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Register a new userPrivacy in the Genomic Era
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Added by
Muhammad Naveed
Publication date
2014
fields
Informatics Engineering
and research's language is
English
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Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.
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In this paper, we attempt to provide a privacy-preserving and efficient solution for the similar patient search problem among several parties (e.g., hospitals) by addressing the shortcomings of previous attempts. We consider a scenario in which each hospital has its own genomic dataset and the goal of a physician (or researcher) is to search for a patient similar to a given one (based on a genomic makeup) among all the hospitals in the system. To enable this search, we let each hospital encrypt its dataset with its own key and outsource the storage of its dataset to a public cloud. The physician can get authorization from multiple hospitals and send a query to the cloud, which efficiently performs the search across authorized hospitals using a privacy-preserving index structure. We propose a hierarchical index structure to index each hospitals dataset with low memory requirements. Furthermore, we develop a novel privacy-preserving index merging mechanism that generates a common search index from individual indices of each hospital to significantly improve the search efficiency. We also consider the storage of medical information associated with genomic data of a patient (e.g., diagnosis and treatment). We allow access to this information via a fine-grained access control policy that we develop through the combination of standard symmetric encryption and ciphertext policy attribute-based encryption. Using this mechanism, a physician can search for similar patients and obtain medical information about the matching records if the access policy holds. We conduct experiments on large-scale genomic data and show the efficiency of the proposed scheme. Notably, we show that under our experimental settings, the proposed scheme is more than $60$ times faster than Wang et al.s protocol and $95$ times faster than Asharov et al.s solution.
Privacy-preserving genomic data sharing is prominent to increase the pace of genomic research, and hence to pave the way towards personalized genomic medicine. In this paper, we introduce ($epsilon , T$)-dependent local differential privacy (LDP) for privacy-preserving sharing of correlated data and propose a genomic data sharing mechanism under this privacy definition. We first show that the original definition of LDP is not suitable for genomic data sharing, and then we propose a new mechanism to share genomic data. The proposed mechanism considers the correlations in data during data sharing, eliminates statistically unlikely data values beforehand, and adjusts the probability distributions for each shared data point accordingly. By doing so, we show that we can avoid an attacker from inferring the correct values of the shared data points by utilizing the correlations in the data. By adjusting the probability distributions of the shared states of each data point, we also improve the utility of shared data for the data collector. Furthermore, we develop a greedy algorithm that strategically identifies the processing order of the shared data points with the aim of maximizing the utility of the shared data. Considering the interdependent privacy risks while sharing genomic data, we also analyze the information gain of an attacker about genomes of a donors family members by observing perturbed data of the genome donor and we propose a mechanism to select the privacy budget (i.e., $epsilon$ parameter of LDP) of the donor by also considering privacy preferences of her family members. Our evaluation results on a real-life genomic dataset show the superiority of the proposed mechanism compared to the randomized response mechanism (a widely used technique to achieve LDP).
Trusted execution environments (TEE) such as Intels Software Guard Extension (SGX) have been widely studied to boost security and privacy protection for the computation of sensitive data such as human genomics. However, a performance hurdle is often generated by SGX, especially from the small enclave memory. In this paper, we propose a new Hybrid Secured Flow framework (called HySec-Flow) for large-scale genomic data analysis using SGX platforms. Here, the data-intensive computing tasks can be partitioned into independent subtasks to be deployed into distinct secured and non-secured containers, therefore allowing for parallel execution while alleviating the limited size of Page Cache (EPC) memory in each enclave. We illustrate our contributions using a workflow supporting indexing, alignment, dispatching, and merging the execution of SGX- enabled containers. We provide details regarding the architecture of the trusted and untrusted components and the underlying Scorn and Graphene support as generic shielding execution frameworks to port legacy code. We thoroughly evaluate the performance of our privacy-preserving reads mapping algorithm using real human genome sequencing data. The results demonstrate that the performance is enhanced by partitioning the time-consuming genomic computation into subtasks compared to the conventional execution of the data-intensive reads mapping algorithm in an enclave. The proposed HySec-Flow framework is made available as an open-source and adapted to the data-parallel computation of other large-scale genomic tasks requiring security and scalable computational resources.
Signatures are primarily used as a mark of authenticity, to demonstrate that the sender of a message is who they claim to be. In the current digital age, signatures underpin trust in the vast majority of information that we exchange, particularly on public networks such as the internet. However, schemes for signing digital information which are based on assumptions of computational complexity are facing challenges from advances in mathematics, the capability of computers, and the advent of the quantum era. Here we present a review of digital signature schemes, looking at their origins and where they are under threat. Next, we introduce post-quantum digital schemes, which are being developed with the specific intent of mitigating against threats from quantum algorithms whilst still relying on digital processes and infrastructure. Finally, we review schemes for signing information carried on quantum channels, which promise provable security metrics. Signatures were invented as a practical means of authenticating communications and it is important that the practicality of novel signature schemes is considered carefully, which is kept as a common theme of interest throughout this review.
The availability of genomic data is often essential to progress in biomedical research, personalized medicine, drug development, etc. However, its extreme sensitivity makes it problematic, if not outright impossible, to publish or share it. As a result, several initiatives have been launched to experiment with synthetic genomic data, e.g., using generative models to learn the underlying distribution of the real data and generate artificial datasets that preserve its salient characteristics without exposing it. This paper provides the first evaluation of the utility and the privacy protection of six state-of-the-art models for generating synthetic genomic data. We assess the performance of the synthetic data on several common tasks, such as allele population statistics and linkage disequilibrium. We then measure privacy through the lens of membership inference attacks, i.e., inferring whether a record was part of the training data. Our experiments show that no single approach to generate synthetic genomic data yields both high utility and strong privacy across the board. Also, the size and nature of the training dataset matter. Moreover, while some combinations of datasets and models produce synthetic data with distributions close to the real data, there often are target data points that are vulnerable to membership inference. Looking forward, our techniques can be used by practitioners to assess the risks of deploying synthetic genomic data in the wild and serve as a benchmark for future work.
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