A community assessment of privacy preserving techniques for human genomes

BMC Medical Informatics and Decision Making

Volumn 14, Issue 1, 2014, Pages

  Jiang, Xiaoqian ^a   Zhao, Yongan ^b   Wang, Xiaofeng ^b   Malin, Bradley ^c   Wang, Shuang ^a   Ohno Machado, Lucila ^a   Tang, Haixu ^b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b INDIANA UNIVERSITY   (United States)

^c VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Data sharing; Differential privacy; Genome wide association studies; Privacy protection

Indexed keywords

ANONYMIZATION; COMMUNITY ASSESSMENT; GENETIC PRIVACY; GENOME-WIDE ASSOCIATION STUDY; HUMAN; HUMAN GENOME; GENETIC ASSOCIATION; INFORMATION DISSEMINATION; STANDARDS;

GENETIC PRIVACY; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INFORMATION DISSEMINATION;

EID: 84964313265     PISSN: None     EISSN: 14726947     Source Type: Journal    
DOI: 10.1186/1472-6947-14-S1-S1     Document Type: Article

References (31)

1. Ohno-Machado L: Sharing data for the public good and protecting individual privacy: informatics solutions to combine different goals. J Am Med Inform Assoc. 2013, 20: 1-10.1136/amiajnl-2012-001513.
2. Willer CJ, Li Y, Abecasis GR: METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics. 2010, 26: 2190-1. 10.1093/bioinformatics/btq340.
3. Green ED, Guyer MS, Institute NHGR, et al: Charting a course for genomic medicine from base pairs to bedside. Nature. 2011, 470: 204-13. 10.1038/nature09764.
4. McGuire AL, Fisher R, Cusenza P, et al: Confidentiality, privacy, and security of genetic and genomic test information in electronic health records: points to consider. Genet Med. 2008, 10: 495-9. 10.1097/GIM.0b013e31817a8aaa.
5. Shoenbill K, Fost N, Tachinardi U, et al: Genetic data and electronic health records: a discussion of ethical, logistical and technological considerations. J Am Med Inform Assoc. 2013, 21: 171-80.
6. Lin Z, Owen AB, Altman RB: Genomic research and human subject privacy. Science (80-). 2004, 305: 183-10.1126/science.1095019.
7. Erlich Y, Narayanan A: Routes for breaching and protecting genetic privacy. Nat Rev Genet. 2014, 15: 409-21. 10.1038/nrg3723.
8. Naveed M, Ayday E, Clayton EW, et al: Privacy and Security in the Genomic Era. arXiv. 2014, 1405.1891v: 1-47.
9. Gymrek M, McGuire AL, Golan D, et al: Identifying personal genomes by surname inference. Science (80-). 2013, 339: 321-4. 10.1126/science.1229566.
10. Homer N, Szelinger S, Redman M, et al: Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet. 2008, 4: e1000167-10.1371/journal.pgen.1000167.
11. Kaye J, Heeney C, Hawkins N, et al: Data sharing in genomics - re-shaping scientific practice. Nat Rev Genet. 2009, 10: 331-5. 10.1038/nrg2573.
12. Craig DW, Goor RM, Wang Z, et al: Assessing and managing risk when sharing aggregate genetic variant data. Nat Rev Genet. 2011, 12: 730-6. 10.1038/nrg3067. (accessed 11 Aug2014), [ http://www.nature.com/nrg/journal/v12/n10/abs/nrg3067.html ]
13. Sankararaman S, Obozinski G, Jordan MI, et al: Genomic privacy and limits of individual detection in a pool. Nat Genet. 2009, 41: 965-7. 10.1038/ng.436. (accessed 18 Apr2014), [ http://dx.doi.org/10.1038/ng.436 ]
14. Kantarcioglu M, Jiang W, Liu Y, et al: A cryptographic approach to securely share and query genomic sequences. IEEE Trans Inf Technol Biomed. 2008, 12: 606-17.
15. Kamm L, Bogdanov D, Laur S, et al: A new way to protect privacy in large-scale genome-wide association studies. Bioinformatics. 2013, 29: 886-93. 10.1093/bioinformatics/btt066.
16. Baldi P, Baronio R, Cristofaro E De: Countering gattaca: efficient and secure testing of fully-sequenced human genomes. CCS '11 Proceedings of the 18th ACM conference on Computer and communications security. 2011, 691-702.
17. B EA, Raisaro JL, Hengartner U, et al: Data Privacy Management and Autonomous Spontaneous Security. 2014, Berlin, Heidelberg:: Springer Berlin Heidelberg
18. Agrawal R, Kiernan J, Srikant R, et al: Order preserving encryption for numeric data. Proceedings of the 2004 ACM SIGMOD international conference on Management of data - SIGMOD '04. 2004, New York, USA: ACM Press, 563-
19. Agrawal R, Srikant R: Privacy-preserving data mining. Proceedings of the 2000 ACM SIGMOD international conference on Management of data - SIGMOD '00. 2000, New York, USA: ACM Press, 439-50.
20. Dwork C: Differential privacy. Int Colloq Autom Lang Program. 2006, 4052: 1-12.
21. Jiang X, Sarwate AD, Ohno-Machado L: Privacy technology to support data sharing for comparative effectiveness research: a systematic review. Med Care. 2013, 51: S58-65.
22. The International HapMap Project. [ http://hapmap.ncbi.nlm.nih.gov/index.html.en ]
23. Church GM: The personal genome project. Mol Syst Biol. 2005, 1: 2005.0030-
24. Dwork C, McSherry F, Nissim K, et al: Calibrating noise to sensitivity in private data analysis. Theory Cryptogr. 2006, 3876: 265-84. 10.1007/11681878-14.
25. McSherry F, Talwar K: Mechanism Design via Differential Privacy. 48th Annual IEEE Symposium on Foundations of Computer Science (FOCS'07). 2007, Providence, RI:: IEEE, 94-103.
26. Chernoff H, Lehmann EL, et al: The use of maximum likelihood estimates in χ tests for goodness of fit. Ann Math Stat. 1954, 25: 579-86. 10.1214/aoms/1177728726.
27. Barrett JC, Fry B, Maller J, et al: Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005, 21: 263-5. 10.1093/bioinformatics/bth457.
28. Scheet P, Stephens M: A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006, 78: 629-44. 10.1086/502802.
29. Wang S, Mohammed N, Chen R: Differentially Private Genome Data Dissemination through Top-Down Specialization. BMC Med informatics Decis Mak. 2014, 14 (S1): S2-
30. Yu F, Ji Z: Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies: An Application to iDASH Healthcare Privacy Protection Challenge. BMC Med Informatics Decis Mak. 2014, 14 (S1): S3-
31. Ohno-Machado L, Bafna V, Boxwala Aa, et al: iDASH. Integrating data for analysis, anonymization, and sharing. J Am Med Informatics Assoc. 2012, 19: 196-201. 10.1136/amiajnl-2011-000538.