Polymorphisms in genes involved in the absorption, distribution, metabolism, and excretion of drugs in the Kazakhs of Kazakhstan

A list of SNPs that were not found in heterozygous or homozygous variants. (DOC 83 kb

Polymorphisms of HLA-DRB1, -DQA1 and -DQB1 in inhabitants of Astana, the capital city of Kazakhstan.

BackgroundKazakhstan has been inhabited by different populations, such as the Kazakh, Kyrgyz, Uzbek and others. Here we investigate allelic and haplotypic polymorphisms of human leukocyte antigen (HLA) genes at DRB1, DQA1 and DQB1 loci in the Kazakh ethnic group, and their genetic relationship between world populations.Methodology/principal findingsA total of 157 unrelated Kazakh ethnic individuals from Astana were genotyped using sequence based typing (SBT-Method) for HLA-DRB1, -DQA1 and -DQB1 loci. Allele frequencies, neighbor-joining method, and multidimensional scaling analysis have been obtained for comparison with other world populations. Statistical analyses were performed using Arlequin v3.11. Applying the software PAST v. 2.17 the resulting genetic distance matrix was used for a multidimensional scaling analysis (MDS). Respectively 37, 17 and 19 alleles were observed at HLA-DRB1, -DQA1 and -DQB1 loci. The most frequent alleles were HLA-DRB1*07:01 (13.1%), HLA-DQA1*03:01 (13.1%) and HLA-DQB1*03:01 (17.6%). In the observed group of Kazakhs DRB1*07:01-DQA1*02:01-DQB1*02:01 (8.0%) was the most common three loci haplotype. DRB1*10:01-DQB1*05:01 showed the strongest linkage disequilibrium. The Kazakh population shows genetic kinship with the Kazakhs from China, Uyghurs, Mongolians, Todzhinians, Tuvinians and as well as with other Siberians and Asians.Conclusions/significanceThe HLA-DRB1, -DQA1 and -DQB1 loci are highly polymorphic in the Kazakh population, and this population has the closest relationship with other Asian and Siberian populations

Genetic risk factors for restenosis after percutaneous coronary intervention in Kazakh population

Background: After coronary stenting, the risk of developing restenosis is from 20 to 35 %. The aim of the present study is to investigate the association of genetic variation in candidate genes in patients diagnosed with restenosis in the Kazakh population. Methods: Four hundred fifty-nine patients were recruited to the study; 91 patients were also diagnosed with diabetes and were excluded from the sampling. DNA was extracted with the salting-out method. The patients were genotyped for 53 single-nucleotide polymorphisms. Genotyping was performed on the QuantStudio 12K Flex (Life Technologies). Differences in distribution of BMI score among different genotype groups were compared by analysis of variance (ANOVA). Also, statistical analysis was performed using R and PLINK v.1.07. Haplotype frequencies and LD measures were estimated by using the software Haploview 4.2. Results: A logistic regression analysis found a significant difference in restenosis rates for different genotypes. FGB (rs1800790) is significantly associated with restenosis after stenting (OR = 2.924, P = 2.3E−06, additive model) in the Kazakh population. CD14 (rs2569190) showed a significant association in the additive (OR = 0.08033, P = 2.11E−09) and dominant models (OR = 0.05359, P = 4.15E−11). NOS3 (rs1799983) was also highly associated with development of restenosis after stenting in additive (OR = 20.05, P = 2.74 E−12) and recessive models (OR = 22.24, P = 6.811E−10). Conclusions: Our results indicate that FGB (rs1800790), CD14 (rs2569190), and NOS3 (rs1799983) SNPs could be genetic markers for development of restenosis in Kazakh population. Adjustment for potential confounder factor BMI gave almost the same results

Neighbor-joining dendrogram based on HLA allele frequencies.

<p>Dendroram constructed by the neighbor-joining method showing the relationship between Kazakh populations with other populations based on the frequencies of HLA-DRB1 loc.</p

The Most frequent of DRB1-DQA1-DQB1 extended haplotypes and their frequencies in the Kazakh population (Astana).

a<p>Found in Buryats (22.0%); Khanty-Mansi (16.9%) Kazakhs (China) (8.3%).</p>b<p>Found in Italians (Sardinia) (25.3%); Russia (North-west) (9.0%); Kazakhs (China) (13.1%).</p>c<p>Found in Khanty-Mansi (8.1%); Italians (7.6%), Todzhinians (6.8%); Russia (North-west) (5.5%). Kazakhs (China) (4.8%);</p>d<p>Found in South Korea (2.9%).</p>e<p>Not found in any other population.</p>f<p>Found in Todzhinians (22.5%); English (14.1%), Australia Aborigine (10.0%); Russia (North-west) (9.0%); Kazakhs (China) (2.4%).</p>g<p>Found in Italians (14.1%); Slovenes (11.4%).</p>h<p>Found in Australia Aborigine (7.0%).</p>i<p>Found in Japan (8.2%); Mongolians (6.5%); Kazakhs (China) (2.4%).</p>j<p>Found in Khanty-Mansi (8.1%); Italians (7.6%); Kazakhs (China) (4.8%).</p>k<p>Found in Cameroon Yaounde (1.2%).</p>l<p>Found in Italians (1.9%); Tuva (1.1%).</p><p>The Most frequent of DRB1-DQA1-DQB1 extended haplotypes and their frequencies in the Kazakh population (Astana).</p

Baseline data on number of alleles in the Kazakh population (Astana) and average heterozygosity.

<p>Baseline data on number of alleles in the Kazakh population (Astana) and average heterozygosity.</p

Haplotype frequency and significant linkage disequilibrium parameter of HLA two-loci haplotypes in Kazakh population (Astana).

a<p>Number of times;</p>b<p>Haplotype frequency;</p>c<p>D Linkage disequilibrium;</p>d<p>Only t values ≥ 2.0 were considered significant.</p><p>Haplotype frequency and significant linkage disequilibrium parameter of HLA two-loci haplotypes in Kazakh population (Astana).</p

Allelic frequency of HLA-DRB1, -DQA1 and -DQB1 loci in the Kazakh population (Astana).

<p>Allelic frequency of HLA-DRB1, -DQA1 and -DQB1 loci in the Kazakh population (Astana).</p

Territory of the Republic of Kazakhstan.

<p>Territory of the Republic of Kazakhstan.</p