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Crowdsourcing the Analysis of Genomes
- 1. Crowdsourcing the Analysis of Genomes 3 Years of Publicly Available Genotypings – Stories from the Frontline
- 5. & open data
- 6. Science & open data
- 7. I firmly believe that the next great breakthrough in bioscience could come from a 15-year-old who downloads the human genome in Egypt. – Thomas Friedman (2005, WIRED)
- 8. If we can put a man on the moon and sequence the human genome, we should be able to devise something close to a universal digital public library – Peter Singer (2011, The Guardian)
- 9. • Collects personalized genetic data from customers of 23andMe, FamilyTreeDNA, etc. • Also collects phenotypic information (medical history etc.) • Data available under Creative Commons Zero (~ Public Domain)
- 10. & end users
- 11. & end users • add value: cross-database annotation • some data visualization • (community aspect) • enable scientific advances?
- 16. is the data used?
- 17. from my inbox: analysis of individual files. I have a program that looks at 23andMe results and finds the 50- 100 most 'rare/uncommon' results out of the 900,000+ tested by 23andMe. Your results show your European background very well. And, you do have just 1 homozygousrecessive result but it comes in an intergenic region so presumably can be ignored. However, you are a 'carrier' for one of the SNPs (rs1805128) in theKCNE1 gene which has been associated with 'torsade de pointes' (but the evidence is very poor!). Also, there is no suggestion of consanguinity in your pedigree.
- 19. replication of published studies
- 20. teaching
- 21. art
- 23. limitations • sample sizes (so far) • usability of the data • usage of the data
- 24. tl;dr • people openly publish their personal genomics data sets • actual usage of that data is limited so far • but: some of the examples show the potential of opening up human genetics
- 25. thx from us Samantha Clark Julia Reda Helge Rausch Philipp Bayer
Notas del editor
- similarity to every other online shopping done, e.g. amazon
- collect saliva, basically just spit into this little tube. if you order it with 23andme it will be at your door via express postage ~2 days after you ordered it
- takes 3-4 weeks until you get an email, notifying you of the results. you will get access to this funny text file on the right hand side, it contains the ~1 million genetic variants (nowadays only ~600k) that 23andme tests for
- 23andme seems keen to be perceived as a company that cares about open data have an api to allow programmatic access, but you need to apply and it’s not widely used also: at the same time researchers can’t easily get access if they want to, access to data is marketable and brings the company lots of money nothing wrong with making money, but…
- …coming from a academic biology background, this is what I’m used to: lots of data is freely available genetic information is made public so that others can a) reproduce your work b) do their own research c) do comparative studies, because they are really really useful
- and academia is not alone with this view, thomas friedman in 2005 said this we with opensnp agree to this sentiment to a great deal, but this requires that data is available
- of course, we’re not the first ones to figure this out, peter singer in 2011 said this. and we agree to this at least as much. creating such a digital public library for genetic information isn’t technically impossible
- so we just did exactly this: data comes from all direct-to-consumer genetic testing companies, even the ones extinct by now we also allow people to publish details about themselves (medical history, but also things like eye color, hair color, etc.) The data is put under CC-0, which for most purposes is the public domain. and the data is not only usable for free, we also offer programmatic interfaces, comparable to the API of 23andMe
- we really don’t want to be coercive in our approach with openSNP people who upload data should do so knowing the risks, that’s why we try to scare people shitless
- why should people do it anyway? cross-database annotation: one-stop-shop for latest publications, whether SNPedia has already entries, community: maybe 2000 messages send through the system, but opensnp is also referenced as a resource in outside forums, e.g. yahoo groups for rare diseases
- how the result looks like on the web single page showing some basic statistics: where is the variation located, how is my own variation, how is the distribution of variations amongst opensnp users, etc. then: what do we know about the impact of those variants? lastly: where are