Muhammad Naveed
Jean-Pierre Hubaux
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Abstract
Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.
- Rakesh Agrawal, Jerry Kiernan, Ramakrishnan Srikant, and Yirong Xu. 2004. Order preserving encryption for numeric data. In ACM International Conference on Management of Data. 563--574. Google Scholar
Digital Library
- Naomi E. Allen, Cathie Sudlow, Tim Peakman, Rory Collins, Rafael Dal-Ré, John P. Ioannidis, Michael B. Bracken, Patricia A. Buffler, An-Wen Chan, Eduardo L. Franco, and others. 2014. UK Biobank data: come and get it. Science Translational Medicine 6, 224.Google ScholarCross Ref
- Russ B. Altman, Ellen Wright Clayton, Isaac S. Kohane, Bradley A. Malin, and Dan M. Roden. 2013. Data re-identification: societal safeguards. Science 339, 6123, 1032.Google ScholarCross Ref
- Russ B. Altman and Teri E. Klein. 2002. Challenges for biomedical informatics and pharmacogenomics. Annual Review of Pharmacology and Toxicology 42, 1, 113--133.Google ScholarCross Ref
- Mary R. Anderlik. 2003. Assessing the quality of DNA-based parentage testing: findings from a survey of laboratories. Jurimetrics 291--314.Google Scholar
- Mikhail J. Atallah, Florian Kerschbaum, and Wenliang Du. 2003. Secure and private sequence comparisons. In ACM Workshop on Privacy in the Electronic Society. 39--44. Google ScholarDigital Library
- Mikhail J. Atallah and Jiangtao Li. 2005. Secure outsourcing of sequence comparisons. International Journal of Information Security 4, 4, 277--287. Google ScholarDigital Library
- Erman Ayday, Emiliano De Cristofaro, Jean-Pierre Hubaux, and Gene Tsudik. 2013a. Whole genome sequencing: Revolutionary medicine or privacy nightmare? Computer 48, 2, 58--66.Google ScholarCross Ref
- Erman Ayday, Jean Louis Raisaro, Urs Hengartner, Adam Molyneaux, and Jean-Pierre Hubaux. 2014. Privacy-preserving processing of raw genomic data. In Data Privacy Management and Autonomous Spontaneous Security. 133--147. Google ScholarDigital Library
- Erman Ayday, Jean Louis Raisaro, and Jean-Pierre Hubaux. 2013b. Personal use of the genomic data: privacy vs. storage cost. In IEEE Global Communications Conference, Exhibition and Industry Forum.Google ScholarCross Ref
- Erman Ayday, Jean Louis Raisaro, and Jean-Pierre Hubaux. 2013c. Privacy-enhancing technologies for medical tests using genomic data. In Network and Distributed System Security Symposium.Google Scholar
- Erman Ayday, Jean Louis Raisaro, Jean-Pierre Hubaux, and Jacques Rougemont. 2013d. Protecting and evaluating genomic privacy in medical tests and personalized medicine. In Workshop on Privacy in the Electronic Society. 95--106. Google ScholarDigital Library
- Erman Ayday, Jean Louis Raisaro, Paul J. McLaren, Jacques Fellay, and Jean-Pierre Hubaux. 2013e. Privacy-preserving computation of disease risk by using genomic, clinical, and environmental data. In Workshop on Health Information Technologies. Google ScholarDigital Library
- William Bains. 2010. Genetic exceptionalism. Nature Biotechnology 28, 3, 212--213.Google ScholarCross Ref
- Pierre Baldi, Roberta Baronio, Emiliano De Cristofaro, Paolo Gasti, and Gene Tsudik. 2011. Countering GATTACA: efficient and secure testing of fully-sequenced human genomes. In ACM Conference on Computer and Communications Security. 691--702. Google ScholarDigital Library
- Suzette J. Bielinski, Janet E. Olson, Jyotishman Pathak, Richard M. Weinshilboum, Liewei Wang, Kelly J. Lyke, Euijung Ryu, Paul V. Targonski, Michael D. Van Norstrand, Matthew A. Hathcock, and others. 2014. Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time: using genomic data to individualize treatment protocol. In Mayo Clinic Proceedings, Vol. 89, 25--33.Google ScholarCross Ref
- Marina Blanton, Mikhail J. Atallah, Keith B. Frikken, and Qutaibah Malluhi. 2012. Secure and efficient outsourcing of sequence comparisons. In European Symposium on Research in Computer Security. 505--522.Google ScholarCross Ref
- Michael Bobellan. 2010. DNA’s dirty little secret. In Washington Monthly. http://goo.gl/cIppNs.Google Scholar
- Philip Bohannon, Markus Jakobsson, and Sukamol Srikwan. 2000. Cryptographic approaches to privacy in forensic DNA databases. In Public Key Cryptography. 373--390. Google ScholarDigital Library
- David Botstein and Neil Risch. 2003. Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nature Genetics 33, 228--237.Google ScholarCross Ref
- Rosemary Braun, William Rowe, Carl Schaefer, Jinghui Zhang, and Kenneth Buetow. 2009. Needles in the haystack: identifying individuals present in pooled Genomic Data. PLoS Genetics 5, 10, e1000668.Google ScholarCross Ref
- Steven E. Brenner. 2013. Be prepared for the big genome leak. Nature 498, 7453, 139.Google ScholarCross Ref
- Fons Bruekers, Stefan Katzenbeisser, Klaus Kursawe, and Pim Tuyls. 2008. Privacy-preserving matching of DNA profiles. IACR Cryptology ePrint Archive 2008, 203.Google Scholar
- Liam R. Brunham and Michael R. Hayden. 2012. Whole-genome sequencing: the new standard of care? Science 336, 1112--1113.Google ScholarCross Ref
- Mustafa Canim, Murat Kantarcioglu, and Bradley Malin. 2012. Secure management of biomedical data with cryptographic hardware. IEEE Transactions on Information Technology in Biomedicine 16, 1, 166--175. Google ScholarDigital Library
- Christopher A. Cassa, Rachel A. Miller, and Kenneth D. Mandl. 2013. A novel, privacy-preserving cryptographic approach for sharing sequencing data. Journal of the American Medical Informatics Association 20, 1, 69--76.Google ScholarCross Ref
- Yangyi Chen, Bo Peng, X. Wang, and Haixu Tang. 2012. Large-scale privacy-preserving mapping of human genomic sequences on hybrid clouds. In Network and Distributed System Security Symposium.Google Scholar
- Zhengming Chen, Junshi Chen, Rory Collins, Yu Guo, Richard Peto, Fan Wu, and Liming Li. 2011. China Kadoorie Biobank of 0.5 million people: survey methods, baseline characteristics and long-term follow-up. International Journal of Epidemiology 40, 6, 1652--1666.Google ScholarCross Ref
- Michael Cheng. 2003. Medical device regulations: global overview and guiding principles. World Health Organization, Geneva, Switzerland.Google Scholar
- George Church, Catherine Heeney, Naomi Hawkins, Jantina de Vries, Paula Boddington, Jane Kaye, Martin Bobrow, Bruce Weir, and others. 2009. Public access to genome-wide data: five views on balancing research with privacy and protection. PLoS Genetics 5, 10, e1000665.Google ScholarCross Ref
- David Clayton. 2010. On inferring presence of an individual in a mixture: a Bayesian approach. Biostatistics 11, 4, 661--673.Google ScholarCross Ref
- Council of Europe. 2008. Additional protocol to the convention on human rights and biomedicine, concerning genetic testing for health purposes. http://goo.gl/hciO0n.Google Scholar
- David W. Craig, Robert M. Goor, Zhenyuan Wang, Justin Paschall, Jim Ostell, Michael Feolo, Stephen T. Sherry, and Teri A. Manolio. 2011. Assessing and managing risk when sharing aggregate genetic variant data. Nature Reviews Genetics 12, 10, 730--736.Google ScholarCross Ref
- George Danezis and Emiliano De Cristofaro. 2014. Fast and private genomic testing for disease susceptibility. In Workshop on Privacy in the Electronic Society. 31--34. Google ScholarDigital Library
- Emiliano De Cristofaro. 2014a. Genomic privacy and the rise of a new research community. IEEE Security and Privacy 12, 2, 80--83.Google ScholarCross Ref
- Emiliano De Cristofaro, Sky Faber, Paolo Gasti, and Gene Tsudik. 2012. Genodroid: are privacy-preserving genomic tests ready for prime time? In ACM Workshop on Privacy in the Electronic Society. 97--108. Google ScholarDigital Library
- Emiliano De Cristofaro. 2014b. An exploratory ethnographic study of issues and concerns with whole genome sequencing. In Workshop on Usable Security.Google ScholarCross Ref
- Mentari Djatmiko, Arik Friedman, Roksana Boreli, Felix Lawrence, Brian Thorne, and Stephen Hardy. 2014. Secure evaluation protocol for personalized medicine. In Workshop on Privacy in the Electronic Society. 159--162. Google ScholarDigital Library
- Cynthia Dwork. 2006. Differential privacy. In Automata, Languages and Programming. 1--12. Google ScholarDigital Library
- David Eppstein, Michael T. Goodrich, and Pierre Baldi. 2011. Privacy-enhanced methods for comparing compressed DNA sequences. arXiv preprint arXiv:1107.3593.Google Scholar
- Yaniv Erlich and Arvind Narayanan. 2013. Routes for breaching and protecting genetic privacy. arXiv abs/1310.3197v1.Google Scholar
- James P. Evans, Wylie Burke, and Muin Khoury. 2010. The rules remain the same for genomic medicine: the case against “reverse genetic exceptionalism.” Genetics in Medicine 12, 6, 342--343.Google ScholarCross Ref
- W. Gregory Feero, Alan E. Guttmacher, Ultan McDermott, James R. Downing, and Michael R. Stratton. 2011. Genomics and the continuum of cancer care. New England Journal of Medicine 364, 340--350.Google ScholarCross Ref
- Stephen E. Fienberg, Aleksandra Slavkovic, and Caroline Uhler. 2011. Privacy preserving GWAS data sharing. In IEEE Data Mining Workshops. 628--635. Google ScholarDigital Library
- Matthew Fredrikson, Eric Lantz, Somesh Jha, Simon Lin, David Page, and Thomas Ristenpart. 2014. Privacy in pharmacogenetics: an end-to-end case study of personalized warfarin dosing. In USENIX Security Symposium. 17--32. Google ScholarDigital Library
- Keith B. Frikken. 2009. Practical private DNA string searching and matching through efficient oblivious automata evaluation. In Data and Applications Security. 81--94. Google ScholarDigital Library
- J. Raphael Gibbs and Andrew Singleton. 2006. Application of genome-wide single nucleotide polymorphism typing: Simple association and beyond. PLoS Genetics 2, 10.Google Scholar
- Natasha Gilbert. 2008. Researchers criticize genetic data restrictions. Nature News. doi:10.1038/news.2008.1083Google Scholar
- Jane Gitschier. 2009. Inferential genotyping of Y chromosomes in Latter-Day Saints founders and comparison to Utah samples in the HapMap project. American Journal of Human Genetics 84, 2, 251--258.Google ScholarCross Ref
- Jill S. Goldman, Susan E. Hahn, Jennifer Williamson Catania, Susan Larusse-Eckert, Melissa Barber Butson, Malia Rumbaugh, Michelle N. Strecker, J. Scott Roberts, Wylie Burke, Richard Mayeux, and others. 2011. Genetic counseling and testing for Alzheimer disease: joint practice guidelines of the American College of Medical Genetics and the National Society of Genetic Counselors. Genetics in Medicine 13, 6, 597--605.Google ScholarCross Ref
- Leo A. Goodman. 1961. Snowball sampling. The Annals of Mathematical Statistics 32, 1.Google ScholarCross Ref
- Michael T. Goodrich. 2009. The mastermind attack on genomic data. In IEEE Symposium on Security and Privacy. 204--218. Google ScholarDigital Library
- Lawrence O. Gostin and James G. Hodge Jr. 1999. Genetic privacy and the law: an end to genetics exceptionalism. Jurimetrics 40, 21--58.Google Scholar
- Omri Gottesman, Helena Kuivaniemi, Gerard Tromp, W. Andrew Faucett, Rongling Li, Teri A. Manolio, Saskia C. Sanderson, Joseph Kannry, Randi Zinberg, Melissa A. Basford, and others. 2013a. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genetics in Medicine 15, 10, 761--771.Google ScholarCross Ref
- Omri Gottesman, Stuart A. Scott, Stephen B. Ellis, Casey L. Overby, Angelika Ludtke, Jean-Sébastien Hulot, Jeffrey Hall, Kumar Chatani, Kristin Myers, Joseph L. Kannry, and others. 2013b. The CLIPMERGE PGx program: clinical implementation of personalized medicine through electronic health records and genomics-pharmacogenomics. Clinical Pharmacology and Therapeutics 94, 2, 214.Google ScholarCross Ref
- Scott Gottlieb. 2001. US employer agrees to stop genetic testing. BMJ: British Medical Journal 322, 7284, 449.Google Scholar
- Henry T. Greely, Daniel P. Riordan, Nanibaa’A Garrison, and Joanna L. Mountain. 2006. Family ties: the use of DNA offender databases to catch offenders’ kin. The Journal of Law, Medicine and Ethics 34, 2, 248--262.Google ScholarCross Ref
- Bastian Greshake, Philipp E. Bayer, Helge Rausch, and Julia Reda. 2014. openSNP--a crowdsourced web resource for personal genomics. PloS One 9, 3, e89204.Google ScholarCross Ref
- Alan E. Guttmacher and Francis S. Collins. 2003. Welcome to the genomic era. New England Journal of Medicine 349, 996--998.Google ScholarCross Ref
- Melissa Gymrek, Amy L. McGuire, David Golan, Eran Halperin, and Yaniv Erlich. 2013. Identifying personal genomes by surname inference. Science 339, 6117, 321--324.Google Scholar
- Eran Halperin and Dietrich A. Stephan. 2009. SNP imputation in association studies. Nature Biotechnology 27, 4, 349--351.Google ScholarCross Ref
- Calvin B. Harley, A. Bruce Futcher, and Carol W. Greider. 1990. Telomeres shorten during ageing of human fibroblasts. Nature 345, 6274, 458--460.Google Scholar
- David Haussler, David A. Patterson, Mark Diekhans, Armando Fox, Michael Jordan, Anthony D. Joseph, Singer Ma, Benedict Paten, Scott Shenker, Taylor Sittler, and others. 2012. A million cancer genome warehouse. Technical Report. DTIC Document.Google Scholar
- Erika Check Hayden. 2013. Privacy protections: The genome hacker. Nature 497, 172--174.Google ScholarCross Ref
- Dan He, Nicholas A. Furlotte, Farhad Hormozdiari, Jong Wha J. Joo, Akshay Wadia, Rafail Ostrovsky, Amit Sahai, and Eleazar Eskin. 2014. Identifying genetic relatives without compromising privacy. Genome Research 24, 4, 664--672.Google ScholarCross Ref
- Nils Homer, Szabolcs Szelinger, Margot Redman, David Duggan, Waibhav Tembe, Jill Muehling, John V. Pearson, Dietrich A. Stephan, Stanley F. Nelson, and David W. Craig. 2008. Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genetics 4, 8.Google ScholarCross Ref
- Farhad Hormozdiari, Jong Wha J. Joo, Akshay Wadia, Feng Guan, Rafail Ostrosky, Amit Sahai, and Eleazar Eskin. 2014. Privacy preserving protocol for detecting genetic relatives using rare variants. Bioinformatics 30, 12, i204--i211.Google ScholarCross Ref
- Yan Huang, David Evans, and Jonathan Katz. 2012. Private set intersection: Are garbled circuits better than custom protocols. In Network and Distributed System Security Symposium.Google Scholar
- Yan Huang, David Evans, Jonathan Katz, and Lior Malka. 2011. Faster secure two-party computation using garbled circuits. In USENIX Security Symposium. Google ScholarDigital Library
- Zhicong Huang, Erman Ayday, Jacques Fellay, Jean-Pierre Hubaux, and Ari Juels. 2015. GenoGuard: Protecting genomic data against brute-force attacks. In IEEE Symposium on Security and Privacy. 447--462.Google ScholarDigital Library
- Mathias Humbert, Erman Ayday, Jean-Pierre Hubaux, and Amalio Telenti. 2013. Addressing the concerns of the Lacks family: quantification of kin genomic privacy. In ACM Conference on Computer and Communications Security. 1141--1152. Google ScholarDigital Library
- Mathias Humbert, Erman Ayday, Jean-Pierre Hubaux, and Amalio Telenti. 2014. Reconciling utility with privacy in genomics. In Workshop on Privacy in the Electronic Society. 11--20. Google ScholarDigital Library
- Hae Kyung Im, Eric R. Gamazon, Dan L. Nicolae, and Nancy J. Cox. 2012. On sharing quantitative trait GWAS results in an era of multiple-omics data and the limits of genomic privacy. American Journal of Human Genetics 90, 4591--598.Google ScholarCross Ref
- Kevin B. Jacobs, Meredith Yeager, Sholom Wacholder, David Craig, Peter Kraft, David J. Hunter, Justin Paschal, Teri A. Manolio, Margaret Tucker, Robert N. Hoover, and others. 2009. A new statistic and its power to infer membership in a genome-wide association study using genotype frequencies. Nature Genetics 41, 11, 1253--1257.Google ScholarCross Ref
- Somesh Jha, Louis Kruger, and Vitaly Shmatikov. 2008. Towards practical privacy for genomic computation. In IEEE Symposium on Security and Privacy. 216--230. Google ScholarDigital Library
- Mark A. Jobling. 2001. In the name of the father: surnames and genetics. Trends in Genetics 17, 6, 353--357.Google ScholarCross Ref
- Elizabeth E. Joh. 2006. Reclaiming “abandoned” DNA: the Fourth Amendment and genetic privacy. Northwestern University Law Review 100, 2, 857--884.Google Scholar
- Aaron Johnson and Vitaly Shmatikov. 2013. Privacy-preserving data exploration in genome-wide association studies. In ACM International Conference on Knowledge Discovery and Data Mining. 1079--1087. Google ScholarDigital Library
- Ari Juels and Thomas Ristenpart. 2014. Honey encryption: Security beyond the brute-force bound. In Advances in Cryptology--EUROCRYPT. 293--310.Google Scholar
- Murat Kantarcioglu, Wei Jiang, Ying Liu, and Bradley Malin. 2008. A cryptographic approach to securely share and query genomic sequences. IEEE Transactions on Information Technology in Biomedicine 12, 5, 606--617. Google ScholarDigital Library
- Nikolaos Karvelas, Andreas Peter, Stefan Katzenbeisser, Erik Tews, and Kay Hamacher. 2014. Privacy-preserving whole genome sequence processing through proxy-aided oram. In Workshop on Privacy in the Electronic Society. 1--10. Google ScholarDigital Library
- David Kaufman, Juli Bollinger, Rachel Dvoskin, and Joan Scott. 2012. Preferences for opt-in and opt-out enrollment and consent models in biobank research: a national survey of Veterans Administration patients. Genetics in Medicine 14, 9, 787--794.Google ScholarCross Ref
- David J. Kaufman, Juli Murphy Bollinger, Joan Scott, and Kathy L. Hudson. 2009. Public opinion about the importance of privacy in biobank research. American Journal of Human Genetics 85, 5, 643--654.Google ScholarCross Ref
- David H. Kaye and Michael E. Smith. 2003. DNA identification databases: legality, legitimacy, and the case for population-wide coverage. Wisconsin Law Review 413.Google Scholar
- Manfred Kayser and Peter de Knijff. 2011. Improving human forensics through advances in genetics, genomics and molecular biology. Nature Reviews Genetics 12, 3, 179--192.Google ScholarCross Ref
- Isaac S. Kohane. 2011. Using electronic health records to drive discovery in disease genomics. Nature Review Genetics 12, 6, 417--428.Google ScholarCross Ref
- Augustine Kong, Gisli Masson, Michael L. Frigge, Arnaldur Gylfason, Pasha Zusmanovich, Gudmar Thorleifsson, Pall I. Olason, Andres Ingason, Stacy Steinberg, Thorunn Rafnar, and others. 2008. Detection of sharing by descent, long-range phasing and haplotype imputation. Nature Genetics 40, 9, 1068--1075.Google ScholarCross Ref
- Rachel Lehmann-Haupt. 2010. Are sperm donors really anonymous anymore? Slate. http://goo.gl/410TLNGoogle Scholar
- Guang Li, Yadong Wang, and Xiaohong Su. 2012. Improvements on a privacy-protection algorithm for DNA sequences with generalization lattices. Computer Programs in Biomedicine 108, 1, 1--9. Google ScholarDigital Library
- Zhen Lin, Michael Hewett, and Russ B. Altman. 2002. Using binning to maintain confidentiality of medical data. In American Medical Informatics Association Annual Symposium. 454.Google Scholar
- Zhen Lin, Art B. Owen, and Russ B. Altman. 2004. Genomic research and human subject privacy. Science 305, 5681, 183.Google ScholarCross Ref
- Noralane M. Lindor. 2012. Personal autonomy in the genomic era. In Video Proceedings of Mayo Clinic Individualizing Medicine Conference. {http://bcove.me/lm00e8z7}Google Scholar
- Abby Lippman. 1991. Prenatal genetic testing and screening: constructing needs and reinforcing inequities. American Journal of Law in Medicine 17, 1--2, 15--50.Google ScholarCross Ref
- Thomas Lumley and Kenneth Rice. 2010. Potential for revealing individual-level information in genome-wide association studies. Journal of the American Medical Association 303, 7, 659--660.Google ScholarCross Ref
- Marcy E. MacDonald, Christine M. Ambrose, Mabel P. Duyao, Richard H. Myers, Carol Lin, Lakshmi Srinidhi, Glenn Barnes, Sherryl A. Taylor, Marianne James, Nicolet Groot, and others. 1993. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington’s disease chromosomes. Cell 72, 6, 971--983.Google ScholarCross Ref
- Bradley Malin. 2006. Re-identification of familial database records. In American Medical Informatics Association Annual Symposium, Vol. 2006. 524--528.Google Scholar
- Bradley A. Malin. 2005a. An evaluation of the current state of genomic data privacy protection technology and a roadmap for the future. Journal of the American Medical Informatics Association 12, 1, 28--34.Google ScholarCross Ref
- Bradley A. Malin. 2005b. Protecting DNA sequence anonymity with generalization lattices. Methods of Information in Medicine 44, 687--692.Google ScholarCross Ref
- Bradley A. Malin and Latanya Sweeney. 2004. How (not) to protect genomic data privacy in a distributed network: using trail re-identification to evaluate and design anonymity protection systems. Journal of Biomedical Informatics 37, 3, 179--192. Google ScholarDigital Library
- Jonathan Marchini and Bryan Howie. 2010. Genotype imputation for genome-wide association studies. Nature Reviews Genetics 11, 7, 499--511.Google ScholarCross Ref
- Nicholas Masca, Paul R. Burton, and Nuala A. Sheehan. 2011. Participant identification in genetic association studies: improved methods and practical implications. International Journal of Epidemiology 40, 6, 1629--1642.Google ScholarCross Ref
- Carol Mastromauro, Richard H. Myers, Barbara Berkman, John M. Opitz, and James F. Reynolds. 1987. Attitudes toward presymptomatic testing in Huntington disease. American Journal of Medical Genetics 26, 2, 271--282.Google ScholarCross Ref
- Amy L. McGuire, Jill M. Oliver, Melody J. Slashinski, Jennifer L. Graves, Tao Wang, P. Adam Kelly, William Fisher, Ching C. Lau, John Goss, Mehmet Okcu, and others. 2011. To share or not to share: a randomized trial of consent for data sharing in genome research. Genetics in Medicine 13, 11, 948--955.Google ScholarCross Ref
- Alison Motluk. 2005. Anonymous sperm donor traced on Internet. New Scientist http://goo.gl/3FOpfc.Google Scholar
- Gautam Naik. 2009. Family secrets: an adopted man’s 26-year quest for his father. The Wall Street Journal http://goo.gl/z9xGBc.Google Scholar
- Muhammad Naveed. 2014. Hurdles for genomic data usage management. In International Workshop on Data Usage Management. Google ScholarDigital Library
- Muhammad Naveed, Shashank Agrawal, Manoj Prabhakaran, XiaoFeng Wang, Erman Ayday, Jean-Pierre Hubaux, and Carl A. Gunter. 2014. Controlled functional encryption. In ACM Conference on Computer and Communications Security. 1280--1291. Google ScholarDigital Library
- Dorothy Nelkin and Susan Lindee. 1995. The DNA mystique. W.H. Freeman & Company.Google Scholar
- Dale R. Nyholt, Chang-En Yu, and Peter M. Visscher. 2008. On Jim Watson’s APOE status: genetic information is hard to hide. European Journal of Human Genetics 17, 2, 147--149.Google ScholarCross Ref
- Casey L. Overby, Peter Tarczy-Hornoch, James I. Hoath, Ira J. Kalet, and David L. Veenstra. 2010. Feasibility of incorporating genomic knowledge into electronic medical records for pharmacogenomic clinical decision support. BMC Bioinformatics 11, Suppl 9, S10.Google ScholarCross Ref
- Andrew J. Pakstis, William C. Speed, Rixun Fang, Fiona CL Hyland, Manohar R. Furtado, Judith R. Kidd, and Kenneth K. Kidd. 2010. SNPs for a universal individual identification panel. Human Genetics 127, 3, 315--324.Google ScholarCross Ref
- Jodyn Platt, Juli Bollinger, Rachel Dvoskin, Sharon L. R. Kardia, and David Kaufman. 2014. Public preferences regarding informed consent models for participation in population-based genomic research. Genetics in Medicine 16, 1, 11--18.Google ScholarCross Ref
- Barbara Prainsack and Effy Vayena. 2013. Beyond the clinic: ‘direct-to-consumer’ genomic profiling services and pharmacogenomics. Pharmacogenomics 14, 4, 403--412.Google ScholarCross Ref
- Presidential Commission for the Study of Bioethical Issues. 2012. Privacy and progress in whole genome sequencing. http://goo.gl/iKL5Zt.Google Scholar
- Jill M. Pulley, Margaret M. Brace, Gordon R. Bernard, and Dan R. Masys. 2008. Attitudes and perceptions of patients towards methods of establishing a DNA biobank. Cell and Tissue Banking 9, 1 (2008), 55--65.Google ScholarCross Ref
- Jill M. Pulley, Joshua C. Denny, Josh F. Peterson, Gordon R. Bernard, Cindy L. Vnencak-Jones, Andrea H. Ramirez, Jessica T. Delaney, Erica Bowton, Kyle Brothers, Kevin Johnson, and others. 2012. Operational implementation of prospective genotyping for personalized medicine: the design of the Vanderbilt PREDICT project. Clinical Pharmacology and Therapeutics 92, 1, 87--95.Google ScholarCross Ref
- Malcolm Ritter. 2013. Henrietta Lacks’ family, feds reach settlement on use of DNA info. http://goo.gl/S4l7bY.Google Scholar
- Mark A. Rothstein. 2005. Genetic exceptionalism & legislative pragmatism. Hastings Center Report 35, 4, 27--33.Google ScholarCross Ref
- Randall K. Saiki, Stephen Scharf, Fred Faloona, Kary B. Mullis, Glenn T. Horn, Henry A. Erlich, and Norman Arnheim. 1985. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230, 4732, 1350--1354.Google Scholar
- Sahel Shariati Samani, Zhicong Huang, Erman Ayday, Mark Elliot, Jacques Fellay, Jean-Pierre Hubaux, and Zoltan Kutalik. 2015. Quantifying genomic privacy via inference attack with high-order SNV correlations. In Workshop on Genome Privacy. 32--40.Google ScholarDigital Library
- Sriram Sankararaman, Guillaume Obozinski, Michael I. Jordan, and Eran Halperin. 2009. Genomic privacy and limits of individual detection in a pool. Nature Genetics 41, 9, 965--967.Google ScholarCross Ref
- Eric E. Schadt, Sangsoon Woo, and Ke Hao. 2012. Bayesian method to predict individual SNP genotypes from gene expression data. Nature Genetics 44, 5, 603--608.Google ScholarCross Ref
- Johanna M. Seddon, Robyn Reynolds, Yi Yu, Mark J. Daly, and Bernard Rosner. 2011. Risk models for progression to advanced age-related macular degeneration using demographic, environmental, genetic, and ocular factors. Ophthalmology 118, 11, 2203--2211.Google ScholarCross Ref
- Rebecca Skloot. 2013. The immortal life of Henrietta Lacks, the sequel. http://goo.gl/Oh8u4A.Google Scholar
- Rebecca Skloot and Bahni Turpin. 2010. The Immortal Life of Henrietta Lacks. Crown Publishers, New York, NY.Google Scholar
- Frank Stajano. 2009. Privacy in the era of genomics. netWorker 13, 4, 40--ff. Google ScholarDigital Library
- Frank Stajano, Lucia Bianchi, Pietro Liò, and Douwe Korff. 2008. Forensic genomics: kin privacy, driftnets and other open questions. In ACM Workshop on Privacy in the Electronic Society. 15--22. Google ScholarDigital Library
- Rob Stein. 2005. Found on the web, with DNA: a boy’s father. The Washington Post http://goo.gl/q6X16E.Google Scholar
- Latanya Sweeney, Akua Abu, and Julia Winn. 2013. Identifying participants in the personal genome project by name (a re-identification experiment). CoRR abs/1304.7605.Google Scholar
- Doug Szajda, Michael Pohl, Jason Owen, Barry G. Lawson, and Virginia Richmond. 2006. Toward a practical data privacy scheme for a distributed implementation of the Smith-Waterman genome sequence comparison algorithm. In Network and Distributed System Security Symposium.Google Scholar
- Ellen S. Tambor, Barbara A. Bernhardt, Joann Rodgers, Neil A. Holtzman, and Gail Geller. 2002. Mapping the human genome: an assessment of media coverage and public reaction. Genetics in Medicine 4, 1, 31--36.Google ScholarCross Ref
- Juan Ramón Troncoso-Pastoriza, Stefan Katzenbeisser, and Mehmet Celik. 2007. Privacy preserving error resilient DNA searching through oblivious automata. In ACM Conference on Computer and Communications Security. 519--528. Google ScholarDigital Library
- Michael C. Turchin and Joel N. Hirschhorn. 2012. Gencrypt: one-way cryptographic hashes to detect overlapping individuals across samples. Bioinformatics 28, 6, 886--888. Google ScholarDigital Library
- United States Supreme Court. 2013. Maryland v. King, 569 U.S. 6 (2013).Google Scholar
- John Craig Venter, Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith, Mark Yandell, Cheryl A. Evans, and others. 2001. The sequence of the human genome. Science 291, 5507, 1304--1351.Google Scholar
- Brittney R. Villalva. 2012. Madonna sterilization, star hires DNA team on tour. In The Christian Post. http://goo.gl/yj9p4v.Google Scholar
- Peter M. Visscher and William G. Hill. 2009. The limits of individual identification from sample allele frequencies: theory and statistical analysis. PLoS Genetics 5, 10, e1000628.Google ScholarCross Ref
- Isabel Wagner. 2015. Genomic privacy metrics: a systematic comparison. In Workshop on Genome Privacy. 50--59.Google ScholarCross Ref
- Rui Wang, Yong Fuga Li, XiaoFeng Wang, Haixu Tang, and Xiaoyong Zhou. 2009a. Learning your identity and disease from research papers: information leaks in genome wide association study. In ACM Conference on Computer and Communications Security. 534--544. Google ScholarDigital Library
- Rui Wang, XiaoFeng Wang, Zhou Li, Haixu Tang, Michael K. Reiter, and Zheng Dong. 2009b. Privacy-preserving genomic computation through program specialization. In ACM Conference on Computer and Communications Security. 338--347. Google ScholarDigital Library
- Wei Xie, Murat Kantarcioglu, William S. Bush, Dana Crawford, Joshua C. Denny, Raymond Heatherly, and Bradley A. Malin. 2014. SecureMA: protecting participant privacy in genetic association meta-analysis. Bioinformatics btu561.Google Scholar
- Fei Yu, Stephen E. Fienberg, Aleksandra B. Slavkovi, and Caroline Uhler. 2014. Scalable privacy-preserving data sharing methodology for genome-wide association studies. Journal of Biomedical Informatics 50, 0, 133--141.Google ScholarCross Ref
- Elias A. Zerhouni and Elizabeth G. Nabel. 2008. Protecting aggregate genomic data. Science 322, 5898, 44a.Google Scholar
Index Terms
- Privacy in the Genomic Era
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