{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T17:48:42Z","timestamp":1770140922556,"version":"3.49.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,12]],"date-time":"2022-02-12T00:00:00Z","timestamp":1644624000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"German Ministry of Research and Education","award":["01ZZ2010"],"award-info":[{"award-number":["01ZZ2010"]}]},{"name":"German Federal Ministry of Education and Research"},{"name":"DIFUTURE","award":["01ZZ1804D"],"award-info":[{"award-number":["01ZZ1804D"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Diagnosis and treatment decisions on genomic data have become widespread as the cost of genome sequencing decreases gradually. In this context, disease\u2013gene association studies are of great importance. However, genomic data are very sensitive when compared to other data types and contains information about individuals and their relatives. Many studies have shown that this information can be obtained from the query-response pairs on genomic databases. In this work, we propose a method that uses secure multi-party computation to query genomic databases in a privacy-protected manner. The proposed solution privately outsources genomic data from arbitrarily many sources to the two non-colluding proxies and allows genomic databases to be safely stored in semi-honest cloud environments. It provides data privacy, query privacy and output privacy by using XOR-based sharing and unlike previous solutions, it allows queries to run efficiently on hundreds of thousands of genomic data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We measure the performance of our solution with parameters similar to real-world applications. It is possible to query a genomic database with 3\u00a0000\u00a0000 variants with five genomic query predicates under 400\u2009ms. Querying 1\u00a0048\u00a0576 genomes, each containing 1\u00a0000\u00a0000 variants, for the presence of five different query variants can be achieved approximately in 6\u2009min with a small amount of dedicated hardware and connectivity. These execution times are in the right range to enable real-world applications in medical research and healthcare. Unlike previous studies, it is possible to query multiple databases with response times fast enough for practical application. To the best of our knowledge, this is the first solution that provides this performance for querying large-scale genomic data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/gitlab.com\/DIFUTURE\/privacy-preserving-variant-queries.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac070","type":"journal-article","created":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T04:17:01Z","timestamp":1643948221000},"page":"2202-2210","source":"Crossref","is-referenced-by-count":12,"title":["Efficient privacy-preserving whole-genome variant queries"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4088-2784","authenticated-orcid":false,"given":"Mete","family":"Akg\u00fcn","sequence":"first","affiliation":[{"name":"Medical Data Privacy and Privacy-Preserving ML on Healthcare Data, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen, Germany"},{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , T\u00fcbingen, Germany"},{"name":"Translational Bioinformatics, University Hospital T\u00fcbingen , T\u00fcbingen, Germany"},{"name":"Department of Computer Engineering, \u0130zmir Institute of Technology , \u0130zmir, Turkey"}]},{"given":"Nico","family":"Pfeifer","sequence":"additional","affiliation":[{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , T\u00fcbingen, Germany"},{"name":"Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen, Germany"},{"name":"Statistical Learning in Computational Biology, Max Planck Institute for Informatics , Saarbr\u00fccken, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1739-4598","authenticated-orcid":false,"given":"Oliver","family":"Kohlbacher","sequence":"additional","affiliation":[{"name":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , T\u00fcbingen, Germany"},{"name":"Translational Bioinformatics, University Hospital T\u00fcbingen , T\u00fcbingen, Germany"},{"name":"Applied Bioinformatics, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen, Germany"}]}],"member":"286","published-online":{"date-parts":[[2022,2,12]]},"reference":[{"key":"2023020109022245400_btac070-B1","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.jbi.2015.05.022","article-title":"Privacy preserving processing of genomic data: a survey","volume":"56","author":"Akg\u00fcn","year":"2015","journal-title":"J. Biomed. Inf"},{"key":"2023020109022245400_btac070-B2","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/j.ajhg.2018.08.007","article-title":"The clinical sequencing evidence-generating research consortium: integrating genomic sequencing in diverse and medically underserved populations","volume":"103","author":"Amendola","year":"2018","journal-title":"Am. J. Hum. Genet"},{"key":"2023020109022245400_btac070-B3","first-page":"535","author":"Asharov","year":"2013"},{"key":"2023020109022245400_btac070-B4","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1515\/popets-2018-0034","article-title":"Privacy-preserving search of similar patients in genomic data","volume":"2018","author":"Asharov","year":"2018","journal-title":"PoPETs"},{"key":"2023020109022245400_btac070-B5","first-page":"887","author":"Aziz","year":"2017"},{"key":"2023020109022245400_btac070-B6","first-page":"192","author":"Bogdanov","year":"2008"},{"key":"2023020109022245400_btac070-B7","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/B978-0-12-420196-5.00022-8","volume-title":"Medical and Health Genomics","author":"B\u00f8rsting","year":"2016"},{"key":"2023020109022245400_btac070-B8","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nature05911","article-title":"Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls","volume":"447","author":"Consortium","year":"2007","journal-title":"Nature"},{"key":"2023020109022245400_btac070-B9","author":"Demmler","year":"2015"},{"key":"2023020109022245400_btac070-B10","author":"Demmler","year":"2017"},{"key":"2023020109022245400_btac070-B11","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.tips.2016.10.013","article-title":"Cancer precision medicine: from cancer screening to drug selection and personalized immunotherapy","volume":"38","author":"Deng","year":"2017","journal-title":"Trends Pharmacol. Sci"},{"key":"2023020109022245400_btac070-B12","author":"Dierks","year":"2008"},{"key":"2023020109022245400_btac070-B13","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/nrg3723","article-title":"Routes for breaching and protecting genetic privacy","volume":"15","author":"Erlich","year":"2014","journal-title":"Nat. Rev. Genet"},{"key":"2023020109022245400_btac070-B14","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1515\/popets-2017-0047","article-title":"Unlynx: a decentralized system for privacy-conscious data sharing","volume":"2017","author":"Froelicher","year":"2017","journal-title":"PoPETs"},{"key":"2023020109022245400_btac070-B15","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1126\/science.aaf6162","article-title":"A federated ecosystem for sharing genomic, clinical data","volume":"352","year":"2016","journal-title":"Science"},{"key":"2023020109022245400_btac070-B16","first-page":"218","author":"Goldreich","year":"1987"},{"key":"2023020109022245400_btac070-B17","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.jbi.2018.03.003","article-title":"Secure count query on encrypted genomic data","volume":"81","author":"Hasan","year":"2018","journal-title":"J. Biomed. Inf"},{"key":"2023020109022245400_btac070-B18","author":"Huang","year":"2011"},{"key":"2023020109022245400_btac070-B19","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1038\/ng.3623","article-title":"Identification of 15 genetic loci associated with risk of major depression in individuals of European descent","volume":"48","author":"Hyde","year":"2016","journal-title":"Nat. Genet"},{"key":"2023020109022245400_btac070-B20","first-page":"216","author":"Jha","year":"2008"},{"key":"2023020109022245400_btac070-B21","first-page":"15","author":"Kamara","year":"2011"},{"key":"2023020109022245400_btac070-B22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-018-1506-1","article-title":"Consumer genomics will change your life, whether you get tested or not","volume":"19","author":"Khan","year":"2018","journal-title":"Genome Biol"},{"key":"2023020109022245400_btac070-B23","first-page":"359","author":"Liu","year":"2015"},{"key":"2023020109022245400_btac070-B24","first-page":"287","author":"Malkhi","year":"2004"},{"key":"2023020109022245400_btac070-B25","doi-asserted-by":"crossref","first-page":"87","DOI":"10.2478\/popets-2019-0006","article-title":"Systematizing genome privacy research: a privacy-enhancing technologies perspective","volume":"2019","author":"Mittos","year":"2019","journal-title":"PoPETs"},{"key":"2023020109022245400_btac070-B26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/2767007","article-title":"Privacy in the genomic era","volume":"486","author":"Naveed","year":"2015","journal-title":"ACM Comput. Surv"},{"key":"2023020109022245400_btac070-B27","first-page":"799","article-title":"Addressing beacon re-identification attacks: quantification and mitigation of privacy risks","volume":"24","author":"Raisaro","year":"2017","journal-title":"JAMIA"},{"key":"2023020109022245400_btac070-B28","doi-asserted-by":"crossref","first-page":"47","DOI":"10.2478\/popets-2019-0004","article-title":"Privacy-preserving similar patient queries for combined biomedical data","volume":"2019","author":"Salem","year":"2019","journal-title":"PoPETs"},{"key":"2023020109022245400_btac070-B29","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1016\/j.ajhg.2015.09.010","article-title":"Privacy risks from genomic data-sharing beacons","volume":"97","author":"Shringarpure","year":"2015","journal-title":"Am. J. Hum. Genet"},{"key":"2023020109022245400_btac070-B30","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s12920-017-0275-0","article-title":"Efficient and secure outsourcing of genomic data storage","volume":"10","author":"Sousa","year":"2017","journal-title":"BMC Med. Genomics"},{"key":"2023020109022245400_btac070-B31","doi-asserted-by":"crossref","first-page":"2316","DOI":"10.1093\/bioinformatics\/btz924","article-title":"Clinvap: a reporting strategy from variants to therapeutic options","volume":"36","author":"S\u00fcr\u00fcn","year":"2020","journal-title":"Bioinformatics"},{"key":"2023020109022245400_btac070-B32","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/bioinformatics\/bty643","article-title":"Re-identification of individuals in genomic data-sharing beacons via allele inference","volume":"35","author":"von Thenen","year":"2019","journal-title":"Bioinformatics"},{"key":"2023020109022245400_btac070-B33","first-page":"492","author":"Wang","year":"2015"},{"key":"2023020109022245400_btac070-B34","first-page":"162","volume-title":"Proceedings of the 27th Annual Symposium on Foundations of Computer Science, SFCS \u201986","author":"Yao","year":"1986"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac070\/42559134\/btac070.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/8\/2202\/49009695\/btac070.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/8\/2202\/49009695\/btac070.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:50:08Z","timestamp":1675284608000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/8\/2202\/6527622"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,2,12]]},"references-count":34,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2022,4,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac070","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,4,15]]},"published":{"date-parts":[[2022,2,12]]}}}