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Genomic privacy and limits of individual detection in a pool

Nature Genetics volume 41, pages 965–967 (2009)Cite this article

Abstract

Recent studies have demonstrated that statistical methods can be used to detect the presence of a single individual within a study group based on summary data reported from genome-wide association studies (GWAS). We present an analytical and empirical study of the statistical power of such methods. We thereby aim to provide quantitative guidelines for researchers wishing to make a limited number of SNPs available publicly without compromising subjects' privacy.

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Figure 1: ROC curves comparing the LR test with a plug-in allele frequency estimate, its theoretical power (denoted “LR theory”) as computed using a modified version of equation (1) corrected to account for the use of the plug-in estimate, and the statistic proposed by Homer et al.1 on a pool of size n = 1,000.
Figure 2: The power attained by the LR test is not population specific.

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References

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Acknowledgements

E.H. was supported by US National Science Foundation grant IIS-0713254. E.H. is a faculty fellow of the Edmond J. Safra Bioinformatics program at Tel-Aviv University. M.I.J., S.S. and G.O. were supported by NIH/NIGMS R01 grant GM071749. This study makes use of data generated by the Wellcome Trust Case Control Consortium; a full list of the investigators who contributed to the generation of the data is available from http://www.wtccc.org.uk. Funding for the project was provided by the Wellcome Trust under award 076113.

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Author notes

  1. Sriram Sankararaman and Guillaume Obozinski: These authors contributed equally to this work.

Authors and Affiliations

  1. Computer Science Division, University of California, Berkeley, Berkeley, California, USA

    Sriram Sankararaman & Michael I Jordan

  2. Department of Statistics, University of California, Berkeley, Berkeley, California, USA

    Guillaume Obozinski & Michael I Jordan

  3. International Computer Science Institute, Berkeley, California, USA

    Eran Halperin

  4. School of Computer Science and the Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv, Israel

    Eran Halperin

Authors
  1. Sriram Sankararaman
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  2. Guillaume Obozinski
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  3. Michael I Jordan
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  4. Eran Halperin
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Contributions

S.S. and G.O. contributed to the design of the experiments and implemented the experiments; they also developed the theoretical analysis and contributed to writing the paper. M.I.J. contributed to the design of the experiments, the theoretical analysis and the writing of the paper as well as to the funding of the project. E.H. initiated the project and proposed the framework, and he contributed to the design of the experiments, the theoretical analysis, the writing of the paper and the funding of the project.

Corresponding author

Correspondence to Eran Halperin.

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Supplementary Figures 1–7, Supplementary Methods and Supplementary Note (PDF 764 kb)

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Sankararaman, S., Obozinski, G., Jordan, M. et al. Genomic privacy and limits of individual detection in a pool. Nat Genet 41, 965–967 (2009). https://doi.org/10.1038/ng.436

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