Crowdsourced Analysis of Family Genomes

This is a guest post by Manuel Corpas. Originally published on Figshare.

Manuel Corpas is the Project Leader for Plant and Animal Genomes at The Genome Analysis Centre in Norfolk. His primary role is to develop software tools for analysis, integration and data mining of genomes and has more than 12 years of experience in the bioinformatics field. He was founder and inaugural chair of International Society for Computational Biology (ISCB) Student Council and has been involved in the Junior PI initiative for mid-career scientists in ISCB and elected Board of Directors for the Society since 2014.

Disclaimer: Manuel Corpas’ current or past employers do not endorse any findings, methods or conclusions, directly or indirectly related to his personal genomics work.

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I believe that anyone, regardless of country, ethnicity or economic situation should have access to his/her personal genomic data and the ability to research them as much as s/he wants with resources that are public and easy to use.

The article published last November 7th on BMC Genomics [1] culminates a 6-years long process of understanding my personal genome and those of my direct family relatives to the full. In 2009 I decided to buy a 23andMe kit for 399 dollars which allowed me to have my personal genotypes analysed for ~0.5M SNPs. As a result I was predicted to have a 50% higher chance of having prostate cancer. Figure 1 shows the profile I got from 23andMe.

 

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Figure 1: My predicted disease risks from 23andMe (Screenshot taken in 2011) 

 

This was something that surprised me, given that no one in my family has had this disease. After having my coding part of the genome (AKA exome) sequenced and not finding much, I then proposed my family to analyse their genomes too. My Mother, Father, Sister and Aunt accepted. Figure 2 shows the saliva spits from my family before sending them to the BGI for sequencing.

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Figure 2: Tubes with saliva from my Mother, Father and Sister,
ready to be sent to Hong Kong for exome sequencing by the BGI.

After this fateful decision, me and my family have gone through a number of ‘firsts’: the first personal genomics crowdfunding initiative to attract funds to sequence our genomes, the first family to publicly put their personal genomes (exomes) on the internet for free download [2] and the first crowdsourced analysis for a set of family genomes [3]. Figure 3 shows the total amount of data that we put on the internet for crowdsourcing analysis.

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Figure 3: Summary of all data sources that were made publicly available
via the internet for crowdsourcing analysis. 

 

Overall, this experience has allowed us to ascertain the extent to which today it is possible to analyse our personal genomes using direct to consumer means. The ethics side of this study has been a lot trickier than anticipated. Some criticisms I have received for ‘coercing’ my family to do these experiments and for not following a clinically approved informed consent procedure, even though I claim everyone provided informed consent. I always reply to this that my family freely embarked into this journey because they wanted and found the experience interesting. It would be kind of difficult to get saliva from all my family members without their consent and knowledge for what this was for! Secondly, I do not believe that even the most experienced geneticist can provide informed consent before receiving results. How can you have informed consent about some risk you do not anticipate or know? There are so many risks associated with any given genome interpretation exercise that no one can ever be truly prepared for all possible eventualities.

I have never feared risking my reputation for following an unconventional/disruptive way of communicating science, which is what we have primarily intended with this work. I believe I have been able to stir some people’s opinions as evidenced by the tremendously positive response we’ve had through our publications and social media. I will continue to work tirelessly on making it possible for ordinary people to have access and explore their personal genomes by themselves, something that I call ‘democratisation of personal genomics’. Sadly, society still has a long way to go on this. I will consider successful my contribution to this field if this work raises at least some awareness about this current challenge we all face.

 

REFERENCES:

[1] BMC Genomics. 2015 Nov 7;16(1):910. doi: 10.1186/s12864-015-1973-7

[2] http://figshare.com/articles/Corpasome/693052 

[3] Source Code Biol Med. 2013 Jun 21;8(1):13. doi: 10.1186/1751-0473-8-13

 

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