I've become really interested in the concept of the quantified self. I believe in the power of data, and we currently have the ability to collect more of it than ever before. I also believe that data should be open and shared for the greater good. As navel gazing as this is, I think self-insight is incredibly valuable and I've chosen to document how I'm doing it - as someone trying to improve their relationship with their body, mind and world, as someone living with chronic health conditions and as a generally curious person. In particular, I'm often asked about my experience with personal genome analysis and I hope this can provide answers to most of the questions I am asked - and making the information available to those who are not willing to compromise their privacy by asking. 

23andMe, Promethease and Personal Genomics

Disclaimer: I have no further education in this subject than high school biology and my own research, which I have approached cautiously and know is very rudimentary. Take this as a broad overview and question the details. None of the following is intended as scientific or medical advice.

I chose 23andMe, after comparing various services; they used the Illumina platform I preferred and allow you to download your raw data. Processing took about 6 weeks and once the results were in, I grabbed the raw data and immediately ran with it. 23andMe do not offer full genome sequencing (this is, as of 2016, still around ~$1000); rather they sequence about ~600,000 known SNPs (on the current v4 chip) and give you data based on that. Keep in mind that this is not an exact science, none of this should be taken as standalone medical advice, and it is mostly for your personal interest and curiosity. 

Ancestry

23andMe's own service is currently restricted to ancestry information. I found out some interesting things! Here's my ancestry composition:

Note the Oceanian and East Asian DNA? Wasn't expecting that, even in such a small amount - as far as I was aware, my ancestry should have been entirely European. with a few expected outliers like the tiny Sub-Saharan African amount. Most people who are entirely European show as 98 - 99% in 23andMe. I had a slightly more detailed look at this using my raw data and GEDMatch - specifically, the 'Admixture (heritage)' tool. It's not a large amount of my DNA, but considering I live in New Zealand, probably I have some kind of Maori or Polynesian heritage - I'm not really qualified to comment on this. Ancestry wasn't my primary reason for taking the test, although I may dig deeper into this in the future. 

Health

I used my raw data file to analyse my DNA with Promethease - this provided access to health data. Promethease appears much less user friendly at first than 23andMe's old health reports, but the level of detail is actually really helpful. It pulls the details of the SNP and any associated info from SNPedia, including links to the original studies, and presents it with as little interpretation or spin as possible. Effort and research are required to parse the results correctly, and should be approached cautiously without jumping to conclusions, especially if you have little to no scientific background. From what I've seen of 23andMe's reports, they oversimplify things - like aggregating SNPs and calculating an overall risk factor, which isn't the most transparent or accurate way to present the data.

I thought I knew what I was looking for, but I got a whole lot more. I have some chronic health conditions that I knew had a genetic component. Often that gives you direct information - for example, what medications your body can process more effectively than others. I did take away a few pieces of health information that I wasn't expecting. Promethease doesn't fuck around - the very first result it gave me is that I carry two copies of APO-ε4, which means I'm part of the ~1.7% of the population who are ~11x times more likely than average to develop Alzheimer's disease. Not exactly cheerful news.

However, I was able to take this knowledge and use it for good - a recent study suggests that for people who have the APO-ε4 allele, eating fish once a week may slow the development of Alzheimers. I'm young, I have a whole life ahead of me, and if eating fish once a week can possibly help, I'm all over that. It probably won't hurt, and I feel empowered that I've amassed this knowledge and can take action. There are a few other markers, like risks for various types of cancer, that I now also know to be aware of.

Privacy, Research and Open Data

When it comes to the wider picture, I think data should be open and shared for the greater good, and that goes for genetic data too. For a start, I opted into sharing my genetic data into 23andMe's research program. I attempted to find more programs, but most, like OpenHumans, GenesForGood or the Harvard Personal Genome Project, only accept data from US residents. Reddit, for example /r/genetics, has been useful for finding smaller scale studies - one I recently contributed to was about sexuality & gender expression, for example. I'm a fan of contributing to these studies, I see it as giving back useful data with such small amount of effort and at low risk. Not that many people are running around with a copy of their genome and actively seeking to participate in research, so I think it's a pretty cool thing to do if you can.

However, it would be amiss not to talk about the privacy ramifications of even taking part in personal genome analysis in the first place. Your genetic data is not only uniquely you, it can also identify your next of kin. In the case of 23andMe, your genetic data and spit sample are now being stored by a privately held US company, who have a history of reckless behaviour i.e. getting on the wrong side of the FDA. If that's not enough, 23andMe have links to Google, who are in the business of exploiting your personal data. Health and life insurance companies are already aware of the existence of these services and are eager to use the data against you. Very few countries currently have genetic nondiscrimination legislation (an example is GINA in the US).

Law enforcement are also seeking out genetic data - see this recent fishing expedition using familial DNA, which means you can be under suspicion without even submitting your DNA to any of these services yourself (this is a great example of how I mentioned previously that you expose your next of kin through your own genetic data). There is no real way to participate anonymously, even using a pseudonym. Overall, I weighed this against my curiosity and what I hoped to gain from the service and went with it. I don't regret it, and I would do it again - I will probably get full genome sequencing when it is affordable.

I have considered open sourcing my genetic data through a service like openSNP. This isn't something to do lightly - as mentioned before, it's not just your genetic data, it's also that which you share with your close relatives. On one hand, open data for the greater good - a whole database of genetic information available for any researcher to use. On the other hand, it's literally any researcher - there is no tracking of who accesses and downloads the data, just a great big blob. You also create a publicly accessible profile, and your data is subject to a Creative Commons Zero license - essentially, sending your most private data out into the world on its own with zero control over how it is used. 

I read this article from 2011 on a guy who uploaded his genome data to GitHub and it resonates strongly with me. The service he talks about wanting to make possible largely exists today in the form of Promethease, but it shows what can be achieved with open data. I am still very cautious about this and unlikely to do it any time soon (take a look at openSNP's disclaimer and that'll certainly sober you up), but it is the extreme extension of the views I already hold. Update: I did this, here's my openSNP profile

CureTogether

CureTogether (part of 23andMe) is a service allowing people to track how they experience their health conditions and measure them against aggregated data from other people. Unlike most of the services here, I would consider this data deeply personal and it's not something I'd consider sharing - and my barrier for sharing is reasonably low compared to other people. Some of my health conditions are public knowledge, even via other services discussed here, but not to the extent covered by CureTogether; some aren't, and I would prefer to keep them that way. Some, well, who really wants to read about my deep personal experience with acid reflux?

The data that CureTogether collects is useful either as part of a large, anonymised dataset, or on a very granular level to the person it concerns. It's excellent for prompting you to quantify the lived experience of your health conditions, and mildly interesting to plot them against other participants. It also contributes to 23andMe research on some level - here's a fluffy diagram of comorbid conditions.