Tag Archives: SNPTips

SNPTips update (1.1)

I did a tip of the week on SNPTips a few months ago (more information there). It’s a great addon to view your genomic data while browsing databases and web sites. They’ve moved to version 1.1. There are two nice new features and some bug fixes. The features are:
*You can now use your deCODEme data, in addition to the 23andme support they started with.
*You can use SNPTips even without raw data to view SNPs on a page.
*and it’s been updated for Firefox 4.x.

You can check our our previous tip here (which still applies :).

SNPTips landing page at 5am Solutions.

Gene Envy. I haz it.

Last night I had a fun conversation with some non-scientists on personal genomics. A lot of my conversations on this topic are “inside baseball” with people who know the field (and the minefields) really well. So it’s fun for me to explore the larger social and ethical issues with people who are just beginning to think about them. And they coined a phrase to describe my feelings on something I had seen: gene envy. They were right :)

We talked at some length about what you can and can’t learn from the “reader’s digest” version of your genome that you get from a SNP scan like 23andMe provides. How SNPs can be informative, but are not the only types of variations that might be important in your genome, and they certainly don’t represent all the SNPs possible. We talked about the kinds of things you can learn from the SNPs right now–silly trait sorts of things like whether you have wet or dry earwax (as if you didn’t know already), as well as some information about potential disease incidence and response to certain medications–but even that data is sometimes preliminary and subject to change still.

That’s all the stuff I expected. One thing I wondered about was if I was going to be affected by knowing about other people’s genes…and how I might react to that. Well, now I know. I haz gene envy. [for my color-blind siblings, I wrote that in green, btw]

I hate to admit it. I want to be better than that. But maybe I lack a gene for that or something…. I should state right off that I’m not mad at anyone personally–nobody has control over what’s in their genes. It’s not about them per se, it’s about my reactions.

I’m not a hugely introspective person, but I have been trying to pay special attention to my responses to the new landscape of personal genomics. We have a front-row seat to this, and a decent copy of the program. So I feel a responsibility to be aware and honest about what my reactions are. And this is one I don’t like in myself. But it’s there.

I’ve downloaded some other people’s genome scans that they made publicly available. I use them to test out some of the software that I run. And if I want to make screen shots of stuff I refuse to reveal my SNPs right now as I don’t feel safe doing so.

One day I was looking around at obesity variations for some project I was working on. I had forgotten that I had my SNPTips tool on. When you have SNPTips on and search the medical literature at PubMed, the abstracts can be a bit of a roller-coaster. You can read about this research, and roll over the SNP IDs and be shown your own variations (or in my case other people’s). It looks like this as you are reading:

Note: that is NOT the paper I was reading nor the SNP and gene I’m referring to; this was just an example image.

So I am reading along the text, and check the genotype of this individual’s SNP. In that case, a result of AA meant that you had the “skinny” version of the gene in that study. It bugged me. I rolled my eyes, and thought of course it’s easy for this person to be thin….sigh. I was jealous.

In another case I was relieved that someone’s genes didn’t carry a variation I have. I saw the results for someone and thought: oh, good, they probably won’t have peanut allergy like I do. I’m glad for them.

One time when reading in the 23andMe discussion boards I found myself looking at the results for people who are probably resistant to HIV. I thought: nice for them. But the ones who didn’t have that–I was sort of shocked to see them telling everyone. I wonder if that’s wise when we know that data scraping is going on at some medical social networking sites. I easily could have written down their results and their names if I had been an insurance investigator. (If you want to check your own data there, search for CCR5 at 23andMe.)

Another “variation” on my response came when the Alzheimer’s alleles were recently released by 23andMe. I saw several people celebrate their alleles. WOOT!! Even before I looked at mine I resented this. Yeah, I think, you lucky dogs: goody for you. Now shut up and stop rubbing it in. Some people are not going to have a good outcome of this.

And I think to myself: it’s easy to be cavalier about the results you get from personal genome scans if you are healthy and have good genes–and stuff that won’t affect your insurability. Or if you live in a place where your health insurance is guaranteed or you are otherwise secure in your insurance. That’s not the case for all of us.

What I’m feeling is a mixture of things. I’m jealous and irritated by other’s “good” genes. I’m relieved in some cases. I’m anxious for my own outcomes in others. Even though I know that what we know today is only part of the story in most cases, and even with “bad” genes there are probably other modifiers or interactions that may mean you can get off scot-free with your alleles. But will insurers want to take a chance on me? I am skeptical that they’ll lean to the liberal side of the interpretations.

I still think we’re likely to see what I called Genorexia Nervosa–where some fraction of people get so wound up about their genes–or their kids’ genes–that they go overboard with how they think they should eat, or exercise, or allow themselves to be exposed to. (There’s probably an OCD sort of gene that influences that….). But I didn’t see the personal envy coming. That’s what happens when you have a front-row seat on a roller-coaster. And that’s exactly why I ended up doing the 23andMe scan–to join the ride, for good and for bad.

I’ll get over it. Although I do think I have a variant of the hold-a-grudge gene. I may mutter things about your skinny genes if I see you in skinny jeans….

Tip of the Week: SNPTips and viewing personal genome data

Today’s tip of the week is on SNPTips. We had a guest post on this earlier. We usually do tips on databases and analysis tools, but after getting our 23andme data, we’ve been using SNPTips often and thought it might be of use to some of our readers. SNPTips was created by 5am Solutions for 23andme* customers to easily view their genomic data while browsing the web. The tip will quickly show you how to install the browser extension and what it does. At the end of the tip, I  briefly show a custom annotation track I created of my 23andme data using UCSC Genome Browsers** Personal Genome SNP format.  The format is not perfect for 23andme data (doesn’t allow for rsID field, has fields of little use with 23andme data, etc), but it does help tremendously if you want to browse your data with the genome browser. You basically take the 23andme data that looks like this:

and rearrange the columns, add a few to make it look like this:

You can do this in a spreadsheet program like I did, it’s a bit labor intensive. If I decide to do it for my daughter’s and husband’s genome data (which is a distinct possibility), I’d created a perl script to change the format (or maybe there is something already out there?).

It basically entails:
*eliminating the  rsID column
*rearranging the columns to the correct order
*adding “chr” to the chromosome number
*adding four columns, 1 with the number of alleles, 2 with 0′s (frequency data the 23andme data doesn’t have)
*changing the genotypes from xx to x and xy to x/y.

Remember also that the 23andme position data is from build 36 (2006, hg18) and the genotypes displayed in 23andme data are oriented with respect to the positive strand on the reference assembly.

It’s not the most elegant solution, but it works and nicely with SNPTips. It has been quite addictive for me :). I’m sure there are more elegant ones that can be done.

*OpenHelix and it’s employees have no commercial connection or financial interest with 5amsolutions or 23andme.
**UCSC sponsors tutorials and outreach with OpenHelix through as a subgrantee.

Guest Post: SNPTips, Andrew Evans

Andrew Evans – Sr. Information Architect and blogger at 5AM Solutions, Inc. This blog post is also published at http://blog.5amsolutions.com/

When I became a customer of the 23andMe personal genomics service back in 2008, I remember the sense of awe I had when I opened up the raw data file for the first time and looked at the actual A’s, G’s C’s and T’s of my genetic makeup. In reality it’s only a tiny portion of it since 23andMe assays 600,000-odd “single nucleotide polymorphisms,” or SNPs (now close to a million with their v3 chip). SNPs are locations in the genome where individuals differ from one another. SNPs (pronounced “snips”) are interesting because they might help explain in part why my personal traits and health have developed the way they have – how I might respond to certain drug treatments, why my eyes are brown, or whether I am a carrier of known Mendelian disorders, for instance. More and more new research arrives every day, attempting to link SNPs to every conceivable health condition and trait.

23andMe does a good job of providing interesting and carefully-researched reports for their customers, available on their website, and tailored to your personal genotype. They sift through the flood of research data and determine what is really worth your time to consider. They also maintain an informative blog that tracks breaking developments that might eventually make it into their official reports.

Those of us who are more adventurous, however, and perhaps better-schooled in the science behind personal genomics, can outgrow 23andMe’s filter. We wander to the scientific literature and other technical online resources where there is a lot more data, much of it preliminary, to explore. Such information can tempt one to jump to erroneous conclusions. But I understand this environment and I’d rather decide for myself.

This is the situation I found myself in not long after becoming a 23andMe customer. I discovered Mike Cariaso’s SNPedia.com, for instance, and ran my data through his Promethease tool – and I realized there was a lot more information on SNPs in the literature than 23andMe was showing us. Also, I became a more technical reader of the 23andMe reports, and now routinely follow up their references and go back to the original journal articles to understand why they draw the conclusions they do.

But there is one problem with all this Web wanderlust – once you leave 23andMe’s website, you must look up your genotype at each SNP on your own if you want to see what impact a particular finding might have on you. This can get quite tedious – especially for journal articles that mention batches of SNPs at a time. To the eye (and my memory), it’s not clear which SNPs are on the 23andMe chip at all, since they assay a subset of the known frequently-occurring SNPs.

This led me to a rather straightforward idea – why not build personal genomics smarts right into the web browser? That way, the browser could enhance web pages that mention SNPs and show you relevant information without you actually having to break your reading flow and go look up genotype information. A browser extension can do this, and so SNPTips was born.

SNPTips is a Firefox browser extension that links to your 23andMe raw data and pre-processes web pages as they are loaded, adding color-coding and tooltips to SNP IDs that are mentioned in web content. If you simply hover your mouse cursor over the SNP RS number, your personal genotype at that SNP is displayed. SNPTips also adds a little icon next to the ID – clicking this icon brings up a balloon with smart links to other web resources, including SNPedia, Google Scholar, and NHGRI’s dbSNP – so you can delve deeper with a single click.

Web page content without SNPTips

Same page, SNPTips-enhanced

(green SNPs are on your chip, gray ones are not)

Looking up each of these SNPs one at a time is a major pain, and a true impediment to getting value out of 23andMe raw data – switching windows, logging in, searching, etc. With SNPTips, a simple mouse gesture is all that’s required, without even losing your place as you read!

SNPTips is currently in public beta. To get SNPTips, simply visit snptips.com with your Firefox 3.6+ browser, and click the Install Now button, and follow the directions on the website to configure. After you’ve tried it out, we’d love to hear from you and hear your questions or suggestions for improvements. Just send e-mail to snptips@5amsolutions.com

I’m excited about our future plans for the tool as well (additional browsers, other personal genomics services, for instance) – stay tuned here (and follow @SNPTips on Twitter) for updates.