A novel, privacy-preserving cryptographic approach for sharing sequencing data

Journal of the American Medical Informatics Association

Volumn 20, Issue 1, 2013, Pages 69-76

  Cassa, Christopher A ^a,b,c   Miller, Rachel A ^c   Mandl, Kenneth D ^b,d  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ARTICLE; COST; DNA SEQUENCE; ERROR; GENE LOCUS; GENE SEQUENCE; GENOTYPE; HUMAN; MEDICAL INFORMATION SYSTEM; PRIVACY;

COMPUTER SECURITY; DATABASES, NUCLEIC ACID; DNA FINGERPRINTING; ELECTRONIC HEALTH RECORDS; GENETIC PRIVACY; HUMANS; INFORMATION DISSEMINATION; MEDICAL RECORD LINKAGE; REPRODUCIBILITY OF RESULTS;

EID: 84871887995     PISSN: 10675027     EISSN: 1527974X     Source Type: Journal    
DOI: 10.1136/amiajnl-2012-001366     Document Type: Article

References (43)

1. Blow N. Biobanking: freezer burn. Nat Methods 2009;6:173-8.
2. Kohane IS, Mandl KD, Taylor PL, et al. Medicine. Reestablishing the researcher-patient compact. Science 2007;316:836-7.
3. Roden DM, Pulley JM, Basford MA, et al. Development of a large-scale de-identified DNA biobank to enable personalized medicine. Clin Pharmacol Ther 2008;84:362-9.
4. McGuire AL. 1000 Genomes on the Road to Personalized Medicine. Per Med 2008;5:195-7.
5. NCBI. Genetests.org. 2012. http://www.ncbi.nlm.nih.gov/sites/GeneTests/ (accessed 24 Oct 2012).
6. Illumina I. BaseSpace: Genomics Cloud Computing. 2012. http://basespace.illumina. com (accessed 24 Oct 2012).
7. Services AW. AWS Genomics Event. 2011. http://aws.amazon.com/ genomicsevent/ (accessed 24 Oct 2012).
8. Lin Z, Owen AB, Altman RB. Genetics. Genomic research and human subject privacy. Science 2004;305:183.
9. Cassa CA, Schmidt B, Kohane IS, et al. My sister's keeper?: genomic research and the identifiability of siblings. BMC Med Genomics 2008;1:32.
10. Bieber FR, Lazer D. Guilt by association: should the law be able to use one person's DNA to carry out surveillance on their family? Not without a public debate. New Sci 2004;184:20.
11. Bieber FR, Brenner CH, Lazer D. Human genetics. Finding criminals through DNA of their relatives. Science 2006;312:1315-6.
12. 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.
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.
14. Wang RYFL, Wang X, Tang H, et al. Learning your identity and disease from research papers: information leaks in genome wide association study. CCS '09: Proc of the 15th ACM Conf Comput Commun Secur 2009;15:534-44.
15. Benjamin EJ, Dupuis J, Larson MG, et al. Genome-wide association with select biomarker traits in the Framingham Heart Study. BMC Med Genet 2007;8(Suppl 1): S11.
16. Genome-Wide Association Studies. 2008. http://www.genome.gov/20019523 (accessed 24 Oct 2012).
17. Morton NE. Into the post-HapMap era. Adv Genet 2008;60:727-42.
18. Cappuccio FP, Oakeshott P, Strazzullo P, et al. Application of Framingham risk estimates to ethnic minorities in United Kingdom and implications for primary prevention of heart disease in general practice: cross sectional population based study. BMJ 2002;325:1271.
19. Colditz GA, Coakley E. Weight, weight gain, activity, and major illnesses: the Nurses' Health Study. Int J Sports Med 1997;18(Suppl 3):S162-70.
20. Empana JP, Ducimetiere P, Arveiler D, et al. Are the Framingham and PROCAM coronary heart disease risk functions applicable to different European populations? The PRIME Study. Eur Heart J 2003;24:1903-11.
21. NCBI. database of Genotypes and Phenotypes (dbGaP). 2012. http://www.ncbi.nlm. nih.gov/gap (accessed 24 Oct 2012).
22. NHLBI. NHLBI GO Exome Sequencing Project. 2012. http://esp.gs.washington.edu/ drupal/ (accessed 24 Oct 2012).
23. EBI. The European Genome-phenome Archive. 2012. http://www.ebi.ac.uk/ega/ (accessed 24 Oct 2012).
24. NCBI. ClinVar. 2012. http://www.ncbi.nlm.nih.gov/clinvar/ (accessed 24 Oct 2012).
25. Vadhan S. Randomness Extractors. 2012. http://people.seas.harvard.edu/~salil/ pseudorandomness/extractors.pdf (accessed 24 Oct 2012).
26. Venkatesan G, Umans C, Vadhan S. Unbalanced expanders and randomness extractors from Parvaresh-Vardy codes. J Assoc Comput Machinery 2009;56:Article 20.
27. Technology NIoSa. NIST Randomness Beacon. 2012. http://www.nist.gov/itl/csd/ ct/nist_beacon.cfm (accessed 24 Oct 2012).
28. EmbeddedSw.net. Cryptography - 256 bit ciphers: 256bit key - 128bit block - AES. 2012. http://embeddedsw.net/Cipher_Reference_Home.html#AES (accessed 24 Oct 2012).
29. Nishida N, Koike A, Tajima A, et al. Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals. BMC Genomics 2008;9:431.
30. Korn JM, Kuruvilla FG, McCarroll SA, et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat Genet 2008;40:1253-60.
31. Holden C. Genetic discrimination. Long-awaited genetic nondiscrimination bill headed for easy passage. Science 2007;316:676.
32. Hudson KL, Holohan MK, Collins FS. Keeping pace with the times-the Genetic Information Nondiscrimination Act of 2008. N Engl J Med 2008;358:2661-3.
33. Malin BA, Sweeney LA. Inferring genotype from clinical phenotype through a knowledge based algorithm. Pac Symp Biocomput 2002;41-52.
34. Henneman L, Timmermans DR, van der Wal G. Public experiences, knowledge and expectations about medical genetics and the use of genetic information. Commun Genet 2004;7:33-43.
35. Levitt DM. Let the consumer decide? The regulation of commercial genetic testing. J Med Ethics 2001;27:398-403.
36. Miller SM, Fleisher L, Roussi P, et al. Facilitating informed decision making about breast cancer risk and genetic counseling among women calling the NCI's Cancer Information Service. J Health Commun 2005;10:119-36.
37. Mouchawar J, Hensley-Alford S, Laurion S, et al. Impact of direct-to-consumer advertising for hereditary breast cancer testing on genetic services at a managed care organization: a naturally-occurring experiment. Genet Med 2005;7:191-7.
38. Mouchawar J, Laurion S, Ritzwoller DP, et al. Assessing controversial direct-to-consumer advertising for hereditary breast cancer testing: reactions from women and their physicians in a managed care organization. Am J Manag Care 2005;11:601-8.
39. Services USDoHH. The Privacy Rule. Health Information Privacy. 2002. http://www. hhs.gov/ocr/privacy/hipaa/administrative/privacyrule/index.html (accessed 24 Oct 2012).
40. Malin B, Loukides G, Benitez K, et al. Identifiability in biobanks: models, measures, and mitigation strategies. Hum Genet 2011;130:383-92.
41. 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.
42. Adida B, Kohane IS. GenePING: secure, scalable management of personal genomic data. BMC Genomics 2006;7:93.
43. (IETF) IETF. HMAC-based Extract-and-Expand Key Derivation Function (HKDF). ISSN:2070-1721 May 2010. http://tools.ietf.org/html/rfc5869 (accessed 24 Oct 2012).