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

Genetics in Medicine : Official Journal of the American College of Medical Genetics
Paul J McLarenAmalio Telenti

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 genomi...Continue Reading

References

Apr 12, 2002·Lancet·Seth HetheringtonAllen D Roses
Sep 20, 2005·The Journal of Infectious Diseases·Margalida RotgerUNKNOWN Swiss HIV Cohort Study
Jun 8, 2006·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·A RauchSimon Mallal
Apr 27, 2007·Clinical Biochemistry·Linnea M BaudhuinDennis J O'Kane
Jun 15, 2007·Pharmacogenomics·Rubin LubomirovAmalio Telenti
Jul 21, 2007·Science·Jacques FellayDavid B Goldstein
Aug 8, 2008·The Journal of Infectious Diseases·Sara ColomboUNKNOWN Swiss HIV Cohort Study
Feb 20, 2009·Clinical Pharmacology and Therapeutics·M Arab-AlameddineUNKNOWN Swiss HIV Cohort Study
Feb 25, 2009·Pharmacogenetics and Genomics·Julia di IulioUNKNOWN Swiss HIV Cohort Study
Apr 1, 2009·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·A FayetL A Decosterd
Sep 18, 2009·Nature·David L ThomasMary Carrington
Dec 2, 2009·International Journal of Epidemiology·UNKNOWN Swiss HIV Cohort StudyPatrick Francioli
Sep 3, 2010·Nature·UNKNOWN International HapMap 3 ConsortiumJean E McEwen
Oct 1, 2010·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Margalida RotgerUNKNOWN Swiss HIV Cohort Study
Nov 6, 2010·Science·UNKNOWN International HIV Controllers StudyMeng Zhao
Feb 4, 2011·The Journal of Infectious Diseases·Rubin LubomirovUNKNOWN Swiss HIV Cohort Study
Mar 2, 2011·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Julia di IulioUNKNOWN Swiss HIV Cohort Study
Nov 1, 2012·Pharmacogenetics and Genomics·Rubin LubomirovUNKNOWN Swiss HIV Cohort Study
Mar 28, 2013·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Margalida RotgerUNKNOWN Swiss HIV Cohort Study
Jun 14, 2013·PloS One·Xiaoming JiaPaul I W de Bakker
Jun 19, 2014·Expert Opinion on Drug Metabolism & Toxicology·Pablo BarreiroVincent Soriano
Jul 20, 2014·JAMA : the Journal of the American Medical Association·Huldrych F GünthardPaul A Volberding
Aug 22, 2014·Pharmacogenomics·Clint MizziGeorge P Patrinos
Sep 26, 2014·F1000Research·Amalio TelentiJean Pierre Hubaux
May 20, 2015·Nature Immunology·Paul J McLaren, Mary Carrington

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Citations

Sep 7, 2017·Proceedings of the National Academy of Sciences of the United States of America·Christoph LippertJ Craig Venter
Jul 14, 2018·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jean Louis RaisaroJean-Pierre Hubaux
Feb 26, 2016·Nature Methods·David W Craig
Jan 17, 2020·Journal of the American Medical Informatics Association : JAMIA·Tsung-Ting KuoRodney A Gabriel
Feb 14, 2019·Briefings in Bioinformatics·Abukari Mohammed Yakubu, Yi-Ping Phoebe Chen
May 16, 2020·Human Genetics·Shanelle N GingrasPaul J McLaren
Aug 9, 2017·BMC Medical Genomics·Feng ChenShuang Wang
Dec 22, 2017·NPJ Genomic Medicine·Shuang WangLucila Ohno-Machado
Sep 16, 2020·Nature Genetics·Amalio Telenti, Xiaoqian Jiang
Mar 7, 2020·Nature Methods·Can KockanS Cenk Sahinalp
Aug 9, 2017·BMC Medical Genomics·João Sá SousaJean-Pierre Hubaux
Dec 29, 2020·Computers in Biology and Medicine·João Rafael AlmeidaJosé Luís Oliveira
May 23, 2021·Briefings in Bioinformatics·Dandan LuHongmin Cai
Mar 13, 2020··Zekeriya ErkinMarcel Reinders

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Methods Mentioned

BETA
genotyping

Software Mentioned

Windows 7
SNP2HLA
R Survival package

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