title: Privacy-preserving genomic testing in the clinic: a model using HIV treatment.
abstract: 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.
  
  
  
  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.
  
  
  
  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%.
  
  
  
  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.
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Paul J
authors.identifier: 0000-0001-6019-7018
authors.initials: PJ
authors.lastname: McLaren
authors.affiliation: School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Jean Louis
authors.initials: JL
authors.lastname: Raisaro
authors.affiliation: Division of Clinical Pharmacology, University Hospital Center, University of Lausanne, Lausanne, Switzerland.
authors.forename: Manel
authors.initials: M
authors.lastname: Aouri
authors.affiliation: Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland.
authors.forename: Margalida
authors.initials: M
authors.lastname: Rotger
authors.affiliation: School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.|Department of Computer Engineering, Bilkent University, Ankara, Turkey.
authors.forename: Erman
authors.initials: E
authors.lastname: Ayday
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: István
authors.identifier: 0000-0003-3360-1999
authors.initials: I
authors.lastname: Bartha
authors.affiliation: Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland.
authors.forename: Maria B
authors.initials: MB
authors.lastname: Delgado
authors.affiliation: Swiss HIV Cohort Data Center, Lausanne, Switzerland.
authors.forename: Yannick
authors.initials: Y
authors.lastname: Vallet
authors.affiliation: Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.|Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
authors.forename: Huldrych F
authors.initials: HF
authors.lastname: Günthard
authors.affiliation: Division of Infectious Diseases, University Hospital and University of Lausanne, Lausanne, Switzerland.
authors.forename: Matthias
authors.identifier: 0000-0003-0933-7833
authors.initials: M
authors.lastname: Cavassini
authors.affiliation: Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.
authors.forename: Hansjakob
authors.identifier: 0000-0002-1375-3146
authors.initials: H
authors.lastname: Furrer
authors.affiliation: Division of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland.
authors.forename: Thanh
authors.initials: T
authors.lastname: Doco-Lecompte
authors.affiliation: Division of Infectious Diseases, University Hospital Basel, Basel, Switzerland.
authors.forename: Catia
authors.initials: C
authors.lastname: Marzolini
authors.affiliation: Division of Infectious Diseases, Kantonsspital St. Gallen, St. Gallen, Switzerland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Schmid
authors.affiliation: Division of Infectious Diseases, Ospedale Regionale di Lugano, Lugano, Switzerland.
authors.forename: Caroline
authors.initials: C
authors.lastname: Di Benedetto
authors.affiliation: Division of Clinical Pharmacology, University Hospital Center, University of Lausanne, Lausanne, Switzerland.
authors.forename: Laurent A
authors.identifier: 0000-0002-9840-1325
authors.initials: LA
authors.lastname: Decosterd
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.|Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Jacques
authors.identifier: 0000-0002-8240-939X
authors.initials: J
authors.lastname: Fellay
authors.affiliation: School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Hubaux
authors.affiliation: J. Craig Venter Institute, La Jolla, California, USA.
authors.forename: Amalio
authors.initials: A
authors.lastname: Telenti
mesh_terms: D016494:Computer Security; D030661:Genetic Privacy; D014644:Genetic Variation; D023281:Genomics / Q000941:ethics; D015658:HIV Infections / Q000235:genetics*; D006801:Humans; D008962:Models, Theoretical