{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:56Z","timestamp":1772138096737,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,8,26]],"date-time":"2019-08-26T00:00:00Z","timestamp":1566777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","award":["DNRF94"],"award-info":[{"award-number":["DNRF94"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","award":["DNRF94"],"award-info":[{"award-number":["DNRF94"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["679330"],"award-info":[{"award-number":["679330"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002808","name":"Carlsberg Foundation","doi-asserted-by":"publisher","award":["CF16-0913"],"award-info":[{"award-number":["CF16-0913"]}],"id":[{"id":"10.13039\/501100002808","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["NIH 1R01GM116044-01"],"award-info":[{"award-number":["NIH 1R01GM116044-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The presence of present-day human contaminating DNA fragments is one of the challenges defining ancient DNA (aDNA) research. This is especially relevant to the ancient human DNA field where it is difficult to distinguish endogenous molecules from human contaminants due to their genetic similarity. Recently, with the advent of high-throughput sequencing and new aDNA protocols, hundreds of ancient human genomes have become available. Contamination in those genomes has been measured with computational methods often developed specifically for these empirical studies. Consequently, some of these methods have not been implemented and tested for general use while few are aimed at low-depth nuclear data, a common feature in aDNA datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We develop a new X-chromosome-based maximum likelihood method for estimating present-day human contamination in low-depth sequencing data from male individuals. We implement our method for general use, assess its performance under conditions typical of ancient human DNA research, and compare it to previous nuclear data-based methods through extensive simulations. For low-depth data, we show that existing methods can produce unusable estimates or substantially underestimate contamination. In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5\u00d7 on the X-chromosome when contamination is below 25%. Moreover, our method still yields meaningful estimates in very challenging situations, i.e. when the contaminant and the target come from closely related populations or with increased error rates. With a running time below 5\u00a0min, our method is applicable to large scale aDNA genomic studies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The method is implemented in C++ and R and is available in github.com\/sapfo\/contaminationX and popgen.dk\/angsd.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz660","type":"journal-article","created":{"date-parts":[[2019,8,22]],"date-time":"2019-08-22T15:38:20Z","timestamp":1566488300000},"page":"828-841","source":"Crossref","is-referenced-by-count":23,"title":["A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7712-4496","authenticated-orcid":false,"given":"J V\u00edctor","family":"Moreno-Mayar","sequence":"first","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , 1015 Lausanne, Switzerland"},{"name":"Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland"},{"name":"National Institute of Genomic Medicine (INMEGEN) , 14610 Mexico City, Mexico"}]},{"given":"Thorfinn Sand","family":"Korneliussen","sequence":"additional","affiliation":[{"name":"Lundbeck Foundation GeoGenetics Centre, GLOBE Institute , University of Copenhagen, 1350 Copenhagen"}]},{"given":"Jyoti","family":"Dalal","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , 1015 Lausanne, Switzerland"},{"name":"Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0630-027X","authenticated-orcid":false,"given":"Gabriel","family":"Renaud","sequence":"additional","affiliation":[{"name":"Lundbeck Foundation GeoGenetics Centre, GLOBE Institute , University of Copenhagen, 1350 Copenhagen"}]},{"given":"Anders","family":"Albrechtsen","sequence":"additional","affiliation":[{"name":"Department of Biology, The Bioinformatics Centre, University of Copenhagen , 2200 Copenhagen, Denmark"}]},{"given":"Rasmus","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Lundbeck Foundation GeoGenetics Centre, GLOBE Institute , University of Copenhagen, 1350 Copenhagen"},{"name":"Department of Statistics , CA 94720, USA"},{"name":"Department of Integrative Biology, University of California , Berkeley, CA 94720, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1001-7511","authenticated-orcid":false,"given":"Anna-Sapfo","family":"Malaspinas","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , 1015 Lausanne, Switzerland"},{"name":"Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2019,8,26]]},"reference":[{"key":"2023013110094062200_btz660-B1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/nature14507","article-title":"Population genomics of Bronze Age Eurasia","volume":"522","author":"Allentoft","year":"2015","journal-title":"Nature"},{"key":"2023013110094062200_btz660-B2","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1038\/nature09298","article-title":"Integrating common and rare genetic variation in diverse human populations","volume":"467","author":"Altshuler","year":"2010","journal-title":"Nature"},{"key":"2023013110094062200_btz660-B3","doi-asserted-by":"crossref","first-page":"14616","DOI":"10.1073\/pnas.0704665104","article-title":"Patterns of damage in genomic DNA sequences from a Neandertal","volume":"104","author":"Briggs","year":"2007","journal-title":"Proc. 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