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

H. G. Koch, J. McClay, E. W. Loh, S. Higuchi, J. H. Zhao, P. Sham, D. Ball, I. W. Craig

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22 Citations (Scopus)

Abstract

There 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.

Original languageEnglish
Pages (from-to)2993-2999
Number of pages7
JournalHuman Molecular Genetics
Volume9
Issue number20
Publication statusPublished - Dec 12 2000
Externally publishedYes

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Linkage Disequilibrium
Microsatellite Repeats
Single Nucleotide Polymorphism
Alleles
Quantitative Trait Loci
Alcoholics
Gene Frequency
Chromosomes, Human, Pair 12
Aldehyde Dehydrogenase
Population
Exons
Genes

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

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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. / Koch, H. G.; McClay, J.; Loh, E. W.; Higuchi, S.; Zhao, J. H.; Sham, P.; Ball, D.; Craig, I. W.

In: Human Molecular Genetics, Vol. 9, No. 20, 12.12.2000, p. 2993-2999.

Research output: Contribution to journalArticle

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AU - Loh, E. W.

AU - Higuchi, S.

AU - Zhao, J. H.

AU - Sham, P.

AU - Ball, D.

AU - Craig, I. W.

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