Using the Ensembl Variant Effect Predictor with your 23andme data

I subscribe to the Ensembl blog and found, in my feed reader this morning, a post which linked to the Variant Effect Predictor (VEP). The original blog post, strangely, has disappeared.

Not to worry: so, the VEP takes genotyping data in one of several formats, compares it with the Ensembl variation + core databases and returns a summary of how the variants affect transcripts and regulatory regions. My first thought – can I apply this to my own 23andme data?

23andme – yes, me – part 3

Results!
The email is titled “Your Genetic Profile is Ready at 23andMe!” It arrived on June 21, a shade under 5 weeks after sample arrival and well ahead of the estimated 6-8 weeks. This is what we’ve been waiting for.

23 and me – yes, me – part 2

Sample journey and arrival

Spitting across the Pacific

My tube of spit arrived at the lab on May 19. Six days door-to-door via Guangzhou, Anchorage and Memphis to LA.

23andMe raw data menu

On arrival, a confirmatory email: “The spit sample you recently submitted to 23andMe for the person listed above has been received by the laboratory and is now pending analysis; the process usually takes 6-8 weeks. You will receive another email notification from us as soon as the data for this sample are ready to be accessed through your 23andMe account.”

In the meantime, there’s plenty to explore at the 23andMe website. Anyone can create a demo account, which allows you to explore anonymous sample data to get a feel for what you’ll see when your own sample is processed. Naturally, I’m most excited by the options to browse and download raw data. You can also participate in around 20 health and genetics surveys which are a good way to kill time, although not many of them provide instant personal gratification.

Next update – some time in July.

23 and me – yes, me – part 1

Until recently, I was not even aware that there is a DNA day. Nor can I tell you exactly when and where I noticed that 23andMe, the personal genomics company, launched a sale to celebrate the day – I imagine it flashed by on Twitter or FriendFeed. I can tell you that like many others I decided that finally, I could justify the expense, signed up (with around 15 minutes to spare – thanks to the 17 hour Sydney/California time difference) and I’m now waiting for sample arrival and processing.

I thought it might be interesting to blog the experience and provided that I don’t discover anything disturbing, I’ll share some of my data here. Related posts will be tagged with “23andme” and here is part 1 which covers sign-up, delivery, sample collection and return.

The 23andme blog

23andme have been blogging for a while, but activity has recently picked up. Entitled “The spittoon” (tagline: more than you’ve come to expectorate…nice one), a recent post is bluntly headed “Why science can’t share” and points us to this NYT article by a cancer biostatistician on the difficulties in accessing raw biomedical data.

Update: the NYT article was free when I posted this, but now requires login. Ah, the irony…

The 23andme post is filed, quite appropriately and correctly, under “big questions”. A blog worth keeping an eye on.

From hype to reality, just like that

If you’ve been wondering whether personalised genomics startup 23andMe were for real, the wait is over. Details of their service are now available. Simply pay USD 999, spit in a tube and mail it to them (in the US only so far) and they promise a personal web-based genome browser with information about disease susceptibility, ancestry and (if your relatives join in), genealogy. The technology used is SNP genotyping – basically DNA is amplified from your sample and hybridised to an Illumina array, generating ~ 600 000 data points. All the details are available here.

Some reactions (first 2 articles by people who have trialled the service):

• Welcome to the Age of Genomics at Wired Magazine
• My Genome, Myself: Seeking Clues in DNA – NYT article
• Expect frequent posts from Pimm – Partial immortalization, Scienceroll and Deepak at BBGM on this topic

So there you go – we talk about the hype, the technical difficulties, the ethical/legal issues and then someone just goes and does it. I suspect that increasingly, this is how the future will unfold. Shall we lay bets on the year of the first cloned human?