My genome analysis part III - the results are in

Lots of excitement today on checking to see if my sample has been processed, the results are ready.

You can see I checked the "please load my health data", I guess 23andMe want to make sure you really really do want to find things out about yourself efore letting you dive into the results.
The next step is to enter my data; year of birth (40 years ago last Tuesday), sex (with an "I'm not sure" option!), height, weight and smoking status. I answered no to all the medical questions (lucky me), except I am a Psoriatic so to finish off I added that I am using Dovonex cream for my Psoriasis.


Health and disease status: My first result is my blood group status, 23adnMe correctly identify me as having an O blood group. I also find out which snps are used to determine this and the reference for the paper. Interesting stuff for a scientist like me.

Immediately available is my health status report. This shows 114 disease, 52 trait, 27 carrier status and 20 drug response reports.

3 of these are locked. The locked reports describe the trait or disease eing reported and exp,lain the genetic susceptibility BEFORE you chose to reveal results. It certainly felt that the website is designed to guide an informed choice, even if you are missing a face-to-face discussion with a genetic counselor. I looked at my ApoE status and see I have twice the risk of the general population. Certainly not a 'nice' result but not likely to make me lose any sleep.

The first 23andMe discovery I read about was curly hair. According to the analysis I should have slightly curlier hair than the average European. Mine is dead straight and was so even when I was a head-banging teen rocker. My brother has slightly curly hair and my dad was curly (all shaved off now).

I am not a carrier for 24 of the diseases reported. I am a haemochromotosis carrier and not ready to look at BRCA status yet.

The most useful result for me personally is an increased risk of Glaucoma. This had been mentioned at my last opticians visit and I had brushed it off a it. Seeing a genetic risk as well makes me think I will speak to the optician a bit more at my next appointment and monitor this closely. I'll also start to look at what I can do and what treatments are available for this condition.

Traits and inheritance: As for traits I was happy to see I am a likely sprinter (CRUK half marathon in March next year). I was a little disappointed to find out I am likely to have a typical IQ. It shows what ard work I must have put in to get where I am today and also says to me my kids won't be able to get away with not doing their homework.

There are no closely related individuals on 23andME, yet. I am 74.24% identical to Neil Hadfield (also on 23andME) however I am 71.19% similar to a Chinese person and 68.49% similar to an African. Neil is probably not my long lost brother.

Impressions so far: I will spend a few days looking through this but so far it has persuaded me my £160 birthday present was worth it. It certainly satisfies my curiosity. For now I will leave BRCA status as there are some family things that need to be discussed efofre diving into that one.

Keeping up with the Joneses, genomics style

23andMe just launched their new programme to perform exome sequencing for individuals. The Exome80 "Personal exome sequencing" will cost just $999! This will now put pressure on some of those who have had their genomes scanned on arrays to pay up for the exome or risk being the social outcast in California high society. In fact 23andMe state on their website "Most excitingly, you'll be a trailblazer, one of the first people on the planet to know their personal exome sequence" that's hamming things up if ever I heard it.

The previous service (which I just signed up to) only scans 1M SNPs. The exome sequencing will provide users sequence data over about 50 million bases of DNA at 80 fold coverage. There will not be any of the very well designed reports that are given with SNP data though, just sequences and variants. This means only those with the skills to access this data will get anything useful out of it and it is debatable what 'useful' means in this context. There is certainly not the same depth of information available on exome variants and linkage to disease.

It sounds like 23andMe will develop tools and so will the community. I expect the Genomes Unzipped team will all be in the first batch of samples, hopefully paid for by 23adndMe. Most of these, if not all, are already customers who are "comfortable managing and understanding raw genetic data" as stated on the 23andMe press release. The release also assays "If you don't know your exons from your introns, this pilot is probably not for you,". I think most undergrads know about exons and introns and they certainly could not do a huge amount with raw data.

This could of course be a great opportunity for a grad school programme to develop tools and interpretations as the data could be shared out across classes.

23andMe's description of what an exome is fails to mention regulatory sequences at all. While they do say "you can think of the exome as the DNA sequence of your genes" and "Your entire genome is made up of your exome plus...DNA that does not code for proteins".The dropping of regulation may seem trivial to a lay person but is becoming increasingly important for biologists. Where are the regulome capture products!

PS: if anyone from 23andMe is reading this and wants to send me an early birthday present my DNA is ready for sequencing on my desk. Courtesy of an Oragene freebie at a conference. It's amazing what you can pick up for free nowadays.

My genome analysis part 1

It's my birthday in a few weeks and I thought I'd get myself genotyped by 23andMe as a birthday present to myself.

The lab I run offers genotyping and whole genome sequencing so it feels a bit crazy to be sending this out to a company when I could run the chips myself. I also thought I could do some of the analysis using some of the web based tools and Galaxy. I also saw Dan MacArthurs blog about a FireFox plugin, this should throw up some interesting tidbits next time I am browsing through UCSC or the literature. There are probably some legal and ethical issues about performing my own genome analysis but perhaps once I get the results I'll ask my boss if I can start using my genome library as the control on our flowcells.

The order has been placed and I now have an account on the 23andMe website.It will soon be time to start spitting and then waiting for results. I don't know if 23andMe use the Illumina multi-sample kit, but if they do hopefully in another year or so 2-5M snps will be the order of the day. The current 23andMe v3 chip is one of Illuminas HumanOmniExpress arrays, genotyping 730,000 SNPs plus 200,000 custom SNPs selected by 23andMe.

I will keep posting about this genome adventure as I get my results and start to look at them. There are some other great sites already bringing these technologies into the public domain. My favourite is Genomes Unzipped, do take a look if your not already aware of what that team is doing. I have also signed up to the personal genome project, but as a non-US citizen can't actually join yet.

PS: Sorry Dan but I am adding one more white european ancestry sample to the 23andMe database.

PPS: If you do want to know I'm after international copies of The Hobbit, which I collect, as my other pressies. If you have an old copy lying around feel free to send it and I'll make a donation to charity for each copy I receive. The older the better but do check yours is not worth a fortune before sending it!!! I am particularly looking for a Spanish copy.