They are still working on the recorded version of the NHGRI GWAS seminar that we attended last week, but I wanted to point you to a useful web page they mentioned. It is a collection of GWAS studies with the top 5 SNPs from each listed, as long as they made a certain threshold.
“As of 11/24/08, this table includes 202 publications and 435 SNPs.” according to the Catalog of Published Genome-Wide Association Studies.
So if you are interested in GWAS data this is a nice collection of that literature. It also comes as an Excel doc you can download.
The traits they cover are quite a range–from freckles to diabetes to bipolar disorder and many more. I think I would like to take some of these data over to the UCSC Genome Brower’s Genome Graphs feature where you can visualize the data on a handy genome graphic. To get this figure, here’s what I did:
1. Took the GWAS excel file.
2. Pulled out the rs IDs for the SNPs. Some cells had to be fixed because the data within it is a series of comma delimited SNPs. Moved each to a single cell.
3. Cleaned up any non rsIDs. I end up with 480 SNPs. I left the duplicates for now.
4. Created a plain text file of these SNPs. I gave each one a value of 1 just for the purposes of the genome graphs software. I just wanted to see all these SNPs on the genome in one graphic. Genome graphs tool tells me:
Loaded 12351941 elements from snp126 table for mapping.
Mapped 479 of 480 (99.8%) of markers
These data are now available in the drop-down menus on the main page for graphing
Off we go…Here are my SNPs on the genome graph–the SNPs are teeny blue dots. Ok, I don’t know what it means either. I just wanted a sense of what was coming out of all the GWAS studies and where they actually were on the genome. I would like to take another look at the data, this was just a quick pass–I’m intrigued by the SNPs that come up in multiple studies and I’m curious about what those genes do. Hmmm…..