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Extent and distribution of linkage disequilibrium in the Old Order Amish

dc.contributor.authorVan Hout, Cristopher V.en_US
dc.contributor.authorLevin, Albert M.en_US
dc.contributor.authorRampersaud, Evadnieen_US
dc.contributor.authorShen, Haiqingen_US
dc.contributor.authorO'Connell, Jeffrey R.en_US
dc.contributor.authorMitchell, Braxton D.en_US
dc.contributor.authorShuldiner, Alan R.en_US
dc.contributor.authorDouglas, Julie A.en_US
dc.date.accessioned2010-02-02T15:29:38Z
dc.date.available2011-03-01T16:26:42Zen_US
dc.date.issued2010-02en_US
dc.identifier.citationVan Hout, Cristopher V.; Levin, Albert M.; Rampersaud, Evadnie; Shen, Haiqing; O'Connell, Jeffrey R.; Mitchell, Braxton D.; Shuldiner, Alan R.; Douglas, Julie A. (2010). "Extent and distribution of linkage disequilibrium in the Old Order Amish." Genetic Epidemiology 34(2): 146-150. <http://hdl.handle.net/2027.42/64895>en_US
dc.identifier.issn0741-0395en_US
dc.identifier.issn1098-2272en_US
dc.identifier.urihttps://hdl.handle.net/2027.42/64895
dc.description.abstractKnowledge of the extent and distribution of linkage disequilibrium (LD) is critical to the design and interpretation of gene mapping studies. Because the demographic history of each population varies and is often not accurately known, it is necessary to empirically evaluate LD on a population-specific basis. Here we present the first genome-wide survey of LD in the Old Order Amish (OOA) of Lancaster County Pennsylvania, a closed population derived from a modest number of founders. Specifically, we present a comparison of LD between OOA individuals and US Utah participants in the International HapMap project (abbreviated CEU) using a high-density single nucleotide polymorphism (SNP) map. Overall, the allele (and haplotype) frequency distributions and LD profiles were remarkably similar between these two populations. For example, the median absolute allele frequency difference for autosomal SNPs was 0.05, with an inter-quartile range of 0.02–0.09, and for autosomal SNPs 10–20 kb apart with common alleles (minor allele frequency≥0.05), the LD measure r 2 was at least 0.8 for 15 and 14% of SNP pairs in the OOA and CEU, respectively. Moreover, tag SNPs selected from the HapMap CEU sample captured a substantial portion of the common variation in the OOA (∼88%) at r 2 ≥0.8. These results suggest that the OOA and CEU may share similar LD profiles for other common but untyped SNPs. Thus, in the context of the common variant-common disease hypothesis, genetic variants discovered in gene mapping studies in the OOA may generalize to other populations. Genet. Epidemiol . 34: 146–150, 2010. © 2009 Wiley-Liss, Inc.en_US
dc.format.extent90598 bytes
dc.format.extent3118 bytes
dc.format.mimetypeapplication/pdf
dc.format.mimetypetext/plain
dc.publisherWiley Subscription Services, Inc., A Wiley Companyen_US
dc.subject.otherLife and Medical Sciencesen_US
dc.subject.otherGeneticsen_US
dc.titleExtent and distribution of linkage disequilibrium in the Old Order Amishen_US
dc.typeArticleen_US
dc.rights.robotsIndexNoFollowen_US
dc.subject.hlbsecondlevelBiological Chemistryen_US
dc.subject.hlbsecondlevelGeneticsen_US
dc.subject.hlbsecondlevelMolecular, Cellular and Developmental Biologyen_US
dc.subject.hlbtoplevelHealth Sciencesen_US
dc.subject.hlbtoplevelScienceen_US
dc.description.peerreviewedPeer Revieweden_US
dc.contributor.affiliationumDepartment of Human Genetics, University of Michigan School of Medicine, Ann Arbor, Michigan ; The first two authors contributed equally to this work.en_US
dc.contributor.affiliationumDepartment of Human Genetics, University of Michigan School of Medicine, Ann Arbor, Michiganen_US
dc.contributor.affiliationumDepartment of Human Genetics, University of Michigan School of Medicine, Ann Arbor, Michigan ; Department of Human Genetics, University of Michigan, 1241 E. Catherine St., 5912 Buhl Building, SPC 5618 Ann Arbor, MI 48109-5618en_US
dc.contributor.affiliationotherDepartment of Medicine, University of Maryland School of Medicine, Baltimore, Marylanden_US
dc.contributor.affiliationotherDepartment of Medicine, University of Maryland School of Medicine, Baltimore, Marylanden_US
dc.contributor.affiliationotherDepartment of Medicine, University of Maryland School of Medicine, Baltimore, Marylanden_US
dc.contributor.affiliationotherDepartment of Medicine, University of Maryland School of Medicine, Baltimore, Marylanden_US
dc.contributor.affiliationotherDepartment of Medicine, University of Maryland School of Medicine, Baltimore, Maryland ; Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, Marylanden_US
dc.identifier.pmid19697356en_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/64895/1/20444_ftp.pdf
dc.identifier.doi10.1002/gepi.20444en_US
dc.identifier.sourceGenetic Epidemiologyen_US
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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