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Article: Further investigation of linkage diequilibrium between SNPs and their ability to identify associated susceptibility loci

TitleFurther investigation of linkage diequilibrium between SNPs and their ability to identify associated susceptibility loci
Authors
Issue Date2004
PublisherBlackwell Publishing Ltd. The Journal's web site is located at http://www.blackwellpublishing.com/journals/AHG
Citation
Annals Of Human Genetics, 2004, v. 68 n. 3, p. 240-248 How to Cite?
AbstractThere is currently considerable interest in the use of single-nucleotide polymorphisms (SNPs) to map disease susceptibility genes. The success of this method will depend on a number of factors including the strength of linkage disequilibrium (LD) between marker and disease loci. We used a data set of SNP genotypings in the region of the APOE disease susceptibility locus to investigate the likely usefulness of SNPs in case-control studies. Using the estimated haplotype structure surrounding and including the APOE locus, and assuming a codominant disease model, we treated each SNP in turn as if it were a disease susceptibility locus and obtained, for each disease locus and markers, the expected likelihood ratio test (LRT) to assess disease association. We were particularly interested in the power to detect association with the susceptibility polymorphism itself, the power of nearby markers to detect association, and the ability to distinguish between the susceptibility polymorphism and marker loci also showing association. We found that the expected LRT depended critically on disease allele frequencies. For disease loci with a reasonably common allele we were usually able to detect association. However, for only a subset of markers in the close neighbourhood of the disease locus was association detectable. In these cases we were usually, but not always, able to distinguish the disease locus from nearby associated marker loci. For some disease loci, no other loci demonstrated detectable association with the disease phenotype. We conclude that one may need to use very dense SNP maps in order to avoid overlooking polymorphisms affecting susceptibility to a common phenotype. © University College London 2004.
Persistent Identifierhttp://hdl.handle.net/10722/175971
ISSN
2015 Impact Factor: 1.889
2015 SCImago Journal Rankings: 1.191
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorNorth, BVen_US
dc.contributor.authorCurtis, Den_US
dc.contributor.authorMartin, ERen_US
dc.contributor.authorLai, EHen_US
dc.contributor.authorRoses, ADen_US
dc.contributor.authorSham, PCen_US
dc.date.accessioned2012-11-26T09:03:08Z-
dc.date.available2012-11-26T09:03:08Z-
dc.date.issued2004en_US
dc.identifier.citationAnnals Of Human Genetics, 2004, v. 68 n. 3, p. 240-248en_US
dc.identifier.issn0003-4800en_US
dc.identifier.urihttp://hdl.handle.net/10722/175971-
dc.description.abstractThere is currently considerable interest in the use of single-nucleotide polymorphisms (SNPs) to map disease susceptibility genes. The success of this method will depend on a number of factors including the strength of linkage disequilibrium (LD) between marker and disease loci. We used a data set of SNP genotypings in the region of the APOE disease susceptibility locus to investigate the likely usefulness of SNPs in case-control studies. Using the estimated haplotype structure surrounding and including the APOE locus, and assuming a codominant disease model, we treated each SNP in turn as if it were a disease susceptibility locus and obtained, for each disease locus and markers, the expected likelihood ratio test (LRT) to assess disease association. We were particularly interested in the power to detect association with the susceptibility polymorphism itself, the power of nearby markers to detect association, and the ability to distinguish between the susceptibility polymorphism and marker loci also showing association. We found that the expected LRT depended critically on disease allele frequencies. For disease loci with a reasonably common allele we were usually able to detect association. However, for only a subset of markers in the close neighbourhood of the disease locus was association detectable. In these cases we were usually, but not always, able to distinguish the disease locus from nearby associated marker loci. For some disease loci, no other loci demonstrated detectable association with the disease phenotype. We conclude that one may need to use very dense SNP maps in order to avoid overlooking polymorphisms affecting susceptibility to a common phenotype. © University College London 2004.en_US
dc.languageengen_US
dc.publisherBlackwell Publishing Ltd. The Journal's web site is located at http://www.blackwellpublishing.com/journals/AHGen_US
dc.relation.ispartofAnnals of Human Geneticsen_US
dc.subject.meshAlzheimer Disease - Geneticsen_US
dc.subject.meshCase-Control Studiesen_US
dc.subject.meshGene Frequencyen_US
dc.subject.meshGenetic Markersen_US
dc.subject.meshGenetic Predisposition To Disease - Geneticsen_US
dc.subject.meshGenetics, Populationen_US
dc.subject.meshHaplotypes - Geneticsen_US
dc.subject.meshHumansen_US
dc.subject.meshLikelihood Functionsen_US
dc.subject.meshLinkage Disequilibriumen_US
dc.subject.meshModels, Geneticen_US
dc.subject.meshPhenotypeen_US
dc.subject.meshPolymorphism, Single Nucleotide - Geneticsen_US
dc.titleFurther investigation of linkage diequilibrium between SNPs and their ability to identify associated susceptibility locien_US
dc.typeArticleen_US
dc.identifier.emailSham, PC: pcsham@hku.hken_US
dc.identifier.authoritySham, PC=rp00459en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1046/j.1529-8817.2004.00086.xen_US
dc.identifier.pmid15180704-
dc.identifier.scopuseid_2-s2.0-4444292821en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-4444292821&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume68en_US
dc.identifier.issue3en_US
dc.identifier.spage240en_US
dc.identifier.epage248en_US
dc.identifier.isiWOS:000222131100007-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridNorth, BV=7005058731en_US
dc.identifier.scopusauthoridCurtis, D=14633020700en_US
dc.identifier.scopusauthoridMartin, ER=7404092528en_US
dc.identifier.scopusauthoridLai, EH=7201466525en_US
dc.identifier.scopusauthoridRoses, AD=35352401800en_US
dc.identifier.scopusauthoridSham, PC=34573429300en_US

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