{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T00:15:57Z","timestamp":1778199357276,"version":"3.51.4"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2021,7,12]],"date-time":"2021-07-12T00:00:00Z","timestamp":1626048000000},"content-version":"vor","delay-in-days":11,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["U01EB023685"],"award-info":[{"award-number":["U01EB023685"]}]},{"name":"National Institute of Health","award":["R01HG010798"],"award-info":[{"award-number":["R01HG010798"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CNS-1838083"],"award-info":[{"award-number":["CNS-1838083"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006733","name":"Indiana University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006733","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Precision Health Initiative"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The availability of human genomic data, together with the enhanced capacity to process them, is leading to transformative technological advances in biomedical science and engineering. However, the public dissemination of such data has been difficult due to privacy concerns. Specifically, it has been shown that the presence of a human subject in a case group can be inferred from the shared summary statistics of the group, e.g. the allele frequencies, or even the presence\/absence of genetic variants (e.g. shared by the Beacon project) in the group. These methods rely on the availability of the target\u2019s genome, i.e. the DNA profile of a target human subject, and thus are often referred to as the membership inference method.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this article, we demonstrate the haplotypes, i.e. the sequence of single nucleotide variations (SNVs) showing strong genetic linkages in human genome databases, may be inferred from the summary of genomic data without using a target\u2019s genome. Furthermore, novel haplotypes that did not appear in the database may be reconstructed solely from the allele frequencies from genomic datasets. These reconstructed haplotypes can be used for a haplotype-based membership inference algorithm to identify target subjects in a case group with greater power than existing methods based on SNVs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The implementation of the membership inference algorithms is available at https:\/\/github.com\/diybu\/Haplotype-based-membership-inferences.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab305","type":"journal-article","created":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T20:46:37Z","timestamp":1619469997000},"page":"i161-i168","source":"Crossref","is-referenced-by-count":8,"title":["Haplotype-based membership inference from summary genomic data"],"prefix":"10.1093","volume":"37","author":[{"given":"Diyue","family":"Bu","sequence":"first","affiliation":[{"name":"Department of Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University , Bloomington, IN 47408, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaofeng","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University , Bloomington, IN 47408, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haixu","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University , Bloomington, IN 47408, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,7,12]]},"reference":[{"key":"2023062410293960900_btab305-B1","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s12920-017-0278-x","article-title":"Aftermath of Bustamante attack on genomic beacon service","volume":"10","author":"Al Aziz","year":"2017","journal-title":"BMC Med. Genomics"},{"key":"2023062410293960900_btab305-B2","first-page":"1","article-title":"Next generation DNA sequencing (ii): techniques, applications","volume":"1","author":"Ansorge","year":"2016","journal-title":"Next Gener. Sequence Appl"},{"key":"2023062410293960900_btab305-B3","author":"Ayoz","year":"2020"},{"key":"2023062410293960900_btab305-B4","doi-asserted-by":"crossref","first-page":"i903","DOI":"10.1093\/bioinformatics\/btaa821","article-title":"The effect of kinship in re-identification attacks against genomic data sharing beacons","volume":"36","author":"Ayoz","year":"2020","journal-title":"Bioinformatics"},{"key":"2023062410293960900_btab305-B5","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","article-title":"Haploview: analysis and visualization of lD and haplotype maps","volume":"21","author":"Barrett","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062410293960900_btab305-B6","doi-asserted-by":"crossref","first-page":"eabc6160","DOI":"10.1126\/sciadv.abc6160","article-title":"A GWAS in Latin Americans identifies novel face shape loci, implicating vps13b and a Denisovan Introgressed region in facial variation","volume":"7","author":"Bonfante","year":"2021","journal-title":"Sci. Adv"},{"key":"2023062410293960900_btab305-B7","first-page":"45","author":"Bu","year":"2018"},{"key":"2023062410293960900_btab305-B8","first-page":"166298","article-title":"Genome-wide genetic data on 500,000 UK biobank participants","author":"Bycroft","year":"2017","journal-title":"BioRxiv"},{"key":"2023062410293960900_btab305-B9","doi-asserted-by":"crossref","first-page":"2005.0030","DOI":"10.1038\/msb4100040","article-title":"The personal genome project","volume":"1","author":"Church","year":"2005","journal-title":"Mol. Syst. Biol"},{"key":"2023062410293960900_btab305-B10","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1038\/s41586-019-1793-z","article-title":"The GenomeAsia 100k project enables genetic discoveries across Asia","volume":"576","year":"2019","journal-title":"Nature"},{"key":"2023062410293960900_btab305-B11","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"2023062410293960900_btab305-B12","first-page":"106","author":"Cupak","year":"2016"},{"key":"2023062410293960900_btab305-B13","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1109\/TCBB.2017.2709740","article-title":"An inference attack on genomic data using kinship, complex correlations, and phenotype information","volume":"15","author":"Deznabi","year":"2018","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf"},{"key":"2023062410293960900_btab305-B14","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":"2023062410293960900_btab305-B15","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":"2023062410293960900_btab305-B16","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. Methods"},{"key":"2023062410293960900_btab305-B100","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with NumPy","volume":"585","author":"Harris","year":"2020","journal-title":"Nature"},{"key":"2023062410293960900_btab305-B17","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 Genet"},{"key":"2023062410293960900_btab305-B18","first-page":"1141","author":"Humbert","year":"2013"},{"key":"2023062410293960900_btab305-B19","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1038\/ng.216","article-title":"Detection of sharing by descent, long-range phasing and haplotype imputation","volume":"40","author":"Kong","year":"2008","journal-title":"Nat. Genet"},{"key":"2023062410293960900_btab305-B21","doi-asserted-by":"crossref","first-page":"10166","DOI":"10.1073\/pnas.1711125114","article-title":"Identification of individuals by trait prediction using whole-genome sequencing data","volume":"114","author":"Lippert","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062410293960900_btab305-B22","doi-asserted-by":"crossref","first-page":"e103","DOI":"10.7717\/peerj-cs.103","article-title":"Sympy: symbolic computing in python","volume":"3","author":"Meurer","year":"2017","journal-title":"PeerJ Comput. Sci"},{"key":"2023062410293960900_btab305-B23","first-page":"65","volume-title":"Pulp: A Linear Programming Toolkit for Python","author":"Mitchell","year":"2011"},{"key":"2023062410293960900_btab305-B24","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1126\/science.aaf6162","article-title":"Genomics. A federated ecosystem for sharing genomic, clinical data. Global alliance for genomics and health","volume":"352","author":"Page","year":"2016","journal-title":"Science"},{"key":"2023062410293960900_btab305-B25","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1038\/ng.3062","article-title":"Data use under the NIH GWAS data sharing policy and future directions","volume":"46","author":"Paltoo","year":"2014","journal-title":"Nat. Genet"},{"key":"2023062410293960900_btab305-B26","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. Inf. Assoc"},{"key":"2023062410293960900_btab305-B27","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":"2023062410293960900_btab305-B28","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nature24286","article-title":"DNA sequencing at 40: past, present and future","volume":"550","author":"Shendure","year":"2017","journal-title":"Nature"},{"key":"2023062410293960900_btab305-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":"2023062410293960900_btab305-B30","volume-title":"Python Reference Manual","author":"Van Rossum","year":"1995"},{"key":"2023062410293960900_btab305-B31","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":"2023062410293960900_btab305-B32","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/s12920-017-0282-1","article-title":"Controlling the signal: practical privacy protection of genomic data sharing through beacon services","volume":"10","author":"Wan","year":"2017","journal-title":"BMC Med. Genomics"},{"key":"2023062410293960900_btab305-B33","first-page":"534","author":"Wang","year":"2009"},{"key":"2023062410293960900_btab305-B34","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1038\/s41525-017-0036-1","article-title":"A community effort to protect genomic data sharing, collaboration and outsourcing","volume":"2","author":"Wang","year":"2017","journal-title":"NPJ Genomic Med"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/Supplement_1\/i161\/50694498\/btab305.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/Supplement_1\/i161\/50694498\/btab305.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,25]],"date-time":"2023-06-25T00:21:53Z","timestamp":1687652513000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/Supplement_1\/i161\/6319711"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,1]]},"references-count":34,"journal-issue":{"issue":"Supplement_1","published-print":{"date-parts":[[2021,8,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab305","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,7,1]]},"published":{"date-parts":[[2021,7,1]]}}}