Controlling the Signal: Practical Privacy Protection of Genomic Data Sharing through Beacon Services

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dc.contributor.ORCID0000-0001-6423-4533 (Kantarcioglu, M)en_US
dc.contributor.VIAF305367293 (Kantarcioglu, M)en_US
dc.contributor.authorWan, Zhiyuen_US
dc.contributor.authorVorobeychik, Yevgeniyen_US
dc.contributor.authorKantarcioglu, Muraten_US
dc.contributor.authorMalin, Bradleyen_US
dc.contributor.utdAuthorKantarcioglu, Muraten_US
dc.date.accessioned2018-09-24T15:29:15Z
dc.date.available2018-09-24T15:29:15Z
dc.date.created2017-07-26en_US
dc.date.issued2018-09-24
dc.description.abstractBackground: 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. Methods: 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. Results: 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. Conclusions: 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.en_US
dc.description.departmentErik Jonsson School of Engineering and Computer Scienceen_US
dc.description.sponsorshipNIH grants R01HG006844, RM1HG009034, U01HG006385, and U01HG006378.en_US
dc.identifier.bibliographicCitationWan, Zhiyu, Yevgeniy Vorobeychik, Murat Kantarcioglu, and Bradley Malin. 2017. "Controlling the signal: Practical privacy protection of genomic data sharing through Beacon services." 10 (Suppl. 2), doi:10.1186/s12920-017-0282-1en_US
dc.identifier.issn1755-8794en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/6108
dc.identifier.volume10 (Suppl. 2)en_US
dc.language.isoenen_US
dc.relation.urihttp://dx.doi.org/10.1186/s12920-017-0282-1en_US
dc.rightsCC BY 4.0 (Attribution)en_US
dc.rights©2017 The Authorsen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.source.journalBMC Medical Genomicsen_US
dc.subjectInformation Disseminationen_US
dc.subjectGeneticsen_US
dc.subjectGenomicsen_US
dc.subjectPerturbation (Mathematics)en_US
dc.subjectPrecision Medicineen_US
dc.subjectPrivacyen_US
dc.subjectGenetic Privacyen_US
dc.titleControlling the Signal: Practical Privacy Protection of Genomic Data Sharing through Beacon Servicesen_US
dc.type.genrearticleen_US

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