Tag Archives: SNPedia

What would you do with your genome?

So last week I treated myself to my first vacation in a long time.  It was my birthday, and I wanted to disconnect a bit and recharge.  Mostly it worked, although the hundreds of emails I’m facing this morning are a bit daunting.  But just before I left I got an email from a colleague who asked me a really great question:

….I would love to know where you would start when you get back a personal genome sequence….

And I couldn’t shake this out of my head.  I was sitting on a bridge outside Windsor Castle thinking about it as the sun set on my first day.  (On subsequent days I found that the far superior ciders in the UK were able to push this question out of my head for some periods of time. And also pie.)

I’ve spent some significant time thinking about the onslaught of personal genomics, of course.  It’s all been very theoretical, because I would have refused to even begin the process of obtaining my personal genome sequence until the GINA legislation fully kicked in.  But now that barrier is down.  I’m still not ready to get mine done for a variety of reasons (cost, quality, informative value).  But it’s still worth thinking about what I would do with it if it was handed to me–in specific terms, with concrete actions.  So here’s what I decided I would do.  Your mileage may vary.  And I’d love to hear what others might do with theirs.  Follow the link for the specific actions I’d take.

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Top SNPs of the year

Interesting post from SNPedia blog (we mentioned being able to view SNPedia SNPS HapMap last year in a post) of the top 10 SNPs of the year.

Of course, as they mention, it’s very subjective.

Because they have chosen SNPs with serious health interest, I’ll semi-frivolously (because hey, no knowledge is necessarily “frivolous” :) nominate either:

The “ear wax” SNP which determines whether you have ‘wet or dry’ earwax, only because (yes, TMI) I have both, one in each ear so now I’m curious as to why.

and

The “Perfect Musical Pitch” SNP, only because my daughter and I seem to have that particular variation, and we know a few people who don’t ;-).

SNPedia on the HapMap GBrowser

SNPs are hot. Everywhere we go for training people want to see SNPs. SNPs from many sources. And we know a lot of places to find them. Although everything gets in to dbSNP, of course, sometimes it helps to look at subsets of SNPs that were the focus of special projects. For example, the genes and SNPs from WashU in the SeattleSNPs project are focused on inflammation. If your genes are on their list, you are golden–you can look at the gene of interest in deep detail. Same for the NIEHS SNPs–those genes and SNPs are environmentally influenced.

Other projects are broader. Of course, the HapMap project identified millions of SNPs in various populations. And they did this genome-wide. The HapMap folks created a browser to focus on their data–but viewed on the official genomic sequence. That browser is based on the GBrowse software, which many people have used to create views of their favorite genomes and data.

Sometimes you can take the SNPs from one project, and load them onto another place to look at them. In the case of SeattleSNPs, you can find any gene page and click to load those SNPs as custom tracks on to the UCSC Genome Browser by clicking the “Golden Path” links in the middle of the page.

I was just looking today at another source of SNP data that you can load into a viewer. SNPedia is a resource that collects SNP information. I just found out today on the SNPedia blog that you can view those SNPs right on the HapMap browser–it is so easy! There are 2 URLs for the SNPedia data (http://www.snpedia.com/files/gbrowse/snpedia and http://www.snpedia.com/files/gbrowse/microarrays, you can see more info about them on their blog). All you have to do is:

  • go to the HapMap browser (sample location from the SNPedia blog)
  • go down to the very bottom of the HapMap page
  • paste each of those SNPedia URLs in the “Add remote annotations:” section one at a time. Click the Update URLs button each time.
  • and the data gets loaded from SNPedia right on to the HapMap browser.

So you get the genomic context, the HapMap context, and the SNPedia data too. I clicked one of the ones in this view (rs7901695) and it took me back to the SNPedia page for that SNP–which links back to a GeneSherpas blog post. Isn’t it amazing what you can learn from blogs?