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Secure searching of biomarkers through hybrid homomorphic encryption scheme.

ABSTRACT: As genome sequencing technology develops rapidly, there has lately been an increasing need to keep genomic data secure even when stored in the cloud and still used for research. We are interested in designing a protocol for the secure outsourcing matching problem on encrypted data.We propose an efficient method to securely search a matching position with the query data and extract some information at the position. After decryption, only a small amount of comparisons with the query information should be performed in plaintext state. We apply this method to find a set of biomarkers in encrypted genomes. The important feature of our method is to encode a genomic database as a single element of polynomial ring.Since our method requires a single homomorphic multiplication of hybrid scheme for query computation, it has the advantage over the previous methods in parameter size, computation complexity, and communication cost. In particular, the extraction procedure not only prevents leakage of database information that has not been queried by user but also reduces the communication cost by half. We evaluate the performance of our method and verify that the computation on large-scale personal data can be securely and practically outsourced to a cloud environment during data analysis. It takes about 3.9 s to search-and-extract the reference and alternate sequences at the queried position in a database of size 4M.Our solution for finding a set of biomarkers in DNA sequences shows the progress of cryptographic techniques in terms of their capability can support real-world genome data analysis in a cloud environment.

SUBMITTER: Kim M

PROVIDER: S-EPMC5547457 | biostudies-other | 2017 Jul

REPOSITORIES: biostudies-other

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Project description:BackgroundProgress in precision psychiatry is predicated on identifying reliable individual-level diagnostic biomarkers. For psychosis, measures of structural and functional connectivity could be promising biomarkers given consistent reports of dysconnectivity across psychotic disorders using magnetic resonance imaging.MethodsWe leveraged data from four independent cohorts of patients with psychosis and control subjects with observations from approximately 800 individuals. We used group-level analyses and two supervised machine learning algorithms (support vector machines and ridge regression) to test within-, between-, and across-sample classification performance of white matter and resting-state connectivity metrics.ResultsAlthough we replicated group-level differences in brain connectivity, individual-level classification was suboptimal. Classification performance within samples was variable across folds (highest area under the curve [AUC] range = 0.30) and across datasets (average support vector machine AUC range = 0.50; average ridge regression AUC range = 0.18). Classification performance between samples was similarly variable or resulted in AUC values of approximately 0.65, indicating a lack of model generalizability. Furthermore, collapsing across samples (resting-state functional magnetic resonance imaging, N = 888; diffusion tensor imaging, N = 860) did not improve model performance (maximal AUC = 0.67). Ridge regression models generally outperformed support vector machine models, although classification performance was still suboptimal in terms of clinical relevance. Adjusting for demographic covariates did not greatly affect results.ConclusionsConnectivity measures were not suitable as diagnostic biomarkers for psychosis as assessed in this study. Our results do not negate that other approaches may be more successful, although it is clear that a systematic approach to individual-level classification with large independent validation samples is necessary to properly vet neuroimaging features as diagnostic biomarkers.

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Secure searching of biomarkers through hybrid homomorphic encryption scheme.

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