{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T02:49:04Z","timestamp":1774320544613,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Sample mix-ups can arise during sample collection, handling, genotyping or data management. It is unclear how often sample mix-ups occur in genome-wide studies, as there currently are no post hoc methods that can identify these mix-ups in unrelated samples. We have therefore developed an algorithm (MixupMapper) that can both detect and correct sample mix-ups in genome-wide studies that study gene expression levels.<\/jats:p>\n               <jats:p>Results: We applied MixupMapper to five publicly available human genetical genomics datasets. On average, 3% of all analyzed samples had been assigned incorrect expression phenotypes: in one of the datasets 23% of the samples had incorrect expression phenotypes. The consequences of sample mix-ups are substantial: when we corrected these sample mix-ups, we identified on average 15% more significant cis-expression quantitative trait loci (cis-eQTLs). In one dataset, we identified three times as many significant cis-eQTLs after correction. Furthermore, we show through simulations that sample mix-ups can lead to an underestimation of the explained heritability of complex traits in genome-wide association datasets.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0MixupMapper is freely available at http:\/\/www.genenetwork.nl\/mixupmapper\/<\/jats:p>\n               <jats:p>Contact: \u00a0lude@ludesign.nl<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr323","type":"journal-article","created":{"date-parts":[[2011,6,9]],"date-time":"2011-06-09T00:23:48Z","timestamp":1307579028000},"page":"2104-2111","source":"Crossref","is-referenced-by-count":82,"title":["MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects"],"prefix":"10.1093","volume":"27","author":[{"given":"Harm-Jan","family":"Westra","sequence":"first","affiliation":[{"name":"1 Department of Genetics, University Medical Center Groningen, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands and 3Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK"}]},{"given":"Ritsert C.","family":"Jansen","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University Medical Center Groningen, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands and 3Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK"}]},{"given":"Rudolf S. N.","family":"Fehrmann","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University Medical Center Groningen, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands and 3Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK"}]},{"given":"Gerard J.","family":"te Meerman","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University Medical Center Groningen, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands and 3Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK"}]},{"given":"David","family":"van Heel","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University Medical Center Groningen, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands and 3Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK"}]},{"given":"Cisca","family":"Wijmenga","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University Medical Center Groningen, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands and 3Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK"}]},{"given":"Lude","family":"Franke","sequence":"additional","affiliation":[{"name":"1 Department of Genetics, University Medical Center Groningen, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands and 3Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK"},{"name":"1 Department of Genetics, University Medical Center Groningen, 2Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9700AB, Groningen, The Netherlands and 3Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK"}]}],"member":"286","published-online":{"date-parts":[[2011,6,7]]},"reference":[{"key":"2023012511524143700_B1","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1038\/ng.381","article-title":"Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes","volume":"41","author":"Barrett","year":"2009","journal-title":"Nat. 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