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

Publication

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

Journal Paper/Review - Jan 14, 2016

McLaren Paul J, Hubaux Jean-Pierre, Fellay Jacques, Decosterd Laurent A, Di Benedetto Caroline, Schmid Patrick, Marzolini Catia, Doco-Lecompte Thanh, Furrer Hansjakob, Cavassini Matthias, Günthard Huldrych F, Vallet Yannick, Delgado Maria B, Bartha István, Ayday Erman, Rotger Margalida, Aouri Manel, Raisaro Jean Louis, Telenti Amalio

Citation

McLaren P, Hubaux J, Fellay J, Decosterd L, Di Benedetto C, Schmid P, Marzolini C, Doco-Lecompte T, Furrer H, Cavassini M, Günthard H, Vallet Y, Delgado M, Bartha I, Ayday E, Rotger M, Aouri M, Raisaro J, Telenti A. Privacy-preserving genomic testing in the clinic: a model using HIV treatment. Genet Med 2016; 18:814-22.

Type

Journal Paper/Review (English)

Journal

Genet Med 2016; 18

Publication Date

Jan 14, 2016

Issn Electronic

1530-0366

Pages

814-22

Brief description/objective

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 18 8, 814-822.