カザフスタン共和国乳がん患者における遺伝的背景とホモシステイン濃度決定因子

長崎大学学位論文 学位記番号:博(医歯薬)乙第34号 学位授与年月日:平成26年9月3日Nagasaki University (長崎大学)論文博

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

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.

Mitochondrial and Y-chromosomal profile of the Kazakh population from East Kazakhstan

Aim To study the genetic relationship of Kazakhs from East Kazakhstan to other Eurasian populations by examining paternal and maternal DNA lineages. Methods Whole blood samples were collected in 2010 from 160 unrelated healthy Kazakhs residing in East Kazakhstan. Genomic DNA was extracted with Wizard® genomic DNA Purification Kit. Nucleotide sequence of hypervariable segment I of mitochondrial DNA (mtDNA) was determined and analyzed. Seventeen Y-short tandem repeat (STR) loci were studied in 67 samples with the Amp- FiSTR Y-filer PCR Amplification Kit. In addition, mtDNA data for 2701 individuals and Y-STR data for 677 individuals were retrieved from the literature for comparison. Results There was a high degree of genetic differentiation on the level of mitochondrial DNA. The majority of maternal lineages belonged to haplogroups common in Central Asia. In contrast, Y-STR data showed very low genetic diversity, with the relative frequency of the predominant haplotype of 0.612. Conclusion The results revealed different migration patterns in the population sample, showing there had been more migration among women. mtDNA genetic diversity in this population was equivalent to that in other Central Asian populations. Genetic evidence suggests the existence of a single paternal founder lineage in the population of East Kazakhstan, which is consistent with verbal genealogical data of the local tribes

Identifying risk factors associated with smear positivity of pulmonary tuberculosis in Kazakhstan

Background Sputum smear-positive tuberculosis (TB) patients have a high risk of transmission and are of great epidemiological and infection control significance. Little is known about the smearpositive populations in high TB burden regions, such as Kazakhstan. The objective of this study is to characterize the smear-positive population in Kazakhstan and identify associated modifiable risk factors. Methods Data on incident TB cases’ (identified between April 2012 and March 2014) socio-demographic, risk behavior, and comorbidity characteristics were collected in four regions of Kazakhstan through structured survey and medical record review. We used multivariable logistic regression to determine factors associated with smear positivity. Results Of the total sample, 193 (34.3%) of the 562 study participants tested smear-positive. In the final adjusted multivariable logistic regression model, sex (adjusted odds ratio (aOR) = 2.0, 95% CI:1.3–3.1, p < 0.01), incarceration (aOR = 3.6, 95% CI:1.2–11.1, p = 0.03), alcohol dependence (aOR = 2.6, 95% CI:1.2–5.7, p = 0.02), diabetes (aOR = 5.0, 95% CI:2.4–10.7, p < 0.01), and physician access (aOR = 2.7, 95% CI:1.3–5.5p < 0.01) were associated with smear-positivity. Conclusions Incarceration, alcohol dependence, diabetes, and physician access are associated with smear positivity among incident TB cases in Kazakhstan. To stem the TB epidemic, screening, treatment and prevention policies should address these factors

The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana

We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged

Genomic research perspectives in Kazakhstan

Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine.   Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well-equipped laboratories, bioinformatics, as well as qualified trained physicians and laboratory staff

Genetic epidemiology of ventricular tachycardia in patients with cardiomyopathy in Kazakhstan: a targeted sequencing study

Ventricular tachycardia (VT) is a common complication in cardiac disorders of different etiology such as coronary heart disease (CHD) and cardiomyopathies. We hypothesized that the underlying molecular mechanism, independent of disease etiology, might originate from a common overlapping pattern of genetic variants in cardiac disease-related genes. <b>Aim:</b> to investigate genetic basis of VT in patients with cardiomyopathy in Kazakhstan using targeted NGS (design of new HaloPlex gene panel). <b>Material and methods.</b> Using a customized HaloPlex Target Enrichment System? (Agilent Technologies, USA) 96 cardiomyopathy associated candidate-genes were enriched and then sequenced on HiSeq2000 platform using 2x150bp paired-end standard sequencing conditions in DNA of 95 patients diagnosed with sporadic (64/95) or familial (26/95) cardiomyopathies (dilated cardiomyopathy (DCM): 37.3%, idiopathic ventricular tachycardia (iVT): 38.9%, CHD with severe episodes of VT: 24.2%, and others: 3%). <b>Results:</b> The candidate gene library design covers a total target region of 463.767kbp with 406.062 analyzable target bases including all exonic and proximal intronic (+/-10bp) sequence and representing by 2,017 target loci. The mean coverage of all 95 samples at the target loci was 707.62-fold. Targeted sequencing and stepwise filtering of the annotated variants identified a total of 319 unique variants in 74 genes totaling up in 475 variants for the overall study group (HGMD listed). More than 50% of the patients carried at least two mutations, irrespective of the clinical phenotype. Furthermore, 215 private (unique) non-synonymous variants were observed in the patient cohort. Prediction scores of the private variants indicated high probability of disease association. Including the newly identified high-probability variants, each patient carried on average >4.8 genetic variants. Interestingly, statistical evaluation revealed no difference in the frequency of genetic variants (HGMD or rare variants) observed for the CHD and the DCM subgroup. The most abundant mutations of the CHD were observed in <i>MYBPC3, DMD, LAMA2, MYH6</i> and <i>GAA</i>. <i>PRKAG2 </i>mutations were overrepresented in the CHD subgroup. <b>Conclusion:</b> Our study indicates that the majority of the investigated patients with cardiomyopathies and VT, irrespective of disease phenotype or subgroup carry multiple disease-linked mutations and additional potentially functional rare variants in cardiac disease genes. We thus have to consider a molecular disease-overlap with converging phenotypes