[The analysis of association between multiple sclerosis and genetic markers identified in genome-wide association studies]. / Analiz assotsiatsii s rasseyannym sklerozom geneticheskikh markerov predraspolozhennosti, vyyavlennykh v rezul'tate polnogenomnykh issledovanii.

OBJECTIVE: Our aim was to analyse the association with multiple sclerosis of the genetic markers of autoimmune disorders identified in genome-wide association studies in ethnically homogenous groups of Russians and Tatars residing in the Republic of Bashkortostan. MATERIAL AND METHODS: We performed genotyping of the genetic variants rs2069762 in IL2 gene, rs759648 in PVT1 gene, rs1800682 in FAS gene and rs12708716 in CLEC16A gene in the study group consisting of 1724 people (547 patients with multiple sclerosis, 1177 representatives of the control group). We analysed the association of the studied genetic markers with multiple sclerosis using logistic regression under additive genetic model implemented in PLINK program with sex a covariate. RESULTS: In the group of Tatars, we detected an association of PVT1 rs759648*Callele with multiple sclerosis (OR=1.42, p=0,023). Meta-analysis of the study results in the two ethnic groups we confirmed the association of the PVT1 rs759648*C allele with the disease (random effects model and fixed effect model: OR=1.29, p=0,018). CONCLUSION: Our results provide an evidence of an association between multiple sclerosis and the PVT1 rs759648 allele in the populations of Russian and Tatars from the Republic of Bashkortostan. No association with any other studied polymorphic variant was found in the two ethnic groups.

[Molecular-genetic analysis of a rare forensic case of partial deletion of the Y-chromosome]. / Molekuliarno-geneticheskii analiz sluchaia chastichnoi deletsii Y-khromosomy v sudebno-meditsinskoi praktike.

The amelogenin gene encodes dental enamel protein and is present in humans in two forms - AMELX and AMELY, located on the X- and Y-chromosomes, respectively. This rare case depicts a partial deletion of the AMELY gene. In the Into-Stil LLC laboratory, we performed the genetic testing of the DNA samples extracted from buccal epithelial cells of the alleged father and the disputed child (a boy). Genotyping was carried out using COrDIS Plus ('Gordis', Russian Federation) and AmpFLSTR Identifiler Direct PCR Amplification ('Applied Biosystems', USA) Kits. Our findings have demonstrated that both the alleged father and the disputed child lacked the fragments corresponding with the AMELY gene. Using both STR-systems, we detected, in the disputed child's genome, the allele formally identical to the allele in the genome of the alleged father. Further analysis using the COrDYS ('Gordis', Russian Federation) kit allowed us to detect the amplified fragments corresponding with all the STR loci of Y chromosome, except DYS576 and DYS449, which confirmed that both studied individuals belonged to male biological sex.

[Association of adiponectin gene alleles with type 2 diabetes mellitus in residents of Bashkortostan].

Type 2 diabetes mellitus (T2DM) is one of the most acute problems of the modern world. The disease is characterized by high ratio of micro- and macrovascular complications. T2DM is a multifactorial and polygenic disease, structure of hereditary predisposition to which may be population-specific. Aim - the analysis of allelic associations of adiponectin gene (ADIPOQ, rs17366743) with T2DM, its clinical and metabolic characteristics and complications in T2DM patients resident in the Republic of Bashkortostan. MATERIAL AND METHODS: 3 PCR-based method of genotyping with polymorphic marker rs17366743 of ADIPOQ gene in 433 T2DM patients and 428 healthy controls, residents of Bashkortostan. RESULTS: The ratio of genotype CT and allele С was higher in T2DM patients compared with controls (15.7% vs. 6.8%; p=0.0002 and 7.8% vs. 3.4%; p<0.0001, respectively). Genotype ТТ and allele Т were less frequent in T2DM than in healthy subjects (84.3 and 93,2%; p=0.0002; 92.2 and 96.6%, p<0.0001, respectively). The association with the development of diabetic retinopathy and cataract was shown (p=0,044, p=0,008, respectively). CONCLUSIONS: Allele C and genotype CT are risk markers of T2DM (OR=2.43 and 2.56 respectively).

[Clinical and molecular genetic analysis of a case of familial multiple sclerosis in the Republic of Bashkortostan]. / Klinicheskii i molekuliarno-geneticheskii analiz sluchaia semeinogo rasseiannogo skleroza v Respublike Bashkortostan.

AIM: To investigate clinical manifestations of multiple sclerosis (MS) and the genetic makeup of six affected members of one family. MATERIAL AND METHODS: Six members of the family of Russian ethnic origin were examined. Pedigree analysis and genotyping of polymorphic markers of candidate genes for multiple sclerosis were performed. RESULTS AND CONCLUSION: The accumulation of alleles that were associated with autoimmune diseases according to the results of genome-wide association studies (rs1109670*C, rs3129934*T, rs9523762*G, rs1570538*T) was found in the family. The results confirm the contribution of several genetic variants to familial forms of MS.

[Analysis of FOXO1A and FOXO3A Gene Allele Association with Human Longevity].

Seeking human longevity association with gene polymorphisms in transcription factors in the Tatar ethnic group, we conducted an analysis for age-related genotype, frequencies in polymorphic sites of FOXO1A (rs4943794, 72327C>G) and FOXO3A (rs3800231, 35-2764A>G) genes. Genotyping was conducted by using the PCR-RFLP approach. According to the results of logistic regression analysis, during maturity and old age periods, a decrease in the number of FOXO1A*G/*G (OR = 0.984, P = 0.004) genotype carriers occurs and an increase in the number of FOXO1A*C/*G (OR = 1.035, P = 0.014) and FOXO1A*C/*C (OR = 1.024, P = 0.033) genotype carriers occurs in the sample of subjects before gender adjustments. In the sample of long-livers, the number of FOXO1A*C/*C (OR = 0.772, P = 0.028) genotype carriers decreased among women, while the number of FOXO3A*G/*G (OR = 1.008, P = 0.0001) genotype carriers increased among both men and women. Therefore, the FOXO1A gene polymorphic site rs4943794 is associated with an acquisition of old and senescent age in a sample before gender adjustments and with women's longevity. FOXO3A gene polymorphic site rs3800231 is associated with longevity in both women and men.

Combinations of Polymorphic Markers of Chemokine Genes, Their Receptors and Acute Phase Protein Genes As Potential Predictors of Coronary Heart Diseases.

Atherosclerosis, the main factor in the development of coronary heart diseases (CHD), is an inflammatory response to endothelial layer damage in the arterial bed. We have analyzed the association between CHD and the polymorphic markers of genes that control the synthesis of proteins involved in the processes of adhesion and chemotaxis of immunocompetent cells: rs1024611 (-2518A>G, CCL2 gene), rs1799864 (V64I, CCR2 gene), rs3732378 (T280M, CX3CR1 gene), rs1136743 (A70V, SAA1 gene), and rs1205 (2042C>T, CRP gene) in 217 patients with CHD and 250 controls. Using the Monte Carlo method and Markov chains (APSampler), we revealed a combination of alleles/genotypes associated with both a reduced and increased risk of CHD. The most significant alleles/genotypes areSAA1*T/T+CRP*C+CX3CR1*G/A (P perm = 0.0056, OR = 0.07 95%CI 0.009-0.55), SAA1*T+CRP*T+CCR2*G/A+CX3CR1*G (P perm = 0.0063, OR = 14.58 95%CI 1.88-113.04), SAA1*T+CCR2*A+CCL2* G/G (P perm = 0.0351, OR = 10.77 95%CI 1.35-85.74).

[Role of PLAT, PKHD1L1, STK38L and TEAD1 genes Alu-polymorphism for longevity].

The distribution of allele and genotype frequencies of Alu(I/D)-polymorphic sites in PLAT (TPA25), PKHD1L1 (Yb8AC702), STK38L (Ya5ac2145) и TEAD1 (Ya5ac2013) genes was first characterized in the ethnically homogeneous group (Tatars from the Republic of Bashkortostan, Russia), and was established (found) the association of each gene polymorphism with age. The study group consisted of 1580 unrelated individuals aged between 21 and 109 years, including 204 long-livers. It was found that STK38L*I/D genotype had positive association with longevity in the total group (OR=1,016, p=0,034). Long-lived women had a high probability of detection of PKHD1L1*I/I (OR=1,289, p=0,009), PLAT*D/D (OR=1,175, p=0,016) and TEAD1*I/I (OR=1,047, p=0,042) genotypes. PKHD1L1*I/D genotype was a significant factor in providing of male longevity (OR=1,713, p=0,030). Therefore, age-dependent changes in genotype frequencies are specific for each studied gene.

[Combined Effect of Genetic Factors, Age, and Smoking on the Risk of Developing Myocardial Infarction].

OBJECTIVE: to elaborate a complex model for myocardial infarction (MI) risk assessment considering the combined effect of genetic predisposition, age and smoking. MATERIALS AND METHODS: The study included two independent samples of ethnic Russians: 325 patients with MI and 185 individuals without history of cardiovascular diseases (controls) from the Moscow region, and 220 patients and 197 controls from the Republic of Bashkortostan. Genotyping of polymorphic loci of genes CRP (rs1130864), IFNG (rs2430561), TGFB1 (rs1982073), FGB (rs1800788) and PTGS1 (rs3842787) was performed. To construct the predictive models, we used logistic regression with stepwise inclusion of variables. The predictive value was evaluated by the area under the curve (AUC) in a ROC-analysis. The factor was considered as a marker at pAUC <0.05 calculated by the method of DeLong. The marker was considered effective at AUC >0.60. RESULTS: Three separate genetic variants FGB rs1800788*T, TGFB1 rs1982073*TT, CRP rs1130864*TT, and biallelic combination IFNG rs2430561*A + PTGS1 rs3842787*T whose association with MI we described earlier, were used to construct the composite genetic marker (AUC=0.66 in the training and test samples) by the logistic regression method. Adding to the obtained composite genetic marker such parameters as age and smoking allowed to create a complex MI risk marker, which was characterized by the predictive value stability (AUC=0.77 in the training sample and 0.82 in the test sample). CONCLUSION: The obtained complex model for MI risk assessment was reproduced in two independent samples of Russian ethnicity individuals from different regions of Russia with different gender identities, and allowed to have a reasonable chance (about 80%) of distinguishing patients and healthy individuals.

[Association of polymorphic markers of chemokine genes, their receptors, and CD14 gene with coronary atherosclerosis].

Atherosclerosis represents an inflammatory response to the disturbance of the endothelial layer in the arterial bloodstream. In the present study, an analysis of associations of polymorphic markers for the genes controlling synthesis of proteins involved in atherosclerosis pathogenesis in coronary atherosclerosis (CA) patients (217 subjects) and in a control group (250 subjects) was conducted. The following genes were examined: rs991804 (CCL2 gene), rs1126579 (CXCR2 gene), rs4074 (CXCL1 gene), rs4073 (CXCL8 gene), rs333 (CCR5 gene), rs2471859 (CXCR4 gene), rs1801157 (CXCL12 gene), and rs2569190 (CD14 gene). Using the Monte Carlo and Markov chain (APSampler) method, allele/genotype combinations associated with both low and high CA risk were revealed. The most important findings included the following: CXCR4*T/T + CCL2*C + CCR5*I/I (P perm = 1 × 10­6, OR = 0.44, 95% CI 0.3­0.63), CXCR2*C + CD14*C + CXCL12*G + CCL2*C + CCR5*D (P perm = 4 × 10­6, OR = 5.78, 95% CI 2.34­14.28), CD14*C + CCL2*C/C + CCR5*D (P perm = 6.3 × 10­6, OR = 5.81, 95% CI 2.17­15.56), CXCL8*A + CXCR2*C + CD14*T + CXCR4*C (P perm = 0.01, OR = 3.21, 95% CI 1.63­6.31).

[Association of variable rs1801282 locus of PPARG2 gene with diabetic nephropathy].

The association of the variable rs1801282 locus of the PPARG2 gene (peroxisome proliferator-activated receptor gamma) with type 2 diabetes mellitus and its complications was analyzed in inhabitants of the Republic of Bashkortostan. The genotype frequencies of the variable rs1801282 locus of the PPARG2 gene did not significantly differ in groups of healthy persons and patients with type 2 diabetes in all three considered inheritance models (codominant, dominant, and recessive). At the same time, it was demonstrated that the risk of one of the diabetic complications, i.e., diabetic nephropathy, was associated with the variable rs1801282 locus of the PPARG2 gene. Diabetic nephropathy was more common in patients with the C/C genotype (62.7%) compared to the C/G and G/G genotypes (37.5%), P = 0.036. The G allele is protective in regard to diabetic nephropathy (OR = 0.36) in patients with type 2 diabetes mellitus.

[Alu insertion-deletion polymorphism of COL13A1 and LAMA2 genes: The analysis of association with longevity].

The distribution of allele and genotype frequencies of Alu(I/D) polymorphic sites in the COL13A1 and LAMA2 genes coding extracellular matrix protein subunits was characterized in an ethnically homogeneous group (Tatars from the Republic of Bashkortostan, Russia). It was established that the frequency of individuals with the COL13A1*D/*D genotype was higher in the senile age period. The LAMA2*I/*D genotype was predisposing to longevity among women. According to the observed results, the frequency of the LAMA2*I/*D genotype was increased in senile individuals older than 90 years. The observed associations can be explained on the basis of the contemporary view by the importance of Alu elements in gene expression regulation at transcriptional and post-transcriptional levels, the involvement of collagen and laminin in maintaining the structure and function of the extracellular matrix, and the relationship between the extracellular matrix state, pathological changes and aging.

[Genetic Association of ADRA2A and ADRB3 Genes with Metabolic Syndrome among the Tatars].

An association study was performed for genetic polymorphisms in ADRB3 (rs4994) and ADRA2A (rs1800544, rs553668) genes to estimate their effect on quantitative parameters, including glucose, insulin, and HOMA-IR index in women from the Tatar population of Russia. It has been shown that CT and CC are associated with metabolic syndrome and increased insulin. It was shown that ADRA2A (rs1800544) gene polymorphism was associated with high levels of insulin and an increased HOMA-IR index in GG- and GC-genotype carriers.

[SOME RESULTS OF MOLECULAR GENETIC RESEARCHES OF AGING AND LONGEVITY].

This review is devoted to the description of research achievements in genetics of aging and longevity. It represents a certain interest for understanding of a problems of aging as a whole. There is a huge amount of results of diverse genetic studies of aging and longevity. Studies were performed with using different experimental strategies on model organisms or samples from different human populations of the world. The search for aging and longevity genes was carried out within international consortiums. The first results of whole genome sequences of super-centenarians were received. The genes influencing life expectancy were revealed in organisms of different systematic groups. Many of these genes are evolutionarily conservative. Associations between APOE, FOXO1A, FOXO3A, AKT1 gene polymorphisms and human longevity were confirmed in independent studies.

[CYP2D6, CYP3A5, and CYP3A4 gene polymorphism in Russian, Tatar, and Bashkir populations].

The allele and genotype frequency distribution at polymorphic loci rs3892097 (184G>A) of CYP2D6 gene, rs776746 (6986A>G) of the CYP3A5 gene and rs2740574 (-392A>G) of the CYP3A4 gene in Russians, Tatars, and Bashkirs was examined. Samples were taken from residents of Bashkortostan Republic (1240 men and women aged from 20 to 109 years and consisted of 443 Russians, 517 Tatars, and 280 Bashkirs). Allele identification was conducted using PCR-RFLP or PCR with TaqMan probes. The "nonfunctional" allele rs3892097*A of the CYP2D6 gene was detected in populations of Russians, Tatars, and Bashkirs in 17.2, 9.5, and 7.1% cases, respectively. The rs776746*G allele of the CYP3A5 gene encoding the CYP3A5 isoenzyme with decreased activity was revealed with a frequency of 94.6% in populations of Russians, 94.3% in the Tatar population, and 91.5% in the Bashkir population. The share of the minor allele rs2740574*G of the CYP3A4 was 4.0% in populations of Russians, 0.5% in the Tatar population, and 0.9% in the Bashkir population. It has been previously shown that the rs3892097*A, rs776746*G, and rs2740574*G allele frequencies vary significantly in different world populations. Since allele variants of CYP2D6, CYP3A5, and CYP3A4 genes can play essential role in interindividual and in interethnic differences in the metabolism of many therapeutic agents, the obtained results could be used in the prognosis of pharmacotherapy efficacy in populations of Russians, Tatars, and Bashkirs.

[[Length polymorphism of minisatellite repeat B2-VNTR of the bradykinin B2 receptor gene in healthy Russians and in patients with coronary heart disease].

Bradykinin B2 receptor is involved in many processes, including the regulation of blood pressure and smooth muscle contraction, vasodilation, inflammation, edema, cell proliferation, pain. It is suggested that this receptor may be one of the factors that have cardioprotective and infarct-limiting effects. It is assumed that certain genetic variants in both coding and non-coding regions ofBDKRB2 gene may influence its expression. In the 3'-untranslated region of BDKRB2 exon 3 the minisatellite repeat B2-VNTR is located. B2-VNTR has previously been shown to affect the BDKRB2 mRNA stability. Therefore, it is important to perform the molecular genetic analysis of this minisatellite in patients with different forms of coronary heart disease in order to reveal possible associations between specific B2-VNTR alleles and certain clinical forms of coronary heart disease. In the present study, a comparative analysis of the allele and genotype frequencies of B2-VNTR was carried out in groups of healthy individuals and patients with two clinical forms of coronary heart disease (angina pectoris and myocardial infarction), ethnically Russian. The results of the B2-VNTR length polymorphism analysis indicate that this tandem repeat may be attributed to a class of low polymorphic and non-hypervariable minisatellite. In all analyzed groups we revealed three B2-VNTR alleles, consisting of 43, 38 and 33 repeat units. Alleles of 43 and 33 repeats were major in all investigated groups. No statistically significant differences were found in the B2-VNTR allele and genotype frequencies between men and women in control group, and also between healthy men and men with angina pectoris and myocardial infarction. Thus, B2-VNTR length polymorphism was not associated with these clinical forms of coronary heart disease in Russian men. However, we do not exclude the possibility of association between the B2-VNTR short alleles (38 and 33 repeats) and cardioprotective effects of bradykinin B2 receptor in women with coronary heart disease. This hypothesis requires further investigation.

[Association between inflanummatory gene polymorphisms and the risk of myocardial infarction].

Allele and genotype frequency distributions of polymorphism rs2076059 (3832T>C) within the SELE gene rs6131 (S290N), within the SELP gene, rs1131498 (F206L), within the SELL gene, rs5498 (K469E) within the ICAM1 gene, rs35569394 (-2549(18)I/D) within the VEGFA gene, and rs1024611 (-2518A>G) within the CCL2 gene were examined in a group of patients after myocardial infarction (MI)(280 individuals) and in a control group (312 individuals). An implementation of the Markov chain and Monte-Carlo method (AP- Sampler) revealed the allele combinations associated with decreased and increased risk of MI. Among these the most important allele combinations were SELE*C + SELP*S + CCL2*A (FDR = 0.0005; OR = 0.42) SELP*S + CCL2*A (FDR = 0.0009; OR= 0.36}, SELL*F + VEGFA*I+ CCL2*G/G(FDR = 0.0009; OR = 4.17) VEGFA*I+ CCL2*G/G (FDR = 0.0009; OR = 3.76), SELE*C + CCL2*A (FDR = 0.0023; OR = 0.47), and SELL*I+ CCL2*G/G (FDR = 0.003; OR = 3.15).

[Age-dependent CYP1A2 gene polymorphism -163C>A in three ethnic groups of Bashkortostan Republic residents].

On a sample of 1240 persons from Bashkortostan, including Russian, Bashkirs and Tatars, the analysis of allele and genotype frequencies distribution of CYP1A2 gene polymorphism -163C>A was performed by PCR-RFLP in view of belonging to a particular age cohort. In Russian and Bashkirs ethnic groups we observed age-dependent decrease of CYP1A2*C allele and CYP1A2*CI*C genotype frequencies (in Russian statistically significant for allele and genotype, the Bashkirs--only for allele) and a statistically significant increase of CYP1A2*A allele and CYP1A2*A/*A genotype frequencies. The set reduction in the frequency of the wild allele CYP1A2*C and increasing the frequency of the mutant allele CYP1A2*A with age may be due to greater survival of persons who are carriers of that allelic variants of CYP1A2 gene, providing a more efficient metabolism of xenobiotics.

[Association of polymorphic markers of CASP8, BCL2 and BAX genes with aging and longevity].

We performed the analysis of genotype frequency dynamics of CASP8, BCL2 and BAX genes polymorphic markers between 21 and 109 years in the group of Ethnic Tatars from Bashkortostan. Genotyping was carried out using PCR and PCR-RFLP. We found associations between age and -652(6N)I/D polymorphism of CASP8 gene (rs3834129), 140016C>T polymorphism of BCL2 gene (rs12454712) and 919A>G polymorphism of BAX gene (rs1805419). An increase of genotype frequency of BCL2*C/*C and decrease of genotype frequency of CASP8*I/*D was observed in male of senile age; and also decrease of genotype frequency of BAX*G/*G among long-livers. In female of longevity age, the number of CASP8*I/*D, BCL2*T/*T and BAX*A/*A genotype carriers was higher and number of CASP8*DI/*D, BCL2*C/*C, BAX*A/*G and BAX *G/*G genotype carriers was reduced.

[Association analysis of polymorphic loci of TP53 and NFKB1 genes with human age and longevity].

TP53 and NFKB1 genes represent considerable interest as candidate genes of human aging and longevity. The allele and genotype frequency distributions of TP53 R72P (rs1042522) polymorphism and NFKB1 2592 + 58T > A (rs4648110) polymorphism were characterized in groups of men and women of 21-109 years in the given research. No statistically significant distinctions in allele and genotype frequencies between long-livers, old people and other age groups were revealed. On the basis of logistic regression analysis results it is obviously possible to make the conclusion that polymorphism R72P of TP53 gene and polymorphism 2592 + 58T > A of NFKB1 genes is associated with the age mainly throughout elderly and senile ranges of years. Relative chances to achieve the age of 80-90 years are higher in carriers of TP53*R/*R and NFKB1*A/*A genotypes. It is also possible to believe that TP53 and NFKB1 genes are frailty genes, instead of longevity ones.