Bilkent University
Department of Computer Engineering
CS 590/690 SEMINAR
Beacon Reconstruction Attack: Reconstruction of genomes in genomic data-sharing beacons using summary statistics
Kousar Kousar
Master Student
(Supervisor: Asst.Prof.Sinem Sav)
Computer Engineering Department
Bilkent University
Abstract: Genomic data sharing beacon protocol, developed by the Global Alliance for Genomics and Health (GA4GH), offers a privacy-preserving mechanism for querying genomic datasets while restricting direct data access. Despite their design, beacons remain vulnerable to privacy attacks. This study introduces a novel privacy vulnerability of the protocol: One can reconstruct large portions of the genomes of all beacon participants by only using the summary statistics reported by the protocol. We introduce a novel optimization-based algorithm that leverages beacon responses and Single Nucleotide Polymorphism (SNP) correlations for reconstruction. By optimizing using the SNP correlations and allele frequencies, the proposed approach achieves genome reconstruction on beacons generated using individuals from the HapMap and OpenSNP datasets. Our findings reveal critical vulnerabilities in beacon protocol, underscoring the need for enhanced privacy-preserving mechanisms to protect genomic data.
DATE: March 24, Monday @ 14:30 Place: EA 502