Privacy-preserving genomic testing in the clinic: a model using HIV treatment.

McLaren PJ1,2, Raisaro JL3, Aouri M4, Rotger M5, Ayday E3,6, Bartha I1,2, Delgado MB5, Vallet Y7, F Günthard H8,9, Cavassini M10, Furrer H11, Doco-Lecompte T12, Marzolini C13, Schmid P14, Di Benedetto C15, Decosterd LA4, Fellay J1,2, Hubaux JP3, Telenti A16.

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Abstract

PURPOSE:

The implementation of genomic-based medicine is hindered by unresolved questions regarding data privacy and delivery of interpreted results to health-care practitioners. We used DNA-based prediction of HIV-related outcomes as a model to explore critical issues in clinical genomics.

METHODS:

We genotyped 4,149 markers in HIV-positive individuals. Variants allowed for prediction of 17 traits relevant to HIV medical care, inference of patient ancestry, and imputation of human leukocyte antigen (HLA) types. Genetic data were processed under a privacy-preserving framework using homomorphic encryption, and clinical reports describing potentially actionable results were delivered to health-care providers.

RESULTS:

A total of 230 patients were included in the study. We demonstrated the feasibility of encrypting a large number of genetic markers, inferring patient ancestry, computing monogenic and polygenic trait risks, and reporting results under privacy-preserving conditions. The average execution time of a multimarker test on encrypted data was 865 ms on a standard computer. The proportion of tests returning potentially actionable genetic results ranged from 0 to 54%.

CONCLUSIONS:

The model of implementation presented herein informs on strategies to deliver genomic test results for clinical care. Data encryption to ensure privacy helps to build patient trust, a key requirement on the road to genomic-based medicine.Genet Med advance online publication 14 January 2016Genetics in Medicine (2016); doi:10.1038/gim.2015.167.