Journal Article

Allele association studies with SSR and SNP markers at known physical distances within a 1 Mb region embracing the <i>ALDH2</i> 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 and I. W. Craig

in Human Molecular Genetics

Volume 9, issue 20, pages 2993-2999
Published in print December 2000 | ISSN: 0964-6906
Published online December 2000 | e-ISSN: 1460-2083 | DOI: http://dx.doi.org/10.1093/hmg/9.20.2993
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

Show Summary Details

Preview

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.

Journal Article.  4792 words.  Illustrated.

Subjects: Genetics and Genomics

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.