New Methods for the Implementation of Joint Investment and Innovation Projects in Developed and Developing Countries: Experience of the Republic of Kazakhstan and the Russian Federation

The primary purpose of the research is to develop new scientific approaches to the implementation of joint innovation and investment projects in the framework of cooperation between developing countries on the example of the Republic of Kazakhstan and the Russian Federation. The methodology of the study included the use of a system of methods: the analytical and induction methods, hypothesis and the synthesis method. As part of the analytical and induction methods, the general theory of investment projects implemented by business entities of two or more countries was investigated. When considering the theory of investment and innovation projects, the following aspects were studied: basic fundamental attributes of project implementation; modelling of investment and innovation projects; modelling of the development of cross-country investment and innovation projects with the participation of two or more countries; factors influencing the effectiveness of cross-country investment and innovation projects. The study focused on the impact of investment and innovation projects on the economic growth of developing countries. Based on the results obtained using the analytical method, the general problems of intensification of investment projects were developed. Based on the identified problems, the method of hypothesis formulation was applied, which allowed formulating postulates on the application of several new methods of integration and economic cooperation of the states. The findings of the research allow in developing a new economic policy of cooperation of developing and, in some aspects, developed countries and applying it in practice in the conditions of increasing global competition

Esophageal Cancer in Kazakhstan: Multi-omic Research Challenges

Introduction. Esophageal cancer (EC) is the sixth most common cancer in Kazakhstan, fifth leading cause of mortality among men, and ninth leading cause of mortality among women. Advances in high-throughput sequencing over the last decade have made mapping the whole genetic variation in genome-wide scale possible. Transcriptome sequencing has become a powerful method for detecting driver mutations in cancer, since somatic point mutations as well as aberrant RNA variants, such as fusion genes and alternative splicing, can be identified. The aim of the study was to identify the genetic basis of EC by performing whole transcriptome sequencing (RNA-Seq) study in Kazakhstani patients.Materials and methods. We included patients with EC who had been admitted to the oncology center in Astana, Kazakhstan during the 2013-2014 year period. A pair of fresh frozen EC, its adjacent normal tissue specimen, and venous blood were obtained. So far, five pairs of EC samples were subjected to RNA-seq. Total RNA was isolated, and its quality was assessed using Agilent Bioanalyzer. The cDNA library was prepared following the standard mRNA protocol by Illumina and sequenced using Illumina HiSeq2000. Bionformatic analysis is ongoing.Results. During 2013, a total of 74 patients with EC were hospitalized in the oncology center, Astana, Kazakhstan. Radical and palliative surgery was performed on 39 and 34 patients, respectively, and 1 patient refused surgery treatment. The median age of the patients was 66 years (range 49-86 years). 88.4% of the patients were diagnosed with advanced stages T3-T4, and 74.5% from them has dysphagia III-IV levels. 83% of the cases were squamous cell carcinoma (ESCC). The major localizations for this type of cancer were the middle section (58.2%), lower section (37.2%), and upper section (4.6%) of the cases.Conclusion. ESCC is the most common histologic subtype of esophageal cancer in our patients and is characterized by a poor prognosis. Most patients were diagnosed with late stages T3-T4. Using high throughput sequencing approach, we could potentially identify a higher number of crucial molecular pathways involved in esophageal carcinogenesis that could facilitate the development of new diagnostic and treatment strategies. The early detection of EC gives hope of a long-term survival for patients

Sequence Alterations of I(Ks) Potassium Channel Genes in Kazakhstani Patients with Atrial Fibrillation

Introduction. Atrial fibrillation (AF) is the most common sustained arrhythmia, and it results in significant morbidity and mortality. However, the pathogenesis of AF remains unclear to date. Recently, more pieces of evidence indicated that AF is a multifactorial disease resulting from the interaction between environmental factors and genetics. Recent studies suggest that genetic mutation of the slow delayed rectifier potassium channel (I(Ks)) may underlie AF.Objective. To investigate sequence alterations of I(Ks) potassium channel genes KCNQ1, KCNE1 and KCNE2 in Kazakhstani patients with atrial fibrillation.Methods. Genomic DNA of 69 cases with atrial fibrillation and 27 relatives were analyzed for mutations in all protein-coding exons and their flanking splice site regions of the genes KCNQ1 (NM_000218.2 and NM_181798.1), KCNE1 (NM_000219.2), and KCNE2 (NM_172201.1) using bidirectional sequencing on the ABI 3730xL DNA Analyzer (Applied Biosystems, Foster City, CA, USA).Results. In total, a disease-causing mutation was identified in 39 of the 69 (56.5%) index cases. Of these, altered sequence variants in the KCNQ1 gene accounted for 14.5% of the mutations, whereas a KCNE1 mutation accounted for 43.5% of the mutations and KCNE2 mutation accounted for 1.4% of the mutations. The majority of the distinct mutations were found in a single case (80%), whereas 20% of the mutations were observed more than once. We found two sequence variants in KCNQ1 exon 13 (S546S G1638A) and exon 16 (Y662Y, C1986T) in ten patients (14.5%). In KCNE1 gene in exon 3 mutation, S59G A280G was observed in 30 of 69 patients (43.5%) and KCNE2 exon 2 T10K C29A in 1 patient (1.4%). Genetic cascade screening of 27 relatives to the 69 index cases with an identified mutation revealed 26.9% mutation carriers  who were at risk of cardiac events such as syncope or sudden unexpected death.Conclusion. In this cohort of Kazakhstani index cases with AF, a disease-causing mutation was identified in 56.5 % of the referred patients. Further screening of mutations in other genes encoding cardiac ion channels is needed to clarify possible disease causing and founder mutations in Kazakhstani atrial fibrillation patients

The First Kazakh Whole Genomes: The First Report of NGS Data

Introduction: The human genome sequence will underpin human biology and medicine in the next century, providing a single, essential reference to all genetic information. Extraordinary technological advances and decreases in the cost of DNA sequencing have made the possibility of whole genome sequencing (WGS) feasible as a highly accessible test for numerous indications. The international project “Genetic architecture of Kazakh population” is well underway to determine the complete DNA. Next generation sequencing is a powerful tool for genetic analysis, which will enable us to uncover the association of loci at specific sites in the genome associated with disease. The aim of this study was to introduce first data on WGS of 6 Kazakh individuals.Methods: This pilot study is among the first WGS performed on 6 healthy Kazakh individuals, using next generation sequencing platform HiSeq2000, Illumina by manufacturer’s protocols. All generated *.bcl files were simultaneously converted and demultiplexed using bcl2fasta application. Alignment of sequence reads performed using bwa-mem against human b19 reference genome. Sorting, removing of intermediate files, *.bam files assembling, and marking duplicates were performed using PicardTools package. GATK haplotype caller tool was used for variant calling. ClinVar, SNPedia, and Cosmic databases were processed to identify clinical genomic variants in 6 Kazakh whole genomes. Java Runtime Environment and R. Bioconductor packages were installed to perform raw data processing and run program scripts.Results: The sequence alignment and mapping procedures on reference genome hg19 of each 6 healthy Kazakh individual were completed. Between 87,308,581,400 and 107,526,741,301 total base pairs were sequenced with average coverage x29.85. Between 98.85% and 99.58% base pairs were totally mapped and on average 96.07% were properly paired. Het/Hom and Ti/Tv ratios for each whole genome ranged from 1.35 to 1.52 and from 2.07 to 2.08, respectively. We compared and analyzed each genome with on existing clinical databases ClinVar, SNPedia, Cosmic and found from 20 to 25, from 269 to 288, from 7 to 12 SNP records, respectively. The availability of a reference Kazakh genome sequences provides the basis for studying the nature of sequence variation, particularly single nucleotide polymorphisms.Conclusion: The first whole genome sequencing of Kazakhs were performed. In this pilot study, we identified SNPs associated with different conditions. Further studies of WGS on Kazakh population are needed to identify possible unique genetic variants in Kazakhs

Whole genome sequencing of M.tuberculosis in Kazakhstan: preliminary data

Background: Tuberculosis is a major public health problem which infects one third of the world’s population, resulting in more than two million deaths every year. The emergence of whole genome sequencing (WGS) technologies as a primary research tool has allowed for the detection of genetic diversity in Mycobacterium tuberculosis (MTB) with unprecedented resolution. WGS has been used to address a broad range of topics, including the dynamics of evolution, transmission, and treatment. To our knowledge, studies involving WGS of Kazakhstani strains of M. tuberculosis have not yet been performed.Aim: To perform whole genome sequencing of M. tuberculosis strains isolated in Kazakhstan and analyze sequence data (first experience and preliminary data).Results: In the present report, we announce the whole-genome sequences of the two clinical isolates of Mycobacterium tuberculosis, MTB-489 and MTB-476, isolated from the Almaty region. These strains were part of a repository that was created during our project “Creating prerequisites of personalized approach in the diagnosis and treatment of tuberculosis, based on whole genome-sequencing of M. tuberculosis”. Two strains were isolated from sputum samples of patients P1 and P2. Phenotypically, two isolates were drug-susceptible M. tuberculosis. Sequence data was compared with the publicly available data on M. tuberculosis laboratory strain H37Rv and others. The sequencing of the strains was performed on a Roche 454 GS FLX+ next-generation sequencing platform using a standard protocol for a shotgun genome library. The whole genome sequencing was performed for two M.tuberculosis isolates MTB-476 and MTB-489. 96 M bp with an average read length of 520 bp, approximately 21.8X coverage and 104.2 M bp with an average read length of 589 bp and approximately 23.7X coverage were generated for the MTB-476 and MTB-489, respectively. The genome of MTB-476 consists of 257 contigs, 4204 CDS, 46 tRNAs and 3 rRNAs. MTB-489 has 187 contigs, 4183 CDS, 45 tRNAs and 3rRNAs.Conclusion: The results of genome assembling have been submitted into NCBI GenBank and are available for public access under the accession numbers AZBA00000000 and AZAZ00000000. These genome assemblies can be useful for comparative genome analysis and for identification of novel SNPs and gene variants in genomes of M.tuberculosis

Vitamin D Receptor Gene Polymorphisms in Susceptibility to Tuberculosis in the Kazakh Population in Almaty and Almaty Area

Introduction: Vitamin D receptor (VDR) plays an important role in activating the immune response against various infectious agents. It is known that the active metabolite of ligand receptor Vitamin D (1,25 – dihydroxyvitamin D) is encoded by VDR and helps mononuclear phagocytes to suppress the intracellular growth of M. tuberculosis. The VDR gene harbors approximately 200 polymorphisms, some of which are linked to differences in receptor Vitamin D uptake and therefore can be considered as candidate disease risk variants. The relation between VDR gene polymorphisms and susceptibility to TB has been studied in different populations. There is not a great deal of information regarding the association of these SNPs with TB risk in the Kazakh population. The four most commonly investigated VDR polymorphisms in association with different diseases, including susceptibility to tuberculosis, are located in exon 2 (rs2228570 or FokI), intron 8 (rs1544410 or BsmI and rs7975232 or ApaI), and exon 9 (rs731236 or TaqI). The aim of our study was to determine whether these four VDR gene single nucleotide polymorphisms were associated with TB and whether they were a risk for the development of TB in the Kazakh Population in Almaty city and Almaty area.Methods: This study was a hospital-based case-control analysis of 283 individuals (99 TB patients and 184 healthy controls). Genotyping was performed by Taqman SNP allelic discrimination using commercial TaqMan SNP Genotyping assays.  Statistical analysis was conducted using SPSS Version 19.0 software.Results: Genotype frequencies for the Kazakh population are close to world (HapMap) data on Asian populations. FokI and ApaI polymorphisms genotypes tend to be associated with TB risk under the co-dominant model [OR=1.18; 95%CI: (0.68, 2.07), p=0.15] for FokI and [OR=1.33; 95%CI: (0.61, 2.91), p=0.6] for ApaI. No significant association between the disease and TaqI, BsmI genotypes was observed.Conclusions: In summary, we explored potential associations between SNPs in the VDR (FokI, ApaI) gene and susceptibility to tuberculosis in the Kazakh Population, which requires further detailed analysis with a larger sample size and greater geographic diversity including other regions of Kazakhstan

Genetic Diversity of IF?, IL1?, TLR2, and TLR8 Loci in Pulmonary Tuberculosis in Kazakhstan

Introduction. Tuberculosis (TB) is caused by bacterium Mycobacterium tuberculosis (MTB), and according to the WHO, up to 30% of world population is infected with latent TB. Pathogenesis of TB is multifactorial, and its development depends on environmental, social, microbial, and genetic factors of both the bacterium and the host. The number of TB cases in Kazakhstan has decreased in the past decade, but multidrug-resistant (MDR) TB cases are dramatically increasing. Polymorphisms in genes responsible for immune response have been associated with TB susceptibility. The objective of this study was to investigate the risk of developing pulmonary TB (PTB) associated with polymorphisms in several inflammatory pathway genes among Kazakhstani population.Methods. 703 participants from 3 regions of Kazakhstan were recruited for a case-control study. 251 participants had pulmonary TB (PTB), and 452 were healthy controls (HC). Males and females represented 42.39% and 57.61%, respectively. Of all participants, 67.4% were Kazakhs, 22.8% Russians, 3.4% Ukrainians, and 6.4% were of other origins. Clinical and epidemiological data were collected from medical records, interviews, and questionnaires. DNA samples were genotyped using TaqMan assay on 4 polymorphisms: IFN? (rs2430561) and IL1? (rs16944), TLR2 (rs5743708) and TLR8 (rs3764880). Statistical data was analyzed using SPSS 19.Results. Genotyping by IF?, IL1?, TLR2 showed no significant association with PTB susceptibility (p > 0.05). TLR8 genotype A/G was significantly higher in females (F/M – 41.5%/1.3%) and G/G in males (M/F – 49%/20.7%) (?2=161.43, p < 0.001). A significantly increased risk of PTB development was observed for TLR A/G with an adjusted OR of 1.48 (95%, CI: 0.96 - 2.28), and a protective feature was revealed for TLR8 G/G genotype (OR: 0.81, 95%, CI: 0.56 - 1.16, p = 0.024). Additional grouping by gender revealed that TLR8 G/G contributes as protective genotype (OR: 1.83, 95%, CI: 1.18 - 2.83, p = 0.036) in males of the control group.Conclusion. Results indicate that heterozygous genotype A/G of TLR8 increases the risk of PTB development, while G/G genotype may serve as protection mechanism. A/A genotype is strongly associated with susceptibility to PTB. To clarify the role of other polymorphisms in susceptibility to PTB in Kazakhstani population, further investigations are needed.

Draft genome sequences of two clinical Isolates of mycobacterium tuberculosis from sputum of Kazakh patients

Here, we report the draft genome sequences of two clinical isolates of Mycobacterium tuberculosis (MTB-476 and MTB-489) isolated from sputum of Kazakh patients

Transcriptome profiling and analysis of patients with esophageal squamous cell carcinoma from Kazakhstan

Esophageal squamous cell carcinoma (ESCC) is the predominant subtype of esophageal cancer in Central Asia, often diagnosed at advanced stages. Understanding population-specific patterns of ESCC is crucial for tailored treatments. This study aimed to unravel ESCC’s genetic basis in Kazakhstani patients and identify potential biomarkers for early diagnosis and targeted therapies. ESCC patients from Kazakhstan were studied. We analyzed histological subtypes and conducted in-depth transcriptome sequencing. Differential gene expression analysis was performed, and significantly dysregulated pathways were identified using KEGG pathway analysis (p-value < 0.05). Protein-protein interaction networks were constructed to elucidate key modules and their functions. Among Kazakhstani patients, ESCC with moderate dysplasia was the most prevalent subtype. We identified 42 significantly upregulated and two significantly downregulated KEGG pathways, highlighting molecular mechanisms driving ESCC pathogenesis. Immune-related pathways, such as viral protein interaction with cytokines, rheumatoid arthritis, and oxidative phosphorylation, were elevated, suggesting immune system involvement. Conversely, downregulated pathways were associated with extracellular matrix degradation, crucial in cancer invasion and metastasis. Protein-protein interaction network analysis revealed four distinct modules with specific functions, implicating pathways in esophageal cancer development. High-throughput transcriptome sequencing elucidated critical molecular pathways underlying esophageal carcinogenesis in Kazakhstani patients. Insights into dysregulated pathways offer potential for early diagnosis and precision treatment strategies for ESCC. Understanding population-specific patterns is essential for personalized approaches to ESCC management

Balanced system of indicators for the assessment of innovative construction projects efficiency

The role of innovations in the construction industry is considered in the article. In the conditions of transition of national economy to the innovative type of development, the indicators that allow estimating the efficiency of innovative activity, where the key aspect is the comprehensive assessment, are important. Innovative projects are especially relevant for the construction industry, which is the key driver of the national economy development. Sustainable construction ensures the development of industries, where innovative projects can partly solve the problems of creating renewable energy sources. The authors offer to expand the list of indicators for the assessment of the innovative project efficiency not only from the financial and investment point of view, but also taking into account quantitative and quality, scientific, technological, operational, marketing indicators, which often are not considered. The assessment of the innovative projects efficiency has to be the central link in the innovation management; so the authors offer to improve the system of the balanced indicators. The balanced system of indicators (BSI) is developed. It is planned to extend and to introduce BSI not only at the level of the enterprises, but also for all the types of economic activity according to their technological effectiveness