Nucleotide sequence diversity in non-coding regions of ALDH2 as revealed by restriction enzyme and SSCP analysis

The simultaneous analysis of closely linked nucleotide substitutions has re cently become possible. However, it is not known whether the construction o f molecular haplotypes will be a generally useful strategy for nuclear gene s. Furthermore, whereas mobility-shift methods are widely used for the disc overy of nucleotide substitutions, the yield of these methods has rarefy be en evaluated. This paper investigates these issues in non-coding regions of ALDH2, the gene that encodes aldehyde dehydrogenase 2 (ALDH2). Screening 2 0 Europeans, 20 native Americans, and 20 Asians by using restriction enzyme and single-strand conformation polymorphism (SSCP) analysis has revealed 1 6 variable sites. SSCP yields slightly fewer than the number of nucleotide substitutions predicted by the restriction enzyme digests. Estimates of nuc leotide diversity are similar to those of other genes, suggesting that the pattern of polymorphism in ALDH2 offers a preview of what can be expected i n many human nuclear genes. Eight of the variable sites discovered here and four sites discovered by others have been genotyped in 756 people from 17 populations across five continents. An expectation-maximization method has used to estimate haplotype states and frequencies. Only three haplotypes ar e common worldwide, and a fourth haplotype is common in, but private to, As ia. Although allele frequencies differ among sites, linkage disequilibrium is almost maximal across ALDH2. This suggests that haplotype construction a t ALDH2 is particularly successful. The ALDH2 result, in conjunction with l inkage disequilibrium results from other genes, indicates that haplotype co nstruction will be a generally useful genomic strategy.