Bioinformatics

Getting My Genome Sequencing Done (Part I)


Readers of this blog may have come across the experiment my family did with Direct-to-consumer (DTC) genetic testing. We analyzed all our samples using 23andMe kits and started sharing and writing about our personal genome data. This experience has changed me dramatically as a person and researcher.  I started off as a bioinformatician with an interest in risks of genetic variants but now these experiences have helped me develop a real insight into the psychology of how these variants may impact on people’s reactions. As a family, we are truly experiencing a really positive and unexpected response from people contacting us via the Internet who are willing to tell us their findings about our family data.

After doing our whole genome genotypes, the next obvious step is to have our whole genomes sequenced. There is quite a lot of debate at the moment as to whether genome sequencing should be accessible to the general public and if so, to what extent. But I figured out that if “the rich and famous” can have their genome sequenced, perhaps with a bit of luck, the “ordinary and poor” (among which I include myself), could have a chance, even with zero budget. Zero budget for this exercise was an essential point of principle, given that we really would not be able to afford even a 10th of the price a genome currently costs (around $9,500; probably cheaper than this price by the time you are reading this).

I wasn’t sure how to do this, but I know that this might be possible and that we would get it done if we could. So I went onto the Internet and searched for whole genome sequencing. I found three potential good candidates that could do it on demand: Complete Genomics, the Illumina personal sequencing services and the Beijin Genomics Institute (BGI).  So the first thing I did, I sent them an email. Given that we had no money to spend and that there is no such a thing as free lunch, we thought that we needed to offer something substantial in return since we were asking them to waive us the fee of ~$50,000. The only substantial thing we could really offer was publicity, so the following proposal was sent to those three companies via their websites:

Dear Sir/Madam: I would like to offer you a deal/proposal. My family would like to have their whole genome sequenced with your company. In exchange for releasing to the public openly and freely on the Internet our genomes we thought you could sponsor us. This action could attract *a lot of attention* to [company name], as this is a pioneering move. Currently a very limited set of people are actually interested in sequencing their genomes. The only way you can reach the ordinary citizen (sooner rather than later) is if ordinary people, like my family publish their experiences and pave the way. My family, an ordinary family, constitutes an example of what this technology could do for any ordinary person, not just a scientist, etc. In addition to this, I want to fully research all of the social/ethical implications that publishing this information can bring. We also hope to share this information with the world. Currently all my family has genotyped their genomes with 23andMe and put all this data in the Internet for free download: http://manuelcorpas.com/five-family-relatives-genome-download/ To our knowledge, this is the first time that anything like that has been done. In barely a month since this information has been published, four different analyses from specialists/hobbyists have reached us, making us learn that dad, for example, is lactose intolerant [1]. Our point is that now, with DNA sequence providers, the door opens for DIY genome mining. The power of the Internet and computers may bring this technology to computer savvy people. For example, our 23andMe genomes are now been taken by SNPedia and several other ancestry projects such as Eurogenes and Artemis: http://www.snpedia.com/index.php/User:Manuelcorpas http://bga101.blogspot.com/2011/03/mds-analysis-of-southern-europe.html http://dioegenesartemis.blogspot.com/2011/04/first-results.html Although up to date the information provided by 23andMe has not revealed any nasty surprises about our genomes, we are aware that now anyone can report new findings that were not initially discovered in our genomes. We believe, however, that as a family we can gain a lot more than lose by sharing our genome data with the world. I believe my proposal could bring a lot of exposure to [company name] and therefore would request whether you could consider this offer. Best wishes, Manuel

Illumina never got back to us. Looking around we learned that their policy is that sequencing should be done with medical prescription. Fair enough.

I couldn’t wait long so I continued researching the matter and found Complete’s contact phone number on their website, so I rang them. To my surprise I was put through and the person was very polite with me and keen to listen to what I had to say. Since I have learned that Complete had already sequenced and published 69 genomes, available via this website:

http://www.completegenomics.com/sequence-data/download-data/

Among these genomes there is a multigenerational family with a bigger pedigree than the one I was proposing. This obviously meant that our offer wasn’t as innovative as we initially thought of. It seems that Complete Genomics will not do (at least for the time being) “Direct-to-consumer” business, but that still, their goal is to become the “Intel Inside” for human genome sequencing efforts, the technology underlying most human genome analyses. I thought that that was a cool objective if attainable.

I still didn’t give up. I tried to see whether there was a chance that Complete might change their mind, so I wrote to them about our incredibly interesting experience of family dynamics and family communication issues while discussing our personal genomes. So far we have not been lucky enough to get our genomes sequenced for free. Despite not achieving our outcome, there is a lot we have learned on the way though. What an interesting experience.

This is the end of part one on Getting My Genome Sequencing Done.

[1] This information was actually available in our 23andMe reports, but we missed it initially. We learned about this condition with the SNPedia tool Promethease

6 replies »

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s