{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:11:02Z","timestamp":1772165462565,"version":"3.50.1"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,9,25]],"date-time":"2021-09-25T00:00:00Z","timestamp":1632528000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,9,25]],"date-time":"2021-09-25T00:00:00Z","timestamp":1632528000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>We present ARCHes, a fast and accurate haplotype-based approach for inferring an individual\u2019s ancestry composition. Our approach works by modeling haplotype diversity from a large, admixed cohort of hundreds of thousands, then annotating those models with population information from reference panels of known ancestry.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The running time of ARCHes does not depend on the size of a reference panel because training and testing are separate processes, and the inferred population-annotated haplotype models can be written to disk and reused to label large test sets in parallel (in our experiments, it averages less than one minute to assign ancestry from 32 populations using 10 CPU). We test ARCHes on public data from the 1000 Genomes Project and the Human Genome Diversity Project (HGDP) as well as simulated examples of known admixture.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our results demonstrate that ARCHes outperforms RFMix at correctly assigning both global and local ancestry at finer population scales regardless of the amount of population admixture.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-021-04350-x","type":"journal-article","created":{"date-parts":[[2021,9,25]],"date-time":"2021-09-25T15:02:53Z","timestamp":1632582173000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Ancestry inference using reference labeled clusters of haplotypes"],"prefix":"10.1186","volume":"22","author":[{"given":"Yong","family":"Wang","sequence":"first","affiliation":[]},{"given":"Shiya","family":"Song","sequence":"additional","affiliation":[]},{"given":"Joshua G.","family":"Schraiber","sequence":"additional","affiliation":[]},{"given":"Alisa","family":"Sedghifar","sequence":"additional","affiliation":[]},{"given":"Jake K.","family":"Byrnes","sequence":"additional","affiliation":[]},{"given":"David A.","family":"Turissini","sequence":"additional","affiliation":[]},{"given":"Eurie L.","family":"Hong","sequence":"additional","affiliation":[]},{"given":"Catherine A.","family":"Ball","sequence":"additional","affiliation":[]},{"given":"Keith","family":"Noto","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,9,25]]},"reference":[{"key":"4350_CR1","doi-asserted-by":"publisher","first-page":"1233","DOI":"10.1534\/genetics.112.147330","volume":"193","author":"P-R Loh","year":"2013","unstructured":"Loh P-R, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B. Inferring admixture histories of human populations using linkage disequilibrium. Genetics. 2013;193:1233\u201354.","journal-title":"Genetics"},{"key":"4350_CR2","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1534\/genetics.112.139808","volume":"191","author":"S Gravel","year":"2012","unstructured":"Gravel S. Population genetics models of local ancestry. Genetics. 2012;191:607\u201319.","journal-title":"Genetics"},{"key":"4350_CR3","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1038\/ng1337","volume":"36","author":"J Marchini","year":"2004","unstructured":"Marchini J, Cardon LR, Phillips MS, Donnelly P. The effects of human population structure on large genetic association studies. Nat Genet. 2004;36:512\u20137.","journal-title":"Nat Genet"},{"key":"4350_CR4","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","volume":"19","author":"DH Alexander","year":"2009","unstructured":"Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655\u201364.","journal-title":"Genome Res"},{"key":"4350_CR5","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1038\/ng1847","volume":"38","author":"AL Price","year":"2006","unstructured":"Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006;38:904\u20139.","journal-title":"Nat Genet"},{"key":"4350_CR6","doi-asserted-by":"publisher","first-page":"e1002453","DOI":"10.1371\/journal.pgen.1002453","volume":"8","author":"DJ Lawson","year":"2012","unstructured":"Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of population structure using dense haplotype data. PLoS Genet. 2012;8:e1002453.","journal-title":"PLoS Genet"},{"key":"4350_CR7","doi-asserted-by":"publisher","first-page":"e1000519","DOI":"10.1371\/journal.pgen.1000519","volume":"5","author":"AL Price","year":"2009","unstructured":"Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 2009;5:e1000519.","journal-title":"PLoS Genet"},{"key":"4350_CR8","doi-asserted-by":"publisher","first-page":"2213","DOI":"10.1093\/genetics\/165.4.2213","volume":"165","author":"N Li","year":"2003","unstructured":"Li N, Stephens M. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics. 2003;165:2213\u201333.","journal-title":"Genetics"},{"key":"4350_CR9","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1016\/j.ajhg.2013.06.020","volume":"93","author":"BK Maples","year":"2013","unstructured":"Maples BK, Gravel S, Kenny EE, Bustamante CD. RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am J Hum Genet. 2013;93:278\u201388.","journal-title":"Am J Hum Genet"},{"key":"4350_CR10","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1086\/521987","volume":"81","author":"SR Browning","year":"2007","unstructured":"Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007;81:1084\u201397.","journal-title":"Am J Hum Genet"},{"key":"4350_CR11","doi-asserted-by":"publisher","unstructured":"Uren C, Hoal EG, M\u00f6ller M. Putting RFMix and ADMIXTURE to the test in a complex admixed population. BMC Genetics.  2020;21(40). https:\/\/doi.org\/10.1186\/s12863-020-00845-3.","DOI":"10.1186\/s12863-020-00845-3"},{"key":"4350_CR12","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/nature09534","volume":"467","author":"GR Abecasis","year":"2010","unstructured":"Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061\u201373.","journal-title":"Nature"},{"key":"4350_CR13","doi-asserted-by":"publisher","first-page":"1100","DOI":"10.1126\/science.1153717","volume":"319","author":"JZ Li","year":"2008","unstructured":"Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, et al. Worldwide human relationships inferred from genome-wide patterns of variation. 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Nature. 2007;449:851\u201361. https:\/\/doi.org\/10.1038\/nature06258.","journal-title":"Nature"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-021-04350-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-021-04350-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-021-04350-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,25]],"date-time":"2021-09-25T15:05:49Z","timestamp":1632582349000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-021-04350-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,25]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["4350"],"URL":"https:\/\/doi.org\/10.1186\/s12859-021-04350-x","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.09.23.310698","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,9,25]]},"assertion":[{"value":"8 April 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 August 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 September 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All data for this research project were from subjects who provided prior informed written consent to participate in AncestryDNA\u2019s Human Diversity Project, as reviewed and approved by our external institutional review board, Advarra (formerly Quorum). All data were de-identified prior to use.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare competing financial interests: authors affiliated with AncestryDNA may have equity in Ancestry. The work described in this manuscript is covered by one or more patents including US patent entitled Local Genetic Ethnicity Determination System US10558930B2.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"459"}}