The need for standardized biobanks in Kazakhstan

Biobanks are an important tool for clinical and research studies conducted on biomarkers of genetic therapy, diagnostic tests and new drugs; however, most biobanks remain incomplete and are often used without uniform standards and criteria. There is also a a lack of high-quality biological samples and many bioethical problems are often overlooked.Currently, Kazakhstan has no standard requirements and protocols for biomedical organizations. However, .an analysis of published data shows that possibly hundreds of samples are analyzed. Therefore, an establishment of biobank with standardized requirements could create better quality research.The National Center for Biotechnology has already started a biobank with more than 1,500 blood samples, with the ultimate goal of creating a biobank including around 10,000 blood samples of healthy volunteers, the same number of samples obtained from individuals with cardiovascular and endocrine diseases with samples stored under special conditions. The database contains demographic characteristics of donor’s medical history. Informed consent for research received from all donors. This biobank can be considered as a national resource for scientific research

Pharmacogenetic research in Kazakhstan

Introduction: Pharmacogenomics is an emerging field of medicine that combines genetics and pharmacology. Pharmacogenomic research is relatively new in Kazahkstan, but, in recent years, significant progress has been made in this field. The National Scientific Laboratory for Biotechnology has launched several government-funded research projects focused on finding genetic markers that determine susceptibility to various drugs. Another goal of pharmacogenetic research in the laboratory is to find the pharmacogenomic markers that target cardiovascular diseases, accounting for allelic frequencies in selected genes in the Kazakh population. In addition, pharmacogenomic testing kits allow patients to choose the drug dosage. For example, the drug Warfarin has been developed within the framework of the "Technology Commercialization Project,” funded jointly by the Ministry of Education and Science of the Republic of Kazakhstan and the World Bank.Material and methods: The pharmacogenomic studies were conducted using the real-time PCR and direct DNA sequencing. DNA was isolated from venous blood or buccal cells, collected from patients.Results: To date, we have identified the most promising areas of research in the field of pharmacogenomics in Kazakhstan. The allelic frequencies of a number of polymorphisms in the Kazakh population have been calculated (CYP2C9, CYP2C19, CYP3A4, VKORC1, CYP4F2, GGCX, CYP2D6, CYP1A2, NAT2, GSTP1, SLC47A1). A unique repository of DNA samples was established and is being replenished during the implementation of aforementioned projects. Development of the testing kit for individual selection of Warfarin dosage is nearing completion. A patent, named "Method of Selection Based Dose Warfarin Genotyping for the Kazakh Population" has been recently obtained. An application for another patent, titled "Express Method of Correction of Warfarin Dosing, Based on Real-time PCR" has received positive evaluation. The results of domestic pharmacogenomic studies will allow a more rational selection of drugs and their dosage regimens specific to the Kazakh population

Frequency of NAT2 and GSTP1 polymorphisms in the Kazakh population

Introduction: Phase II xenobiotic biotransformation enzymes perform detoxification of hydrophilic and often toxic Phase I products by glutathionetransferase (GST), UDP-glucuronosyltransferase (UDF), N-acetyltransferase (NAT) families and other enzymes. GST protein family metabolizes a large number of electrophilic xenobiotics, including drugs, by conjugating them with glutathione. Arylamine-N-acetyltransferase (NAT) catalyzes the acetylation of the aromatic and heterocyclic amines.Materials and methods: The current study has assessed the frequencies of NAT2 and GSTP1 genes polymorphisms in 326 healthy individuals from different regions of Kazakhstan by using Real-Time PCR and direct sequencing methods.Results: Allele frequencies were derived for NAT2*5 (0.54) and GSTP1 (0.27). GSTP1 alleles were in Hardy – Weinberg equilibrium (p > 0.05), while NAT2*5 (p = 0.00) were not.  The population differences between North, Northeast and South Kazakhstan regions were determined. Statistically significant differences in the frequency of genotypes were not found.Conclusion: Allelic polymorphisms of NAT2*5 and GSTP1 genes vary widely in different populations. Kazakh population was significantly different from Asian, Caucasoid, African-American and Hispanic ones by NAT2*5 and GSTP1 genes. Allelic variants of the NAT2*5 were detected with a low frequency in Asian populations. Allelic frequency in other world populations varies from 30 to 50%. The differences between Kazakh (0.54) and the world population were statistically significant (p < 0.05). The frequency of GSTP1 (rs1695) in the African American population is 42%. The frequency of GSTP1 in Asian populations varies from 11% to 23%, in Caucasoid populations it is about 30%. The differences between Kazakh population (0.27) and other populations selected from the literature were statistically significant (p < 0.05).The study of mutations in GSTP1 and NAT2 genes is necessary to assess the risk of the development of various diseases, such as cancer. Information on allelic polymorphisms also might be useful for personalized drug prescription for such drugs as cyclophosphamide, cisplatin, methotrexate, isoniazid, pyrazinamide, and rifampin

Estrogen Receptor Gene (ESR1) PVUII and XBAI Polymorphisms and Bone Mineral Density in Kazakh Women

Introduction: Osteoporosis is a common age-related disease that is strongly influenced by genetics. Polymorphisms of the estrogen receptor gene alpha (ESR1) are consistently been associated with bone mineral density (BMD) and fracture.The purpose of this investigation was to evaluate potential association of single nucleotide polymorphism (SNP) variants of the ESR1 gene and bone mineral density (BMD) of the lumbar spine in Kazakh women.Methods: 140 female participants in Pavlodar clinics with varying measures of BMD. We are examined the potential association of BMD with 2 SNPs from the ESR1 gene (rs2234693 [PvuII] and rs9340799 [XbaI]). Genotyping of the PvuII and XbaI polymorphisms was performed by direct sequencing of the gene fragments containing restriction sites with the identification of genotypes PP, Pp, pp and XX, Xx, xx respectively.Results: Unadjusted mean BMD values ranged from 1.14±0.14 g/cm2 in Caucasian women and 1.03±0.11 g/cm2 in Asian women. The association between PvuII polymorphism and BMD at the lumbar spine (p= 0.04 for PP=Pp=pp) was statistically significant in all women. The XbaI polymorphism was not associated with BMD at lumbar spine. The relative risk for low BMD was higher for the marker PvuII (RR=1.51) than for the marker XbaI (RR=1.35).Conclusion: The PvuII polymorphism had a weak association with lumbar spine BMD.  XbaI polymorphism was unlikely to be a predictor of lumbar spine BMD in Kazakh women. These conclusions could help to determine the genetic risk factors for osteoporosis; however, further studies on the association between gene polymorphisms and BMD are needed including larger numbers of participants and genes to clarify genetic risks

Vitamin D Receptor Gene Polymorphisms and Breast Cancer Risk in Kazakhstan

Introduction: The steroid hormone 1,25-dihydroxyvitamin D3 is thought to protect against breast cancer. The activity of 1,25-dihydroxyvitamin D3 is mediated via the vitamin D receptor (VDR), and a number of polymorphisms in the VDR gene have been identified. These result in distinct genotypes, some of which may alter susceptibility to breast cancer. Two common single nucleotide polymorphisms (SNP) in the VDR gene (VDR), rs1544410 (BsmI) and rs2228570 (FokI), have been inconsistently associated with breast cancer risk. Increased risk has been reported for the FokI ff genotype, which encodes a less transcriptionally active isoform of VDR. A reduced risk has been reported for the BsmI BB genotype which may influence VDR mRNA stability.Aim: We have investigated whether specific VDR gene polymorphisms are associated with breast cancer risk in Kazakhstan women.Material and Methods: In a case–control study, female breast cancer patients (315) and a female control group (n=604) were tested for two VDR polymorphisms. Statistical analysis was conducted using SPSS19.0.Results: The VDR rs2228570 (FokI) polymorphism was associated with an increased occurence of BC [rs2228570 (folk) ff vs. FF genotype: OR=1.71; 95% CI=1.21-2.43]. No association was noted between rs1544410 (BsmI) BB and breast cancer risk [OR=0.68; 95% CI=0.49-0.95].Conclusion: Although the factors that increase breast cancer susceptibility remain uncertain, future large studies should integrate genetic variation in VDR with biomarkers of vitamin D status. Additional testing on the effect of varying genotypes on the functional mechanisms of the VDR could help to improve future testing and treatment of woman at risk for breast cancer

BRCA1 and BRCA2 Gene Mutations Screening In Sporadic Breast Cancer Patients In Kazakhstan.

Background: A large number of distinct mutations in the BRCA1 and BRCA2 genes have been reported worldwide, but little is known regarding the role of these inherited susceptibility genes in breast cancer risk among Kazakhstan women.Aim: To evaluate the role of BRCA1/2 mutations in Kazakhstan women presenting with sporadic breast cancer.Methods: We investigated the distribution and nature of polymorphisms in BRCA1 and BRCA2 entire coding regions in 156 Kazakhstan sporadic breast cancer cases and 112 age-matched controls using automatic direct sequencing.Results: We identified 22 distinct variants, including 16 missense mutations and 6 polymorphisms in BRCA1/2 genes. In BRCA1, 9 missense mutations and 3 synonymous polymorphisms were observed. In BRCA2, 7 missense mutations and 3 polymorphisms were detected. There was a higher prevalence of observed mutations in Caucasian breast cancer cases compared to Asian cases (p<0.05); higher frequencies of sequence variants were observed in Asian controls. No recurrent or founder mutations were observed in BRCA1/2 genes. There were no statistically significant differences in age at diagnosis, tumor histology, size of tumor, and lymph node involvement between women with breast cancer with or without the BRCA sequence alterations.Conclusions:Considering the majority of breast cancer cases are sporadic, the present study will be helpful in the evaluation of the need for the genetic screening of BRCA1/2 mutations and reliable genetic counseling for Kazakhstan sporadic breast cancer patients. Evaluation of common polymorphisms and mutations and breast cancer risk in families with genetic predisposition to breast cancer is ongoing in another current investigation.

Genomic analyses inform on migration events during the peopling of Eurasia.

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.Support was provided by: Estonian Research Infrastructure Roadmap grant no 3.2.0304.11-0312; Australian Research Council Discovery grants (DP110102635 and DP140101405) (D.M.L., M.W. and E.W.); Danish National Research Foundation; the Lundbeck Foundation and KU2016 (E.W.); ERC Starting Investigator grant (FP7 - 261213) (T.K.); Estonian Research Council grant PUT766 (G.C. and M.K.); EU European Regional Development Fund through the Centre of Excellence in Genomics to Estonian Biocentre (R.V.; M.Me. and A.Me.), and Centre of Excellence for Genomics and Translational Medicine Project No. 2014-2020.4.01.15-0012 to EGC of UT (A.Me.) and EBC (M.Me.); Estonian Institutional Research grant IUT24-1 (L.S., M.J., A.K., B.Y., K.T., C.B.M., Le.S., H.Sa., S.L., D.M.B., E.M., R.V., G.H., M.K., G.C., T.K. and M.Me.) and IUT20-60 (A.Me.); French Ministry of Foreign and European Affairs and French ANR grant number ANR-14-CE31-0013-01 (F.-X.R.); Gates Cambridge Trust Funding (E.J.); ICG SB RAS (No. VI.58.1.1) (D.V.L.); Leverhulme Programme grant no. RP2011-R-045 (A.B.M., P.G. and M.G.T.); Ministry of Education and Science of Russia; Project 6.656.2014/K (S.A.F.); NEFREX grant funded by the European Union (People Marie Curie Actions; International Research Staff Exchange Scheme; call FP7-PEOPLE-2012-IRSES-number 318979) (M.Me., G.H. and M.K.); NIH grants 5DP1ES022577 05, 1R01DK104339-01, and 1R01GM113657-01 (S.Tis.); Russian Foundation for Basic Research (grant N 14-06-00180a) (M.G.); Russian Foundation for Basic Research; grant 16-04-00890 (O.B. and E.B); Russian Science Foundation grant 14-14-00827 (O.B.); The Russian Foundation for Basic Research (14-04-00725-a), The Russian Humanitarian Scientific Foundation (13-11-02014) and the Program of the Basic Research of the RAS Presidium “Biological diversity” (E.K.K.); Wellcome Trust and Royal Society grant WT104125AIA & the Bristol Advanced Computing Research Centre (http://www.bris.ac.uk/acrc/) (D.J.L.); Wellcome Trust grant 098051 (Q.A.; C.T.-S. and Y.X.); Wellcome Trust Senior Research Fellowship grant 100719/Z/12/Z (M.G.T.); Young Explorers Grant from the National Geographic Society (8900-11) (C.A.E.); ERC Consolidator Grant 647787 ‘LocalAdaptatio’ (A.Ma.); Program of the RAS Presidium “Basic research for the development of the Russian Arctic” (B.M.); Russian Foundation for Basic Research grant 16-06-00303 (E.B.); a Rutherford Fellowship (RDF-10-MAU-001) from the Royal Society of New Zealand (M.P.C.)

REGULARITIES OF HYPOCHLORITE MINERAL-ANION INTERACTION WITH LIPIDS OF MAN'S BLOOD LIPOPROTEINS AND LIPOSOMES

It has been determined on the lipoproteins of the man's blood that the lipids LNP have been subjected to the largest oxidation changes under action of the hypochlorite in the comparison with LONP and LVP. It has been determined in the investigated oxidation systems (liposomes from egg phosphatidyl choline, dimyristoylphosphatidyl choline, colloid dispesion and LNP) the same set of the oxidation products is formed. The set of the formed cholesterin oxyderivatives doesn't depend upon the access rate to the hypochlorite. At interaction of the hypochlorite with cholesterin it has been determined that the cholesterin structure change takes place only accrording to the C3, C6 and C7 position. No one derivative oxidated according to the hydrocarbon tail has been discoverd in the mixture of the products. The methods for preparative extraction and identification of the cholesterin oxyderivatives and its esters have been developedAvailable from VNTIC / VNTIC - Scientific & Technical Information Centre of RussiaSIGLERURussian Federatio

The need for standardized biobanks in Kazakhstan

Biobanks are an important tool for clinical and research studies conducted on biomarkers of genetic therapy, diagnostic tests and new drugs; however, most biobanks remain incomplete and are often used without uniform standards and criteria. There is also a a lack of high-quality biological samples and many bioethical problems are often overlooked. Currently, Kazakhstan has no standard requirements and protocols for biomedical organizations. However, .an analysis of published data shows that possibly hundreds of samples are analyzed. Therefore, an establishment of biobank with standardized requirements could create better quality research. The National Center for Biotechnology has already started a biobank with more than 1,500 blood samples, with the ultimate goal of creating a biobank including around 10,000 blood samples of healthy volunteers, the same number of samples obtained from individuals with cardiovascular and endocrine diseases with samples stored under special conditions. The database contains demographic characteristics of donor’s medical history. Informed consent for research received from all donors. This biobank can be considered as a national resource for scientific research

Frequency of NAT2 and GSTP1 polymorphisms in the Kazakh population

Introduction: Phase II xenobiotic biotransformation enzymes perform detoxification of hydrophilic and often toxic Phase I products by glutathionetransferase (GST), UDP-glucuronosyltransferase (UDF), N-acetyltransferase (NAT) families and other enzymes. GST protein family metabolizes a large number of electrophilic xenobiotics, including drugs, by conjugating them with glutathione. Arylamine-N-acetyltransferase (NAT) catalyzes the acetylation of the aromatic and heterocyclic amines. Materials and methods: The current study has assessed the frequencies of NAT2 and GSTP1 genes polymorphisms in 326 healthy individuals from different regions of Kazakhstan by using Real-Time PCR and direct sequencing methods. Results: Allele frequencies were derived for NAT2*5 (0.54) and GSTP1 (0.27). GSTP1 alleles were in Hardy – Weinberg equilibrium (p > 0.05), while NAT2*5 (p = 0.00) were not.  The population differences between North, Northeast and South Kazakhstan regions were determined. Statistically significant differences in the frequency of genotypes were not found. Conclusion: Allelic polymorphisms of NAT2*5 and GSTP1 genes vary widely in different populations. Kazakh population was significantly different from Asian, Caucasoid, African-American and Hispanic ones by NAT2*5 and GSTP1 genes. Allelic variants of the NAT2*5 were detected with a low frequency in Asian populations. Allelic frequency in other world populations varies from 30 to 50%. The differences between Kazakh (0.54) and the world population were statistically significant (p < 0.05). The frequency of GSTP1 (rs1695) in the African American population is 42%. The frequency of GSTP1 in Asian populations varies from 11% to 23%, in Caucasoid populations it is about 30%. The differences between Kazakh population (0.27) and other populations selected from the literature were statistically significant (p < 0.05). The study of mutations in GSTP1 and NAT2 genes is necessary to assess the risk of the development of various diseases, such as cancer. Information on allelic polymorphisms also might be useful for personalized drug prescription for such drugs as cyclophosphamide, cisplatin, methotrexate, isoniazid, pyrazinamide, and rifampin