{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T20:15:36Z","timestamp":1780604136882,"version":"3.54.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Inference of ancestry using genetic data is motivated by applications in genetic association studies, population genetics and personal genomics. Here, we provide methods and software for improved ancestry inference using genome-wide single nucleotide polymorphism (SNP) weights from external reference panels. This approach makes it possible to leverage the rich ancestry information that is available from large external reference panels, without the administrative and computational complexities of re-analyzing the raw genotype data from the reference panel in subsequent studies.<\/jats:p>\n               <jats:p>Results: We extensively validate our approach in multiple African American, Latino American and European American datasets, making use of genome-wide SNP weights derived from large reference panels, including HapMap 3 populations and 6546 European Americans from the Framingham Heart Study. We show empirically that our approach provides much greater accuracy than either the prevailing ancestry-informative marker (AIM) approach or the analysis of genome-wide target genotypes without a reference panel. For example, in an independent set of 1636 European American genome-wide association study samples, we attained prediction accuracy (R2) of 1.000 and 0.994 for the first two principal components using our method, compared with 0.418 and 0.407 using 150 published AIMs or 0.955 and 0.003 by applying principal component analysis directly to the target samples. We finally show that the higher accuracy in inferring ancestry using our method leads to more effective correction for population stratification in association studies.<\/jats:p>\n               <jats:p>Availability: The SNPweights software is available online at http:\/\/www.hsph.harvard.edu\/faculty\/alkes-price\/software\/.<\/jats:p>\n               <jats:p>Contact: \u00a0aprice@hsph.harvard.edu or cychen@mail.harvard.edu.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt144","type":"journal-article","created":{"date-parts":[[2013,3,29]],"date-time":"2013-03-29T03:31:53Z","timestamp":1364527913000},"page":"1399-1406","source":"Crossref","is-referenced-by-count":207,"title":["Improved ancestry inference using weights from external reference panels"],"prefix":"10.1093","volume":"29","author":[{"given":"Chia-Yen","family":"Chen","sequence":"first","affiliation":[{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuela","family":"Pollack","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David J.","family":"Hunter","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel N.","family":"Hirschhorn","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Kraft","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alkes L.","family":"Price","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"},{"name":"1 Department of Epidemiology, 2Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 3Broad Institute of Harvard and MIT, Cambridge, MA 02142, 4Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, 5Divisions of Genetics and Endocrinology, Children's Hospital and 6Department of Genetics, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,3,28]]},"reference":[{"key":"2023062610153107800_btt144-B1","doi-asserted-by":"crossref","first-page":"e29033","DOI":"10.1371\/journal.pone.0029033","article-title":"Association of systemic lupus erythematosus clinical features with European population genetic substructure","volume":"6","author":"Alonso-Perez","year":"2011","journal-title":"PLoS One"},{"key":"2023062610153107800_btt144-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":"2023062610153107800_btt144-B3","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1111\/j.0006-341X.1999.00997.x","article-title":"Genomic control for association studies","volume":"55","author":"Devlin","year":"1999","journal-title":"Biometrics"},{"key":"2023062610153107800_btt144-B4","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/ng826","article-title":"Identification of a variant associated with adult-type hypolactasia","volume":"30","author":"Enattah","year":"2002","journal-title":"Nat. Genet."},{"key":"2023062610153107800_btt144-B5","doi-asserted-by":"crossref","first-page":"e1002554","DOI":"10.1371\/journal.pgen.1002554","article-title":"Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas","volume":"8","author":"Galanter","year":"2012","journal-title":"PLoS Genet."},{"key":"2023062610153107800_btt144-B6","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":"2023062610153107800_btt144-B7","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1002\/art.23166","article-title":"The HLA-DRB1 shared epitope is associated with susceptibility to rheumatoid arthritis in African Americans through European genetic admixture","volume":"58","author":"Hughes","year":"2008","journal-title":"Arthritis Rheum."},{"key":"2023062610153107800_btt144-B8","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1038\/ng2075","article-title":"A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer","volume":"39","author":"Hunter","year":"2007","journal-title":"Nat. Genet."},{"key":"2023062610153107800_btt144-B9","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1056\/NEJMoa0907897","article-title":"Genetic ancestry in lung-function predictions","volume":"363","author":"Kumar","year":"2010","journal-title":"N. Engl. J. Med."},{"key":"2023062610153107800_btt144-B10","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1038\/nature09410","article-title":"Hundreds of variants clustered in genomic loci and biological pathways affect human height","volume":"467","author":"Lango Allen","year":"2010","journal-title":"Nature"},{"key":"2023062610153107800_btt144-B11","doi-asserted-by":"crossref","first-page":"3605","DOI":"10.1214\/10-AOS821","article-title":"Convergence and prediction of principal component scores in high-dimensional settings","volume":"38","author":"Lee","year":"2010","journal-title":"Ann. Stat."},{"key":"2023062610153107800_btt144-B12","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1038\/nature07331","article-title":"Genes mirror geography within Europe","volume":"456","author":"Novembre","year":"2008","journal-title":"Nature"},{"key":"2023062610153107800_btt144-B13","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1038\/ng.139","article-title":"Interpreting principal component analyses of spatial population genetic variation","volume":"40","author":"Novembre","year":"2008","journal-title":"Nat. Genet."},{"key":"2023062610153107800_btt144-B14","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/ng.2283","article-title":"Extremely low-coverage sequencing and imputation increases power for genome-wide association studies","volume":"44","author":"Pasaniuc","year":"2012","journal-title":"Nat. Genet."},{"key":"2023062610153107800_btt144-B15","doi-asserted-by":"crossref","first-page":"e1000114","DOI":"10.1371\/journal.pgen.1000114","article-title":"Tracing sub-structure in the European American population with PCA-informative markers","volume":"4","author":"Paschou","year":"2008","journal-title":"PLoS Genet."},{"key":"2023062610153107800_btt144-B16","doi-asserted-by":"crossref","first-page":"e190","DOI":"10.1371\/journal.pgen.0020190","article-title":"Population structure and eigenanalysis","volume":"2","author":"Patterson","year":"2006","journal-title":"PLoS Genet."},{"key":"2023062610153107800_btt144-B17","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/ng1847","article-title":"Principal components analysis corrects for stratification in genome-wide association studies","volume":"38","author":"Price","year":"2006","journal-title":"Nat. Genet."},{"key":"2023062610153107800_btt144-B18","doi-asserted-by":"crossref","first-page":"e236","DOI":"10.1371\/journal.pgen.0030236","article-title":"Discerning the ancestry of European Americans in genetic association studies","volume":"4","author":"Price","year":"2008","journal-title":"PLoS Genet."},{"key":"2023062610153107800_btt144-B19","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/nrg2813","article-title":"New approaches to population stratification in genome-wide association studies","volume":"11","author":"Price","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"2023062610153107800_btt144-B20","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1086\/302959","article-title":"Association mapping in structured populations","volume":"67","author":"Pritchard","year":"2000","journal-title":"Am. J. Hum. Genet."},{"key":"2023062610153107800_btt144-B21","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: a tool set for whole-genome association and population-based linkage analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"2023062610153107800_btt144-B22","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/nature08365","article-title":"Reconstructing Indian population history","volume":"461","author":"Reich","year":"2009","journal-title":"Nature"},{"key":"2023062610153107800_btt144-B23","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1038\/nature11258","article-title":"Reconstructing native American population history","volume":"488","author":"Reich","year":"2012","journal-title":"Nature"},{"key":"2023062610153107800_btt144-B24","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1137\/080736417","article-title":"A randomized algorithm for principal component analysis","volume":"31","author":"Rokhlin","year":"2009","journal-title":"SIAM. J. Matrix Anal. Appl."},{"key":"2023062610153107800_btt144-B25","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/j.ajhg.2010.03.011","article-title":"Inferring genetic ancestry: opportunities, challenges, and implications","volume":"86","author":"Royal","year":"2010","journal-title":"Am. J. Hum. Genet."},{"key":"2023062610153107800_btt144-B26","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1093\/aje\/kwq401","article-title":"Validation of a small set of ancestral informative markers for control of population admixture in African Americans","volume":"173","author":"Ruiz-Narv\u00e1ez","year":"2011","journal-title":"Am. J. Epidemiol."},{"key":"2023062610153107800_btt144-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":"2023062610153107800_btt144-B28","doi-asserted-by":"crossref","first-page":"e5","DOI":"10.1371\/journal.pgen.0040005","article-title":"Application of ancestry informative markers to association studies in European Americans","volume":"4","author":"Seldin","year":"2008","journal-title":"PLoS Genet."},{"key":"2023062610153107800_btt144-B29","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1093\/aje\/kwm021","article-title":"The third generation cohort of the national heart, lung, and blood institute\u2019s framingham heart study: design, recruitment, and initial examination","volume":"165","author":"Splansky","year":"2007","journal-title":"Am. J. Epidemiol."},{"key":"2023062610153107800_btt144-B30","doi-asserted-by":"crossref","first-page":"e4","DOI":"10.1371\/journal.pgen.0040004","article-title":"Analysis and application of European genetic substructure using 300 K SNP information","volume":"4","author":"Tian","year":"2008","journal-title":"PLoS Genet."},{"key":"2023062610153107800_btt144-B31","doi-asserted-by":"crossref","first-page":"e1000628","DOI":"10.1371\/journal.pgen.1000628","article-title":"The limits of individual identification from sample allele frequencies: theory and statistical analysis","volume":"5","author":"Visscher","year":"2009","journal-title":"PLoS Genet."},{"key":"2023062610153107800_btt144-B32","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1038\/ng.763","article-title":"Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia","volume":"43","author":"Yang","year":"2011","journal-title":"Nat. Genet."},{"key":"2023062610153107800_btt144-B33","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/j.ajhg.2007.10.009","article-title":"A unified association analysis approach for family and unrelated samples correcting for stratification","volume":"82","author":"Zhu","year":"2008","journal-title":"Am. J. Hum. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/11\/1399\/50700946\/bioinformatics_29_11_1399.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/11\/1399\/50700946\/bioinformatics_29_11_1399.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T10:17:32Z","timestamp":1687774652000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/11\/1399\/219940"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,3,28]]},"references-count":33,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2013,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt144","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,6,1]]},"published":{"date-parts":[[2013,3,28]]}}}