Semi-Parallel logistic regression for GWAS on encrypted data.

BMC Medical Genomics
Miran KimDaniele Micciancio

Abstract

The sharing of biomedical data is crucial to enable scientific discoveries across institutions and improve health care. For example, genome-wide association studies (GWAS) based on a large number of samples can identify disease-causing genetic variants. The privacy concern, however, has become a major hurdle for data management and utilization. Homomorphic encryption is one of the most powerful cryptographic primitives which can address the privacy and security issues. It supports the computation on encrypted data, so that we can aggregate data and perform an arbitrary computation on an untrusted cloud environment without the leakage of sensitive information. This paper presents a secure outsourcing solution to assess logistic regression models for quantitative traits to test their associations with genotypes. We adapt the semi-parallel training method by Sikorska et al., which builds a logistic regression model for covariates, followed by one-step parallelizable regressions on all individual single nucleotide polymorphisms (SNPs). In addition, we modify our underlying approximate homomorphic encryption scheme for performance improvement. We evaluated the performance of our solution through experiments on real-world dataset. It...Continue Reading

References

Jul 1, 1967·Journal of Chronic Diseases·J TruettW Kannel
Mar 19, 2011·BMC Bioinformatics·Xavier RobinMarkus Müller
Apr 12, 2012·Bioinformatics·Andrey A Shabalin
Jan 7, 2016·BMC Medical Informatics and Decision Making·Miran Kim, Kristin Lauter
Aug 9, 2017·BMC Medical Genomics·Miran KimJung Hee Cheon
Apr 19, 2018·JMIR Medical Informatics·Miran KimXiaoqian Jiang
Oct 13, 2018·BMC Medical Genomics·Andrey KimJung Hee Cheon
Oct 13, 2018·BMC Medical Genomics·Hao ChenKristin Lauter
Dec 24, 2018·BMC Bioinformatics·Charlotte BonteFrederik Vercauteren
Jan 1, 2018·Selected Areas in Cryptography : ... Annual International Workshop, SAC ... Proceedings·Jung Hee CheonYongsoo Song

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Software Mentioned

AllSum
NumIter
RNS
Gemonic
KeySwitch
HEAAN
iDASH ( integrating Data for Analysis , Anonymization , Sharing )
mathbb
ReScale

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