Dataset Information

HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS.

ABSTRACT: Genome-wide association studies (GWAS) have been widely used in discovering the association between genotypes and phenotypes. Human genome data contain valuable but highly sensitive information. Unprotected disclosure of such information might put individual's privacy at risk. It is important to protect human genome data. Exact logistic regression is a bias-reduction method based on a penalized likelihood to discover rare variants that are associated with disease susceptibility. We propose the HEALER framework to facilitate secure rare variants analysis with a small sample size.We target at the algorithm design aiming at reducing the computational and storage costs to learn a homomorphic exact logistic regression model (i.e. evaluate P-values of coefficients), where the circuit depth is proportional to the logarithmic scale of data size. We evaluate the algorithm performance using rare Kawasaki Disease datasets.Download HEALER at http://research.ucsd-dbmi.org/HEALER/ CONTACT: shw070@ucsd.eduSupplementary data are available at Bioinformatics online.

SUBMITTER: Wang S

PROVIDER: S-EPMC4739182 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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Publications

HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS.

Wang Shuang S Zhang Yuchen Y Dai Wenrui W Lauter Kristin K Kim Miran M Tang Yuzhe Y Xiong Hongkai H Jiang Xiaoqian X

Bioinformatics (Oxford, England) 20151006 2

<h4>Motivation</h4>Genome-wide association studies (GWAS) have been widely used in discovering the association between genotypes and phenotypes. Human genome data contain valuable but highly sensitive information. Unprotected disclosure of such information might put individual's privacy at risk. It is important to protect human genome data. Exact logistic regression is a bias-reduction method based on a penalized likelihood to discover rare variants that are associated with disease susceptibilit ...[more]

PMID: 26446135

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Project description:BackgroundThere is limited capacity to assess the comparative risks of medications after they enter the market. For rare adverse events, the pooling of data from multiple sources is necessary to have the power and sufficient population heterogeneity to detect differences in safety and effectiveness in genetic, ethnic and clinically defined subpopulations. However, combining datasets from different data custodians or jurisdictions to perform an analysis on the pooled data creates significant privacy concerns that would need to be addressed. Existing protocols for addressing these concerns can result in reduced analysis accuracy and can allow sensitive information to leak.ObjectiveTo develop a secure distributed multi-party computation protocol for logistic regression that provides strong privacy guarantees.MethodsWe developed a secure distributed logistic regression protocol using a single analysis center with multiple sites providing data. A theoretical security analysis demonstrates that the protocol is robust to plausible collusion attacks and does not allow the parties to gain new information from the data that are exchanged among them. The computational performance and accuracy of the protocol were evaluated on simulated datasets.ResultsThe computational performance scales linearly as the dataset sizes increase. The addition of sites results in an exponential growth in computation time. However, for up to five sites, the time is still short and would not affect practical applications. The model parameters are the same as the results on pooled raw data analyzed in SAS, demonstrating high model accuracy.ConclusionThe proposed protocol and prototype system would allow the development of logistic regression models in a secure manner without requiring the sharing of personal health information. This can alleviate one of the key barriers to the establishment of large-scale post-marketing surveillance programs. We extended the secure protocol to account for correlations among patients within sites through generalized estimating equations, and to accommodate other link functions by extending it to generalized linear models.

Dataset Information

HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS.

Publications

HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS.

Similar Datasets

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