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Aftermath of bustamante attack on genomic beacon service.

ABSTRACT: With the enormous need for federated eco-system for holding global genomic and clinical data, Global Alliance for Genomic and Health (GA4GH) has created an international website called beacon service which allows a researcher to find out whether a specific dataset can be utilized to his or her research beforehand. This simple webservice is quite useful as it allows queries like whether a certain position of a target chromosome has a specific nucleotide. However, the increased integration of individuals genomic data into clinical practice and research raised serious privacy concern. Though the answer of such queries are yes or no in Bacon network, it results in serious privacy implication as demonstrated in a recent work from Shringarpure and Bustamante. In their attack model, the authors demonstrated that with a limited number of queries, presence of an individual in any dataset can be determined.We propose two lightweight algorithms (based on randomized response) which captures the efficacy while preserving the privacy of the participants in a genomic beacon service. We also elaborate the strength and weakness of the attack by explaining some of their statistical and mathematical models using real world genomic database. We extend their experimental simulations for different adversarial assumptions and parameters.We experimentally evaluated the solutions on the original attack model with different parameters for better understanding of the privacy and utility tradeoffs provided by these two methods. Also, the statistical analysis further elaborates the different aspects of the prior attack which leads to a better risk management for the participants in a beacon service.The differentially private and lightweight solutions discussed here will make the attack much difficult to succeed while maintaining the fundamental motivation of beacon database network.

SUBMITTER: Aziz MMA

PROVIDER: S-EPMC5547468 | biostudies-other | 2017 Jul

REPOSITORIES: biostudies-other

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Project description:Genomic data is increasingly collected by a wide array of organizations. As such, there is a growing demand to make summary information about such collections available more widely. However, over the past decade, a series of investigations have shown that attacks, rooted in statistical inference methods, can be applied to discern the presence of a known individual's DNA sequence in the pool of subjects. Recently, it was shown that the Beacon Project of the Global Alliance for Genomics and Health, a web service for querying about the presence (or absence) of a specific allele, was vulnerable. The Integrating Data for Analysis, Anonymization, and Sharing (iDASH) Center modeled a track in their third Privacy Protection Challenge on how to mitigate the Beacon vulnerability. We developed the winning solution for this track.This paper describes our computational method to optimize the tradeoff between the utility and the privacy of the Beacon service. We generalize the genomic data sharing problem beyond that which was introduced in the iDASH Challenge to be more representative of real world scenarios to allow for a more comprehensive evaluation. We then conduct a sensitivity analysis of our method with respect to several state-of-the-art methods using a dataset of 400,000 positions in Chromosome 10 for 500 individuals from Phase 3 of the 1000 Genomes Project. All methods are evaluated for utility, privacy and efficiency.Our method achieves better performance than all state-of-the-art methods, irrespective of how key factors (e.g., the allele frequency in the population, the size of the pool and utility weights) change from the original parameters of the problem. We further illustrate that it is possible for our method to exhibit subpar performance under special cases of allele query sequences. However, we show our method can be extended to address this issue when the query sequence is fixed and known a priori to the data custodian, so that they may plan stage their responses accordingly.This research shows that it is possible to thwart the attack on Beacon services, without substantially altering the utility of the system, using computational methods. The method we initially developed is limited by the design of the scenario and evaluation protocol for the iDASH Challenge; however, it can be improved by allowing the data custodian to act in a staged manner.

Project description:OBJECTIVES:The aim of this study was to examine the impact of transient ischaemic attack (TIA) service modification in two hospitals on costs and clinical outcomes. DESIGN:Discrete event simulation model using data from routine electronic health records from 2011. PARTICIPANTS:Patients with suspected TIA were followed from symptom onset to presentation, referral to specialist clinics, treatment and subsequent stroke. INTERVENTIONS:Included existing versus previous (less same day clinics) and hypothetical service reconfiguration (7-day service with less availability of clinics per day). OUTCOME MEASURES:The primary outcome of the model was the prevalence of major stroke after TIA. Secondary outcomes included service costs (including those of treating subsequent stroke) and time to treatment and attainment of national targets for service provision (proportion of high-risk patients (according to ABCD2 score) seen within 24?hours). RESULTS:The estimated costs of previous service provision for 490 patients (aged 74±12 years, 48.9% female and 23.6% high risk) per year at each site were £340?000 and £368?000, respectively. This resulted in 31% of high-risk patients seen within 24?hours of referral (47/150) with a median time from referral to clinic attendance/treatment of 1.15 days (IQR 0.93-2.88). The costs associated with the existing and hypothetical services decreased by £5000 at one site and increased £21?000 at the other site. Target attainment was improved to 79% (118/150). However, the median time to clinic attendance was only reduced to 0.85 days (IQR 0.17-0.99) and thus no appreciable impact on the modelled incidence of major stroke was observed (10.7 per year, 99%?CI 10.5 to 10.9 (previous service) vs 10.6 per year, 99%?CI 10.4 to 10.8 (existing service)). CONCLUSIONS:Reconfiguration of services for TIA is effective at increasing target attainment, but in services which are already working efficiently (treating patients within 1-2 days), it has little estimated impact on clinical outcomes and increased investment may not be worthwhile.

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Aftermath of bustamante attack on genomic beacon service.

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