openSNP
Genetic Testing
meets Open Data
DTC Genetic Testing
?
What’s the
point?
Genotype-To-Phenotype
GWAS
ramping up
N
mo money mo science
I firmly believe that the next great breakthrough in
bioscience could come from a 15-year-old who
downloads the human geno...
Personal Open Data
• data sets spread on
• github
• personal websites
• …
• dead links
• no contact details
openSNP
• central repository structure
• users can be contacted
• accessible
• open (surprise!)
Data
• Genotypes
• Phenotypes (Hair/Eye Color, Diseases,
Quantified Self…)
• Primary Literature (PLOS/Mendeley, …)
• Genot...
Access ?
• Export via:
• Complete Dumps
• JSON-API
• XML (Distributed Annotation System)
•
people are
doing this?
Usecases
• “Code Review”
• Ancestry
• Pharmacogenomics
• Replication
• Privacy!!11
• Artsy Stuff
I have a program that looks at 23andMe results and finds the 50-
100 most 'rare/uncommon' results out of the 900,000+ test...
Ancestry
Privacy
Privacy
Privacy
ToS
Artsy Stuff
openSNP are:
Samantha Clark
Julia Reda
Helge Rausch
Philipp Bayer
special thx to:
@wilbanks
~3700 users
Bended Realities 2015
Bended Realities 2015
Bended Realities 2015
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Bended Realities 2015

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Bended Realities 2015

  1. 1. openSNP Genetic Testing meets Open Data
  2. 2. DTC Genetic Testing
  3. 3. ?
  4. 4. What’s the point?
  5. 5. Genotype-To-Phenotype
  6. 6. GWAS
  7. 7. ramping up N
  8. 8. mo money mo science
  9. 9. 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) 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)
  10. 10. Personal Open Data • data sets spread on • github • personal websites • … • dead links • no contact details
  11. 11. openSNP • central repository structure • users can be contacted • accessible • open (surprise!)
  12. 12. Data • Genotypes • Phenotypes (Hair/Eye Color, Diseases, Quantified Self…) • Primary Literature (PLOS/Mendeley, …) • Genotype<->Phenotype-Associations (PGP, SNPedia)
  13. 13. Access ? • Export via: • Complete Dumps • JSON-API • XML (Distributed Annotation System) •
  14. 14. people are doing this?
  15. 15. Usecases • “Code Review” • Ancestry • Pharmacogenomics • Replication • Privacy!!11 • Artsy Stuff
  16. 16. 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. Code Review
  17. 17. Ancestry
  18. 18. Privacy
  19. 19. Privacy
  20. 20. Privacy
  21. 21. ToS
  22. 22. Artsy Stuff
  23. 23. openSNP are: Samantha Clark Julia Reda Helge Rausch Philipp Bayer special thx to: @wilbanks ~3700 users

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