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Article: Linkage disequilibrium mapping of complex traits using SNP and microsatellite markers

TitleLinkage disequilibrium mapping of complex traits using SNP and microsatellite markers
Authors
Issue Date2000
PublisherJohn Wiley & Sons, Inc. The Journal's web site is located at http://www.interscience.wiley.com/jpages/0148-7299:1/
Citation
American Journal Of Medical Genetics - Neuropsychiatric Genetics, 2000, v. 96 n. 4, p. 485 How to Cite?
AbstractLinkage analysis of the major psychoses, schizophrenia and bipolar affective disorder, is providing increasing evidence in support of several genetic loci. Some of including chromo-somes 13q and 22q, appear to be shared between the two diagnoses. Linkage disequilibrium mapping, using simple sequence repeat markers and SNPs, followed by the analysis of positional candidate genes, is the most likely route by which susceptibility alleles at loci such as these will be found. However little is known about linkage disequilibrium relationships between different classes of genetic markers and between ethnic groups. We demonstrate that substantial differences exist in allele frequencies for both SNP and microsatellite markers between subjects of Chinese and European origin, which has significant implications for LD mapping. Analysis of about 30 SNPs in brain-expressed candidate genes reveals that about half of those polymorphic in UK populations are monomorphic in the Chinese, and many of the remainder differ significantly in allele frequency. Likewise although almost all of over 100 microsatellites tested are polymorphic in both populations, allele frequencies differ substantially for most, with common alleles present in one population often being infrequent or absent in the other. Using the high/low activity phenotype at the COMT locus (chromosome 22q11) as a phenotype, we have modeled the linkage disequilibrium mapping process with both SNPs and microsatellites. We demonstrate the linkage disequilibrium relationships between markers in this region, the advantages of each marker type, and provide information on the sample size and power required for LD mapping. We also present methods for LD mapping using familial transmission of haplotypes with the program TRANSMIT.
Persistent Identifierhttp://hdl.handle.net/10722/175956
ISSN
2015 Impact Factor: 3.391
2015 SCImago Journal Rankings: 1.771

 

DC FieldValueLanguage
dc.contributor.authorCollier, DAen_US
dc.contributor.authorLi, Ten_US
dc.contributor.authorBreen, Gen_US
dc.contributor.authorHu, Xen_US
dc.contributor.authorZhao, JHen_US
dc.contributor.authorJawaid, Aen_US
dc.contributor.authorLiu, Xen_US
dc.contributor.authorSt Clair, Den_US
dc.contributor.authorSham, Pen_US
dc.date.accessioned2012-11-26T09:02:52Z-
dc.date.available2012-11-26T09:02:52Z-
dc.date.issued2000en_US
dc.identifier.citationAmerican Journal Of Medical Genetics - Neuropsychiatric Genetics, 2000, v. 96 n. 4, p. 485en_US
dc.identifier.issn1552-4841en_US
dc.identifier.urihttp://hdl.handle.net/10722/175956-
dc.description.abstractLinkage analysis of the major psychoses, schizophrenia and bipolar affective disorder, is providing increasing evidence in support of several genetic loci. Some of including chromo-somes 13q and 22q, appear to be shared between the two diagnoses. Linkage disequilibrium mapping, using simple sequence repeat markers and SNPs, followed by the analysis of positional candidate genes, is the most likely route by which susceptibility alleles at loci such as these will be found. However little is known about linkage disequilibrium relationships between different classes of genetic markers and between ethnic groups. We demonstrate that substantial differences exist in allele frequencies for both SNP and microsatellite markers between subjects of Chinese and European origin, which has significant implications for LD mapping. Analysis of about 30 SNPs in brain-expressed candidate genes reveals that about half of those polymorphic in UK populations are monomorphic in the Chinese, and many of the remainder differ significantly in allele frequency. Likewise although almost all of over 100 microsatellites tested are polymorphic in both populations, allele frequencies differ substantially for most, with common alleles present in one population often being infrequent or absent in the other. Using the high/low activity phenotype at the COMT locus (chromosome 22q11) as a phenotype, we have modeled the linkage disequilibrium mapping process with both SNPs and microsatellites. We demonstrate the linkage disequilibrium relationships between markers in this region, the advantages of each marker type, and provide information on the sample size and power required for LD mapping. We also present methods for LD mapping using familial transmission of haplotypes with the program TRANSMIT.en_US
dc.languageengen_US
dc.publisherJohn Wiley & Sons, Inc. The Journal's web site is located at http://www.interscience.wiley.com/jpages/0148-7299:1/en_US
dc.relation.ispartofAmerican Journal of Medical Genetics - Neuropsychiatric Geneticsen_US
dc.titleLinkage disequilibrium mapping of complex traits using SNP and microsatellite markersen_US
dc.typeArticleen_US
dc.identifier.emailSham, P: pcsham@hku.hken_US
dc.identifier.authoritySham, P=rp00459en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.scopuseid_2-s2.0-33749091913en_US
dc.identifier.volume96en_US
dc.identifier.issue4en_US
dc.identifier.spage485en_US
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridCollier, DA=26642980600en_US
dc.identifier.scopusauthoridLi, T=36072008200en_US
dc.identifier.scopusauthoridBreen, G=15742166000en_US
dc.identifier.scopusauthoridHu, X=7404709241en_US
dc.identifier.scopusauthoridZhao, JH=7410311266en_US
dc.identifier.scopusauthoridJawaid, A=12787441800en_US
dc.identifier.scopusauthoridLiu, X=7409286408en_US
dc.identifier.scopusauthoridSt Clair, D=35354078200en_US
dc.identifier.scopusauthoridSham, P=34573429300en_US

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