Alleles Frequency and Polymorphic Genes Genotypes Associated with Alcoholism in Kazakh Population

Background: There is a category of people with a congenial predisposition to alcohol abuse among the total population. The identification of such persons by molecular genetic diagnostics and the implementation of appropriate preventive measures can significantly reduce the incidence of alcoholism. Objectives: This research aimed to study the genetic foundations of alcohol dependence development in Kazakhs based on the analysis of population frequencies of polymorphic variants of predisposition to alcoholism genes. Materials and Methods: The material for the research was the DNA recovered from the peripheral blood of the recruited control group population, which was represented by 1,800 conditionally healthy individuals of Kazakh nationality. Isolated DNA samples were genotyped by PCR. Conclusions: Kazakhs take an intermediate position between the previously studied European and Asian populations by allele frequencies of nine polymorphic variants of ADH1B (rs2066701, rs1789891), ADH1C (rs1693425, rs698), HTR2C (rs6318), ALDH2 (rs671), CADM2 (rs9841829), KLB (rs11940694), DRD2 (rs1076560) genes. Possible markers of an increased risk of alcoholism development in Kazakhs are G alleles of polymorphic loci rs2066701 of the ADH1B gene and rs671 of the ALDH2 gene, and the protective effect is possible in the presence of A alleles rs2066701 of the ADH1B gene and rs671 of the ALDH2 gene.

Frequency of ADH1B RsaI (rs2066701) single nucleotide polymorphism in a population of Bosnia and Herzegovina

Apart from its physiological role in the cellular oxidation of ethanol interesting feature of the ADH1B gene locus is its characteristic geographical distribution in which certain variants of ADH1B peak in different parts of the world. Therefore, ADH1B rs2066701 polymorphism is exploited as a genetic marker in tracing of the evolutionary processes and human migrations in the past. Taking into consideration the complexity of population genetic structure and several migrations in the history of the Balkan populations, including Bosnian and Herzegovinian, this study aimed to estimate the frequency of ADH1B rs2066701 polymorphism in the population of Bosnia and Herzegovina. The total of 101 randomly sampled individuals was genotyped for rs2066701 polymorphism in ADH1B gene using PCR-RFLP method. The obtained frequencies were used to calculate heterozygosity, fixation indices and Hardy-Weinberg equilibrium. Observed population-structure parameters were compared with other population values available in ALFRED database. Dimensional relations between the investigated populations were visualised with the NM-MDS (non metric multidimensional scaling) analysis using PAST. The minor allele frequency for rs2066701 was 0,257. Inter-population analysis including other European and non-European populations from the ALFRED database proved the above-mentioned European genetic background of the B&H population.

Fast principal components analysis reveals convergent evolution of ADH1B gene in Europe and East Asia

Searching for genetic variants with unusual differentiation between subpopulations is an established approach for identifying signals of natural selection. However, existing methods generally require discrete subpopulations. We introduce a method that infers selection using principal components (PCs) by identifying variants whose differentiation along top PCs is significantly greater than the null distribution of genetic drift. To enable the application of this method to large data sets, we developed the FastPCA software, which employs recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using the PC-based test for natural selection, we replicate previously known selected loci and identify three new genome-wide significant signals of selection, including selection in Europeans at the ADH1B gene. The coding variant rs1229984*T has previously been associated to a decreased risk of alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. We also detect new selection signals at IGFBP3 and IGH, which have also previously been associated to human disease.