Ascertainment Bias and the Pattern of Nucleotide Diversity at the Human ALDH2 Locus in a Japanese Population

Confirmation of ALDH2 as a Major locus of drinking behavior and of its variants regulating multiple metabolic phenotypes in a Japanese population

BACKGROUND

Normative alcohol use (or drinking behavior) influences the risk of cardiovascular disease in a multi-faceted manner. To identify susceptibility gene variants for drinking behavior, a 2-staged genome-wide association study was performed in a Japanese population.

METHODS AND RESULTS

In the stage-1 scan, 733 cases and 729 controls were genotyped with 456,827 SNP markers. The associated loci without redundancy of linkage disequilibrium were further examined in the stage-2 general population panel comprising 2,794 drinkers (≥ once per week), 1,521 chance drinkers (< once per week), and 1,351 non-drinkers. Along with genome-wide exploration, we aimed to replicate the trait association of a candidate gene SNP previously reported (rs1229984 in ADH1B). A cluster of 12 SNPs on 12q24 were found to significantly (P<5×10(-8)) associate with drinking behavior in stage 1, among which rs671 (a Glu-to-Lys substitution at position 504) in the ALDH2 gene showed the strongest association (odds ratio (OR)=0.16, P=3.6×10(-211) in the joint analysis). The association was also replicated for rs1229984 (OR=1.20, P<3.6×10(-4)). Furthermore, ALDH2 504Lys was associated with several metabolic traits, eg, lower levels of high-density lipoprotein cholesterol and liver enzymes-AST, ALT, and γGTP-by interacting with alcohol intake.

CONCLUSIONS

Our results confirm ALDH2 as a major locus regulating drinking behavior in the Japanese, indicating that the ALDH2 504Lys variant exerts pleiotropic effects on risk factors of cardiovascular disease among drinkers.

Molecular population genetics of SLC4A1 and Southeast Asian ovalocytosis

Southeast Asian ovalocytosis (SAO) is an erythrocyte abnormality that protects affected individuals from cerebral malaria. This trait is caused by a 27-bp deletion in the SLC4A1 gene, which is lethal when homozygous. We reseqeunced approximately 5 kb of SLC4A1 in an Indonesian population where SAO is prevalent to better understand the evolution of this clinically important trait. The four SAO chromosomes we resequenced share a single haplotype that differs from a sampled non-SAO haplotype only by the 27-bp deletion. Comparison of Indonesian sequence data to that from two other Asian populations (aboriginal Taiwanese and Japanese) shows Indonesian SLC4A1 to be strongly differentiated from the Taiwanese, but not the Japanese. Indeed, the Taiwanese sample contains only chromosomes that are highly divergent from all sampled SAO chromosomes. Because earlier studies have found an association between Austronesian-speakers (who most likely originated in Taiwan) and SAO, our failure to find SAO-like chromosomes in Taiwan is unexpected. Finally, our data find a strong excess of high-frequency derived alleles in all three populations. These alleles include the non-synonymous 'Memphis' variant, which is known to affect anion transport across the erythrocyte membrane. Our data suggest a role for recent natural selection acting on Memphis or a linked variant.

Origin and dispersal of atypical aldehyde dehydrogenase ALDH2487Lys

The East Asian respond with a marked facial flushing and mild to moderate symptoms of intoxication after drinking the amounts of alcohol that has no detectable effect on European. The alcohol sensitivity in Orientals is due to a delayed oxidation of acetaldehyde by an atypical aldehyde dehydrogenase ALDH2487Lys, which is resulted from a structural mutation in gene ALDH2. The atypical ALDH2487Lys allele has been associated with various phenotypic statuses, such as protective against alcohol dependence and the risk of alcohol-related digestive tract cancers. Here, we have examined this SNP, adjacent four non-coding SNPs, and one downstream STRP on ALDH2 gene, in total of 1072 unrelated healthy individuals from 14 Chinese populations and 130 Indian individuals. Five major haplotypes based on five SNPs across the ALDH2 gene 40 kb were found in all East Asian populations. The frequencies of the ancestral haplotype GCCTG and the East Asian special haplotype GCCTA containing the atypical ALDH2487Lys allele were 44.8% and 14.9%, respectively. The frequency of the atypical ALDH2487Lys allele or the East Asian specific haplotype GCCTA is high in Yunnan, South coastal, east coastal of China, and decreased gradually toward inland China, West, Northwest and North China. Combined with demographic history in East Asian, our results showed that the presence of ALDH2487Lys allele in peripheral regions of China might be the results of historical migration events from China to these regions. The origin of ALDH2487Lys could be possibly traced back to ancient Pai-Yuei tribe in South China.