Inference Attacks and Controls on Genotypes and Phenotypes for Individual Genomic Data

The rapid growth of DNA-sequencing technologies motivates more personalized and predictive genetic-oriented services, which further attract individuals to increasingly release their genome information to learn about personalized medicines, disease predispositions, genetic compatibilities, etc. Individual genome information is notoriously privacy-sensitive and highly associated with relatives. In this paper, we present an inference attack algorithm to predict target genotypes and phenotypes based on belief propagation in factor graphs. With this algorithm, an attacker can effectively predict the target genotypes and phenotypes of target individuals based on genome information shared by individuals or their relatives, and genotype and phenotype association from genome-wide association study (GWAS). To address the privacy threats resulted from such inference attacks, we elaborate the metrics to evaluate data utility and privacy and then present a data sanitization method. We evaluate our inference attack algorithm and data sanitization method on real GWAS dataset: Age-related macular degeneration (AMD) case/control dataset. The evaluation results show that our work can effectively defense against genome threats while guaranteeing data utility.