{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T22:58:52Z","timestamp":1771455532392,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,29]],"date-time":"2023-05-29T00:00:00Z","timestamp":1685318400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 HG010959"],"award-info":[{"award-number":["R01 HG010959"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["DP5 OD029574"],"award-info":[{"award-number":["DP5 OD029574"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["RM1 HG011558"],"award-info":[{"award-number":["RM1 HG011558"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Broad Institute\u2019s Schmidt Fellowship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Advances in genomics are increasingly depending upon the ability to analyze large and diverse genomic data collections, which are often difficult to amass due to privacy concerns. Recent works have shown that it is possible to jointly analyze datasets held by multiple parties, while provably preserving the privacy of each party\u2019s dataset using cryptographic techniques. However, these tools have been challenging to use in practice due to the complexities of the required setup and coordination among the parties. We present sfkit, a secure and federated toolkit for collaborative genomic studies, to allow groups of collaborators to easily perform joint analyses of their datasets without compromising privacy. sfkit consists of a web server and a command-line interface, which together support a range of use cases including both auto-configured and user-supplied computational environments. sfkit provides collaborative workflows for the essential tasks of genome-wide association study (GWAS) and principal component analysis (PCA). We envision sfkit becoming a one-stop server for secure collaborative tools for a broad range of genomic analyses. sfkit is open-source and available at: https:\/\/sfkit.org.<\/jats:p>","DOI":"10.1093\/nar\/gkad464","type":"journal-article","created":{"date-parts":[[2023,5,29]],"date-time":"2023-05-29T10:21:49Z","timestamp":1685355709000},"page":"W535-W541","source":"Crossref","is-referenced-by-count":14,"title":["sfkit: a web-based toolkit for secure and federated genomic analysis"],"prefix":"10.1093","volume":"51","author":[{"given":"Simon","family":"Mendelsohn","sequence":"first","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA, USA"}]},{"given":"David","family":"Froelicher","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA, USA"},{"name":"Computer Science and AI Laboratory , MIT, Cambridge, MA, USA"}]},{"given":"Denis","family":"Loginov","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA, USA"}]},{"given":"David","family":"Bernick","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2724-7228","authenticated-orcid":false,"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA, USA"},{"name":"Computer Science and AI Laboratory , MIT, Cambridge, MA, USA"},{"name":"Department of Mathematics , MIT, Cambridge, MA, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2713-0150","authenticated-orcid":false,"given":"Hyunghoon","family":"Cho","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard , Cambridge, MA, USA"}]}],"member":"286","published-online":{"date-parts":[[2023,5,29]]},"reference":[{"key":"2023070504565497800_B1","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1038\/s41586-021-04064-3","article-title":"The power of genetic diversity in genome-wide association studies of lipids","volume":"600","author":"Graham","year":"2021","journal-title":"Nature"},{"key":"2023070504565497800_B2","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1038\/s41586-022-04434-5","article-title":"Mapping genomic loci implicates genes and synaptic biology in schizophrenia","volume":"604","author":"Trubetskoy","year":"2022","journal-title":"Nature"},{"key":"2023070504565497800_B3","first-page":"1","article-title":"Sociotechnical safeguards for genomic data privacy","author":"Wan","year":"2022","journal-title":"Nat. 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Genet."},{"key":"2023070504565497800_B12","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1111\/j.1467-789X.2009.00569.x","article-title":"The polymorphisms of UCP2 and UCP3 genes associated with fat metabolism, obesity and diabetes","volume":"10","author":"Jia","year":"2009","journal-title":"Obesity Rev."},{"key":"2023070504565497800_B13","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a toolset for whole-genome association and population-based linkage analysis","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. 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U.S.A."},{"key":"2023070504565497800_B17","article-title":"Deep leakage from gradients","volume-title":"Proceedings of Advances in Neural Information Processing Systems (NeurIPS)","author":"Zhu","year":"2019"},{"key":"2023070504565497800_B18","first-page":"691","article-title":"Exploiting unintended feature leakage in collaborative learning","volume-title":"Proceedings of IEEE Symposium on Security and Privacy (SP)","author":"Melis","year":"2019"},{"key":"2023070504565497800_B19","doi-asserted-by":"crossref","first-page":"100210","DOI":"10.1016\/j.xgen.2022.100210","article-title":"Meta-analysis fine-mapping is often miscalibrated at single-variant resolution","volume":"2","author":"Kanai","year":"2022","journal-title":"Cell Genom."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W535\/50736393\/gkad464.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W535\/50736393\/gkad464.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T08:59:34Z","timestamp":1688547574000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/W1\/W535\/7184156"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,29]]},"references-count":19,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2023,5,29]]},"published-print":{"date-parts":[[2023,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad464","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,5]]},"published":{"date-parts":[[2023,5,29]]}}}