Monday 26 July 2010

Exploring my genome with 23andMe - disease risks

In recent months I have been following with interest the experiences of my friends in the genetic genealogy community who have tested with the personal genomics company 23andMe. The 23andMe test looks at over 500,000 SNPs (pronounced snips) - markers in your DNA known as single-nucleotide polymorphisms - and provides you with information on your ancestry and your predisposition to 163 traits and diseases. The Complete Edition 23andMe test normally costs US $499 (about £321). It is also possible to purchase separately the Ancestry Edition at $399 or the Health Edition at $429. The Complete Edition is however the only 23andMe test which gives you access to your raw data, and is therefore the most useful. Although I have been curious about the process I really could not justify spending nearly £400 on such a test. However, when 23andMe had a one-off sale on DNA Day at the end of April I jumped at the opportunity to purchase the Complete Edition test for just $99 (£63). I had to pay an additional $70 for Fedex delivery. The total cost charged to my credit card was £117. I have had my results for several weeks now but it has taken me a while to explore and digest all the information. I will share my experiences of my 23andMe test in a series of  blog posts, and will focus first of all on my disease risks. I should caution that I have no scientific or medical qualifications. There is a growing body of healthcare professionals and government agencies in America who believe that consumers such as me should not be permitted to purchase these tests without the intermediary of a doctor or genetics counsellor because we are supposedly incapable of understanding the results and, despite lack of evidence, there is a theoretical risk that we might make inappropriate health care decisions based on our findings.

By far the hardest part of the test was grappling with the packaging and then working out how to send the kit back to America. The Fedex instructions were very confusing, and no UK contact details were given. I eventually found a UK telephone number on the Fedex website and was then able to ring up and make arrangements for a courier to come and collect the kit. Before my test could be processed I was required to read and agree to a very lengthy and thorough consent document which reminded me first and foremost that it is "not a test or kit designed to diagnose disease or medical conditions, and it is not intended to be medical advice". The full text of the consent form can be read on the 23andMe website.

The results are all made available through a personal account on the 23andMe website. I have provided below a few sample screenshots. You will need to click on the images to enlarge them. 23andMe distinguishes between "established research" and "preliminary research". For results to be classified as  "established research" (shown on the screenshots with four yellow stars) the association must be widely accepted in the scientific community or validated by at least two studies on more than 750 people with the trait or condition. "Preliminary research" reports are shown with grey stars and are graded depending on the size of the study or studies in question. These findings have not been replicated in other studies and have therefore not yet been confirmed by the scientific community. The results for Parkinson's disease and breast cancer are initially locked, and you are required to read the warnings before deciding whether or not to access these results.
My most elevated risk was for type 2 diabetes, for which 23andMe tell me that I have a 23.6% risk versus an average risk of 18.2%. The screenshot below shows the way that my diabetes risk is presented and explained.
As an illustration of the complexity of so many diseases 23andMe reports on nine markers which have been associated with type 2 diabetes. I have a slightly increased risk on five of those markers but a slightly decreased risk on the remaining four markers. It is however still possible to contract a disease even if you have a reduced risk or, conversely, you might have a higher than normal risk of a disease but never suffer from the condition. For each disease or trait a large amount of information is given which is explained very clearly and presented in a way which makes it very easy to understand. My only criticism is that in the resources section all the links are specific to the US. The majority of 23andMe's customers are in the US so this is understandable, but it is not particularly helpful for those of us who do not live in America. You are also encouraged to consult with a genetic counsellor about your results and a link is provided to a commercial company in America which charges between $99 and $375 for a consultation. Although there is nothing in my results which gives me any cause for concern, if I did have any worries it would have been useful to know who to approach. I'm not aware that we have similar networks of private genetic counsellors in the UK and presumably access to a counsellor would only be possible on the National Health Service with a referral from a general practitioner.

My results also show that I have a slightly elevated risk of age-related macular degeneration and exfoliation glaucoma. I have no family history of either condition and I have never smoked, both of which can be contributory factors.  I have been short-sighted since childhood and, because I wear contact lenses, I go for regular check-ups with my optician. I will be therefore be able to alert my optician to the report, and ask her advice when I next go for a check-up.

Amongst the preliminary research reports I was particularly interested to see that I have a genotype which, if the results of the preliminary study on just one marker can be replicated, would put me at substantially higher odds of contracting diffuse-type stomach cancer. My maternal grandmother died of stomach cancer, albeit at the advanced age of 89, so I quite possibly do have a genetic predisposition. The study cited looked at 925 patients and 1,396 healthy controls from Japan. It will be interesting to see if these results can be replicated in other studies and particularly in European populations. One of the most useful features of the 23andMe service is that your results are continually updated with new findings from published papers.

The remaining results are organised into two further sections - those for which I have a decreased risk and those for which I have a typical risk. The way that the risks are presented is somewhat confusing. According to 23andMe my biggest risk is for obesity. I have a typical risk of 50.6% which is slightly lower than the average of 59%. It seems odd that obesity, my highest risk factor, is not highlighted in red at the top of the page whereas bipolar disease, for which I have only a 0.2% risk versus the average of 0.1% is flagged in red.
I was also very surprised at the figures that 23andMe quotes for obesity. I am advised that on average "59.0 out of 100 women of European ethnicity will get obesity between the ages of 13 and 59". The source for this figure is not given but I rather suspect the figure applies to American women of European ethnicity and not to the European population as a whole, especially as the obesity page is accompanied by a map of America with a breakdown of the obesity levels in each individual state. If so then the percentages for my other disease risks, and especially diabetes which has a strong association with obesity, would need to be suitably adjusted.

I have had no big surprises from the 23andMe test, but it has certainly been an interesting experience exploring my results. I will write more about some of the other features in future posts.
Update 31 July 2010
In today's Times newspaper there was a report from Mark Henderson, the Science Correspondent, on the contradictory population risk data provided by the leading personal genetics companies. If you have a subscription to The Times (you can sign up for a weekly subscription for a nominal fee) you can read the full story here along with the associated commentary from Daniel MacArthur here. Mark had his DNA tested with three different companies: 23andMe, deCODEme and Pathway Genomics. He discusses his results here and in a blog posting hereThe Times story begins: 
Personal genetic testing companies are to change the way that they present health risks after an investigation by The Times exposed how they can mislead people about their chances of developing disease. Three services have agreed to correct problems that can produce confusing and potentially inaccurate personal risk predictions for serious conditions such as heart attacks and diabetes.
The companies are giving the same individuals widely different risk estimates for some diseases because of uncertainty about how widespread the conditions are in the general population. This uncertainty affects the personal risks sent to customers but is not declared in their results... 
All three companies have announced that they will be reviewing their services and have said that "they would provide clear sources for population risk of diseases, and warn customers that the personal risks calculated might not be accurate for everybody." 23andMe have advised that they would "make adjustments within weeks".  I have been very impressed by the commendable way in which the companies have responded to these concerns and I look forward to seeing the amendments to my 23andMe results in due course.

See also

Part 2 Carrier status and drug responses

Part 3 Traits

Part 4 Ancestry

© Debbie Kennett 2010


Keith Grimaldi said...

Nice summary Debbie! It's definitely not refined yet for markets outside USA though - "get obesity" ??!

Also, even if the health related information is not so useful (but not totally useless) - you have your results and can follow up as research brings up new findings.

Look forward to the next posts

Debbie Kennett said...

Thanks Keith. It's definitely worth having the raw data so that you can play around with it. A nice feature of the 23andMe service is that your results are constantly updated in the light of the latest research, and they are also very good at providing commentary on their blog. Just in the last four days I've had new results in for my leprosy susceptibility, based on a Chinese study. I'm not sure that it has any practical value, but it's still interesting to know. 23andMe also seem very responsive to customer needs so I would hope that with more Europeans testing they will eventually tailor their service accordingly.

Your Genetic Genealogist said...

Very nice job explaining the risk analysis, Debbie! I think you made it thoroughly understandable for the layman which can be a challenge. I will also look forward to more.