Privacy-preserving and robust watermarking on sequential genome data using belief propagation and local differential privacy

• Published in: Bioinformatics (Oxford, England) Vol. 37; no. 17; pp. 2668 - 2674
• Main Authors: Öksüz, Abdullah Çağlar, Ayday, Erman, Güdükbay, Uğur
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 09.09.2021; Oxford Publishing Limited (England)
• Subjects: Availability; Bioinformatics; Collusion; Embedding; Gene frequency; Gene sequencing; Genomes; Human Genome Project; Liability; Linkage disequilibrium; Original Papers; Phenotypes; Privacy; Robustness; Watermarking
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/btab128

Abstract Motivation Genome data is a subject of study for both biology and computer science since the start of the Human Genome Project in 1990. Since then, genome sequencing for medical and social purposes becomes more and more available and affordable. Genome data can be shared on public websites or with service providers (SPs). However, this sharing compromises the privacy of donors even under partial sharing conditions. We mainly focus on the liability aspect ensued by the unauthorized sharing of these genome data. One of the techniques to address the liability issues in data sharing is the watermarking mechanism. Results To detect malicious correspondents and SPs—whose aim is to share genome data without individuals’ consent and undetected—, we propose a novel watermarking method on sequential genome data using belief propagation algorithm. In our method, we have two criteria to satisfy. (i) Embedding robust watermarks so that the malicious adversaries cannot temper the watermark by modification and are identified with high probability. (ii) Achieving ϵ-local differential privacy in all data sharings with SPs. For the preservation of system robustness against single SP and collusion attacks, we consider publicly available genomic information like Minor Allele Frequency, Linkage Disequilibrium, Phenotype Information and Familial Information. Our proposed scheme achieves 100% detection rate against the single SP attacks with only 3% watermark length. For the worst case scenario of collusion attacks (50% of SPs are malicious), 80% detection is achieved with 5% watermark length and 90% detection is achieved with 10% watermark length. For all cases, the impact of ϵ on precision remained negligible and high privacy is ensured. Availability and implementation https://github.com/acoksuz/PPRW\_SGD\_BPLDP Supplementary information Supplementary data are available at Bioinformatics online.