Protecting data
for personalized health

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P4 (Predictive, Preventive, Personalized and Participatory) medicine is called to revolutionize healthcare by providing better diagnoses and targeted preventive and therapeutic measures. However, to accelerate its adoption and maximize its potential, clinical and research data on large numbers of individuals must be efficiently shared between all stakeholders. The privacy risks stemming from disclosing medical data raise serious concerns, and have become a barrier that can hold back the advances in P4 medicine if effective privacy-preserving technologies are not adopted to enable privacy-conscious medical data sharing. The evolution of the regulation towards further guarantees (e.g., HIPAA in USA and the new GDPR in EU) reflects this urgent need.

The combination of data sharing with recent advances in the field of *omics and, in particular, in high-throughput sequencing technology, leads to an explosive growth in the amounts of available data; this big data scale can usually not be handled with current hospital computing facilities, hence the need for elastic computing resources that can cope with huge amounts of data in a secure and privacy-aware infrastructure, supporting data processing and sharing.

At EPFL, we are working on different aspects of health data privacy and security with strong collaboration with medical doctors, bioinformaticians, geneticists, and other specialists. We focus, in particular, in the following main research directions:

• Data protection: we make use of decentralized cryptographic protocols to prevent data leakage during computation
  
• Privacy: we quantify the risk of inference attacks and propose techniques to minimize it.

EPFL/LDS Researchers

Prof. Jean-Pierre Hubaux
Dr. Juan Ramon Troncoso-Pastoriza
David Froelicher
Mickaël Misbach
Christian Mouchet
Joao Sa

Academic Partners

Prof. Erman Ayday, Case Western University
Prof. Jacques Fellay, EPFL and CHUV
Prof. Bryan Ford, EPFL
Dr. Mathias Humbert, Swiss Data Science Center
Prof. Ari Juels, Cornell Tech
Prof. Bradley Malin, Vanderbilt University
Prof. Shawn Murphy , Harvard University / Partners Healthcare
Dr. Jean Louis Raisaro, EPFL and CHUV
Prof. Amalio Telenti, Scripps Institute.
Prof. XiaoFeng Wang, Indiana University at Bloomington

Contact

Prof. Jean-Pierre Hubaux

Related Website

https://genomeprivacy.org

Journal/Magazine Articles

• Jean Louis Raisaro, Juan Ramon Troncoso-Pastoriza, Mickael Misbach, Joao Sa Sousa, Sylvain Pradervand, Edoardo Missiaglia, Olivier Michielin, Bryan Ford and Jean-Pierre Hubaux.  MedCo: Enabling Secure and Privacy-Preserving Exploration of Distributed Clinical and Genomic Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 16, no. 4, pp. 1328-1341, 1 July-August 2019.
• Jean Louis Raisaro, Gwangbae Choi, Sylvain Pradervand, Raphael Colsenet, Nathalie Jacquemont, Nicolas Rosat, Vincent Mooser and Jean-Pierre Hubaux.  Protecting Privacy and Security of Genomic Data in i2b2 With Homomorphic Encryption and Differential Privacy. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2018.
• Zhicong Huang, Huang Lin, Jacques Fellay, Zoltan Kutalik and Jean-Pierre Hubaux. SQC: Secure Quality Control for Meta-Analysis of Genome-Wide Association Studies. Bioinformatics, 33(15):2273-2280, 2017.
  
• Joao Sa Sousa, Cédric Lefebvre, Zhicong Huang, Jean Louis Raisaro, Carlos Aguilar, Marc-Olivier Killijian and Jean-Pierre Hubaux. Efficient and Secure Outsourcing of Genomic Data Storage. To appear in BMC Medical Genomics.
• Jean Louis Raisaro, Florian Tramèr, Zhanglong Ji, Diyue Bu, Yongan Zhao, Knox Carey, David Lloyd, Heidi Sofia, Dixie Baker, Paul Flicek, Suyash Shringarpure, Carlos Bustamante, Shuang Wang, Xiaoqian Jiang, Lucila Ohno-Machado, Haixu Tang, XiaoFeng Wang and Jean-Pierre Hubaux. Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks. Journal of the American Medical Informatics Association, Feb. 2017.
• Zhicong Huang, Erman Ayday, Huang Lin, Raeka S. Aiyar, Adam Molyneaux, Zhenyu Xu, Jacques Fellay, Lars M. Steinmetz, and Jean-Pierre Hubaux. A Privacy-Preserving Solution for Compressed Storage and Selective Retrieval of Genomic Data. Genome Research, Dec. 2016, 26(12), pp.1687-1696.
• Paul J. McLaren, Jean Louis Raisaro, Manel Aouri, Margalida Rotger, Erman Ayday, Istvan Bartha, Maria B. Delgado, Yannick Vallet, Huldrych Gunthard, Mathias Cavassini, Hansjakob Furrer, Than Lecompte, Catia Marzolini, Patrick Schmid, Caroline Di Benedetto, Laurent A. Decosterd, Jacques Fellay, Jean-Pierre Hubaux, and Amalio Telenti, the Swiss HIV Cohort Study . Privacy-Preserving Genomic Testing In The Clinic: A Model Using HIV Treatment. Genetics in Medicine. Jan. 2016. Nature Publishing Group.
• Erman Ayday, Emiliano De Cristofaro, Jean-Pierre Hubaux, and Gene Tsudik. Whole Genome Sequencing: Revolutionary Medicine or Privacy Nightmare? Computer, vol.48, no. 2, pp. 58-66, Feb. 2015.
• Muhammad Naveed, Erman Ayday, Ellen W. Clayton, Jacques Fellay, Carl A. Gunter, Jean-Pierre Hubaux, Bradley A. Malin, and XiaoFeng Wang. Privacy in the Genomic Era. ACM Computing Surveys, vol. 48, num. 1, 2015.
• Amalio Telenti, Erman Ayday, and Jean-Pierre Hubaux. On Genomics, Kin, and Privacy. F1000Research 3:80 (doi: 10.12688/f1000research.4089), 2014.
• Jean Louis Raisaro, Erman Ayday, and Jean-Pierre Hubaux. Patient Privacy in the Genomic Era. Praxis, 7 May 2014.

Conference/Workshop Papers

• Juan Ramon Troncoso-Pastoriza, Jean Louis Raisaro, Linus Gasser, Bryan Ford and Jean-Pierre Hubaux.  MedChain: Accountable and Auditable Data Sharing in Distributed Medical Scenarios. 4th International Workshop of Genome Privacy and Security co-located with GA4GH (GenoPri’18). Basel, Oct. 2018.
• Jean Louis Raisaro, Juan Ramon Troncoso-Pastoriza, Mickael Misbach, Joao Sa Sousa, Sylvain Pradervand, Edoardo Missiaglia, Olivier Michielin, Bryan Ford and Jean-Pierre Hubaux. MedCo: Enabling Privacy-Conscious Exploration of Distributed Clinical and Genomic Data. 4th International Workshop of Genome Privacy and Security co-located with GA4GH (GenoPri’17). Orlando, Oct. 2017.
• Gwangbae Choi, Jean Louis Raisaro, Sylvain Pradervand, Raphael Colsonet, Nathalie Jacquemont, Nicolas Rosat, and Jean-Pierre Hubaux. Privacy-Preserving Exploration of Genetic Cohorts with i2b2 At Lausanne University Hospital. 3rd International Workshop of Genome Privacy and Security co-located with AMIA (GenoPri’16). Chicago, Nov. 2016.
• Florian Tramèr, Zhicong Huang, Jean-Pierre Hubaux, and Erman Ayday. Differential Privacy with Bounded Priors: Reconciling Utility and Privacy in Genome-Wide Association Studies.  ACM Conference on Computer and Communications Security (CCS 2015), Denver, Colorado, USA, October 2015.
• Mathias Humbert, Kévin Huguenin, Joachim Hugonot, Erman Ayday, and Jean-Pierre Hubaux. De-anonymizing Genomic Databases with Phenotypic Traits.  Proceedings on Privacy Enhancing Technologies (PETS 2015), Philadelphia, PA, USA, June 2015.
• Zhicong Huang, Erman Ayday, Jacques Fellay, Jean-Pierre Hubaux, and Ari Juels. GenoGuard: Protecting Genomic Data against Brute-Force Attacks.  36th IEEE Symposium on Security and Privacy (S&P 2015), San Jose, CA, USA, May 2015.
• Sahel Shariati Samani, Zhicong Huang, Erman Ayday, Mark Elliot, Jacques Fellay, Jean-Pierre Hubaux, Zoltán Kutalik. Quantifying Genomic Privacy via Inference Attack with High-Order SNV Correlations.  2nd International Workshop on Genome Privacy and Security (in conjunction with IEEE S&P 2015), San Jose, CA, USA, May 2015.
• Ludovic Barman, Mohammed Taha Elgraini, Jean Louis Raisaro, Erman Ayday, Jean-Pierre Hubaux. Privacy Threats and Practical Solutions for Genetic Risk Tests.  2nd International Workshop on Genome Privacy and Security (in conjunction with IEEE S&P 2015), San Jose, CA, USA, May 2015.
• Mathias Humbert, Erman Ayday, Jean-Pierre Hubaux, and Amalio Telenti. On Non-cooperative Genomic Privacy.  19th International Conference on Financial Cryptography and Data Security (FC), 2015.
• Muhammad Naveed, Shashank Agrawal, Manoj Prabhakaran, Xiaofeng Wang, Erman Ayday, Jean-Pierre Hubaux, and Carl A. Gunter. Controlled Functional Encryption.  21st ACM Conference on Computer and Communications Security (CCS 2014), Scottsdale, AZ, USA Nov. 2014.
• Mathias Humbert, Erman Ayday, Jean-Pierre Hubaux, and Amalio Telenti. Reconciling Utility with Privacy in Genomics.  ACM Workshop on Privacy in the Electronic Society (WPES 2014), Scottsdale, AZ, USA Nov. 2014.
• Jean Louis Raisaro, Erman Ayday, Jean-Pierre Hubaux, Paul J. McLaren, Jean-Pierre Hubaux, and Amalio Telenti. Privacy-Preserving HIV Pharmacogenetics: A Real Use Case of Genomic Data Protection.  Workshop on Genome Privacy (in conjunction with PETS 2014), Amsterdam, Netherlands, Jul. 2014.
• Erman Ayday, Jean Louis Raisaro, and Jean-Pierre Hubaux. Personal Use of the Genomic Data: Privacy vs. Storage Cost.  IEEE Global Communications Conference, Exhibition and Industry Forum – GLOBECOM, Atlanta, GA, USA, Dec. 2013.
• Erman Ayday, Jean Louis Raisaro, Jacques Rougemont, and Jean-Pierre Hubaux. Protecting and Evaluating Genomic Privacy in Medical Tests and Personalized Medicine. ACM Workshop on Privacy in the Electronic Society (WPES 2013), Berlin, Germany, Nov. 2013.
• Mathias Humbert, Erman Ayday, Jean-Pierre Hubaux, and Amalio Telenti. Addressing the Concerns of the Lacks Family: Quantification of Kin Genomic Privacy. 20th ACM Conference on Computer and Communications Security (CCS 2013), Berlin, Germany, Nov. 2013.
• Erman Ayday, Jean Louis Raisaro, Urs Hengartner, Adam Molyneaux, and Jean-Pierre Hubaux. Privacy-Preserving Processing of Raw Genomic Data. 8th Data Privacy Management (DPM 2013) International Workshop (in conjunction with ESORICS 2013), Egham, UK, Sep. 2013.
• Erman Ayday, Jean Louis Raisaro, Paul J. McLaren, Jacques Fellay, and Jean-Pierre Hubaux. Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data. USENIX Security Workshop on Health Information Technologies (HealthTech ’13), Aug. 2013.
• Erman Ayday, Jean Louis Raisaro and Jean-Pierre Hubaux. Privacy-Enhancing Technologies for Medical Tests Using Genomic Data (short talk). 20th Annual Network & Distributed System Security Symposium – NDSS 2013, San Diego, CA, USA, Feb., 2013.

Posters

• Jacques Fellay, Jean Louis Raisaro, Zhicong Huang, Mathias Humbert, Erman Ayday, Paul J McLaren, Jean-Pierre Hubaux, and Amalio Telenti. Practical Solutions for Protecting Individual Genomic Privacy. American Society of Human Genetics (ASHG), San Diego, CA, USA, October 2014.
• Erman Ayday, Jean Louis Raisaro, Mathias Humbert, and Jean-Pierre Hubaux. Towards Quantifying and Preventing the Leakage of Genomic Data Using Privacy-Enhancing Technologies. 22nd USENIX Security Symposium, Washington, DC, USA, Aug. 2013.
• Erman Ayday, Emiliano De Cristofaro, Jean-Pierre Hubaux, and Gene Tsudik. Whole Genome Sequencing: Innovation Dream or Privacy Nightmare? 22nd USENIX Security Symposium, Washington, DC, USA, Aug. 2013.
• Erman Ayday, Jean Louis Raisaro, Urs Hengartner, Adam Molyneaux, and Jean-Pierre Hubaux. Towards Privacy Compliance in the Management of Raw Genomic Data. USENIX Security Workshop on Health Information Technologies (HealthTech ’13), Washington, DC, USA, Aug. 2013.
• Erman Ayday, Jean Louis Raisaro, Paul J. McLaren, Jacques Fellay, and Jean-Pierre Hubaux. Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data (poster version). USENIX Security Workshop on Health Information Technologies (HealthTech ’13), Aug. 2013.

Technical Reports

• Zhicong Huang, Erman Ayday, Jacques Fellay, Jean-Pierre Hubaux, and Ari Juels. GenoGuard: Protecting Genomic Data Against Brute-Force Attacks.  EPFL-REPORT-205068, March. 2015.
• Mathias Humbert, Erman Ayday, Jean-Pierre Hubaux, and Amalio Telenti. Reconciling Utility with Privacy in Genomics.  EPFL-REPORT-201547, Sep. 2014.
• Erman Ayday, Jean Louis Raisaro, Urs Hengartner, Adam Molyneaux, and Jean-Pierre Hubaux. Privacy-Preserving Processing of Raw Genomic Data. EPFL-REPORT-187573, Jul. 2013.
• Erman Ayday, Emiliano De Cristofaro, Jean-Pierre Hubaux, and Gene Tsudik. The Chills and Thrills of Whole Genome Sequencing. EPFL-REPORT-186866, Jun. 2013.
• Erman Ayday, Jean Louis Raisaro and Jean-Pierre Hubaux. Privacy-Enhancing Technologies for Medical Tests Using Genomic Data. EPFL-REPORT-182897, Sep. 2012.

Patents

• Jean-Pierre Hubaux, Erman Ayday, Jean Louis Raisaro, Urs Hengartner, Adam Molyneaux, Zhenyu Xu, Jurgi Camblong, and Pierre Hutter Privacy-Preserving Processing of Raw Genomic Data Provisional patent application has been filed, No. 13172607.7, June 2013.
• Erman Ayday, Mathias Humbert, Jacques Fellay, Paul J. McLaren, Jacques Rougemont, Jean Louis Raisaro, Amalio Telenti and Jean-Pierre Hubaux Genomic Privacy Protection Provisional patent application has been filed, No 12184372.6 and 61/700,897, September 2012.

Press Coverage

• Le Temps, “L’EPFL lance un logiciel pour exploiter de manière sûre les données médicales”, 11 March 2019
• Le Temps, “Génome chiffré, génome protégé”, 24 April 2017
• National Television (RTS), “36.9: Votre santé numérique: un trafic lucratif!”, 11 May 2016
• L’Hebdo, (weekly French-language news magazine), 9 May 2016
• Le Tribune de Genève, (cantonal French-language newspaper), “tdg.ch : Médecine génomique: La médecine du Big Data n’est pas sans danger”, 9 May 2016
• Magazine Heise online, 3 June 2015 (text in German, interview in English)
• National News, Radio Télévision Suisse, April 2015 (in French)
• Nature News, 23 March 2015
• Nature Medicine, 05 June 2014
• Le Temps, 28 September 2013 (in French)