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  • 1
    Online Resource
    Online Resource
    Whole-Genome Sequencing Among Kazakhstani Children with Early-Onset Epilepsy Revealed New Gene Variants and Phenotypic Variability
    Springer Science and Business Media LLC ; 2023
    In:  Molecular Neurobiology Vol. 60, No. 8 ( 2023-08), p. 4324-4335
    Details
    In: Molecular Neurobiology, Springer Science and Business Media LLC, Vol. 60, No. 8 ( 2023-08), p. 4324-4335
    Abstract: In Kazakhstan, there is insufficient data on genetic epilepsy, which has its own clinical and management implications. Thus, this study aimed to use whole genome sequencing to identify and evaluate genetic variants and genetic structure of early onset epilepsy in the Kazakhstani pediatric population. In this study, for the first time in Kazakhstan, whole genome sequencing was carried out among epilepsy diagnosed children. The study involved 20 pediatric patients with early onset epilepsy and no established cause of the disease during the July–December, 2021. The average age at enrolment was 34.5 months, with a mean age at seizure onset of 6 months. Six patients (30%) were male, and 7 were familial cases. We identified pathogenic and likely pathogenic variants in 14 (70%) cases, among them, 6 novel disease gene variants ( KCNQ2 , CASK , WWOX , MT-CO3 , GRIN2D , and SLC12A5 ). Other genes associated with the disease were SCN1A (x2), SLC2A1 , ARX , CACNA1B , PCDH19 , KCNT1 , and CHRNA2 . Identification of the genetic causes in 70% of cases confirms the general structure of the etiology of early onset epilepsy and the necessity of using NGS in diagnostics. Moreover, the study describes new genotype-phenotypic correlations in genetic epilepsy. Despite certain limitations of the study, it can be concluded that the genetic etiology of pediatric epilepsy in Kazakhstan is very broad and requires further research.
    Type of Medium: Online Resource
    ISSN: 0893-7648 , 1559-1182
    URL: Article
    DOI: 10.1007/s12035-023-03346-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2079384-4
    SSG: 12
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  • 2
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    Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan
    Elsevier BV ; 2020
    In:  Data in Brief Vol. 33 ( 2020-12), p. 106416-
    Details
    In: Data in Brief, Elsevier BV, Vol. 33 ( 2020-12), p. 106416-
    Type of Medium: Online Resource
    ISSN: 2352-3409
    URL: Article
    DOI: 10.1016/j.dib.2020.106416
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2020
    detail.hit.zdb_id: 2786545-9
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  • 3
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    The First Kazakh Whole Genomes: The First Report of NGS Data
    University Library System, University of Pittsburgh ; 2014
    In:  Central Asian Journal of Global Health Vol. 3 ( 2014-12-12)
    Details
    In: Central Asian Journal of Global Health, University Library System, University of Pittsburgh, Vol. 3 ( 2014-12-12)
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2166-7403
    URL: Article
    DOI: 10.5195/cajgh.2014.146
    Language: Unknown
    Publisher: University Library System, University of Pittsburgh
    Publication Date: 2014
    detail.hit.zdb_id: 2708701-3
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  • 4
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    Genetic Diversity of IFγ, IL1β, TLR2, and TLR8 Loci in Pulmonary Tuberculosis in Kazakhstan
    University Library System, University of Pittsburgh ; 2014
    In:  Central Asian Journal of Global Health Vol. 3 ( 2014-12-12)
    Details
    In: Central Asian Journal of Global Health, University Library System, University of Pittsburgh, Vol. 3 ( 2014-12-12)
    Abstract: 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: IFNγ (rs2430561) and IL1β (rs16944), TLR2 (rs5743708) and TLR8 (rs3764880). Statistical data was analyzed using SPSS 19.Results. Genotyping by IFγ, IL1β, 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%) (χ2=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. 
    Type of Medium: Online Resource
    ISSN: 2166-7403
    URL: Article
    DOI: 10.5195/cajgh.2014.181
    Language: Unknown
    Publisher: University Library System, University of Pittsburgh
    Publication Date: 2014
    detail.hit.zdb_id: 2708701-3
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  • 5
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    Vitamin D Receptor Gene Polymorphisms in Susceptibility to Tuberculosis in the Kazakh Population in Almaty and Almaty Area
    University Library System, University of Pittsburgh ; 2014
    In:  Central Asian Journal of Global Health Vol. 2 ( 2014-01-24)
    Details
    In: Central Asian Journal of Global Health, University Library System, University of Pittsburgh, Vol. 2 ( 2014-01-24)
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2166-7403
    URL: Article
    DOI: 10.5195/cajgh.2013.102
    Language: Unknown
    Publisher: University Library System, University of Pittsburgh
    Publication Date: 2014
    detail.hit.zdb_id: 2708701-3
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  • 6
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    Online Resource
    Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures
    Biomedical Informatics ; 2012
    In:  Bioinformation Vol. 8, No. 16 ( 2012-8-24), p. 773-776
    Details
    In: Bioinformation, Biomedical Informatics, Vol. 8, No. 16 ( 2012-8-24), p. 773-776
    Type of Medium: Online Resource
    ISSN: 0973-8894 , 0973-2063
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.6026/008.016
    DOI: 10.6026/bioinformation
    DOI: 10.6026/97320630008773
    Language: Unknown
    Publisher: Biomedical Informatics
    Publication Date: 2012
    detail.hit.zdb_id: 2203786-X
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  • 7
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    Whole-Genome Sequence-Based Characterization of Pre-XDR M. tuberculosis Clinical Isolates Collected in Kazakhstan
    MDPI AG ; 2023
    In:  Diagnostics Vol. 13, No. 12 ( 2023-06-08), p. 2005-
    Details
    In: Diagnostics, MDPI AG, Vol. 13, No. 12 ( 2023-06-08), p. 2005-
    Abstract: Background: Kazakhstan has a high burden of multidrug-resistant tuberculosis in the Central Asian region. This study aimed to perform genomic characterization of Mycobacterium tuberculosis strains obtained from Kazakhstani patients with pre-extensively drug-resistant tuberculosis diagnosed in Kazakhstan. Methods: Whole-genome sequencing was performed on 10 pre-extensively drug-resistant M. tuberculosis strains from different regions of Kazakhstan. All strains had high-confidence resistance mutations according to the resistance grading system previously established by the World Health Organization. The genome analysis was performed using TB-Profiler, Mykrobe, CASTB, and ResFinder. Results: Valuable information for understanding the genetic diversity of tuberculosis in Kazakhstan can also be obtained from whole-genome sequencing. The results from the Phenotypic Drug Susceptibility Testing (DST) of bacterial strains were found to be consistent with the drug resistance information obtained from genomic data that characterized all isolates as pre-XDR. This information can help in developing targeted prevention and control strategies based on the local epidemiology of tuberculosis. Furthermore, the data obtained from whole-genome sequencing can help in tracing the transmission pathways of tuberculosis and facilitating early detection of outbreaks. Conclusions: The results from whole-genome sequencing of tuberculosis clinical samples in Kazakhstan provide important insights into the drug resistance patterns and genetic diversity of tuberculosis in the country. These results can contribute to the improvement of tuberculosis control and management programs in Kazakhstan.
    Type of Medium: Online Resource
    ISSN: 2075-4418
    URL: Article
    DOI: 10.3390/diagnostics13122005
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2662336-5
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  • 8
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    Online Resource
    Blind source separation methods for deconvolution of complex signals in cancer biology
    Elsevier BV ; 2013
    In:  Biochemical and Biophysical Research Communications Vol. 430, No. 3 ( 2013-01), p. 1182-1187
    Details
    In: Biochemical and Biophysical Research Communications, Elsevier BV, Vol. 430, No. 3 ( 2013-01), p. 1182-1187
    Type of Medium: Online Resource
    ISSN: 0006-291X
    URL: Article
    DOI: 10.1016/j.bbrc.2012.12.043
    RVK:
    WA 15000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2013
    detail.hit.zdb_id: 1461396-7
    SSG: 12
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  • 9
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    Online Resource
    Whole-genome sequencing data of Kazakh individuals
    Springer Science and Business Media LLC ; 2021
    In:  BMC Research Notes Vol. 14, No. 1 ( 2021-12)
    Details
    In: BMC Research Notes, Springer Science and Business Media LLC, Vol. 14, No. 1 ( 2021-12)
    Abstract: Kazakhstan is a Central Asian crossroad of European and Asian populations situated along the way of the Great Silk Way. The territory of Kazakhstan has historically been inhabited by nomadic tribes and today is the multi-ethnic country with the dominant Kazakh ethnic group. We sequenced and analyzed the whole-genomes of five ethnic healthy Kazakh individuals with high coverage using next-generation sequencing platform. This whole-genome sequence data of healthy Kazakh individuals can be a valuable reference for biomedical studies investigating disease associations and population-wide genomic studies of ethnically diverse Central Asian region. Data description Blood samples have been collected from five ethnic healthy Kazakh individuals living in Kazakhstan. The genomic DNA was extracted from blood and sequenced. Sequencing was performed on Illumina HiSeq2000 next-generation sequencing platform. We sequenced and analyzed the whole-genomes of ethnic Kazakh individuals with the coverage ranging from 26 to 32X. Ranging from 98.85 to 99.58% base pairs were totally mapped and aligned on the human reference genome GRCh37 hg19. Het/Hom and Ts/Tv ratios for each whole genome ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Sequencing data are available in the National Center for Biotechnology Information SRA database under the accession number PRJNA374772.
    Type of Medium: Online Resource
    ISSN: 1756-0500
    URL: Article
    DOI: 10.1186/s13104-021-05464-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2413336-X
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  • 10
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    Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets
    MDPI AG ; 2019
    In:  International Journal of Molecular Sciences Vol. 20, No. 18 ( 2019-09-07), p. 4414-
    Details
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 20, No. 18 ( 2019-09-07), p. 4414-
    Abstract: Independent component analysis (ICA) is a matrix factorization approach where the signals captured by each individual matrix factors are optimized to become as mutually independent as possible. Initially suggested for solving source blind separation problems in various fields, ICA was shown to be successful in analyzing functional magnetic resonance imaging (fMRI) and other types of biomedical data. In the last twenty years, ICA became a part of the standard machine learning toolbox, together with other matrix factorization methods such as principal component analysis (PCA) and non-negative matrix factorization (NMF). Here, we review a number of recent works where ICA was shown to be a useful tool for unraveling the complexity of cancer biology from the analysis of different types of omics data, mainly collected for tumoral samples. Such works highlight the use of ICA in dimensionality reduction, deconvolution, data pre-processing, meta-analysis, and others applied to different data types (transcriptome, methylome, proteome, single-cell data). We particularly focus on the technical aspects of ICA application in omics studies such as using different protocols, determining the optimal number of components, assessing and improving reproducibility of the ICA results, and comparison with other popular matrix factorization techniques. We discuss the emerging ICA applications to the integrative analysis of multi-level omics datasets and introduce a conceptual view on ICA as a tool for defining functional subsystems of a complex biological system and their interactions under various conditions. Our review is accompanied by a Jupyter notebook which illustrates the discussed concepts and provides a practical tool for applying ICA to the analysis of cancer omics datasets.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    URL: Article
    DOI: 10.3390/ijms20184414
    Language: English
    Publisher: MDPI AG
    Publication Date: 2019
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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