. The results from the SNP array are fed into statistical software to analyse the data:
statistical software

It is only because of the strength of the computing power now available that this work can actually occur - and why the costs of doing this research have become achievable.