1. bookVolume 2019 (2019): Issue 1 (January 2019)
Journal Details
License
Format
Journal
eISSN
2299-0984
First Published
16 Apr 2015
Publication timeframe
4 times per year
Languages
English
access type Open Access

My Genome Belongs to Me: Controlling Third Party Computation on Genomic Data

Published Online: 24 Dec 2018
Volume & Issue: Volume 2019 (2019) - Issue 1 (January 2019)
Page range: 108 - 132
Received: 31 May 2018
Accepted: 16 Sep 2018
Journal Details
License
Format
Journal
eISSN
2299-0984
First Published
16 Apr 2015
Publication timeframe
4 times per year
Languages
English
Abstract

An individual’s genetic information is possibly the most valuable personal information. While knowledge of a person’s DNA sequence can facilitate the diagnosis of several heritable diseases and allow personalized treatment, its exposure comes with significant threats to the patient’s privacy. Currently known solutions for privacy-respecting computation require the owner of the DNA to either be heavily involved in the execution of a cryptographic protocol or to completely outsource the access control to a third party. This motivates the demand for cryptographic protocols which enable computation over encrypted genomic data while keeping the owner of the genome in full control. We envision a scenario where data owners can exercise arbitrary and dynamic access policies, depending on the intended use of the analysis results and on the credentials of who is conducting the analysis. At the same time, data owners are not required to maintain a local copy of their entire genetic data and do not need to exhaust their computational resources in an expensive cryptographic protocol.

In this work, we present METIS, a system that assists the computation over encrypted data stored in the cloud while leaving the decision on admissible computations to the data owner. It is based on garbled circuits and supports any polynomially-computable function. A critical feature of our system is that the data owner is free from computational overload and her communication complexity is independent of the size of the input data and only linear in the size of the circuit’s output. We demonstrate the practicality of our approach with an implementation and an evaluation of several functions over real datasets.

Keywords

[1] Breast cancer risk factors - genetics. http://www.breastcancer.org/risk/factors/genetics.Search in Google Scholar

[2] Python cryptography toolkit (pycrypto). https://pypi.python.org/pypi/pycrypto. Accessed: 2017-05-18.Search in Google Scholar

[3] Research – 23andme. https://www.23andme.com/enint/research/. [Online; accessed 28-May-2018].Search in Google Scholar

[4] Researchkit. http://researchkit.org/. [Online; accessed 28-May-2018].Search in Google Scholar

[5] Initial sequencing and analysis of the human genome. Nature, 409(6822):860–921, 02 2001.10.1038/3505703911237007Search in Google Scholar

[6] Gail-Joon Ahn, Moti Yung, and Ninghui Li, editors. ACM CCS 14, Scottsdale, AZ, USA, November 3–7, 2014. ACM Press.Search in Google Scholar

[7] Gilad Asharov, Yehuda Lindell, Thomas Schneider, and Michael Zohner. More efficient oblivious transfer and extensions for faster secure computation. In Ahmad-Reza Sadeghi, Virgil D. Gligor, and Moti Yung, editors, ACM CCS 13, pages 535–548, Berlin, Germany, November 4–8, 2013. ACM Press.10.1145/2508859.2516738Search in Google Scholar

[8] Erman Ayday, Emiliano De Cristofaro, Jean-Pierre Hubaux, and Gene Tsudik. Whole genome sequencing: Revolutionary medicine or privacy nightmare? Computer, 48(2):58–66, 2015.10.1109/MC.2015.59Search in Google Scholar

[9] Erman Ayday, Jean Louis Raisaro, and Jean-Pierre Hubaux. Privacy-enhancing technologies for medical tests using genomic data. Technical report, 2012.Search in Google Scholar

[10] 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. In HealthTech, 2013.Search in Google Scholar

[11] Pierre Baldi, Roberta Baronio, Emiliano De Cristofaro, Paolo Gasti, and Gene Tsudik. Countering gattaca: efficient and secure testing of fully-sequenced human genomes. In Proceedings of the 18th ACM conference on Computer and communications security, pages 691–702. ACM, 2011.10.1145/2046707.2046785Search in Google Scholar

[12] Donald Beaver, Silvio Micali, and Phillip Rogaway. The round complexity of secure protocols. In Proceedings of the twenty-second annual ACM symposium on Theory of computing, pages 503–513. ACM, 1990.10.1145/100216.100287Search in Google Scholar

[13] Mihir Bellare, Viet Tung Hoang, and Phillip Rogaway. Adaptively secure garbling with applications to one-time programs and secure outsourcing. Cryptology ePrint Archive, Report 2012/564, 2012. http://eprint.iacr.org/2012/564.10.1007/978-3-642-34961-4_10Search in Google Scholar

[14] Mihir Bellare, Viet Tung Hoang, and Phillip Rogaway. Foundations of garbled circuits. Cryptology ePrint Archive, Report 2012/265, 2012. http://eprint.iacr.org/2012/265.10.1145/2382196.2382279Search in Google Scholar

[15] Mihir Bellare, Viet Tung Hoang, and Phillip Rogaway. Foundations of garbled circuits. In Yu et al. [69], pages 784–796.Search in Google Scholar

[16] Mihir Bellare and Phillip Rogaway. Random oracles are practical: A paradigm for designing efficient protocols. In V. Ashby, editor, ACM CCS 93, pages 62–73, Fairfax, Virginia, USA, November 3–5, 1993. ACM Press.10.1145/168588.168596Search in Google Scholar

[17] Ran Canetti and Juan A. Garay, editors. CRYPTO 2013, Part II, volume 8043 of LNCS, Santa Barbara, CA, USA, August 18–22, 2013. Springer, Heidelberg, Germany.Search in Google Scholar

[18] Ran Canetti, Oded Goldreich, and Shai Halevi. The random oracle methodology, revisited (preliminary version). In 30th ACM STOC, pages 209–218, Dallas, TX, USA, May 23–26, 1998. ACM Press.10.1145/276698.276741Search in Google Scholar

[19] Henry Carter, Charles Lever, and Patrick Traynor. Whitewash: Outsourcing garbled circuit generation for mobile devices. In Proceedings of the 30th Annual Computer Security Applications Conference, pages 266–275. ACM, 2014.10.1145/2664243.2664255Search in Google Scholar

[20] Henry Carter, Benjamin Mood, Patrick Traynor, and Kevin Butler. Secure outsourced garbled circuit evaluation for mobile devices. In Presented as part of the 22nd USENIX Security Symposium (USENIX Security 13), pages 289–304, Washington, D.C., 2013. USENIX.Search in Google Scholar

[21] J.Lawrence Carter and Mark N. Wegman. Universal classes of hash functions. Journal of Computer and System Sciences, 18(2):143 – 154, 1979.10.1016/0022-0000(79)90044-8Search in Google Scholar

[22] Seung Geol Choi, Jonathan Katz, Ranjit Kumaresan, and Hong-Sheng Zhou. On the security of the Free-XOR technique. Cryptology ePrint Archive, Report 2011/510, 2011. http://eprint.iacr.org/2011/510.Search in Google Scholar

[23] Peter JA Cock, Christopher J Fields, Naohisa Goto, Michael L Heuer, and Peter M Rice. The sanger fastq file format for sequences with quality scores, and the solexa/illumina fastq variants. Nucleic acids research, 38(6):1767–1771, 2010.10.1093/nar/gkp1137284721720015970Search in Google Scholar

[24] Francis S Collins, Lisa D Brooks, and Aravinda Chakravarti. A dna polymorphism discovery resource for research on human genetic variation. Genome research, 8(12):1229–1231, 1998.10.1101/gr.8.12.12299872978Search in Google Scholar

[25] Ronald Cramer and Victor Shoup. Universal hash proofs and a paradigm for adaptive chosen ciphertext secure public-key encryption. In Lars R. Knudsen, editor, EUROCRYPT 2002, volume 2332 of LNCS, pages 45–64, Amsterdam, The Netherlands, April 28 – May 2, 2002. Springer, Heidelberg, Germany.10.1007/3-540-46035-7_4Search in Google Scholar

[26] Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A Albers, Eric Banks, Mark A DePristo, Robert E Handsaker, Gerton Lunter, Gabor T Marth, Stephen T Sherry, et al. The variant call format and vcftools. Bioinformatics, 27(15):2156–2158, 2011.10.1093/bioinformatics/btr330313721821653522Search in Google Scholar

[27] Cynthia Dwork. Differential privacy: A survey of results. In International Conference on Theory and Applications of Models of Computation, pages 1–19. Springer, 2008.10.1007/978-3-540-79228-4_1Search in Google Scholar

[28] Keith B Frikken. Practical private dna string searching and matching through efficient oblivious automata evaluation. In IFIP Annual Conference on Data and Applications Security and Privacy, pages 81–94. Springer, 2009.10.1007/978-3-642-03007-9_6Search in Google Scholar

[29] Craig Gentry, Shai Halevi, and Vinod Vaikuntanathan. i-Hop homomorphic encryption and rerandomizable Yao circuits. In Tal Rabin, editor, CRYPTO 2010, volume 6223 of LNCS, pages 155–172, Santa Barbara, CA, USA, August 15–19, 2010. Springer, Heidelberg, Germany.10.1007/978-3-642-14623-7_9Search in Google Scholar

[30] Ran Gilad-Bachrach, Kim Laine, Kristin Lauter, Peter Rindal, and Mike Rosulek. Secure data exchange: A marketplace in the cloud. Cryptology ePrint Archive, Report 2016/620, 2016. http://eprint.iacr.org/2016/620.Search in Google Scholar

[31] Oded Goldreich, Shafi Goldwasser, and Silvio Micali. How to construct random functions. Journal of the ACM, 33(4):792–807, October 1986.10.1145/6490.6503Search in Google Scholar

[32] Yan Huang, David Evans, Jonathan Katz, and Lior Malka. Faster secure two-party computation using garbled circuits. In USENIX Security Symposium, volume 201, 2011.10.1007/978-3-642-25560-1_2Search in Google Scholar

[33] Yan Huang, Jonathan Katz, and David Evans. Quid-proquo-tocols: Strengthening semi-honest protocols with dual execution. In Security and Privacy (SP), 2012 IEEE Symposium on, pages 272–284. IEEE, 2012.10.1109/SP.2012.43Search in Google Scholar

[34] Yan Huang, Jonathan Katz, and David Evans. Efficient secure two-party computation using symmetric cut-and-choose. In Canetti and Garay [17], pages 18–35.10.1007/978-3-642-40084-1_2Search in Google Scholar

[35] Yuval Ishai, Joe Kilian, Kobbi Nissim, and Erez Petrank. Extending oblivious transfers efficiently. In Dan Boneh, editor, CRYPTO 2003, volume 2729 of LNCS, pages 145–161, Santa Barbara, CA, USA, August 17–21, 2003. Springer, Heidelberg, Germany.10.1007/978-3-540-45146-4_9Search in Google Scholar

[36] Thomas P Jakobsen, Jesper Buus Nielsen, and Claudio Orlandi. A framework for outsourcing of secure computation. In Proceedings of the 6th edition of the ACM Workshop on Cloud Computing Security, pages 81–92. ACM, 2014.10.1145/2664168.2664170Search in Google Scholar

[37] Mark A Jensen, Vincent Ferretti, Robert L Grossman, and Louis M Staudt. The nci genomic data commons as an engine for precision medicine. Blood, 130(4):453–459, 2017.10.1182/blood-2017-03-735654553320228600341Search in Google Scholar

[38] Somesh Jha, Louis Kruger, and Vitaly Shmatikov. Towards practical privacy for genomic computation. In Security and Privacy, 2008. SP 2008. IEEE Symposium on, pages 216–230. IEEE, 2008.Search in Google Scholar

[39] Lynn B Jorde and Stephen P Wooding. Genetic variation, classification and’race’. Nature genetics, 36:S28–S33, 2004.10.1038/ng143515508000Search in Google Scholar

[40] Madhu Kalia. Personalized oncology: recent advances and future challenges. Metabolism, 62:S11–S14, 2013.Search in Google Scholar

[41] Seny Kamara, Payman Mohassel, and Mariana Raykova. Outsourcing multi-party computation. IACR Cryptology ePrint Archive, 2011:272, 2011.Search in Google Scholar

[42] Seny Kamara, Payman Mohassel, and Ben Riva. Salus: a system for server-aided secure function evaluation. In Yu et al. [69], pages 797–808.Search in Google Scholar

[43] Murat Kantarcioglu, Wei Jiang, Ying Liu, and Bradley Malin. A cryptographic approach to securely share and query genomic sequences. IEEE Transactions on information technology in biomedicine, 12(5):606–617, 2008.10.1109/TITB.2007.90846518779075Search in Google Scholar

[44] Nikolaos Karvelas, Andreas Peter, Stefan Katzenbeisser, Erik Tews, and Kay Hamacher. Privacy-preserving whole genome sequence processing through proxy-aided oram. In Proceedings of the 13th Workshop on Privacy in the Electronic Society, WPES ‘14, pages 1–10, New York, NY, USA, 2014. ACM.10.1145/2665943.2665962Search in Google Scholar

[45] David J Kaufman, Juli Murphy-Bollinger, Joan Scott, and Kathy L Hudson. Public opinion about the importance of privacy in biobank research. The American Journal of Human Genetics, 85(5):643–654, 2009.10.1016/j.ajhg.2009.10.002277583119878915Search in Google Scholar

[46] Jane Kaye, Liam Curren, Nick Anderson, Kelly Edwards, Stephanie M Fullerton, Nadja Kanellopoulou, David Lund, Daniel G MacArthur, Deborah Mascalzoni, James Shepherd, et al. From patients to partners: participant-centric initiatives in biomedical research. Nature Reviews Genetics, 13(5):371, 2012.Search in Google Scholar

[47] Miran Kim and Kristin Lauter. Private genome analysis through homomorphic encryption. Cryptology ePrint Archive, Report 2015/965, 2015. http://eprint.iacr.org/2015/965.Search in Google Scholar

[48] Vladimir Kolesnikov, Payman Mohassel, and Mike Rosulek. FleXOR: Flexible garbling for XOR gates that beats free-XOR. In Juan A. Garay and Rosario Gennaro, editors, CRYPTO 2014, Part II, volume 8617 of LNCS, pages 440–457, Santa Barbara, CA, USA, August 17–21, 2014. Springer, Heidelberg, Germany.10.1007/978-3-662-44381-1_25Search in Google Scholar

[49] Vladimir Kolesnikov and Thomas Schneider. Improved garbled circuit: Free xor gates and applications. Automata, Languages and Programming, pages 486–498, 2008.10.1007/978-3-540-70583-3_40Search in Google Scholar

[50] Vladimir Kolesnikov and Thomas Schneider. Improved garbled circuit: Free XOR gates and applications. In Luca Aceto, Ivan Damgård, Leslie Ann Goldberg, Magnús M. Halldórsson, Anna Ingólfsdóttir, and Igor Walukiewicz, editors, ICALP 2008, Part II, volume 5126 of LNCS, pages 486–498, Reykjavik, Iceland, July 7–11, 2008. Springer, Heidelberg, Germany.Search in Google Scholar

[51] Benjamin Kreuter, Abhi Shelat, Benjamin Mood, and Kevin RB Butler. Pcf: A portable circuit format for scalable two-party secure computation. In Usenix Security, volume 13, pages 321–336, 2013.Search in Google Scholar

[52] Benjamin Kreuter, Abhi Shelat, and Chih-Hao Shen. Billion-gate secure computation with malicious adversaries. In USENIX Security Symposium, volume 12, pages 285–300, 2012.Search in Google Scholar

[53] Yehuda Lindell. Fast cut-and-choose based protocols for malicious and covert adversaries. In Canetti and Garay [17], pages 1–17.10.1007/978-3-642-40084-1_1Search in Google Scholar

[54] Yehuda Lindell and Benny Pinkas. Privacy preserving data mining. In Mihir Bellare, editor, CRYPTO 2000, volume 1880 of LNCS, pages 36–54, Santa Barbara, CA, USA, August 20–24, 2000. Springer, Heidelberg, Germany.10.1007/3-540-44598-6_3Search in Google Scholar

[55] Yehuda Lindell and Benny Pinkas. A proof of security of yao’s protocol for two-party computation. Journal of cryptology, 22(2):161–188, 2009.10.1007/s00145-008-9036-8Search in Google Scholar

[56] Dahlia Malkhi, Noam Nisan, Benny Pinkas, Yaron Sella, et al. Fairplay-secure two-party computation system. In USENIX Security Symposium, volume 4. San Diego, CA, USA, 2004.Search in Google Scholar

[57] Neil A. Miller, Emily G. Farrow, Margaret Gibson, Laurel K. Willig, Greyson Twist, Byunggil Yoo, Tyler Marrs, Shane Corder, Lisa Krivohlavek, Adam Walter, Josh E. Petrikin, Carol J. Saunders, Isabelle Thiffault, Sarah E. Soden, Laurie D. Smith, Darrell L. Dinwiddie, Suzanne Herd, Julie A. Cakici, Severine Catreux, Mike Ruehle, and Stephen F. Kingsmore. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Medicine, 7(1):100, 2015.10.1186/s13073-015-0221-8458825126419432Search in Google Scholar

[58] Benjamin Mood, Debayan Gupta, Kevin R. B. Butler, and Joan Feigenbaum. Reuse it or lose it: More efficient secure computation through reuse of encrypted values. In Ahn et al. [6], pages 582–596.Search in Google Scholar

[59] Moni Naor and Benny Pinkas. Oblivious transfer and polynomial evaluation. In 31st ACM STOC, pages 245–254, Atlanta, GA, USA, May 1–4, 1999. ACM Press.10.1145/301250.301312Search in Google Scholar

[60] Moni Naor, Benny Pinkas, and Reuban Sumner. Privacy preserving auctions and mechanism design. In EC, pages 129–139, 1999.10.1145/336992.337028Search in Google Scholar

[61] Moni Naor and Omer Reingold. Number-theoretic constructions of efficient pseudo-random functions. In 38th FOCS, pages 458–467, Miami Beach, Florida, October 19–22, 1997. IEEE Computer Society Press.Search in Google Scholar

[62] Muhammad Naveed, Shashank Agrawal, Manoj Prabhakaran, XiaoFeng Wang, Erman Ayday, Jean-Pierre Hubaux, and Carl A. Gunter. Controlled functional encryption. In Ahn et al. [6], pages 1280–1291.Search in Google Scholar

[63] Boris Pasche and Devin Absher. Whole-genome sequencing: a step closer to personalized medicine. JAMA, 305(15):1596–1597, 2011.Search in Google Scholar

[64] Chris Peikert, Vinod Vaikuntanathan, and Brent Waters. A framework for efficient and composable oblivious transfer. In David Wagner, editor, CRYPTO 2008, volume 5157 of LNCS, pages 554–571, Santa Barbara, CA, USA, August 17–21, 2008. Springer, Heidelberg, Germany.10.1007/978-3-540-85174-5_31Search in Google Scholar

[65] Juan Ramón Troncoso-Pastoriza, Stefan Katzenbeisser, and Mehmet Celik. Privacy preserving error resilient dna searching through oblivious automata. In Proceedings of the 14th ACM conference on Computer and communications security, pages 519–528. ACM, 2007.10.1145/1315245.1315309Search in Google Scholar

[66] Xiao Shaun Wang, Yan Huang, Yongan Zhao, Haixu Tang, XiaoFeng Wang, and Diyue Bu. Efficient genome-wide, privacy-preserving similar patient query based on private edit distance. In Indrajit Ray, Ninghui Li, and Christopher Kruegel:, editors, ACM CCS 15, pages 492–503, Denver, CO, USA, October 12–16, 2015. ACM Press.Search in Google Scholar

[67] Mick Watson. Illuminating the future of dna sequencing. Genome biology, 15(2):108, 2014.10.1186/gb4165405484425001875Search in Google Scholar

[68] Andrew Chi-Chih Yao. How to generate and exchange secrets (extended abstract). In 27th FOCS, pages 162–167, Toronto, Ontario, Canada, October 27–29, 1986. IEEE Computer Society Press.Search in Google Scholar

[69] Ting Yu, George Danezis, and Virgil D. Gligor, editors. ACM CCS 12, Raleigh, NC, USA, October 16–18, 2012. ACM Press.Search in Google Scholar

[70] Samee Zahur and David Evans. Obliv-c: A language for extensible data-oblivious computation. IACR Cryptology ePrint Archive, 2015:1153, 2015.Search in Google Scholar

[71] Samee Zahur, Mike Rosulek, and David Evans. Two halves make a whole - reducing data transfer in garbled circuits using half gates. In Elisabeth Oswald and Marc Fischlin, editors, EUROCRYPT 2015, Part II, volume 9057 of LNCS, pages 220–250, Sofia, Bulgaria, April 26–30, 2015. Springer, Heidelberg, Germany.10.1007/978-3-662-46803-6_8Search in Google Scholar

Recommended articles from Trend MD

Plan your remote conference with Sciendo