{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,4]],"date-time":"2025-12-04T14:30:24Z","timestamp":1764858624209},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: In many situations, genome-wide association studies are performed in populations presenting stratification. Mixed models including a kinship matrix accounting for genetic relatedness among individuals have been shown to correct for population and\/or family structure. Here we extend this methodology to generalized linear mixed models which properly model data under various distributions. In addition we perform association with ancestral haplotypes inferred using a hidden Markov model.<\/jats:p><jats:p>Results: The method was shown to properly account for stratification under various simulated scenari presenting population and\/or family structure. Use of ancestral haplotypes resulted in higher power than SNPs on simulated datasets. Application to real data demonstrates the usefulness of the developed model. Full analysis of a dataset with 4600 individuals and 500 000 SNPs was performed in 2 h 36 min and required 2.28 Gb of RAM.<\/jats:p><jats:p>Availability: The software GLASCOW can be freely downloaded from www.giga.ulg.ac.be\/jcms\/prod_381171\/software.<\/jats:p><jats:p>Contact: \u00a0francois.guillaume@jouy.inra.fr<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts348","type":"journal-article","created":{"date-parts":[[2012,6,19]],"date-time":"2012-06-19T00:19:39Z","timestamp":1340065179000},"page":"2467-2473","source":"Crossref","is-referenced-by-count":40,"title":["Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification"],"prefix":"10.1093","volume":"28","author":[{"given":"Z.","family":"Zhang","sequence":"first","affiliation":[{"name":"1 Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Li\u00e8ge (B34), 1 avenue de l\u2019H\u00f4pital and 2Unit of Animal Productions, Faculty of Veterinary Medicine, University of Li\u00e8ge (B43), 20 boulevard de Colonster, B-4000 Li\u00e8ge, Belgium"}]},{"given":"F.","family":"Guillaume","sequence":"additional","affiliation":[{"name":"1 Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Li\u00e8ge (B34), 1 avenue de l\u2019H\u00f4pital and 2Unit of Animal Productions, Faculty of Veterinary Medicine, University of Li\u00e8ge (B43), 20 boulevard de Colonster, B-4000 Li\u00e8ge, Belgium"}]},{"given":"A.","family":"Sartelet","sequence":"additional","affiliation":[{"name":"1 Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Li\u00e8ge (B34), 1 avenue de l\u2019H\u00f4pital and 2Unit of Animal Productions, Faculty of Veterinary Medicine, University of Li\u00e8ge (B43), 20 boulevard de Colonster, B-4000 Li\u00e8ge, Belgium"}]},{"given":"C.","family":"Charlier","sequence":"additional","affiliation":[{"name":"1 Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Li\u00e8ge (B34), 1 avenue de l\u2019H\u00f4pital and 2Unit of Animal Productions, Faculty of Veterinary Medicine, University of Li\u00e8ge (B43), 20 boulevard de Colonster, B-4000 Li\u00e8ge, Belgium"}]},{"given":"M.","family":"Georges","sequence":"additional","affiliation":[{"name":"1 Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Li\u00e8ge (B34), 1 avenue de l\u2019H\u00f4pital and 2Unit of Animal Productions, Faculty of Veterinary Medicine, University of Li\u00e8ge (B43), 20 boulevard de Colonster, B-4000 Li\u00e8ge, Belgium"}]},{"given":"F.","family":"Farnir","sequence":"additional","affiliation":[{"name":"1 Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Li\u00e8ge (B34), 1 avenue de l\u2019H\u00f4pital and 2Unit of Animal Productions, Faculty of Veterinary Medicine, University of Li\u00e8ge (B43), 20 boulevard de Colonster, B-4000 Li\u00e8ge, Belgium"}]},{"given":"T.","family":"Druet","sequence":"additional","affiliation":[{"name":"1 Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Li\u00e8ge (B34), 1 avenue de l\u2019H\u00f4pital and 2Unit of Animal Productions, Faculty of Veterinary Medicine, University of Li\u00e8ge (B43), 20 boulevard de Colonster, B-4000 Li\u00e8ge, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2012,6,17]]},"reference":[{"key":"2023012513061740300_bts348-B1","doi-asserted-by":"crossref","first-page":"e1274","DOI":"10.1371\/journal.pone.0001274","article-title":"A genomic background based method for association analysis in related individuals","volume":"2","author":"Amin","year":"2007","journal-title":"PLoS 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