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Laboratory of Genomic and Personalized Medicine
1.Research area
The main research objects:
  • Genomic and Multi-omic research in Biomedicine
  • Genetic research of multifactorial disorders (oncological diseases, cardiovascular diseases, etc.)
  • Genetic research of tuberculosis
  • Study of genetic architecture of Kazakhstani population
  • Applied genetics
Laboratory of Genomic and Personalized Medicine was established at the Center for Life Sciences, Nazarbayev University in 2015 on the basis of Department of Genomic and Personalized Medicine.

Main scientific researches of Laboratory focused on development of new approaches of ICA application for analysis and interpretation of tumor heterogeneity, on the study of gene expression and genomic variants in cancer/normal tissues, on analysis of whole genomes/exomes of Kazakh individuals and identification of Kazakh specific genomic variants with developing national genomic reference database, on the study of differential expression in plants in different states and parts, genome organization and genetic variants of drug-resistant M.tuberculosis strains circulating in Kazakhstan, on development of bioinformatics tools implementing a machine learning approaches as applied to DNA detection and amplification technologies as well as development of novel bioinformatics tools and databases.
Mission
The mission of the LGPM is to promote and apply genomic science to make new biomedical discoveries in Kazakhstan, using the most modern methods of genomic sequencing, bioinformatics and validation methods. It aims to create the basis for the development of genomic personalized medicine in Kazakhstan - a qualified team of scientists, laboratory infrastructure, technical capacity and a database of genomic knowledge.

It is planned that the database of genomic variants will be one of the main results of the LGPM projects for the entire medical community in Kazakhstan and around the world. This will help to understand the genetic basis of diseases and determine the best treatments, which will effectively contribute to the future development of personalized medicine and genomic sciences
Laboratory areas
The LGPM works in three areas:
RESEARCH WORK
  • Our experienced staff and research specialists use various modern genomic platforms to obtain high-quality genomic data and then analyze it
  • We focus our efforts on improving the prevention, diagnosis and treatment of diseases and studying the molecular genetic basis of various conditions
  • Our staff conducts a lot of research to introduce personalized medicine into clinical practice and to incorporate genetic medicine into standard medical care in Kazakhstan
  • Genomic data will be analyzed and used to create the Kazakhstan database, which will serve as the basis for the future development of personalized medicine in the country, which is the most comprehensive approach to identify disease-causing genes for the country's population.
APPLIED GENOMICS
  • Use of genetics/genomics in clinical genetic testing - diagnostic testing, predictive genetic testing, presymptomatic genetic testing, mutation carrier testing, prenatal diagnosis
SERVICES
  • We plan to provide genomic technologies and services to researchers and clinicians at Nazarbayev University, as well as to external academic and industry scientists in Kazakhstan and abroad
  • Genome sequencing and analysis
  • High-quality, next-generation genome, exome, and RNA sequencing services and help in extracting information from genomic data
Laboratory carries out research in the following directions:
  • Studying the genetic architecture of the Kazakh population and other populations of Central Asia using high-throughput genomic platforms to assess the risk of development and prediction of various conditions, creating a reference database.
  • Investigation of molecular mechanisms of major multifactorial diseases in Kazakhstan (cardiovascular, oncological, metabolic syndrome, neurodegenerative diseases)
  • Research of tuberculosis and infectious diseases in Kazakhstan: epidemiology, genetics, environmental risk factors, lifestyle, search of new diagnostic biomarkers, host-vector interaction, antibiotic resistance, preventive strategies, studying epidemiology of SARS-CoV2 coronavirus, COVID-19, etc.
  • Development and implementation of new next-generation (NGS) and third-generation (TGS, nanopore sequencing) sequencing methods and translation of genomic technologies into clinical practice and development of applied genetics in biomedicine, population genetics, sports genetics and agriculture.
Methods required for the full genome analysis
  • Obtaining genomic DNA libraries for full genomic analysis
  • Obtaining RNA libraries for full-genome analysis of gene expression
  • Full-genome mapping of protein and transcription factor binding sites
Bioinformatic methods of analysis in cooperation with the Laboratory of Bioinformatics and Systems Biology
  • Development and creation of the Kazakhstan base of genomic variants
  • Processing and analysis of data from whole-genome sequencing (DNAseq, RNAseq, de novo assembly)
  • Regulatory functional genomics
  • Multivariate data analysis and machine learning methods
  • Statistical analysis methods
The main technologies used in LGPM
  • Next generation sequencing (NGS), (whole genome/exome, transcriptome, targeted sequencing, microbiome)
  • Third generation sequencing (TGS), nanopore sequencing
  • Sanger sequencing
  • Microsatellite analysis
  • Real-time PCR
  • PCR
2.Lab team
  • Ainur Akilzhanova
    Head of the Laboratory for Genomic and Personalized Medicine
    Doctor of Medicine, PhD, professor, leading researcher

    Research profile NU
  • Ulan Kozhamkulov
    Leading Researcher
    Candidate of Medical Sciences, Associate Professor

    Research profile NU
  • Saule Rakhimova
    Leading Researcher
    D. Candidate in Biology, Associate Professor

    Research profile NU
  • Dauren Yerezhepov
    Senior Researcher
  • Diana Samatkyzy
    Junior Researcher
  • Nazerke Satvaldina
    junior researcher
  • Zhannur Abilova
    Researcher
  • Madina Zhalbinova
    Junior Researcher
  • Aidana Gabdulkayum
    Assistant Researcher
    Research profile NU
  • Ayaulym Chamoyeva
    Assistant Researcher
  • Akbota Aitkulova
    Assistant Researcher
  • Altynai Kasymkhanova
    Junior Researcher
  • Nurai Tynyshtykbayeva
    Assistant Researcher
  • Galym Muratuly
    Project Administrator
3.Research projects
    Equipment, instrument, inventory of the laboratory
    4.Publications
    List of selected publications of LBSB:


    • Daniyarov A, Molkenov A, Rakhimova S, Akhmetova A, Nurkina Z, Yerezhepov D, Chingissova L, Bismilda V, Toxanbaeva B, Akilzhanova A, Kozhamkulov U, Kairov U. Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan // Data Brief, 2020 Oct 17, doi:10.1016/j.dib.2020.106416. [Full text]

    • M-M Aynaud, O Mirabeau, N Gruel, S Grossetête, V Boeva, S Durand, D Surdez, O Saulnier, S Zaïdi, S Gribkova, U Kairov, V Raynal, F Tirode, TGP Grünewald, M Bohec, S Baulande, I Janoueix-Lerosey, J-P Vert, E Barillot, O Delattre, A Zinovyev. Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution // Cell reports, 2020, doi: 10.1016/j.celrep.2020.01.049. [Full text]

    • N. Sompairac, P. Nazarov, U. Czerwinska, L. Cantini, A. Molkenov, Zh. Zhumadilov, E. Barillot, F. Radvanyi, A. Gorban, U. Kairov and A. Zinovyev. Independent component analysis for unraveling complexity of cancer omics datasets // International Journal of Molecular Science, 2019, 20(18), 4414; [Full text]

    • Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A. Assessing reproducibility of matrix factorization methods in independent transcriptomes // Bioinformatics, 2019 Apr 2, doi: 10.1093/bioinformatics/btz225. [Full text]

    • A. Molkenov, A. Zhelambayeva, A. Yermekov, S. Mussurova, A. Sarkytbayeva, Y. Kalykhbergenov, Zh. Zhumadilov, U. Kairov. Transcriptomic Databases // Reference Module in Life Sciences. Chapter in Encyclopedia of Bioinformatics and Computational Biology, Elsevier press, June 2018, https://doi.org/10.1016/B978-0-12-809633-8.20208-2.

    • Czerwinska U., Kairov U., Cantini L., Barillot E., Zinovyev A. Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals // Chapter in Book Latent Variable Analysis and Signal Separation. Lecture Notes in Computer Science, vol. 10891. 2018, Springer, doi.org/10.1007/978-3-319-93764-9_46. [Full text]

    • U. Kairov, L. Cantini, A. Greco, A. Molkenov, U. Czerwinska, E. Barillot, A. Zinovyev. Determining the optimal number of reproducible independent components for transcriptomic data analysis. BMC Genomics. 2017, Sep 11;18(1):712. doi: 10.1186/s12864-017-4112-9. [Full text]

    • Saliev T, Begimbetova D, Baiskhanova D, Abetov D, Kairov U, Gilman CP, Matkarimov B, Tachibana K. Apoptotic and genotoxic effects of low-intensity ultrasound on healthy and leukemic human peripheral mononuclear blood cells. // Journal of Medical Ultrasonics, 2017 Jul 8. doi: 10.1007/s10396-017-0805-6. [Full text]

    • Kozhamkulov U.A., Kairov U.E., Yerezhepov D.A., Akhmetova A.Zh., Molkenov A.B., Akilzhanova A.R. Whole-genome sequencing of clinical mycobacterium tuberculosis isolates with different drug sensitivity profiles // Eurasian Journal of Applied Biotechnology, 2016. Issue 2, P. 20-29. [Full text]

    • S.Е. Rakhimova, U.E. Kairov, D.A. Yerezhepov, A.B. Molkenov, M.R. Zhalbinova, A.T. Abilmazhinova, Y.V. Zhukov, M.Kh. Omarov, A.R. Akilzhanova. RNA-sequencing of squamous esophageal cancer: from collection of the biomaterial until sequencing on hiseq2000 // Science and Healthcare. 2016, Vol.5, P.53-63. [Full text]

    • A. Akilzhanovа, U. Kozhamkulov, U. Kairov, S. Rakhimova, A. Akhmetova, D. Yerezhepov, A. Molkenov, Zh. Abilova, Zh. Zhumadilov. Determination of genetic variants associated with hypertension, obesity and diabetes in kazakh population to study interaction of genetic variants and metabolome // Science and Healthcare. 2016, Vol.5, P.30-42. [Full text]

    • Kozhakhmetov SS, Kushugulova AR, Saduakhasova SA, Shakhabayeva GS, Khassenbekova ZR, Molkenov AB3, Kairov UE, Issayeva RB, Nurgozhin TS, Zhumadilov ZS. Draft Genome Sequence of Lactobacillus rhamnosus CLS17. Genome Announcements. 2015 May 14; 3(3). e00478-15. doi: 10.1128/genomeA.00478-15. [Full text]

    • Kairov U., U. Kozhamkulov, A. Molkenov, S. Rakhimova, A. Askapuli, M. Zhabagin, A. Akhmetova, D. Yerezhepov, Zh. Abilova, A. Abilmazhinova, V. Bismilda, L. Chingisova, Zh. Zhumadilov, A. Akilzhanova.. Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients. Genome Announcements. 2015 May 14; 3(3). e00466-15. doi: 10.1128/genomeA.00466-15. [Full text]

    • Dmitriev, U.Kairov, T.Robert, A.Barat, V.Lazar, G.Garnac, Y.Vassetzky. Cancer-related genes in the transcription signature of facioscapulohumeral dystrophy myoblasts and myotubes // Journal of Cellular and Molecular Medicine.2014 Feb;18(2):208-17 [Full text]
    5.Collaborations
    6.Life in the Lab