The Global Alliance for Genomics and Health (GA4GH) created the Beacon Project as a means of testing the willingness of data holders to share genetic data in the simplest technical context—a query for the presence of a specified nucleotide at a given position within a chromosome. Each participating site (or “beacon”) is responsible for assuring that genomic data are exposed through the Beacon service only with the permission of the individual to whom the data pertains and in accordance with the GA4GH policy and standards.While recognizing the inference risks associated with large-scale data aggregation, and the fact that some beacons contain sensitive phenotypic associations that increase privacy risk, the GA4GH adjudged the risk of re-identification based on the binary yes/no allele-presence query responses as acceptable. However, recent work demonstrated that, given a beacon with specific characteristics (including relatively small sample size and an adversary who possesses an individual’s whole genome sequence), the individual’s membership in a beacon can be inferred through repeated queries for variants present in the individual’s genome.In this paper, we propose three practical strategies for reducing re-identification risks in beacons. The first two strategies manipulate the beacon such that the presence of rare alleles is obscured; the third strategy budgets the number of accesses per user for each individual genome. Using a beacon containing data from the 1000 Genomes Project, we demonstrate that the proposed strategies can effectively reduce re-identification risk in beacon-like datasets.

Edit distance has been proven to be an important and frequentlyused metric in many human genomic research, with Similar Patient Query (SPQ) being a particularly promising and attractive example. However, due to the widespread privacy concerns on revealing personal genomic data, the scope and scale of many novel use of genome edit distance are substantially limited. While the problem of private genomic edit distance has been studied by the research community for over a decade [5], the state-of-the-art solution [30] is far from even close to be applicable to real genome sequences. In this paper, we propose several private edit distance protocols that feature unprecedentedly high efficiency and precision. Our construction is a combination of a novel genomic edit distance approximation algorithm and new construction of private set difference size protocols. With the private edit distance based secure SPQ primitive, we propose GENSETS, a genome-wide, privacypreserving similar patient query system. It is able to support searching large-scale, distributed genome databases across the nation. We have implemented a prototype of GENSETS. The experimental results show that, with 100 Mbps network connection, it would take GENSETS less than 200 minutes to search through 1 million breast cancer patients (distributed nationwide in 250 hospitals, each having 4000 patients), based on edit distances between their genomes of lengths about 75 million nucleotides each.

Membership Inference Attack (MIA) determines the presence of a record in a machine learning model's training data by querying the model. Prior work has shown that the attack is feasible when the model is overfitted to its training data or when the adversary controls the training algorithm. However, when the model is not overfitted and the adversary does not control the training algorithm, the threat is not well understood. In this paper, we report a study that discovers overfitting to be a sufficient but not a necessary condition for an MIA to succeed. More specifically, we demonstrate that even a well-generalized model contains vulnerable instances subject to a new generalized MIA (GMIA). In GMIA, we use novel techniques for selecting vulnerable instances and detecting their subtle influences ignored by overfitting metrics. Specifically, we successfully identify individual records with high precision in real-world datasets by querying black-box machine learning models. Further we show that a vulnerable record can even be indirectly attacked by querying other related records and existing generalization techniques are found to be less effective in protecting the vulnerable instances. Our findings sharpen the understanding of the fundamental cause of the problem: the unique influences the training instance may have on the model.

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The human genome can reveal sensitive information and is potentially re-identifiable, which raises privacy and security concerns about sharing such data on wide scales. In 2016, we organized the third Critical Assessment of Data Privacy and Protection competition as a community effort to bring together biomedical informaticists, computer privacy and security researchers, and scholars in ethical, legal, and social implications (ELSI) to assess the latest advances on privacy-preserving techniques for protecting human genomic data. Teams were asked to develop novel protection methods for emerging genome privacy challenges in three scenarios: Track (1) data sharing through the Beacon service of the Global Alliance for Genomics and Health. Track (2) collaborative discovery of similar genomes between two institutions; and Track (3) data outsourcing to public cloud services. The latter two tracks represent continuing themes from our 2015 competition, while the former was new and a response to a recently established vulnerability. The winning strategy for Track 1 mitigated the privacy risk by hiding approximately 11% of the variation in the database while permitting around 160,000 queries, a significant improvement over the baseline. The winning strategies in Tracks 2 and 3 showed significant progress over the previous competition by achieving multiple orders of magnitude performance improvement in terms of computational runtime and memory requirements. The outcomes suggest that applying highly optimized privacy-preserving and secure computation techniques to safeguard genomic data sharing and analysis is useful. However, the results also indicate that further efforts are needed to refine these techniques into practical solutions.