The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination
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Date
2004
Journal Title
Journal ISSN
Volume Title
Publisher
Annals of human genetics
Abstract
Summary
The catalytic deficiency of human aldehyde dehydrogenase 2 (ALDH2) is caused by a nucleotide
substitution (G1510A; Glu487Lys) in exon 12 of the ALDH2 locus. This SNP, and four
non‐coding SNPs, including one in the promoter, span 40 kb of ALDH2; these and one
downstream STRP have been tested in 37 worldwide populations. Only four major SNP‐defined
haplotypes account for almost all chromosomes in all populations. A fifth haplotype harbours the
functional variant and is only found in East Asians. Though the SNPs showed virtually no
historic recombination, LD values are quite variable because of varying haplotype frequencies,
demonstrating that LD is a statistical abstraction and not a fundamental aspect of the genome,
and is not a function solely of recombination. Among populations, different sets of tagging
SNPs, sometimes not overlapping, can be required to identify the common haplotypes. Thus,
solely because haplotype frequencies vary, there is no common minimum set of tagging SNPs
globally applicable. The Fst values of the promoter region SNP and the functional SNP were
about two S.D. above the mean for a reference distribution of 117 autosomal biallelic markers.
These high Fst values may indicate selection has operated at these or very tightly linked sites.
Description
Keywords
Human Aldehyde Dehydrogenase 2, Genetics, Evolution
Citation
Oota, H., Pakstis, A.J., Bonne‐Tamir, B., Goldman, D., Grigorenko, E., Kajuna, S.L., Karoma, N.J., Kungulilo, S., Lu, R.B., Odunsi, K. and Okonofua, F., 2004. The evolution and population genetics of the ALDH2 locus: random genetic drift, selection, and low levels of recombination. Annals of human genetics, 68(2), pp.93-109.