Dataset Information

Privacy-preserving genotype imputation with fully homomorphic encryption.

ABSTRACT: Genotype imputation is the inference of unknown genotypes using known population structure observed in large genomic datasets; it can further our understanding of phenotype-genotype relationships and is useful for QTL mapping and GWASs. However, the compute-intensive nature of genotype imputation can overwhelm local servers for computation and storage. Hence, many researchers are moving toward using cloud services, raising privacy concerns. We address these concerns by developing an efficient, privacy-preserving algorithm called p-Impute. Our method uses homomorphic encryption, allowing calculations on ciphertext, thereby avoiding the decryption of private genotypes in the cloud. It is similar to k-nearest neighbor approaches, inferring missing genotypes in a genomic block based on the SNP genotypes of genetically related individuals in the same block. Our results demonstrate accuracy in agreement with the state-of-the-art plaintext solutions. Moreover, p-Impute is scalable to real-world applications as its memory and time requirements increase linearly with the increasing number of samples. p-Impute is freely available for download here: https://doi.org/10.5281/zenodo.5542001.

SUBMITTER: Gursoy G

PROVIDER: S-EPMC8857019 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Privacy-preserving genotype imputation with fully homomorphic encryption.

Gürsoy Gamze G Chielle Eduardo E Brannon Charlotte M CM Maniatakos Michail M Gerstein Mark M

Cell systems 20211109 2

Genotype imputation is the inference of unknown genotypes using known population structure observed in large genomic datasets; it can further our understanding of phenotype-genotype relationships and is useful for QTL mapping and GWASs. However, the compute-intensive nature of genotype imputation can overwhelm local servers for computation and storage. Hence, many researchers are moving toward using cloud services, raising privacy concerns. We address these concerns by developing an efficient, p ...[more]

PMID: 34758288

Similar Datasets

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

Privacy-preserving genotype imputation with fully homomorphic encryption.

Publications

Privacy-preserving genotype imputation with fully homomorphic encryption.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets