Genotyping Of SNP Research Articles

Interaction between angiotensin-converting enzyme gene rs4343 polymorphism, environment factors, and angiotensin II level on susceptibility to knee osteoarthritis

ObjectivesOsteoarthritis (OA) is a complex multifactorial disease. The association of knee OA risk with ACE gene rs4343 polymorphism, gene environment synergistic effect, and angiotensin II serum level has not been previously examined. Therefore, we investigate the ACE gene rs4343 polymorphism in knee OA, and its association with severity of knee OA, and angiotensin II serum level. MethodsUsing a case–control design, we recruited 200 subjects (100 cases and 100 controls) and all were subjected to genotyping of rs4343 SNP by real-time polymerase chain reaction and assay of serum angiotensin II level by ELISA. ResultsG containing genotypes (AG and GG) and G allele frequencies of the ACE rs4343 polymorphism were significantly higher in the case group than that in the control group. There was significant association between ACE rs4343 genotypes and risk of knee OA under the following genetic inheritance models: GG vs. AA (P=0.003), AA vs. GG/AG (P=0.014), AG/AA vs. GG (P=0.037), and G vs. A (P<0.001). Stratified analyses showed ACE rs4343 polymorphism was evidently associated with a significantly increased risk of knee OA among those had BMI≥25% (adjusted OR=3.016; 95% CI 1.052–8.648; P=0.040). Additionally, knee OA patients with GG genotype had greater knee specific WOMAC index, Kellgren score, and serum angiotensin II level than those with AA or GA genotypes. ConclusionThe investigated polymorphism in the ACE gene rs4343 may reflect the risk and severity of knee OA in the Egyptian population, particularly with the GG genotype. The interaction between ACE gene rs4343 polymorphism and obesity further increased the risk of knee OA. Moreover, the higher angiotensin II level may be involved in the pathogenesis of knee OA.

FNDC5 Geni Polimorfizmleri, Serum İrisin Düzeyleri ve Alerjik Rinit Arasındaki İlişkinin Yokluğu

Aim: Allergic rhinitis (AR) is an inflammatory nasal mucosa disease caused by type 1 immunoglobulin E-mediated reactions to allergen exposure. Irisin is a hormone released by skeletal muscles in response to exercise. There are studies that demonstrate the relationship of irisin with inflammation. We aimed to investigate the potential association between irisin coding fibronectin type III domain 5 (FNDC5) gene polymorphisms, serum irisin levels, and AR. Method: A case-control study was designed, involving 100 AR patients and 100 healthy controls. Genotyping of rs726344 and rs1746661 SNPs within the FNDC5 gene was performed using PCR-RFLP method. Serum irisin levels were measured using ELISA. Results: Genotyping of rs726344 SNP in patients revealed 90% GG and 10% GA genotypes, while in controls, it was 94% GG and 6% GA. The AA genotype was not detected in any case. For rs1746661 SNP, patients had 57% GG, 39% GT, and 4% TT genotypes, while controls had 58% GG, 36% GT, and 6% TT genotypes. No significant difference was found in rs726344 and rs1746661 SNPs between the patients and the control group. Serum irisin level was 406.3±56.09 ng/ml in patients and 354.3±46.06 ng/ml in controls with no significant difference. Conclusion: This is the first study aiming to investigate the relationship between the irisin protein, its encoding gene, and AR. No significant association was identified between FNDC5 gene polymorphisms, serum irisin levels, and allergic rhinitis. While these findings suggest a limited role of these factors in AR, further studies are needed for more comprehensive understanding of the irisin-AR relationship.

Genotyping of rs228666 SNP of the human gene ACE2 in mild, moderate and severe COVID-19 patients.

The ACE2-converting enzyme has been identified as the specific receptor for coronavirus, but the effect of the ACE2 gene polymorphism is still unknown, so the expression of human ACE2 independently may affect the susceptibility to infection with COVID-19. Coronavirus is an infectious and pandemic disease caused by it. To evaluate the association between the ACE2 gene polymorphism and the severity of COVID-19 infection, we used PCR polymerase reaction and polymorphism methods to examine 80 patients classified into severe infection based on symptoms and 80 control factors. Results demonstrated statistical significance in this high-risk group and the function of rs228666 SNP in the risk of infection with the independent ACE2 gene rs228666. Individuals who have the variation A allele may be more vulnerable to infection than those who carry G in a condition with the GA genotype when compared to other genotypes GG and GA. In contrast, the AA genotype was not significant. Coronavirus susceptibility and disease severity were related to inflammation and genetic polymorphism, while there was no clear evidence linking this rs228666 SNP to the severity of COVID19 infection. At the 0.01 % probability level, the prediction of the GG genotype for control was not significant. In the case of mild infections, the ACE2 rs228666 SNP genotype was found to be a protective factor for infection with COVID-19 illness in Iraqi patients. Furthermore, patients with this GA genotype are more likely to develop COVID-19 illness than the other genotypes, although the AA genotype had no significant effect on this disease. Individuals with the A allele are also more likely to be infected with COVID-19 than those with the G allele, according to the findings. The GG genotype of the ACE2 rs228666 SNP was substantially more significant at the 0.01 % probability level in the medium cases compared to the control group, showing that the GG genotype of the ACE2 rs228666 SNP is a protective factor against the incidence of infection. With COVID-19 in Iraqi patients, however, the values of the AA genotype are not significant, implying that an individual who carries the A allele is more likely to get COVID-19 disease than those who possess the GG allele. Keywords: Coronavirus, SNP, ACE2.

The association of Sirtuin1 (SIRT1) polymorphism and downregulation of STAT4 gene expression with increased susceptibility to COVID-19 infection

ABSTRACT Sirtuin1 (SIRT1) is an epigenetic modulator that belongs to sirtuins family and participates in many physiologic reactions, as genomic stabilization, apoptosis, proliferation, and inflammation. STAT4 (signal transducer and activator of transcription 4) gene is a component of JAK-STAT signaling pathway, which plays key role in activating cellular-mediated immune responses. The present study aimed to investigate the association between SIRT1 rs12778366 SNP, expression level of STAT4 gene and susceptibility to COVID-19 infections as well as their correlation to clinicopathological data. The present study included 100 ICU patients with severe COVID-19 infection and 100 age- and sex-matched healthy controls. DNA was extracted. Genotyping of SNP in SIRT1 (rs12778366) was performed, Total RNA was extracted from PBMCs. Reverse transcription was done. STAT4 gene expression levels were evaluated with GAPDH as internal control using real-time PCR. We found a significantly higher frequency of ‘C’ allele and C/T genotype in case vs. control. The association was of low strength (φ = 0.105 for alleles, and 0.154 for genotypes). This was associated with higher expression of STAT4 gene (P < 0.001) and increased tendency for lower respiratory complications. Median STAT4 (FC) (Median = 0.18, 95% CI = 0.15–0.27) was lower than normal control value of 1.0. This difference was statistically significant (Hodges-Lehmann location estimator = 0.217, P < 0.001). SIRT1 polymorphism and decreased expression of STAT4 gene are associated with increased susceptibility to COVID-19 infection and correlate to its phenotypic manifestations.

Association of Met420del Variant of Metformin Transporter Gene SLC22A1 with Metformin Treatment Response in Ethiopian Patients with Type 2 Diabetes.

This study aimed to evaluate whether the M420del variants of SLC22A1 (rs72552763) is associated with metformin treatment response in Ethiopian patients with type 2 diabetes mellitus (T2DM). A prospective observational cohort study was conducted on 86 patients with T2DM who had been receiving metformin monotherapy for <1 year. Patients showing ≥0.5% reduction in HbA1c levels from baseline within 3 months and remained low for at least another 3 months were defined as responders while those patients with <0.5% reduction in HbA1c levels and/or those whom started a new class of glucose-lowering drug(s) because of unsatisfactory reduction were defined as non-responders. In addition, good glycemic control was observed when HbA1c ≤7.0%, and the above values were regarded as poor. Genotyping of rs72552763 SNP was performed using TaqMan® Drug Metabolism Enzyme Genotyping Assay and its association with metformin response and glycemic control were assessed by measuring the change in HbA1c and fasting blood glucose levels using Chi-square, logistic regression and Mann-Whitney U-test. Statistical significance was set at p <0.05. The minor allele frequency of the rs72552763 SNP of SLC22A1 was 9.3%. Metformin response was significantly higher in deletion_GAT (del_G) genotypes as compared to the wild-type GAT_GAT (G_G) genotypes. Furthermore, a significantly lower median treatment HbA1 level was found in del_G genotypes as compared to G_G genotypes. However, the association of rs72552763 with metformin response was not replicated at the allele level. In contrast, the minor del_allele was significantly associated with good glycemic control compared to the G_allele, though not replicated at del_G genotypes level. This study demonstrated that metformin response was significantly higher in study participants with a heterozygous carrier of M420del variants of SLC22A1 as compared to the wild-type G_G genotypes after 3 months of treatment.

Exome-based new allele-specific PCR markers and transferability for sodicity tolerance in bread wheat (Triticum aestivum L.).

Targeted exome-based genotype by sequencing (t-GBS), a sequencing technology that tags SNPs and haplotypes in gene-rich regions was used in previous genome-wide association studies (GWAS) for sodicity tolerance in bread wheat. Thirty-nine novel SNPs including 18 haplotypes for yield and yield-components were identified. The present study aimed at developing SNP-derived markers by precisely locating new SNPs on ~180 bp allelic sequence of t-GBS, marker validation, and SNP functional characterization based on its exonic location. We identified unknown locations of significant SNPs/haplotypes by aligning allelic sequences on to IWGSC RefSeqv1.0 on respective chromosomes. Eighteen out of the target 39 SNP locations fulfilled the criteria for producing PCR markers, among which only eight produced polymorphic signals. These eight markers associated with yield, plants m-2, heads m-2, and harvest index, including a pleiotropic marker for yield, harvest index, and grains/head were validated for its amplification efficiency and phenotypic effects in focused identification germplasm strategy (FIGS) wheat set and a doubled haploid (DH) population (Scepter/IG107116). The phenotypic variation explained by these markers are in the range of 4.1-37.6 in the FIGS population. High throughput PCR-based genotyping using new markers and association with phenotypes in FIGS wheat set and DH population validated the effect of functional SNP on closely associated genes-calcineurin B-like- and dirigent protein, basic helix-loop-helix (BHLH-), plant homeodomain (PHD-) and helix-turn-helix myeloblastosis (HTH myb) type -transcription factor. Further, genome-wide SNP annotation using SnpEff tool confirmed that these SNPs are in gene regulatory regions (upstream, 3'-UTR, and intron) modifying gene expression and protein-coding. This integrated approach of marker design for t-GBS alleles, SNP functional annotation, and high-throughput genotyping of functional SNP offers translation solutions across crops and complex traits in crop improvement programs.

Association of transcription factor 7-like 2 rs12255372 polymorphism with susceptibility of type 2 diabetes mellitus in Bangladeshi population.

Polymorphism of transcription factor 7-like 2 (TCF7L2) has a link with type 2 diabetes mellitus (T2DM) through β cell dysfunction that causes defect in blood glucose homeostasis. This case-control study recruited 67 T2DM as cases and 65 age-matched healthy individuals as controls to determine whether the polymorphism rs12255372 (G > T) in the TCF7L2 gene have an association with T2DM in Bangladeshi population. Genomic DNA was purified from peripheral whole blood sample and direct Sanger sequencing was done for genotyping of SNP. Bivariate logistic regression was done to find out the association between genetic variant and T2DM. In our study, the minor T allele frequency was significantly more frequent in T2DM group than healthy controls (29.1% vs. 16.9%). After adjusting with confounding factors, heterozygous-genotype GT had higher odds of developing T2DM (OR 2.4; 95% CI: 1.0-5.5; p value = 0.04) and in dominant model, having SNP in TCF7L2 increased the risk of T2DM 2.3 times (95% CI: 1.0-5.2; p value = 0.04). In interaction model, genetic susceptible SNP cases interacted significantly with increasing age and BMI, female gender, and having family history of diabetes mellitus to develop T2DM (pinteraction < 0.001). Having minor T allele either in heterozygous or homozygous variant form of rs12255372 (G > T) TCF7L2 had significant association with T2DM. In conclusion, TCF7L2 gene variant increases risk of developing T2DM among the Bangladeshi population.

Phosphodiesterase 4 D(PDE4D) gene polymorphisms and risk of ischemic stroke: A systematic review and meta-analysis.

Studies on the relationship between Phosphodiesterase 4 D (PDE4D) gene polymorphism with the risk of ischemic stroke (IS) have shown discordant results. The present meta-analysis was aimed to clarify the relationship between PDE4D gene polymorphism with the risk of IS by estimating pooled analysis of published epidemiological studies. A comprehensive literature search for all the published articles was performed in various electronic databases, including PubMed, EMbase, Cochrane Library, Trip Database, Worldwide Science, CINAHL, and Google Scholar up to 22nd December 2021. Pooled Odds ratios (ORs) with 95% Confidence Intervals (CIs) under dominant, recessive, and allelic models were calculated. Subgroup analysis based on ethnicity (Caucasian vs. Asian) was performed to examine the reliability of these findings. Sensitivity analysis was also performed to detect the heterogeneity between studies. Finally, Begg's funnel plot was used to assess the potential for publication bias. In our meta-analysis, we identified a total of 47 case-control studies with 20,644 ischemic stroke (IS) cases and 23,201 control subjects, including 17 studies of Caucasian descent and 30 studies of Asian descent. Our findings suggest that there was a significant relationship between SNP45 gene polymorphism and risk of IS (Recessive model: OR = 2.06, 95% CI 1.31-3.23), SNP83 overall (allelic model: OR = 1.22, 95% CI 1.04-1.42), Asian (allelic model: OR = 1.20, 95% CI 1.05-1.37), and SNP89 Asian (Dominant model: OR = 1.43, 95% CI 1.29-1.59, recessive model: OR = 1.42, 95% CI 1.28-1.58) respectively. However, no significant relationship was found between SNP32, SNP41, SNP26, SNP56, and SNP87 gene polymorphisms and risk of IS. Findings of this meta-analysis conclude that SNP45, SNP83, and SNP89 polymorphism could be capable of increasing stroke susceptibility in Asians but not in the Caucasian population. Genotyping of SNP 45, 83, 89 polymorphisms may be used as a predictor for the occurrence of IS.

Association of vitamin D receptor Cdx-2 polymorphism with COVID-19: A case-control study

Background: Host genetic variability has been suggested as an important explanation for inter-individual differences in COVID-19 susceptibility and severity. Most vitamin D actions in the regulation of immunity are mediated by vitamin D receptors (VDRs). Polymorphisms in the VDR gene have been associated with several health outcomes; however, their effects on COVID-19 still need more clarification. This study aims to investigate the association of the VDR SNP (rs11568820, Cdx-2) with susceptibility and inter-individual variability of the severity of COVID-19. Methods: A total of 100 confirmed COVID-19 patients and 100 age and sex-matched controls were enrolled in this study between July and September 2021. COVID-19 patients were further subdivided into severe (n=50) and non-severe (n=50) cases. All participants were subjected to genotyping of Cdx-2 SNP using the allelic discrimination of the Real-time PCR technique and assay of serum 25(OH)D levels by ELISA. Results: The results showed that the homozygous ‘GG’ genotype was significantly higher in patients vs. controls, whereas the heterozygous ‘AG’ genotype was significantly lower in COVID-19 patients. Thus, the heterozygous ‘AG’ genotype is considered the protective genotype. This protection was more significant among males vs. females (P=0.02). However, there were no statistically significant differences in the genotype distributions of VDR Cdx-2 SNP between severe and non-severe patients. Moreover, COVID-19 patients with the ‘AG’ genotype presented higher 25(OH)D levels than the ‘GG’ genotype(P=0.02). Conclusions: VDR SNP (rs11568820, Cdx-2) might be a potential risk factor for COVID-19, particularly among male patients.

Association of interferon gamma inducible protein-10, monocyte chemoattractant protein-1, macrophage inflammatory protein-1 alpha, interleukin-6, and rs12252 single nucleotide polymorphism of interferon-induced transmembrane protein-3 gene with the severity of COVID-19 infection

BackgroundEvaluating the serum levels of IP-10, MCP-1, MIP-1α, and IL-6 and genotyping of rs12252 SNP of IFITM3 gene among different categories of COVID-19 patients might aid in understanding the pathogenesis of COVID-19 and contribute to developing disease-specific biomarkers and therapeutic strategies.MethodsThis is a cross-sectional study involving a total of 84 COVID-19 patients confirmed by positive RT-PCR and 28 healthy controls. COVID-19 patients were recruited from the intensive care unit (ICU) and COVID unit of Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka. COVID-19 patients were categorized into moderate, severe, and critically ill groups according to the World Health Organization classification. The serum IP-10, MCP-1, and MIP-1α levels were measured by cytometric bead array assay by flow cytometry, and serum IL-6 level was detected by the chemiluminescence method. rs12252 SNP of the IFITM3 gene was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR RFLP).ResultsThe serum IP-10, MCP-1, MIP-1α, and IL-6 levels among critically ill COVID-19 patients were significantly higher than that in patients with moderate disease and healthy controls (p < 0.001). Genotype distribution for rs12252 (42 T/C) SNP of the IFITM3 gene between the different groups of COVID-19 patients and healthy controls showed that CC genotype was statistically associated with disease severity (p < 0.001).ConclusionsIP-10 and MCP-1, MIP-α, IL-6, and CC genotype of rs12252 (42 T/C) SNP of IFITM3 gene are associated with COVID-19 severity.

MRNA expression analysis confirms CD44 splicing impairment in systemic lupus erythematosus patients.

Systemic Lupus Erythematosus (SLE) is a complex chronic autoimmune disease characterized by several immunological alterations. T cells have a peculiar role in SLE pathogenesis, moving from the bloodstream to the peripheral tissues, causing organ damage. This process is possible for their increased adherence and migration capacity mediated by adhesion molecules, such as CD44. Ten different variant isoforms of this molecule have been described, and two of them, CD44v3 and CD44v6 have been found to be increased on SLE T cells compared to healthy controls, being proposed as biomarkers of disease and disease activity. The process of alternative splicing of CD44 transcripts is not fully understood. We investigated the mRNA expression of CD44v3 and CD44v6 and also analyzed possible CD44 splicing regulators (ESRP1 molecule and rs9666607 CD44 polymorphism) in a cohort of SLE patients compared to healthy controls. This study involved 18 SLE patients and 18 healthy controls. Total RNA and DNA were extracted by peripheral blood mononuclear cells. The expression study was conducted by quantitative RT-polymerase chain reaction, using SYBR Green protocol. Genotyping of rs9666607 SNP was performed by direct sequencing. CD44v6 mRNA expression was higher in SLE patients compared to healthy controls (p = 0.028). CD44v3/v6 mRNA ratio in healthy controls was strongly unbalanced towards isoform v3 compared to SLE patients (p = 0.002) and decreased progressively from healthy controls to the SLE patients in remission and those with active disease (p = 0.015). The expression levels of CD44v3 and CD44v6 mRNA correlated with the disease duration (p = 0.038, Pearson r = 0.493 and p = 0.038, Pearson r = 0.495, respectively). Splicing regulator ESRP1 expression positively correlated with CD44v6 expression in healthy controls (p = 0.02, Pearson r = 0.532) but not in SLE patients. The variant A allele of rs9666607 of CD44 was associated with higher level of global CD44 mRNA (p = 0.04) but not with the variant isoforms. In SLE patients, the increase in CD44v6 protein correlates with a higher transcript level of this isoform, confirming an impairment of CD44 splicing in the disease, whose regulatory mechanisms require further investigation.

The Association of prolactin receptor gene polymorphism with recurrent miscarriage in a sample of Iraqi women

Recurrent miscarriage (RM) is a common occurrence, about 15% of all clinically recognized pregnant women resulting in pregnancy failure. RM has been inconsistently defined. When defined as 3 consecutive pregnancy losses prior to 20 weeks from the last menstrual period, it affects about (1- 2) % of women. our study study whether the polymorphisms in PRL-R gene are correlated with the risk of RM. RM casas was (n=25) and apparently healthy control subject (n=15), were enrolled genotyping of PRL-R gene SNP (rs37389 G>T) polymorphism were determined by using Taqman genotyping assay. This study was carried out in the laboratory of institute of genetic angering and biotechnology for postgraduate study- university of Baghdad from November 2018 to February 2019, and the sample were collected from several laboratories in Baghdad. the distribution of genotypes and alleles frequencies results showed that at rs37389‎ SNP of PRL-R gene, as related with TT, TG and combined TG+GG genotypes, significant differences in frequency percentage were recorded between RM patients and apparently healthy subjects, the frequency of wild TT genotype was significantly lower in patients with RM than in apparently healthy subjects. In contrast, the frequency of heterozygous TG genotype and mutant genotype were significant higher in patients with RM compared with apparently healthy subjects. This study found an association between both heterozygous and homozygous mutants genotype at rs37389 of PRL-R gene with a risk for RM susceptibility.

Polymorphisms of CYP1A1 Genes and Its Correlation with Clinical Variant of Pterygium

&#x0D; Background and Objective: CYP1A1 gene, which has role in carcinogenic metabolisms, is also detected in pterygium tissue. The aim of the study is to determine the polymorphisms of CYP1A1 m2 (rs1048943) and m4 (rs1799814) gene and its correlation with clinical variant of the pterygium.&#x0D; Methods: DNA isolation was performed from blood sample of 80 pterygium patients consisting of 40 inflammatory and 40 non-inflammatory pterygium. Genotyping of rs1048943 SNP AG (m2) in the CYP1A1 gene was performed using Alel Specific Polymerase Chain reaction (AS-PCR) and rs1048943) SNP Genotyping was performed using PCR. Polymorphism results are characterized as wild type (AA), mutant homozygote (GG), and mutant heterozygote (AG).&#x0D; Results: CYP1A1 m2 and m4 gene polymorphism consist of wild type (AA), mutant homozygote (GG), and mutant heterozygote (AG). Both CYP1A1 m2 and m4 genes polymorphism of both groups of inflammatory and non-inflammatory pterygium was mostly consist of wild type polymorphism, followed by the mutant heterozygote polymorphism. The wild type polymorphism was found to be higher in inflammatory pterygium, meanwhile the mutant heterozygote was found to be higher in non-inflammatory pterygium.&#x0D; Conclusion: There were differences in CYP1A1 m2 and m4 gene polymorphism in both pterygium group, but none has been shown to be statistically associated with the clinical variant of the pterygium.

Increased expression of serine palmitoyl transferase and ORMDL3 polymorphism are associated with eosinophilic inflammation and airflow limitation in aspirin-exacerbated respiratory disease.

BackgroundPatients with aspirin-exacerbated respiratory disease (AERD) are known to have poor clinical outcomes. The pathogenic mechanisms have not yet been completely understood.ObjectiveWe aimed to assess the involvement of the de-novo synthetic pathway of sphingolipid metabolism in patients with AERD compared to those with aspirin tolerant asthma (ATA).MethodsA total of 63 patients with AERD and 79 patients with ATA were enrolled in this study. Analysis of mRNA expression of serine palmitoyl transferase, long-chain base subunit 2 (SPTLC2) and genotyping of ORMDL3 SNP (rs7216389) was performed.ResultsSignificantly higher levels of SPTLC2 mRNA expression were noted in patients with AERD, which showed significant positive correlations with peripheral/sputum eosinophil counts and urine LTE4 (all P<0.05). The levels of SPTLC2 mRNA expression showed significant negative correlations with the level of FEV1 and FEV1/FVC (P = 0.033, r = −0.274; P = 0.019, r = −0.299, respectively). Genotype frequencies of ORMDL3 SNP (rs7216389) showed no significant differences between the AERD and ATA groups. Patients with AERD carrying the TT genotype of ORMDL3 had significantly lower levels of FVC (%) and PC20 methacholine than those carrying the CT or CC genotype (P = 0.026 and P = 0.030).Conclusion & clinical relevanceThis is the first study that shows the dysregulated de novo synthetic pathway of sphingolipids may be involved in the eosinophilic inflammation and airflow limitation in AERD.

SINGLE-NUCLEOTIDE POLYMORPHISMS OF THE ESR1 [RS 2234693], IL-1 [RS1143627], RANKL [RS9594738] AND [RS9594759] GENES AS POSSIBLE RISK MARKERS FOR VARIOUS VARIANTS OF THE COURSE OF PERIODONTAL DISEASE IN PATIENTS BORN MACROSOMIC

The article is concerned with the research for genetic predictors of periodontal tissue diseases in individuals born to macosomіс.&#x0D; Purpose of this study is to identify the association between the polymorphic variants of the CYP19A1 [rs2414096, rs936306], ESR1 [rs2234693, rs9340799], IL-1b [rs1143627], IL-6 [rs1800796], IL-10 [rs1800896], RANKL [rs9597575] and VDR [rs 1544410, rs10735810] genes and the formation of periodontal tissue disorders with a predominance of inflammatory (periodontitis) or dystrophic (paradontosis) flow patterns in of Kharkiv and the population of adjacent district who were born by macrosomic delivery.&#x0D; Object and Methods. The molecular genetic method was used to examine 81 persons of different ages (from 18 to 55 years old) who live in the Kharkiv and adjacent districts (Ukraine). The participants in the study were divided into 3 groups. The pathological changes in periodontal tissues were recorded by the classification of periodontal diseases (M.F. Danylevskyi, 1994).&#x0D; The macrosomic-at-birth participants who were diagnosed with chronic periodontitis (of the initial, first, or second degree) were assigned to the general group with a predominance of inflammatory processes in periodontal tissues. The macrosomic-at-birth participants who were diagnosed with parodontosis (of the initial, first or second degree), were assigned to the general group with a predominance of dystrophic processes in periodontal tissues. The comparison group consisted of the individuals with a conventionally healthy periodontium.&#x0D; The DNA was isolated from the buccal epithelium. The genotyping of SNP was carried out by Real-Time PCR.&#x0D; Conclusions. 1. The risk of dystrophically-inflammatory diseases of periodontal tissues with prevalence of both dystrophic (parodontosis) and inflammatory (periodontitis) flow patterns is associated with variants of the IL-1b gene: [rs1143627] (an over-dominant model of inheritance) in individuals born macrosomic. 2. The protective effect during periodontal tissue diseases with a tendency to inflammatory course was associated with the ESR gene variants [rs 2234693] (recessive model of inheritance) and IL-1b [rs1143627] (dominant and multiplicative model of inheritance). 3. A more pronounced effect of the IL-1b gene variant: [rs1143627] on the development of processes with a tendency to inflammatory course in the periodontal tissues (additive, dominant, over-dominant and multiplicative models of inheritance versus over-dominant model of the tendency to dystrophic flow) was recorded. 4. The risk of developing of pathological processes in periodontal tissues with a tendency to a dystrophic course rather than to an inflammatory course, associated with the RANKL [rs9594738] gene variants (dominant and multiplicative models of inheritance) and RANKL [rs9594759] variant (dominant model of inheritance). 5. Analysis of variants of the ESR1 [rs 2234693], IL-1b [rs1143627] and RANKL [rs9594738], [rs95944738], [rs95944738] gene variants is proposed to be used for DNA diagnostics at the preclinical stage of the disease in order to highlight the risk group for the development of periodontal tissue disorders and increase the effectiveness of personalized preventive measures in individuals born macrosomic.

Detection of polymorphism in the promoter region of TNF-alpha gene of water buffalo (Bubalus bubalis) and its association with disease resistance

Tumour necrosis factor (TNF), a proinflammatory cytokine, plays an important role in the regulation of cell differentiation, proliferation and death, as well as in innate and adaptive immune response. In this study we have sequence characterized upstream regulatory region of TNF-á gene of buffalo. Ten single polymorphic nucleotides (SNPs) -541A/T, -553A/G, -563,C/G, -619A/G, -659A/G, -706C/G, -730G/T, -794A/G, -898G/T, -981A/G) along with one indel at position -783 were identified. Further when analysed, among riverine and swamp types, 16 and 17 transcription factor–binding sites (TFBS) respectively were observed. Riverine and swamp buffaloes differed by PAX-2 transcription factor binding site at position -541 present in riverine and absent in swamp, important in the proliferation of multiple cell lines and development of organs. Comparative analysis of TNF-á upstream region revealed presence of additional NF-k binding site in buffalo and v-Myb binding site in cattle only. Genotyping of SNP -794A/G by tetra-ARMS PCR revealed variable allele frequencies among riverine and swamp buffaloes, however in clinical mastitis affected and non-affected Murrah buffaloes this SNP didn’t show any significant association with mastitis resistance. Overall study reveals the sequence variation in TNF-á promoter, possibly leading to modification of transcriptional regulation in swamp and riverine buffalo.

Significant association between IL10-1082/-819 and TNF-308 haplotypes and the susceptibility to cervical carcinogenesis in women infected by Human papillomavirus

Human papillomavirus (HPV) is responsible for high-grade cervical lesions and cervical cancer. The inflammation plays a key role in cervical cancer progression. In this context, studies propose an association between TNFα and IL10 SNPs and susceptibility to HPV infection. The present work aimed to investigate the possible association between IL10 and TNFα promoter polymorphisms and HPV infection in the cervical carcinogenesis risk in women from Brazil. A total of 654 samples was evaluated in this study. HPV detection was performed by PCR and HPV genotyping was performed by PCR and sequencing of positive MY09/11 PCR product. Genotyping of IL10 SNPs (rs1800871 and rs1800896) was performed by High Resolution Melt analysis. Genotyping of TNFα SNP (rs1800629) was performed by fluorogenic allele-specific probes. The distribution of TNF-308 (rs1800629) allelic (p = 0.03) and genotype (p = 0.03) frequencies and HPV-58 infection has showed a statistically significant difference between case and control groups for the assessed TNFα polymorphism. When it comes to TNFα (rs1800629) allelic and genotypic distribution and HPVs 18 and 31 infections, no statistically significant differences between case and control groups were observed for the studied TNFα polymorphism. The allelic and genotypic distribution of IL10-819 (rs1800871) and IL10-1082 (rs1800896) and HPV infection (HPVs 58, 18 and 31) has showed no statistically significant differences between case and control groups for the assessed IL10 polymorphisms. Furthermore, it was observed that haplotypes were associated with an increased cervical cancer risk in HPVs 16, 18 and 58-positive women. It was observed that women carrying the GTA and ATG haplotypes had 3.85 and 17.99-fold, respectively, increased cervical cancer susceptibility when infected by HPV-58. In women infected with HPV-16 and HPV-18, statistically significant results in women carrying the GTA and ATA haplotypes was observed. They had a 2.32 and 3.67-fold, respectively, increased cervical cancer susceptibility when infected by these two HPV types. The analysis of the haplotypes distribution in women infected with HPV-31 has showed no statistically significant results. Our study indicates that the association of genetic polymorphism in inflammation-related genes represents a risk to the susceptibility in the development of cervical cancer in women infected by HPVs 16, 18 and 58.

Gender-Specific Association Between ABCC2 -24C>T SNP and Reduction in Triglycerides in Chilean Patients Treated With Atorvastatin.

Statins are the first-line therapy prescribed to lower plasma cholesterol levels. Although being safe and showing several beneficial cholesterol-independent pleiotropic effects, a significant variability regarding statin's therapeutic goals has been abundantly documented, but less understood. We aimed to investigate the influence of the ABCC2 -24C>T single nucleotide polymorphism on Chilean hypercholesterolaemic individuals treated for 4 weeks with 10 mg/day atorvastatin. A total of 127 individuals medicated with atorvastatin 10 mg/day/4 weeks were included. Lipid profiles were determined before and after drug administration by conventional assays. Genotyping of the ABCC2 rs717620 SNP (-24C>T) was performed with TaqMan® Drug Metabolism Genotyping Assays. As expected, atorvastatin reduced TC, LDL-C and TG concentrations (p < 0.05). Also, HDL-C levels were increased (p < 0.05). Minor allele frequency for the rs717620 was 0.232. Overall, atorvastatin response was not associated with the ABCC2 rs717620 SNP (p > 0.05). Nonetheless, in male individuals carrying the -24T allele, we observed an attenuated reduction in both TG values and the TG/HDL-C ratio after 10 mg/day atorvastatin. This study indicates that TG levels and the TG/HDL-C ratio are affected by the rs717620 SNP in Chilean males but not female individuals after atorvastatin treatment.

Polymorphisms of BCL2 Gene in Acute Lymphoblastic Leukemia Patients in Pakistan and Screening of Phytochemicals to Overcome its Expression

Leukemia is a third fatal disease in developing countries. According to Punjab cancer registry 2014 report, leukemia incidence in Pakistan is 18.8%. Many treatments are available for leukemia now days but still there is a mortality rate measured. BCL2 controls cell apoptosis but when overexpressed due to the presence of promoter region single nucleotide polymorphism 938C>A, it causes anticancer drug resistance and represses apoptosis of malfunctioned cells resulting in immature leucocytes. The aim of the present study was genotyping of promoter region SNP in acute lymphoblastic leukemia patients of Pakistan and screening of naturally occurring phytochemical to identify BCL2 active site targeting compounds to control its expression. Study was performed on 104 cases taking similar control size showing allelic frequency C=0.466 and A=0.534 in cases, indicating an association with the disease by having chi-square p-value 0.0032. Screening of 90 phytochemicals was performed out of which one compound was selected as a lead compound based upon drug likeliness properties, binding with protein, and natural existence that may cause the least harm to human body and greater effect on leukemia cells. The information provided by this research can be used to make new-targeted drugs to control leukemia by inhibiting the mutated proteins.

MPS 08-05 Association of CETP gene D442G polymorphisms with myocardial infarction and stroke in Chinese population

Objective: Genetic variants of proteins involved in lipid metabolism may play an important role in determining the susceptibility for complications associated with cardiovascular and cerebrovascular diseases. Goal of the present study was to determine the association of cholesteryl ester transfer (CETP) gene D442G (rs2303790) polymorphisms with myocardial infarction and stroke. Design and Method: We conducted two case–control association studies (one cohort of 2325 myocardial infarction patients and 2620 unrelated controls, another cohort of 3960 stroke patients and 3654 controls)from the Chinese population. Genotyping of the rs2303790 SNP was performed by the TaqMan Real Time PCR method. Results: In both cohorts CETP D442G (rs2303790) polymorphisms was associated with levels of HDL cholesterol and ApoA1 (all p < 0.001). After adjusting for age, sex, BMI and other factors, CETP D442G has no association with myocardial infarction and hemorrhagic stroke. In subgroup of stroke, the SNP showed a significant association with Ischemic stroke adjusting by HDL cholesterol (odds ratio 1.39, 95%CI: 1.098–1.772, p = 0.0065, dominant model) or ApoA1 (odds ratio 1.47, 95%CI: 1.152–1.876, p = 0.0024, dominant model). Conclusions: The present study has shown that in the Chinese population CETP D442G polymorphisms was associated with HDL cholesterol and ApoA1 levels, but not myocardial infarction and hemorrhagic stroke. The detailed physiological effects of SNP and Ischemic stroke needed to be future defined.