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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.

Generative machine learning models such as Generative Adversarial Networks (GANs) have been shown to be especially successful in generating realistic synthetic data in image and tabular domains. However, it has been shown that such generative models, as well as the generated synthetic data, can reveal information contained in their privacy-sensitive training data, and therefore must be carefully evaluated before being used. The gold standard method through which such privacy leakage can be estimated is simulating membership inference attacks (MIAs), in which an attacker attempts to learn whether a given sample was part of the training data of a generative model. The state-of-the art MIAs against generative models, however, rely on strong assumptions (knowledge of the exact training dataset size), or require a lot of computational power (to retrain many “surrogate” generative models), which make them hard to use in practice. In this work, we propose a technique for evaluating privacy risks in GANs which exploits the outputs of the discriminator part of the standard GAN architecture. We evaluate our attacks in terms of performance in two synthetic image generation applications in radiology and ophthalmology, showing that our technique provides a more complete picture of the threats by performing worst-case privacy risk estimation and by identifying attacks with higher precision than the prior work. [ABSTRACT FROM AUTHOR]

Predictive modeling holds a large potential in clinical decision-making, yet its effectiveness can be hindered by inherent data imbalances in clinical datasets. This study investigates the utility of synthetic data for improving the performance of predictive modeling on realistic small imbalanced clinical datasets. We compared various synthetic data generation methods including Generative Adversarial Networks, Normalizing Flows, and Variational Autoencoders to the standard baselines for correcting for class underrepresentation on four clinical datasets. Although results show improvement in F1 scores in some cases, even over multiple repetitions, we do not obtain statistically significant evidence that synthetic data generation outperforms standard baselines for correcting for class imbalance. This study challenges common beliefs about the efficacy of synthetic data for data augmentation and highlights the importance of evaluating new complex methods against simple baselines. [ABSTRACT FROM AUTHOR]

In a national effort aiming at cross-hospitals data interoperability, the Swiss Personalized Health Network elected RDF as preferred data and meta-data representation format. Yet, most clinical research software solutions are not designed to interact with RDF databases. We present a modular Python toolkit allowing easy conversion from RDF graphs to i2b2, adaptable to other common data models (CDM) with reasonable efforts. The tool was designed with feedback from clinicians in both oncology and laboratory research. [ABSTRACT FROM AUTHOR]

Medical studies are usually time consuming, cumbersome and extremely costly to perform, and for exploratory research, their results are also difficult to predict a priori. This is particularly the case for rare diseases, for which finding enough patients is difficult and usually requires an international-scale research. In this case, the process can be even more difficult due to the heterogeneity of data protection regulations, making the data sharing process particularly hard. In this short paper, we propose MedCo² (pronounced MedCo square), a distributed system that streamlines the process of a medical study by bridging and enabling both data discovery and data analysis among multiple databases, while protecting data confidentiality and patients’ privacy. MedCo² relies on interactive protocols, homomorphic encryption and differential privacy. It enables the privacy preserving computations of multiple statistics such as cosine similarity and variance, and the training of machine learning models, on patients that are obliviously selected according to specific criteria among multiple databases. [ABSTRACT FROM AUTHOR]

One major obstacle to developing precision medicine to its full potential is the privacy concerns related to genomic-data sharing. Even though the academic community has proposed many solutions to protect genomic privacy, these so far have not been adopted in practice, mainly due to their impact on the data utility. We introduce GenoShare, a framework that enables individual citizens to understand and quantify the risks of revealing genome-related privacy-sensitive attributes (e.g., health status, kinship, physical traits) from sharing their genomic data with (potentially untrusted) third parties. GenoShare enables informed decision-making about sharing exact genomic data, by jointly simulating genome-based inference attacks and quantifying the risk stemming from a potential data disclosure. [ABSTRACT FROM AUTHOR]

Background: Cloud computing is becoming the preferred solution for efficiently dealing with the increasing amount of genomic data. Yet, outsourcing storage and processing sensitive information, such as genomic data, comes with important concerns related to privacy and security. This calls for new sophisticated techniques that ensure data protection from untrusted cloud providers and that still enable researchers to obtain useful information. Methods: We present a novel privacy-preserving algorithm for fully outsourcing the storage of large genomic data files to a public cloud and enabling researchers to efficiently search for variants of interest. In order to protect data and query confidentiality from possible leakage, our solution exploits optimal encoding for genomic variants and combines it with homomorphic encryption and private information retrieval. Our proposed algorithm is implemented in C++ and was evaluated on real data as part of the 2016 iDash Genome Privacy-Protection Challenge. Results: Results show that our solution outperforms the state-of-the-art solutions and enables researchers to search over millions of encrypted variants in a few seconds. Conclusions: As opposed to prior beliefs that sophisticated privacy-enhancing technologies (PETs) are unpractical for real operational settings, our solution demonstrates that, in the case of genomic data, PETs are very efficient enablers. [ABSTRACT FROM AUTHOR]

The biomedical community is lagging in the adoption of cloud computing for the management of medical data. The primary obstacles are concerns about privacy and security. In this paper, we explore the feasibility of using advanced privacy-enhancing technologies in order to enable the sharing of sensitive clinical data in a public cloud. Our goal is to facilitate sharing of clinical data in the cloud by minimizing the risk of unintended leakage of sensitive clinical information. In particular, we focus on homomorphic encryption, a specific type of encryption that offers the ability to run computation on the data while the data remains encrypted. This paper demonstrates that homomorphic encryption can be used efficiently to compute aggregating queries on the ciphertexts, along with providing end-to-end confidentiality of aggregate-level data from the i2b2 data model.