Dataset Information

SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases.

ABSTRACT: Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function. Advances in synthetic biology and the decreased cost of sequencing are increasing the amount of privately held genomic data. As the quantity and value of private genomic data grows, so does the incentive to acquire and protect such data, which creates a need to store and process these data securely. We present an algorithm for the Secure Interrogation of Genomic DataBases (SIG-DB). The SIG-DB algorithm enables databases of genomic sequences to be searched with an encrypted query sequence without revealing the query sequence to the Database Owner or any of the database sequences to the Querier. SIG-DB is the first application of its kind to take advantage of locality-sensitive hashing and homomorphic encryption to allow generalized sequence-to-sequence comparisons of genomic data.

SUBMITTER: Titus AJ

PROVIDER: S-EPMC6138421 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Publications

SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases.

Titus Alexander J AJ Flower Audrey A Hagerty Patrick P Gamble Paul P Lewis Charlie C Stavish Todd T O'Connell Kevin P KP Shipley Greg G Rogers Stephanie M SM

PLoS computational biology 20180904 9

Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function. Advances in synthetic biology and the decreased cost of sequencing are increasing the amount of privately held genomic data. As the quantity and value of private genomic data grows, so does the incentive to acquire and protect such data, which creates a need to store and process these data securely. W ...[more]

PMID: 30180163

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Project description:BackgroundData sharing in multicenter medical research can improve the generalizability of research, accelerate progress, enhance collaborations among institutions, and lead to new discoveries from data pooled from multiple sources. Despite these benefits, many medical institutions are unwilling to share their data, as sharing may cause sensitive information to be leaked to researchers, other institutions, and unauthorized users. Great progress has been made in the development of secure machine learning frameworks based on homomorphic encryption in recent years; however, nearly all such frameworks use a single secret key and lack a description of how to securely evaluate the trained model, which makes them impractical for multicenter medical applications.ObjectiveThe aim of this study is to provide a privacy-preserving machine learning protocol for multiple data providers and researchers (eg, logistic regression). This protocol allows researchers to train models and then evaluate them on medical data from multiple sources while providing privacy protection for both the sensitive data and the learned model.MethodsWe adapted a novel threshold homomorphic encryption scheme to guarantee privacy requirements. We devised new relinearization key generation techniques for greater scalability and multiplicative depth and new model training strategies for simultaneously training multiple models through x-fold cross-validation.ResultsUsing a client-server architecture, we evaluated the performance of our protocol. The experimental results demonstrated that, with 10-fold cross-validation, our privacy-preserving logistic regression model training and evaluation over 10 attributes in a data set of 49,152 samples took approximately 7 minutes and 20 minutes, respectively.ConclusionsWe present the first privacy-preserving multiparty logistic regression model training and evaluation protocol based on threshold homomorphic encryption. Our protocol is practical for real-world use and may promote multicenter medical research to some extent.

Dataset Information

SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases.

Publications

SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases.

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