The hitchhiker’s guide to genome hacking

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Yaniv Erlich

ASHG 2018 session on genetic privacy

Science

Yaniv Erlich@erlichya10/17/18
We need to share data
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary
Zielinski et al., 2013. Guardian provided permission to share this photo.

Yaniv Erlich@erlichya10/17/18
The hitchhiker’s guide to genome hacking
Genetic Privacy
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Taxonomy of genome hacking techniques
Attribute disclosure
(whose is this phenotype, anyhow?)
Identity tracing
(whose is this genome, anyhow?)
Attacks
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary
Genealogical
triangulation Side-channel
Phenotype
prediction

Yaniv Erlich@erlichya10/17/18
The shape of identity tracing attacks
Anonymity means being lost in the crowd.
Identity tracing: narrow down the crowd from the sample
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
How much information do we need?
Identify every person in the US: log2(325*106) = 28bits
Surprisingly small!
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Information in common identifiers
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Correlation between Y-chr and surnames
www.ysearch.org:Y
Y
Smith
Smith
Y
Smith
Erlich
Genetic privacy
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Surname inference
In total:
5 successful surname recoveries
Patrilineal line from source to target
Person tested by genetic genealogy service (source)
Genetic privacy
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Long range familial searches
Genetic privacy
Come to my Plenary Abstract talk on Friday at 6:40pm
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Side channel attacks
Genetic privacy
Sweeney et al., 2013
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Side channel @ Personal Genomes Project
Genetic privacy
Sweeney et al., 2013
Oops: default filename has the name of the individual!
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
PGP made it looks like everything is fine (but it is not)
Genetic privacy
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Can we use DNA phenotyping for identity tracing?
We can predict phenotypes from genetic data!
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Not so fast…
Genetic privacy
Height at a single cm resolution
Perfect
knowledge
Theoretical limit(h2)Current knowledge
(Lello et al., Genetics, 2018)
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Face prediction?
Genetic privacy
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Not very promising…
Genetic privacy
Accuracy of prediction(R2)
[bits]
Current knowledge
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Challenges in face prediction
Genetic privacy
Working hypothesis: identifying individuals based on
phenotype inferences is a typically a limited approach
Fig. S11 in Venter
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Do we really understand privacy?
Genetic Privacy
AshleyMadison.com JoinAllofUS.org
Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

Yaniv Erlich@erlichya10/17/18
Melissa Gymrek
Amy McGuire
David Golan
Eran Halperin
Arvind Narayanan
Tal Shor
Shai Carmi
Itsik Pe’er
Acknowledgements
MyHeritage Science team!

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The hitchhiker’s guide to genome hacking

1. Yaniv Erlich@erlichya10/17/18 The hitchhiker’s guide to genome hacking Chief Science Officer, MyHeritage Associate Professor of Computer Science, Columbia University Adjunct Core Member, New York Genome Center Dr. Yaniv Erlich @erlichya Slides are publicly available on:

2. Yaniv Erlich@erlichya10/17/18 We need to share data Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary Zielinski et al., 2013. Guardian provided permission to share this photo.

3. Yaniv Erlich@erlichya10/17/18 The hitchhiker’s guide to genome hacking Genetic Privacy Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

4. Yaniv Erlich@erlichya10/17/18 Taxonomy of genome hacking techniques Attribute disclosure (whose is this phenotype, anyhow?) Identity tracing (whose is this genome, anyhow?) Attacks Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary Genealogical triangulation Side-channel Phenotype prediction

5. Yaniv Erlich@erlichya10/17/18 The shape of identity tracing attacks Anonymity means being lost in the crowd. Identity tracing: narrow down the crowd from the sample Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

6. Yaniv Erlich@erlichya10/17/18 How much information do we need? Identify every person in the US: log2(325*106) = 28bits Surprisingly small! Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

7. Yaniv Erlich@erlichya10/17/18 Information in common identifiers Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

8. Yaniv Erlich@erlichya10/17/18 Correlation between Y-chr and surnames www.ysearch.org:Y Y Smith Smith Y Smith Erlich Genetic privacy Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

9. Yaniv Erlich@erlichya10/17/18 Surname inference In total: 5 successful surname recoveries Patrilineal line from source to target Person tested by genetic genealogy service (source) Genetic privacy Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

10. Yaniv Erlich@erlichya10/17/18 Long range familial searches Genetic privacy Come to my Plenary Abstract talk on Friday at 6:40pm Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

11. Yaniv Erlich@erlichya10/17/18 Side channel attacks Genetic privacy Sweeney et al., 2013 Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

12. Yaniv Erlich@erlichya10/17/18 Side channel @ Personal Genomes Project Genetic privacy Sweeney et al., 2013 Oops: default filename has the name of the individual! Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

13. Yaniv Erlich@erlichya10/17/18 PGP made it looks like everything is fine (but it is not) Genetic privacy Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

14. Yaniv Erlich@erlichya10/17/18 Can we use DNA phenotyping for identity tracing? We can predict phenotypes from genetic data! Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

15. Yaniv Erlich@erlichya10/17/18 Not so fast… Genetic privacy Height at a single cm resolution Perfect knowledge Theoretical limit(h2)Current knowledge (Lello et al., Genetics, 2018) Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

16. Yaniv Erlich@erlichya10/17/18 Face prediction? Genetic privacy Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

17. Yaniv Erlich@erlichya10/17/18 Not very promising… Genetic privacy Accuracy of prediction(R2) [bits] Current knowledge Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

18. Yaniv Erlich@erlichya10/17/18 Challenges in face prediction Genetic privacy Working hypothesis: identifying individuals based on phenotype inferences is a typically a limited approach Fig. S11 in Venter Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

19. Yaniv Erlich@erlichya10/17/18 Do we really understand privacy? Genetic Privacy AshleyMadison.com JoinAllofUS.org Intro. Genealogical attacks Side-channel attacks Phenotypic attacks Summary

20. Yaniv Erlich@erlichya10/17/18 Melissa Gymrek Amy McGuire David Golan Eran Halperin Arvind Narayanan Tal Shor Shai Carmi Itsik Pe’er Acknowledgements MyHeritage Science team!

The hitchhiker’s guide to genome hacking

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