Develop recommendations for making changes to the clinical practice of the Republic of Kazakhstan in order to use genetic predisposition to the development of diseases and the effectiveness of drugs in preventive measures and pharmacotherapy
- STUDIES OF THE GENETIC EPIDEMIOLOGY OF CORONAVIRUS INFECTION IN KAZAKHSTAN WITH ANALYSIS OF DNA OF PERSONS SUFFERING COVID-19 TO ASSESS PREDICTION OF THE COURSE, SEVERITY AND OUTCOMES OF CORONAVIRUS INFECTION as part of the implementation of the scientific and technical program "National Program for the Implementation of Personalized and Preventive Medicine in the Republic of Kazakhstan"
- DNA ANALYSIS OF PERSONS OF THE KAZAKH ETHNIC SUFFERING SIGNIFICANT DISEASES AND CONTROL PERSONS OF THE KAZAKH ETHNOUS TO DETERMINE THE POLYMORPHISM OF THE GENES ASSOCIATED WITH THE DEVELOPMENT OF THESE DISEASES WITH THE SUBSEQUENT DEVELOPMENT OF RECOMMENDATIONS IN THE REPUBLIC OF KAZAKHSTAN AND THE NATIONALIZED PERSONALIZED PROGRAM
- DEVELOPMENT OF RECOMMENDATIONS FOR AMENDING THE CLINICAL PRACTICE OF THE REPUBLIC OF KAZAKHSTAN WITH THE PURPOSE OF USE IN PHARMACOTHERAPY OF GENETIC PREDISPOSITION TO EFFECTIVENESS AND DEVELOPMENT OF SIDE EFFECTS FROM MEDICATIONS within the framework of the implementation of the scientific and technical program "National Program for the Introduction of Personalized Preventive Medicine in the Republic of Kazakhstan"
- Genetic passportation and analysis of polymorphisms in genes associated with resistance to fluoroquinalons and aminoglycosides to select M. Tuberculosis strains allocated from patients in the Republic of Kazakhstan, as well as Targetic security of genes in case of divergence of phenotypical and genetic signs of these strains to determine new STATISTICALLY SIGNIFICANT MARKERS AND DEVELOPMENT OF RECOMMENDATIONS as part of the implementation of the scientific and technical program "National Program for the Implementation of Personalized and Preventive Medicine in the Republic of Kazakhstan"
Relevance
The COVID-19 pandemic has affected more than 23 million patients with higher death rates in 200 countries. Given the current situation in the world and in our country in connection with the COVID-19 pandemic, the entire medical community and the Government of the Republic of Kazakhstan are busy developing measures against the spread of the virus in the country and providing treatment. While real-time reverse transcriptase PCR (RT-qPCR) aimed at detecting SARS-CoV-2 RNA is known to be effective in identifying infected individuals for isolation and contact tracing, it is not effective in determining which viral strains circulate in the community. It is important to know the origin of strains, which in turn influences public health policy decisions. In addition, it is vital to identify superspreader events as they can be influenced by the strain of the virus. Research has been initiated in the world on the genetics of coronavirus, human genetics, the relationship between the course and severity of coronavirus infection from various external and internal (human body) risk factors. Genetic analysis and observation make it possible to characterize circulating viral lines, draw conclusions about events introductions and reconstruct transmission schemes. Viral genome sequencing is used to study the spread of disease during disease outbreaks. To date, it is not known what the consequences of a coronavirus infection may be, and what prognosis to expect from the epidemiological situation in the world, and the course and severity of the disease varies from person to person. The study of the epidemiology of coronavirus infection, genetic epidemiology, factors influencing the course of the disease and outcomes, genetics of the virus will help develop measures to combat the virus epidemic. Together with epidemiological data, genetic epidemiology is a powerful tool to support public health initiatives and ensure preparedness. Real-time genomic surveillance is important for managing viral outbreaks because it can provide insight into how viruses are transmitted, spread and evolve. Such work depends on the rapid sequencing of viral material directly from clinical specimens, i.e. without the need to isolate the virus in pure cultures. As part of this subtask, the DNA of patients infected with coronavirus infection will be studied, sequencing of the genomes of patients with coronavirus will be carried out to identify the relationship between the clinical course of the infectious process and the individual characteristics of the human body, thereby the results can be used in the fight against the coronavirus epidemic,
Purpose of this study
Assess the prediction of the predisposition, course and outcomes of coronavirus infection by analyzing the DNA of people who have recovered from COVID-19 and genotyping the pathogen.
Research Objectives
1. Formation of a sample of study participants. 2. Isolation of coronavirus RNA. Genetic study of coronavirus circulating in Kazakhstan. 3. DNA isolation. 4. Conduct and analyze whole genome sequencing data.
Scientific novelty: For the first time, a study will be conducted on the genetic epidemiology of coronavirus infection in Kazakhstan with DNA analysis of individuals with a positive PCR test result for the presence of COVID-19 to assess the prediction of the course, severity and outcomes of coronavirus infection
Study Design
Target selection Total number: 1200 people, continuous sample, the sample is made in 16 regions of the Republic of Kazakhstan
The study is planned to be carried out on the basis of the branches of the INVIVO laboratories and on the basis of the collective use laboratory of KazNMU named after S.D. Asfendiyarov. A study to assess the prediction of the predisposition, course and outcomes of coronavirus infection with DNA analysis of people who recovered from COVID-19 and genotyping of the pathogen will be carried out in 2 stages: The 1st stage of the study will be carried out on the basis of the INVIVO laboratory. Using the continuous sampling method, 1200 patients with a confirmed diagnosis of COVID-19 will be randomly recruited based on the results of PCR testing, taking into account compliance with all quarantine and safety measures. Individuals with confirmed COVID-19 will be selected with different course and severity of the disease, from different age groups, men and women. A smear from the nasopharynx and throat will be taken from the test subjects, isolation and extraction of SARS-CoV-2 RNA will be carried out from the obtained sample. Virus isolation and RNA extraction will be carried out in an INVIVO biosafety level (BSL) 2+ laboratory with BSL-3 protection. There will beswabs from the nasopharynx and oropharynx in 1200 patients with positive RT-qPCR results living in 16 regions of the Republic of Kazakhstan: Almaty, Almaty region, Zhambyl, Turkestan, Aktobe regions, Pavlodar, Karaganda, North Kazakhstan, Mangistau, Nur-Sultan , West Kazakhstan, Atyrau, Akmola, Kostanay, East Kazakhstan, Kyzylorda regions. Samples will be selected based on cycle threshold (Ct) values ≤ 32 with COVID-19 confirmed by qPCR. Epidemiological data will also be collected, such as symptoms, clinical and demographic data from medical records accompanying the collected samples. The 2nd stage of the study will be carried out on the basis of the Laboratory for Collective Use of KazNMU named after. S.D. Asfendiyarov. Data on RNA materials obtained from samples directly by the INVIVO laboratory will be sent and transported to the Collective Use Laboratory of KazNMU named after. S.D. Asfendiyarov.
Target indicators: Database with the results of whole genome sequencing of the SARS-COV 2 virus. Database of clinically significant genetic markers of COVID-19. COVID-19 seroprevalence base and their association with the course of the disease and poor prognosis.
Researcher: KazNMU named after S.D. Asfendiyarov
Relevance
Today, such genetic databases as ClinVar (NIH), HGMD (Institute of Medical Genetics, Cardiff), etc., as well as a huge number of publications contain information on predictive polymorphisms with proven other ethnic groups (Europeans, Far Eastern peoples, etc.) by association with the development of diseases. At the same time, in order to introduce the above results into the clinical practice of the Republic of Kazakhstan, it becomes necessary to validate these gene polymorphisms in individuals of the Kazakh ethnic group, i.e. identifying the presence or absence and the strength of the connection of selected polymorphisms with diseases in individuals of the Kazakh ethnic group. In addition, given that within the framework of this subtask it is planned to genotype about 2.5 million polymorphisms for each nosology, there is a possibility of finding new significant polymorphisms of predisposition to the development of diseases. As a result, gene polymorphisms with high prognostic and, therefore, clinical significance in individuals of the Kazakh ethnic group will be identified or validated. The implementation stage of this subtask is to develop recommendations and additions to the clinical protocols of the Republic of Kazakhstan, describing the procedure for identifying a genetic predisposition to the development of the studied diseases, as well as describing the procedure for managing people with an identified genetic predisposition. For example, if a patient with gastric cancer is admitted, the patient will be assigned a PCR analysis, and in case of detection of polymorphisms, the high significance of which in the development of gastric cancer has been proven in the Program (i.e. included in clinical protocols), all close relatives of the patient ( parents, siblings, children) will be ordered to undergo a test for the presence of mutations found in the patient. If they are identified, a close relative will be informed that he has an increased risk and will be given recommendations for the prevention of stomach cancer. At the same time, as you know, awareness of the risk of a disease does not always guarantee compliance with all prescriptions. In this regard, a relative with an identified predisposition will be included in the risk group, from which a list of persons for mandatory screening will be formed, the control of which, in the future and according to the experience of OECD countries, will be carried out by increasing the amount of deductions from wages in favor of the Mandatory Screening Fund. health insurance in case of ignoring screening. Clinically significant polymorphisms for inclusion in clinical protocols for individuals of the Russian ethnic group will be selected based on the publications of numerous genetic studies already conducted in the Russian Federation. In addition, due to the extremely high genetic similarity of the East Slavic ethnic groups, the results obtained can be extrapolated to the Ukrainian and Belarusian ethnic groups, thus (together with the Kazakh ethnic group), covering over 90% of the population of the Republic of Kazakhstan.
Purpose of this study
The study of genetic factors predisposing to the development of 12 types of significant diseases in the Kazakh population.
Research Objectives
1. Development of inclusion and exclusion criteria. 2. Collection of biomaterial (blood samples) from persons of Kazakh nationality with 12 types of significant nosologies in history 3. Genotyping on high-density DNA chips of persons with 12 types of significant nosologies in history and persons from control groups.
Study Design Persons of Kazakh nationality (in the third generation) (grandparents on the paternal and maternal lines) will take part in the study. Study scope: 2.5 million polymorphisms, with an incidence of more than 1% in the general population (GWAS). List of nosologies and sample size: • Breast cancer (1200 patients); • Arterial hypertension (1200 patients); • Epilepsy (600 patients and 300 controls); • Acute cerebrovascular accident in preeclampsia (100 patients and 100 controls); • Schizophrenia (1200 patients); • Liver cirrhosis (1000 patients and controls); • Bronchial asthma (300 patients and 300 controls); • Myocardial infarction (1200 patients); • B-linear lymphoma and leukemia in children (200 patients and 200 controls); • Atopic dermatitis (900 patients); • Idiopathic gonarthrosis (300 patients and 300 controls); • Idiopathic scoliosis (200 patients and 200 controls); • Persons who recovered from COVID-19 (1200 patients); • Population control 3000. Research methods: • Genotyping on high-density chips (high-density biochip scanner iScan System with automated sample preparation system, Illumina); • Medium density genotyping by real-time PCR; • Bionformatic analysis.
Research collaborators: NAO KazNMU andm.s.d. Asfendiyarova, NJSC "Astana Medical University", JSC "Scientific Center for Obstetrics, Gynecology and Perinatology", JSC "Kazakh Research Institute of Oncology and Radiology", RSE "Hospital of the Medical Center of the Administration of the President of the Republic of Kazakhstan", JSC "Scientific Research Institute cardiology and internal diseases”, JSC “National Scientific Cardiac Surgery Center”, Republican State Enterprise on the REM “Republican Scientific and Practical Center for Mental Health” of the Ministry of Health of the Republic of Kazakhstan, JSC “National Scientific Center for Surgery named after. A.N. Syzganov", JSC "Scientific Center of Pediatrics and Pediatric Surgery", RSE on REM "National Scientific Center for Phthisiopulmonology" of the Ministry of Health of the Republic of Kazakhstan, RSE "Research Institute of Traumatology and Orthopedics" of the Ministry of Health of the Republic of Kazakhstan, RSE on REM "Research and Production Center for Transfusiology" of the Ministry of Health of the Republic of Kazakhstan .
Figure 1 - Overview of sequential steps for conducting a GWAS study
Relevance
As part of this subtask, a review of publications on pharmacogenetic studies, as well as the PharmGKB (NIH) pharmacogenetic database, will be carried out in order to select drugs that have reliably proven genetic associations with absorption efficiency and the development of side effects. effects. The second selection criterion will be the relevance of the need for timely selection of the correct drug and its dosage. Then, a statistical analysis of the frequency of occurrence of polymorphisms associated with the efficiency of assimilation and the development of side effects of the selected drugs will be carried out. Based on the results obtained, recommendations will be developed for making changes to the clinical protocols of the Republic of Kazakhstan, which describe the procedure for identifying pharmacogenetic features when taking medicines, i.e. genetic predisposition to the effectiveness of drugs and the development of side effects before their appointment by a doctor. For example, if it is planned to prescribe an anticoagulant with pharmacogenetic characteristics to a patient after a surgery, the patient must first undergo a PCR study, based on the results of which an individual dosage of the drug is calculated. If a genetic predisposition to excessively high digestibility or the development of serious side effects is detected, the patient is prescribed another drug. Thus, for example, the risk of thrombosis in the postoperative period is significantly reduced. Another prime example is anticonvulsants. Timely selection of the right drugs is extremely important for children with epileptics, since with each attack there is a degradation of his mental activity, which ultimately leads to irreversible disability. Timely selection of the correct antipsychotic prevents desocialization and hospitalization in the case of an aggressive or extremely desocialized form of mental disorder. In the Republic of Kazakhstan, over 50% of mentally ill patients belong to this group. Timely identification of genetic predictors of effective immunosuppressive therapy after transplantation will make it possible to individualize the prescription of cytostatics and reduce the risk of rejection, thereby saving the patient's life. In general, personalized pharmacotherapy is most important in oncology, since today expensive oncological drugs (1-3 million tenge) in the Republic of Kazakhstan are prescribed blindly, as a result of which the country's budget suffers, and most importantly, people who could have been saved die, in the case of timely selection of a drug that is effective for this particular patient. In addition, another important result of this task will be the revision of the types and volumes of medicines purchased by the state, taking into account the statistically proven genetic predisposition of Kazakhstanis to drugs.
Perspectives in pharmacogenetic research
To date, several pharmacogenomic associations of the world scientific community have been created, whose goal is to evaluate the outcomes of a drug reaction, for example: - PharmGKB is a pharmacogenomics knowledge resource that includes clinical information, including clinical guidelines on gene-drug association and genotype-phenotype relationships. PharmGKB collects, stores and disseminates information on the impact of human genetic variations on drug efficacy Cooperation within the framework of this task with international participation will allow: - Develop genetic variants and determine the relationship between genome, drug and disease (using a literature review). - Summarize important pharmacogenomic SNPs and explore their relationship between SNP genetic variants and drugs - Supervise and participate in the writing of drug dosing guidelines based on pharmacogenomics - Publication of dosing guidelines based on the pharmacogenome Thus, genome-wide association studies (GWAS) have proven to be one of the main tools for mapping human genes, and also demonstrate their potential in pharmacogenomic studies. Practice guidelines related to study design and available sample sizes emphasize the need for creative replication methods that go beyond the traditional replication cohorts that are used for general genetics.
Purpose of this study
Develop recommendations for making changes to the clinical practice of the Republic of Kazakhstan in order to use genetic predisposition to efficacy and the development of side effects from drugs in pharmacotherapy.
Research objectives • Selection of drugs withx genetic predisposition to effectiveness and the development of side effects.
• Statistical analysis of the prevalence of polymorphisms associated with abnormal susceptibility to efficacy and side effects
Study Design
Sample size: persons of the Kazakh ethnic group in the third generation according to the following nosologies:
Nosology Osn. group response. organization for analysis 1. Breast cancer 700 KazNIOR 2. Arterial hypertension 400 NNCC 400 3. Epilepsy 600 MUA 4. Schizophrenia 700 RNPTSPZ 5. Myocardial infarction 500 NIIKVB 300 6. Atopic dermatitis 600 KazNMU 7. Persons who recovered from COVID-2019 600 KazNMU
Researcher: KazNMU named after S.D. Asfendiyarov
Relevance
Kazakhstan, with a rate of primary multidrug-resistant tuberculosis (MDR-TB) of 24.6%, ranks second out of 27 countries in the WHO Euro with a high burden of MDR-TB, a large development and spread of which formed in the 1990s. The duration of MDR-TB therapy in accordance with WHO recommendations is at least 20 months or more, requires the use of more expensive and poorly tolerated second-line drugs, and treatment success does not exceed an average of 55% worldwide. Moreover, the cost of MDR-TB treatment exceeds the cost of treatment of drug-susceptible TB by 8 times or more and requires large organizational efforts on the part of national TB programs. Thus, the cost of MDR-TB treatment in different regions of the world varies from 3,000 to 10,000 US dollars for a standard course of therapy. Today, the treatment of MDR-TB is a major public health problem in many parts of the world. When MDR-TB is not properly treated, or when first infected, a more severe form of TB called pre-extensively drug-resistant TB (XDR-TB) develops. XDR-TB can develop during MDR-TB treatment with reserve drugs if they are misused, misused, or missed. In this connection, the possibilities of XDR-TB therapy today are extremely limited due to the lack of the necessary list of active drugs - the effectiveness of treatment with available second-line drugs does not exceed 30%. The mortality rate among patients with XDR-TB today exceeds 70% within two years after diagnosis and, moreover, such patients pose a serious danger to others. In Kazakhstan, the number of reported cases of extensively drug-resistant tuberculosis is also growing from year to year. To date, more than 550 cases of XDR-TB have been registered, and another 10% of registered MDR-TB (6998 patients) have pre-XDR-TB, i.e. resistance to either fluoroquinolones or second-line injectables. In the absence of proper treatment, the predicted number of XDR-TB patients in the country by 2020 will be more than 2000 people. Of the population infected from them, 1-2 people per year will develop tuberculosis with primary XDR. The current XDR-TB treatment regimen is ineffective (36.8%) with a high relapse rate. At the same time, the cost of this treatment regimen is an average of 10 thousand dollars, not counting their content and other services. The presence of the problem of nosocomial spread of drug-resistant strains of M. tuberculosis through their transmission from patient to patient makes the selected treatment regimen ineffective, since the resistance profile of the new strain does not match the profile of the primary one. In this situation, it is absolutely necessary to introduce innovative personalized approaches to DNA fingerprinting of the pathogen to control its stability at the stages of patient treatment. At the same time, the introduction of individual treatment regimens with new anti-TB drugs is the only measure to control the growth and spread of pre-XDR and XDR-TB. In the current situation, issues related to the laboratory diagnosis of tuberculosis and drug resistance are of particular relevance for the development of a new methodology for a personalized approach in the treatment of severe pre-XDR and XDR-TB. The thoughtful application of available quality diagnostic methods and the reasonable design of patient treatment regimens will ensure the rational use of resources. For the first time in Kazakhstan, a project is proposed that combines the use of such a large-scale complex of molecular genetic and bacteriological methods to study strains of M. tuberculosis with pre-XDR and XDR TB circulating in the country. As a result of the project, an array of clinical and genetic data will be accumulated and analyzed, obtained using a personalized approach, provided by the methods of DNA fingerprinting of microorganisms, with a detailed study of the nature of the extensive drug resistance of the causative agent of tuberculosis.
Purpose of this study
Assess polymorphisms in genes associated with resistance to fluoroquinalones and aminoglycosides for a sample of M. tuberculosis strains isolated from patients in the Republic of Kazakhstan, as well as targeted gene sequencing in case of discrepancy phenotypic and genetic signs of drug resistance of these strains. Research objectives
Collecting, organizing and storing mycobacterial cultures Determination of drug susceptibility of clinical isolates to second-line drugs using phenotypic and molecular genetic tests DNA isolation from obtained mycobacterial cultures Carrying out a detailed molecular genetic typing of lecaries-resistant sampling by MIRU-VNTR and/or spoligotyping, as well as subtyping of the most common strains of the Beijing, LAM and Ural families in the population Identification of DNA-DNA hybridization methods genetic polymorphisms that cause the presence of pre-XDR and XDR among common M. Tuberculosis genotypes in Kazakhstan (continued) Comparison of the results of bacteriological and genetic tests of drug resistance and to form a sample of samples for sequencing of target genes Sequencing of target genes for strains with discrepancies in the results of phenotypic and genetic drug resistance analyzes
Study Design
Sample size: 1500 mycobacterial cultures isolated from patients with drug-resistant TB. Research methods: • Inoculation and testing for drug susceptibility to first and second line drugs on solid Lowenstein-Jensen medium; • Carrying out tests for drug sensitivity to drugs of the first line on a liquid medium using an automated system MGIT BACTEC -960; • Automated system GeneXpert (Xpert MTB / RIF) for the detection of the causative agent of tuberculosis and resistance to rifampicin; • Line Probe Assay LPA (Line Probe Assay) MTBDRplus for the detection of tuberculosis and tuberculosis with multidrug resistance on the HAIN system; • Automated system Exiprep/Existation for detection of tuberculosis and multidrug-resistant tuberculosis; • Isolation of DNA from mycobacterial cultures and methods of sample preparation for sequencing and other types of genetic analysis; • Genotyping methods: MIRU-VNTR, spoligotyping and DNA fingerprinting based on the analysis of specific single nucleotide polymorphisms; • Statistical and phylogenetic analysis; • Analysis of a panel of 120 single nucleotide polymorphisms associated with drug resistance to first and second line drugs by DNA-DNA hybridization on biological chips; • Targeted sequencing of individual genes and genome-wide strains in case of ineffectiveness of the targeted approach. Co-executor of the study: RSE on REM "National Scientific Center for Phthisiopulmonology" of the Ministry of Health of the Republic of Kazakhstan
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