Article (Scientific journals)
DyPS: Dynamic, Private and Secure GWAS
Pascoal, Túlio; Decouchant, Jérémie; Boutet, Antoine et al.
2021In Proceedings on Privacy Enhancing Technologies
Peer Reviewed verified by ORBi


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Keywords :
Federated GWAS; Genomic Privacy; Dynamic workload; Collusion-resistance
Abstract :
[en] Genome-Wide Association Studies (GWAS) identify the genomic variations that are statistically associated with a particular phenotype (e.g., a disease). The confidence in GWAS results increases with the number of genomes analyzed, which encourages federated computations where biocenters would periodically share the genomes they have sequenced. However, for economical and legal reasons, this collaboration will only happen if biocenters cannot learn each others’ data. In addition, GWAS releases should not jeopardize the privacy of the individuals whose genomes are used. We introduce DyPS, a novel framework to conduct dynamic privacy-preserving federated GWAS. DyPS leverages a Trusted Execution Environment to secure dynamic GWAS computations. Moreover, DyPS uses a scaling mechanism to speed up the releases of GWAS results according to the evolving number of genomes used in the study, even if individuals retract their participation consent. Lastly, DyPS also tolerates up to all-but-one colluding biocenters without privacy leaks. We implemented and extensively evaluated DyPS through several scenarios involving more than 6 million simulated genomes and up to 35,000 real genomes. Our evaluation shows that DyPS updates test statistics with a reasonable additional request processing delay (11% longer) compared to an approach that would update them with minimal delay but would lead to 8% of the genomes not being protected. In addition, DyPS can result in the same amount of aggregate statistics as a static release (i.e., at the end of the study), but can produce up to 2.6 times more statistics information during earlier dynamic releases. Besides, we show that DyPS can support a larger number of genomes and SNP positions without any significant performance penalty.
Disciplines :
Engineering, computing & technology: Multidisciplinary, general & others
Computer science
Author, co-author :
Pascoal, Túlio ;  University of Luxembourg > Interdisciplinary Centre for Security, Reliability and Trust (SNT) > CritiX
Decouchant, Jérémie ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Computer Science (DCS)
Boutet, Antoine;  University of Lyon > INSA, INRIA
Esteves-Verissimo, Paulo ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Computer Science (DCS)
External co-authors :
Language :
Title :
DyPS: Dynamic, Private and Secure GWAS
Publication date :
Journal title :
Proceedings on Privacy Enhancing Technologies
Publisher :
Peer reviewed :
Peer Reviewed verified by ORBi
Focus Area :
Security, Reliability and Trust
Systems Biomedicine
FnR Project :
FNR8149128 - Strategic Rtnd Program On Information Infrastructure Security And Dependability, 2014 (01/01/2015-31/12/2021) - Marcus Völp
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