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Bioinformatics. 2015 Jun 1;31(11):1701-7. doi: 10.1093/bioinformatics/btv018. Epub 2015 Jan 27.

Deterministic identification of specific individuals from GWAS results.

Author information

1
School of Computer Science and Technology, Guangdong University of Technology, Guangzhou, China, 510000, Advanced Digital Sciences Center, Illinois at Singapore Pte. Ltd., Singapore, 138632, Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, 61801-2302, School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, College of Science, Engineering and Technology, Hamad Bin Khalifa University, Doha, Qatar and School of Computing, Fudan University, Shanghai, China, 200433 School of Computer Science and Technology, Guangdong University of Technology, Guangzhou, China, 510000, Advanced Digital Sciences Center, Illinois at Singapore Pte. Ltd., Singapore, 138632, Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, 61801-2302, School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, College of Science, Engineering and Technology, Hamad Bin Khalifa University, Doha, Qatar and School of Computing, Fudan University, Shanghai, China, 200433.
2
School of Computer Science and Technology, Guangdong University of Technology, Guangzhou, China, 510000, Advanced Digital Sciences Center, Illinois at Singapore Pte. Ltd., Singapore, 138632, Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, 61801-2302, School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, College of Science, Engineering and Technology, Hamad Bin Khalifa University, Doha, Qatar and School of Computing, Fudan University, Shanghai, China, 200433.

Abstract

MOTIVATION:

Genome-wide association studies (GWASs) are commonly applied on human genomic data to understand the causal gene combinations statistically connected to certain diseases. Patients involved in these GWASs could be re-identified when the studies release statistical information on a large number of single-nucleotide polymorphisms. Subsequent work, however, found that such privacy attacks are theoretically possible but unsuccessful and unconvincing in real settings.

RESULTS:

We derive the first practical privacy attack that can successfully identify specific individuals from limited published associations from the Wellcome Trust Case Control Consortium (WTCCC) dataset. For GWAS results computed over 25 randomly selected loci, our algorithm always pinpoints at least one patient from the WTCCC dataset. Moreover, the number of re-identified patients grows rapidly with the number of published genotypes. Finally, we discuss prevention methods to disable the attack, thus providing a solution for enhancing patient privacy.

AVAILABILITY AND IMPLEMENTATION:

Proofs of the theorems and additional experimental results are available in the support online documents. The attack algorithm codes are publicly available at https://sites.google.com/site/zhangzhenjie/GWAS_attack.zip. The genomic dataset used in the experiments is available at http://www.wtccc.org.uk/ on request.

PMID:
25630377
PMCID:
PMC4443672
DOI:
10.1093/bioinformatics/btv018
[Indexed for MEDLINE]
Free PMC Article

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