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Article: Allele association studies with SSR and SNP markers at known physical distances within a 1 Mb region embracing the ALDH2 locus in the Japanese, demonstrates linkage disequilibrium extending up to 400 kb

TitleAllele association studies with SSR and SNP markers at known physical distances within a 1 Mb region embracing the ALDH2 locus in the Japanese, demonstrates linkage disequilibrium extending up to 400 kb
Authors
Issue Date2000
PublisherOxford University Press. The Journal's web site is located at http://hmg.oxfordjournals.org/
Citation
Human Molecular Genetics, 2000, v. 9 n. 20, p. 2993-2999 How to Cite?
AbstractThere has been considerable recent debate concerning the distances over which levels of allelic association useful for genomic quantitative trait locus (QTL) scans can be detected. We have examined simple sequence repeat (SSR) polymorphisms and two single nucleotide polymorphisms (SNPs) in the region flanking the aldehyde dehydrogenase 2 locus, ALDH2, in populations of Japanese alcoholics and controls. These groups differ significantly in the allele frequencies for the functional SNP in exon XII of this gene located on chromosome 12. The results obtained with SSR markers complement recent investigations with SNPs over similar distances at the TCR α/δ locus. Significant allelic association with this marker could be detected for SSRs over distances up to 400 kb and over 37 kb for the SNP thereby extending the distance over which LD at this locus could be detected by an order of magnitude. Furthermore, as a proof of principle, we show that comparisons of allele frequency differences for the SSR markers in the case (alcoholics) and control populations would have detected the ALDH2 marker as a putative QTL. Extending the tests to include alleles at two or three flanking loci suggests that the power to detect QTLs through association can be enhanced significantly.
Persistent Identifierhttp://hdl.handle.net/10722/175830
ISSN
2015 Impact Factor: 5.985
2015 SCImago Journal Rankings: 4.288
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorKoch, HGen_US
dc.contributor.authorMcclay, Jen_US
dc.contributor.authorLoh, EWen_US
dc.contributor.authorHiguchi, Sen_US
dc.contributor.authorZhao, JHen_US
dc.contributor.authorSham, Pen_US
dc.contributor.authorBall, Den_US
dc.contributor.authorCraig, IWen_US
dc.date.accessioned2012-11-26T09:01:39Z-
dc.date.available2012-11-26T09:01:39Z-
dc.date.issued2000en_US
dc.identifier.citationHuman Molecular Genetics, 2000, v. 9 n. 20, p. 2993-2999en_US
dc.identifier.issn0964-6906en_US
dc.identifier.urihttp://hdl.handle.net/10722/175830-
dc.description.abstractThere has been considerable recent debate concerning the distances over which levels of allelic association useful for genomic quantitative trait locus (QTL) scans can be detected. We have examined simple sequence repeat (SSR) polymorphisms and two single nucleotide polymorphisms (SNPs) in the region flanking the aldehyde dehydrogenase 2 locus, ALDH2, in populations of Japanese alcoholics and controls. These groups differ significantly in the allele frequencies for the functional SNP in exon XII of this gene located on chromosome 12. The results obtained with SSR markers complement recent investigations with SNPs over similar distances at the TCR α/δ locus. Significant allelic association with this marker could be detected for SSRs over distances up to 400 kb and over 37 kb for the SNP thereby extending the distance over which LD at this locus could be detected by an order of magnitude. Furthermore, as a proof of principle, we show that comparisons of allele frequency differences for the SSR markers in the case (alcoholics) and control populations would have detected the ALDH2 marker as a putative QTL. Extending the tests to include alleles at two or three flanking loci suggests that the power to detect QTLs through association can be enhanced significantly.en_US
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://hmg.oxfordjournals.org/en_US
dc.relation.ispartofHuman Molecular Geneticsen_US
dc.subject.meshAlcohol Dehydrogenase - Geneticsen_US
dc.subject.meshAllelesen_US
dc.subject.meshGene Frequencyen_US
dc.subject.meshGenotypeen_US
dc.subject.meshHumansen_US
dc.subject.meshJapanen_US
dc.subject.meshLinkage Disequilibrium - Geneticsen_US
dc.subject.meshMinisatellite Repeats - Geneticsen_US
dc.subject.meshPolymorphism, Single Nucleotide - Geneticsen_US
dc.titleAllele association studies with SSR and SNP markers at known physical distances within a 1 Mb region embracing the ALDH2 locus in the Japanese, demonstrates linkage disequilibrium extending up to 400 kben_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.doi10.1093/hmg/9.20.2993-
dc.identifier.pmid11115843-
dc.identifier.scopuseid_2-s2.0-0034642290en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0034642290&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume9en_US
dc.identifier.issue20en_US
dc.identifier.spage2993en_US
dc.identifier.epage2999en_US
dc.identifier.isiWOS:000165965400008-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridKoch, HG=14633753400en_US
dc.identifier.scopusauthoridMcClay, J=8627461600en_US
dc.identifier.scopusauthoridLoh, EW=7102994165en_US
dc.identifier.scopusauthoridHiguchi, S=7202930847en_US
dc.identifier.scopusauthoridZhao, JH=7410311266en_US
dc.identifier.scopusauthoridSham, P=34573429300en_US
dc.identifier.scopusauthoridBall, D=7202703810en_US
dc.identifier.scopusauthoridCraig, IW=7102548208en_US

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