Choosing blindly but wisely: differentially private solicitation of DNA datasets for disease marker discovery

J Am Med Inform Assoc. 2015 Jan;22(1):100-8. doi: 10.1136/amiajnl-2014-003043. Epub 2014 Oct 28.


Objective: To propose a new approach to privacy preserving data selection, which helps the data users access human genomic datasets efficiently without undermining patients' privacy.

Methods: Our idea is to let each data owner publish a set of differentially-private pilot data, on which a data user can test-run arbitrary association-test algorithms, including those not known to the data owner a priori. We developed a suite of new techniques, including a pilot-data generation approach that leverages the linkage disequilibrium in the human genome to preserve both the utility of the data and the privacy of the patients, and a utility evaluation method that helps the user assess the value of the real data from its pilot version with high confidence.

Results: We evaluated our approach on real human genomic data using four popular association tests. Our study shows that the proposed approach can help data users make the right choices in most cases.

Conclusions: Even though the pilot data cannot be directly used for scientific discovery, it provides a useful indication of which datasets are more likely to be useful to data users, who can therefore approach the appropriate data owners to gain access to the data.

Keywords: Differential Privacy; Genome-wide association studies; Haplotype blocks; Privacy-preserving techniques; Single nucleotide polymorphisms (SNPs); Test statistics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Confidentiality*
  • DNA
  • Datasets as Topic*
  • Genetic Markers*
  • Genome, Human*
  • Genome-Wide Association Study
  • Humans
  • Polymorphism, Single Nucleotide


  • Genetic Markers
  • DNA