{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,12,14]],"date-time":"2023-12-14T21:59:10Z","timestamp":1702591150301},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,3,7]],"date-time":"2018-03-07T00:00:00Z","timestamp":1520380800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"German Federal Ministry of Health","award":["IIA5-2512-FSB-725"],"award-info":[{"award-number":["IIA5-2512-FSB-725"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>In next-generation sequencing, re-identification of individuals and other privacy-breaching strategies can be applied even for anonymized data. This also holds true for applications in which human DNA is acquired as a by-product, e.g. for viral or metagenomic samples from a human host. Conventional data protection strategies including cryptography and post-hoc filtering are only appropriate for the final and processed sequencing data. This can result in an insufficient level of data protection and a considerable time delay in the further analysis workflow.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present PriLive, a novel tool for the automated removal of sensitive data while the sequencing machine is running. Thereby, human sequence information can be detected and removed before being completely produced. This facilitates the compliance with strict data protection regulations. The unique characteristic to cause almost no time delay for further analyses is also a clear benefit for applications other than data protection. Especially if the sequencing data are dominated by known background signals, PriLive considerably accelerates consequent analyses by having only fractions of input data. Besides these conceptual advantages, PriLive achieves filtering results at least as accurate as conventional post-hoc filtering tools.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>PriLive is open-source software available at https:\/\/gitlab.com\/rki_bioinformatics\/PriLive.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty128","type":"journal-article","created":{"date-parts":[[2018,3,6]],"date-time":"2018-03-06T20:11:00Z","timestamp":1520367060000},"page":"2376-2383","source":"Crossref","is-referenced-by-count":3,"title":["PriLive: privacy-preserving real-time filtering for next-generation sequencing"],"prefix":"10.1093","volume":"34","author":[{"given":"Tobias P","family":"Loka","sequence":"first","affiliation":[{"name":"Bioinformatics Division (MF 1), Department for Methods Development and Research Infrastructure"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon H","family":"Tausch","sequence":"additional","affiliation":[{"name":"Bioinformatics Division (MF 1), Department for Methods Development and Research Infrastructure"},{"name":"Centre for Biological Threats and Special Pathogens: Highly Pathogenic Viruses (ZBS 1)"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Piotr W","family":"Dabrowski","sequence":"additional","affiliation":[{"name":"Bioinformatics Division (MF 1), Department for Methods Development and Research Infrastructure"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksandar","family":"Radoni\u0107","sequence":"additional","affiliation":[{"name":"Centre for Biological Threats and Special Pathogens: Highly Pathogenic Viruses (ZBS 1)"},{"name":"Genome Sequencing Unit (MF 2), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Nitsche","sequence":"additional","affiliation":[{"name":"Centre for Biological Threats and Special Pathogens: Highly Pathogenic Viruses (ZBS 1)"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernhard Y","family":"Renard","sequence":"additional","affiliation":[{"name":"Bioinformatics Division (MF 1), Department for Methods Development and Research Infrastructure"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,3,6]]},"reference":[{"key":"2023012712585397700_bty128-B1","first-page":"1","volume-title":"Proceedings of the 2013 USENIX Conference on Safety, Security, Privacy and Interoperability of Health Information Technologies","author":"Ayday","year":"2013"},{"key":"2023012712585397700_bty128-B2","doi-asserted-by":"crossref","first-page":"7861","DOI":"10.3390\/ijms12117861","article-title":"Applications of next-generation sequencing technologies to diagnostic virology","volume":"12","author":"Barzon","year":"2011","journal-title":"Int. J. Mol. Sci"},{"key":"2023012712585397700_bty128-B3","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.virusres.2012.11.013","article-title":"Cowpox virus but not Vaccinia virus induces secretion of CXCL1, IL-8 and IL-6 and chemotaxis of monocytes in vitro","volume":"171","author":"Bourquain","year":"2013","journal-title":"Virus Res"},{"key":"2023012712585397700_bty128-B4","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1093\/bioinformatics\/btw758","article-title":"PRINCESS: privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS","volume":"33","author":"Chen","year":"2017","journal-title":"Bioinformatics"},{"key":"2023012712585397700_bty128-B5","doi-asserted-by":"crossref","first-page":"265","DOI":"10.5501\/wjv.v4.i3.265","article-title":"Next-generation sequencing in clinical virology: discovery of new viruses","volume":"4","author":"Datta","year":"2015","journal-title":"World J. Virol"},{"key":"2023012712585397700_bty128-B6","doi-asserted-by":"crossref","first-page":"2956","DOI":"10.1109\/TKDE.2013.91","article-title":"Composite bloom filters for secure record linkage","volume":"26","author":"Durham","year":"2014","journal-title":"IEEE Trans. Knowledge Data Eng"},{"key":"2023012712585397700_bty128-B7","first-page":"1","volume-title":"Automata, Languages and Programming: 33rd International Colloquium, ICALP 2006, Venice, Italy, July 10-14, 2006, Proceedings, Part II","author":"Dwork","year":"2006"},{"key":"2023012712585397700_bty128-B8","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":"2023012712585397700_bty128-B9","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1101\/gr.135780.111","article-title":"lobSTR: a short tandem repeat profiler for personal genomes","volume":"22","author":"Gymrek","year":"2012","journal-title":"Genome Res"},{"key":"2023012712585397700_bty128-B10","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1126\/science.1229566","article-title":"Identifying personal genomes by surname inference","volume":"339","author":"Gymrek","year":"2013","journal-title":"Science"},{"key":"2023012712585397700_bty128-B11","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.ygeno.2015.04.005","article-title":"CS-SCORE: rapid identification and removal of human genome contaminants from metagenomic datasets","volume":"106","author":"Haque","year":"2015","journal-title":"Genomics"},{"key":"2023012712585397700_bty128-B12","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/nmeth.3746","article-title":"Quantification of private information leakage from phenotype-genotype data: linking attacks","volume":"13","author":"Harmanci","year":"2016","journal-title":"Nat. Meth"},{"key":"2023012712585397700_bty128-B13","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1186\/1471-2105-14-184","article-title":"Benchmarking short sequence mapping tools","volume":"14","author":"Hatem","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023012712585397700_bty128-B14","volume-title":"Freie Universit\u00e4t Berlin, Fachbereich Mathematik Und Informatik: Ser. B, Informatik; [20]10, 06","author":"Holtgrewe","year":"2010"},{"key":"2023012712585397700_bty128-B15","doi-asserted-by":"crossref","first-page":"e1000167","DOI":"10.1371\/journal.pgen.1000167","article-title":"Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays","volume":"4","author":"Homer","year":"2008","journal-title":"PLOS Genetics"},{"key":"2023012712585397700_bty128-B16","doi-asserted-by":"crossref","first-page":"1687","DOI":"10.1101\/gr.206870.116","article-title":"A privacy-preserving solution for compressed storage and selective retrieval of genomic data","volume":"26","author":"Huang","year":"2016","journal-title":"Genome Res"},{"key":"2023012712585397700_bty128-B17","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1038\/ng.455","article-title":"A new statistic and its power to infer membership in a genome-wide association study using genotype frequencies","volume":"41","author":"Jacobs","year":"2009","journal-title":"Nat. Genet"},{"key":"2023012712585397700_bty128-B18","first-page":"122","article-title":"On the privacy risks of sharing clinical proteomics data","volume":"2016","author":"Li","year":"2016","journal-title":"AMIA Summits Trans. Sci. Proc"},{"key":"2023012712585397700_bty128-B19","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows\u2013Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012712585397700_bty128-B20","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1093\/bioinformatics\/btw659","article-title":"HiLive: real-time mapping of illumina reads while sequencing","volume":"33","author":"Lindner","year":"2017","journal-title":"Bioinformatics"},{"key":"2023012712585397700_bty128-B21","first-page":"277","author":"Machanavajjhala","year":"2008"},{"key":"2023012712585397700_bty128-B22","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1093\/jamia\/ocw167","article-title":"Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks","volume":"24","author":"Raisaro","year":"2017","journal-title":"J. Am. Med. Informatics Assoc"},{"key":"2023012712585397700_bty128-B23","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1146\/annurev-genom-090413-025358","article-title":"Alignment of next-generation sequencing reads","volume":"16","author":"Reinert","year":"2015","journal-title":"Ann. Rev. Genomics Human Genetics"},{"key":"2023012712585397700_bty128-B24","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1038\/ng.436","article-title":"Genomic privacy and limits of individual detection in a pool","volume":"41","author":"Sankararaman","year":"2009","journal-title":"Nat. Genet"},{"key":"2023012712585397700_bty128-B25","doi-asserted-by":"crossref","first-page":"e17288.","DOI":"10.1371\/journal.pone.0017288","article-title":"Fast identification and removal of sequence contamination from genomic and metagenomic datasets","volume":"6","author":"Schmieder","year":"2011","journal-title":"Plos One"},{"key":"2023012712585397700_bty128-B26","doi-asserted-by":"crossref","first-page":"41.","DOI":"10.1186\/1472-6947-9-41","article-title":"Privacy-preserving record linkage using Bloom filters","volume":"9","author":"Schnell","year":"2009","journal-title":"BMC Med. Informatics Decision Making"},{"key":"2023012712585397700_bty128-B27","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1038\/nmeth.4458","article-title":"Critical assessment of metagenome interpretation\u2013a benchmark of metagenomics software","volume":"14","author":"Sczyrba","year":"2017","journal-title":"Nat. Meth"},{"key":"2023012712585397700_bty128-B28","doi-asserted-by":"crossref","first-page":"1652","DOI":"10.1093\/bioinformatics\/btw050","article-title":"Efficient privacy-preserving string search and an application in genomics","volume":"32","author":"Shimizu","year":"2016","journal-title":"Bioinformatics"},{"key":"2023012712585397700_bty128-B29","first-page":"23","article-title":"The present and future of de novo whole-genome assembly","volume":"19","author":"Sohn","year":"2016","journal-title":"Brief. Bioinformatics"},{"key":"2023012712585397700_bty128-B30","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pbio.1002195","article-title":"Big Data: astronomical or Genomical?","volume":"13","author":"Stephens","year":"2015","journal-title":"PLOS Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/14\/2376\/48917778\/bioinformatics_34_14_2376.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/14\/2376\/48917778\/bioinformatics_34_14_2376.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T12:49:33Z","timestamp":1693572573000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/14\/2376\/4924210"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,3,6]]},"references-count":30,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2018,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty128","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,7,15]]},"published":{"date-parts":[[2018,3,6]]}}}