Gene expression and methylation profiles as a biomarker for human radiation exposure

Taking into account the fact that Kazakhstan is one of the world's leaders in uranium mining, and given the extent of the damage suffered as a result of the work on the Semipalatinsk nuclear test site, the general background radiation in some regions came under the influence of additional effects of chronic exposure to low doses of radiation, the study and search for new methods of dosimetry, as an integral part of the radiological protection of the population, is a priority for the state. The purpose of this study is the search for and development of potential biomarkers by assessing the impact if ionising radiation on gene expression and quantification of global methylation and hydroxymethylation of uranium industry workers

Gene expression and methylation profiles as a biomarker for human radiation exposure

Taking into account the fact that Kazakhstan is one of the world's leaders in uranium mining, and given the extent of the damage suffered as a result of the work on the Semipalatinsk nuclear test site, the general background radiation in some regions came under the influence of additional effects of chronic exposure to low doses of radiation, the study and search for new methods of dosimetry, as an integral part of the radiological protection of the population, is a priority for the state. The purpose of this study is the search for and development of potential biomarkers by assessing the impact if ionising radiation on gene expression and quantification of global methylation and hydroxymethylation of uranium industry workers

Association of vitamin D receptor (FOKI, TAQI, APAI & BSMI) and IF-y genes' polymorphisms with risk of developing pulmonary TB (PTB) among Kazakhstani population

Almost one third of the world's population is infected with Mycobacterium tuberculosis (MTB) and only 10% of them will develop any active form of the disease. TB is second (1s t is HIV/AIDS) greatest killer worldwide due to a single infectious agent. In 2012, 8.6 million people developed active TB and 1.3 million died. Over 95% of TB deaths occur in developing countries. In 2012, an estimated more than half million children became ill with TB and 74 000 of them died. The TB cases are declining annually, but very slowly. Multi-drug resistant TB (MDR-TB) and extensively drug-resistant tuberculosis (XDRTB) is present in almost all surveyed countries. Kazakhstan is not highly burdened by TB. Kazakhstan is the list of MDR-TB and XDR-TB burden countries. Our aim is to investigate an association of Vitamin D receptor (FokI, TaqI, ApaI & BsmI) and IF-y genes" polymorphisms with risk of developing pulmonary TB (PTB) among Kazakhstani population

Whole genome sequencing of mycobacterium tuberculosis in Kazakhstan: first sequence results of two clinical isolates

The project is aimed to create the prerequisites for a personalized approach to the diagnosis and treatment of tuberculosis (TB) by identifying and comparing the whole genome sequences of M.tuberculosis strains isolated in Kazakhstan. Analysis for whole genome sequences obtained using the next generation sequencing technology will clarify the factors cause of the formation of highly virulent strains of M.tuberculosis, the evolution of local strains, and genetic markers of drug resistance

Reconstructing the genetic structure of the Kazakh from clan distribution data

Applying quasigenetic markers - non-biological traits which are nevertheless inherited in generations - is one of the research fields within human population genetics. For the West European, East European, and Caucasus populations, surnames are typical quasigenetic markers. For Central Asian populations, particularly Kazakh, the clan affiliation serves as a good marker: a set of papers demonstrated that many clans include mainly persons which biologically descent from a recent common ancestor. In this study, we analyzed a large (~4.2 million persons) dataset on quasigenetic markers - the geographic distribution of 50 Kazakh clans at the beginning of the 20th century, and compared the dataset with the direct data of the Y-chro-mosomal diversity in modern Kazakh populations. The analysis included three steps: the isonymy method, which is standard for quasigenetic markers, comparing frequencies of quasigenetic markers, and comparing the quasigenetic and genetic datasets. We constructed 50 maps of frequency of the distribution of each clan and revealed that these maps correlate with the maps of genetic distances. The Mantel test also demonstrated a significant correlation between geographic and quasigenetic distances (г = 0.60; p < 0.05). The analysis of inter-population variability revealed the largest diversity between geographic territories corresponding to the social-territorial groups of the Kazakh Khanate (zhuzes) rather than to other historical groups that existed on the territory of Kazakhstan in preceding and modern epochs. The same is evidenced by the principal components and multidimensional scaling plots, which grouped geographic populations into three clusters corresponding to three zhuzes. This indicates that the final structuring of the Kazakh gene pool might have occurred during the Kazakh Khanate period

Estimating the impact of the Mongol expansion upon the gene pool of Tuvans

With a view to trace the Mongol expansion in Tuvinian gene pool we studied two largest Tuvinian clans – those in which, according to data of humanities, one could expect the highest Central Asian ancestry, connected with the Mongol expansion. Thus, the results of Central Asian ancestry in these two clans component may be used as upper limit of the Mongol influence upon the Tuvinian gene pool in a whole. According to the data of 59 Y-chromosomal SNP markers, the haplogroup spectra in these Tuvinian tribal groups (Mongush, N = 64, and Oorzhak, N = 27) were similar. On average, two-thirds of their gene pools (63 %) are composed by North Eurasian haplogroups (N*, N1a2, N3a, Q) connected with autochtonous populations of modern area of Tuvans. The Central Asian haplogroups (C2, O2) composed less then fifth part (17 %) of gene pools of the clans studied. The opposite ratio was revealed in Mongols: there were 10 % North Eurasian haplogroups and 75 % Central Asian haplogroups in their gene pool. All the results derived – “genetic portraits”, the matrix of genetic distances, the dendrogram and the multidimensional scaling plot, which mirror the genetic connections between Tuvinian clans and populations of South Siberia and East Asia, demonstrated the prominent similarity of the Tuvinian gene pools with populations from and Khakassia and Altai. It could be therefore assumed that Tuvinian clans Mongush and Oorzhak originated from autochtonous people (supposedly, from the local Samoyed and Kets substrata). The minor component of Central Asian haplogroups in the gene pool of these clans allowed to suppose that Mongol expansion did not have a significant influence upon the Tuvinan gene pool at a whole

The genetic history of admixture across inner Eurasia

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this record.Data Availability. Genome-wide sequence data of two Botai individuals (BAM format) are available at the European Nucleotide Archive under the accession number PRJEB31152 (ERP113669). Eigenstrat format array genotype data of 763 present-day individuals and 1240K pulldown genotype data of two ancient Botai individuals are available at the Edmond data repository of the Max Planck Society (https://edmond.mpdl.mpg.de/imeji/collection/Aoh9c69DscnxSNjm?q=).The indigenous populations of inner Eurasia, a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra, harbor tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine, and Uzbekistan. We furthermore report additional damage-reduced genome-wide data of two previously published individuals from the Eneolithic Botai culture in Kazakhstan (~5,400 BP). We find that present-day inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries, mirroring geography. The Botai and more recent ancient genomes from Siberia show a decrease in contribution from so-called “ancient North Eurasian” ancestry over time, detectable only in the northern-most “forest-tundra” cline. The intermediate “steppe-forest” cline descends from the Late Bronze Age steppe ancestries, while the “southern steppe” cline further to the South shows a strong West/South Asian influence. Ancient genomes suggest a northward spread of the southern steppe cline in Central Asia during the first millennium BC. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.Max Planck SocietyEuropean Research Council (ERC)Russian Foundation for Basic Research (RFBR)Russian Scientific FundNational Science FoundationU.S. National Institutes of HealthAllen Discovery CenterUniversity of OstravaCzech Ministry of EducationXiamen UniversityFundamental Research Funds for the Central UniversitiesMES R

Mapping of eco-social and genetic factors of susceptibility of tuberculosis among the population of the Rebuplic of Kazakhstan

In this study combined design was used, which included: 1) Case-control study; 2) Molecular epidemiological study; and 3) Study of human genetic susceptibility to tuberculosis.This work is the first case-control study in Kazakhstan where complex factors of TB risk and their effects are estimated. The study confirmed the role of main risk factors of tuberculosis development in Kazakhstan: young age, single relationship status, living in rent apartment, smoking, diabetes and migration

The possible role of social selection in the distribution of major haplotypes of Y-chromosome haplogroup C3 in Central Asian populations

There is a strong connection between social selection and birth rate of the descendants, whose fathers had achieved high social status during the expansion of the Mongol Empire and associated historical events. We suppose this major ancestral haplotype to be the “proto-Mongolian haplotype”, inherited by Genghis Khan and his descendants. It can be assumed that the four common haplotypes also spread as a result of positive social selection, because some clans were endowed with a number of privileges and high status during the Mongol expansion

The possible role of social selection in the distribution of major haplotypes of Y-chromosome haplogroup C3 in Central Asian populations

There is a strong connection between social selection and birth rate of the descendants, whose fathers had achieved high social status during the expansion of the Mongol Empire and associated historical events. We suppose this major ancestral haplotype to be the “proto-Mongolian haplotype”, inherited by Genghis Khan and his descendants. It can be assumed that the four common haplotypes also spread as a result of positive social selection, because some clans were endowed with a number of privileges and high status during the Mongol expansion