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VNTR
Terms modified by VNTR Selected AbstractsInterleukin-1 receptor antagonist and tumour necrosis factor-alpha gene polymorphisms in Turkish patients with allergic contact dermatitisCONTACT DERMATITIS, Issue 2 2009Ilgen Ertam Background: It has been shown that the family of interleukin-1 receptor antagonist (IL-1 RA) and tumour necrosis factor-alpha (TNF,) genes are polymorphic and related to some inflammatory diseases. Allergic contact dermatitis is the classic presentation of delayed-type hypersensitivity responses to exogenous agents. A number of genes playing role in inflammatory response may be associated with allergic contact dermatitis. Objectives: To investigate whether there is an association between IL-1RA and TNF, gene polymorphisms and allergic contact dermatitis in Turkish patients with allergic contact dermatitis. Methods: This study was performed by the collaboration of Departments of Dermatology and Medical Genetics, Ege University, Faculty of Medicine. A total of 50 patients (31 females and 19 males) with allergic contact dermatitis, and 100 age- and sex-matched controls (58 females and 42 males) were included in the study. IL-1RA Variable Number of Tandem Repeats (VNTR) polymorphism in intron 2 and TNF,-308G-A polymorphism were genotyped by using polymerase chain reaction and agarose gel electrophoresis. Results: The frequency of IL-1RA 1/2 (48%) genotype was significantly higher (P = 0.002) in patient group than that is found in control group (22%). The frequency of TNF, (TNF G-308A) G/G genotype was significantly higher in patient group (68%) than that is found in control group (31%) (P = 0.008). Conclusions: Our findings suggest that TNF, (G/G) gene polymorphism may play role in susceptibility to allergic contact dermatitis in Turkish patients. [source] Interferon-, +874A/T and interleukin-4 intron3 VNTR gene polymorphisms in Chinese patients with idiopathic thrombocytopenic purpuraEUROPEAN JOURNAL OF HAEMATOLOGY, Issue 3 2007Xiaoli Chen Abstract Objectives:, The polarization of Th1/Th2 towards Th1 contributes to the pathogenesis of idiopathic thrombocytopenic purpura (ITP). Cytokines may play crucial roles in the pathogenesis of ITP. The purpose of this study was to investigate whether the interferon (IFN)-, +874(A/T) and interleukin-4 (IL-4) variable number of tandem repeats (VNTR) in intron3 polymorphisms may be responsible in part for genetic susceptibility to ITP. Methods:, Genotyping of IFN-, +874A/T and IL-4 intron3 VNTR was performed in 196 patients with ITP and 128 healthy individuals by polymerase chain reaction sequence-specific primers and direct PCR respectively. Results:, There was no association between IFN-, +874A/T and IL-4 intron3 VNTR polymorphism and ITP risk when all patients, as a group, were analyzed. When the patients were subdivided into two groups: childhood ITP and adult ITP, no statistical differences were found in the genotype and allele frequencies of IFN-, +874A/T and IL-4 intron3 VNTR between the two groups and the controls. Similar results were observed between acute childhood ITP, chronic childhood ITP, acute adult ITP or chronic adult ITP and the controls. Conclusion:, These polymorphisms were distributed similarly between the patients with ITP and the controls, demonstrating that these two candidate gene polymorphisms are not attributed to ITP susceptibility. [source] A systematic approach to molecular quantitative determination of mixed chimaerism following allogeneic bone marrow transplantation: an analysis of its applicability in a group of patients with severe aplastic anaemiaEUROPEAN JOURNAL OF HAEMATOLOGY, Issue 3 2004Rocío Hassan Abstract:, Mixed chimaerism (MC) following allogeneic bone marrow transplantation (allo-BMT) is defined as the persistent cohabitation of haematopoietic cells from recipients and donors. Its kinetics, clinical implications and more efficient laboratory approaches for MC detection are the object of ongoing research in view of the possibility of developing useful markers. Here we describe a sequential analysis of chimaerism using variable number of tandem repeat (VNTR) polymerase chain reaction (PCR) followed by quantitative, fluorescent labelled, short tandem repeat (STR) PCR. A set of four, highly discriminative VNTR and four STR markers was used to assess chimaerism. Sensitivity and regression analysis indicated that this approach was reliable for routine application in a single BMT centre. We studied 12 patients with severe aplastic anaemia (SAA) who had received allo-BMT, and had been conditioned with cyclosphosphamide (Cy) with or without anti-thymocyte globulin (ATG). We found a 50% prevalence of MC in the whole group, with levels between 4% and 37% of recipient cells. A sustained stable MC pattern after BMT was characteristic of the Cy-only conditioned patients but was also recorded in one patient treated with the Cy + ATG regime who showed a sustained MC pattern over a period of 24 months post-BMT. In none of our patients, MC was associated with an increased risk of graft rejection in a median follow-up of 39.5 months. [source] GENETIC STUDY: The interaction between the dopamine transporter gene and age at onset in relation to tobacco and alcohol use among 19-year-oldsADDICTION BIOLOGY, Issue 4 2009Brigitte Schmid ABSTRACT Recent evidence suggests that heterogeneity in the age at onset could explain the inconsistent findings of association studies relating the dopamine transporter (DAT1) gene with alcohol and nicotine consumption. The aim of this study was to examine interactions between two DAT1 polymorphisms and different initiation ages with regard to alcohol and tobacco consumption levels and dependence. Two hundred and ninety-one young adults (135 males, 156 females) participating in the Mannheim Study of Children at Risk were genotyped for the 40-bp variable number of tandem repeats (VNTR) and rs27072 polymorphisms of DAT1. Age at initiation was assessed at age 15 and 19 years. Information about current alcohol and tobacco consumption was obtained at age 19 years using self-report measures and structured interviews. Results suggest that age at onset of intensive consumption moderated the association of the DAT1 gene with early adult substance use and dependence, revealing a DAT1 effect only among individuals homozygous for the 10r allele of the 40-bp VNTR who had started daily smoking or being intoxicated early in life. Equally, carriers of the T allele of the rs27072 polymorphism reporting an early age at first intoxication showed higher current alcohol consumption at age 19 years. In contrast, no interaction between rs27072 and the age at first cigarette with regard to later smoking was observed. These findings provide evidence that the DAT1 gene interacts with an early heavy or regular drug exposure of the maturing adolescent brain to predict substance (ab)use in young adulthood. Further studies are required to confirm these findings. [source] GENETIC STUDY: The dopamine D4 Receptor (DRD4) gene exon III polymorphism, problematic alcohol use and novelty seeking: direct and mediated genetic effectsADDICTION BIOLOGY, Issue 2 2009Lara A. Ray ABSTRACT The present study sought to integrate convergent lines of research on the associations among the dopamine D4 receptor (DRD4) gene, novelty seeking and drinking behaviors with the overall goal of elucidating genetic influences on problematic drinking in young adulthood. Specifically, this study tested a model in which novelty seeking mediated the relationship between DRD4 variable number of tandem repeats (VNTR) genotype and problematic alcohol use. Participants (n = 90, 40 females) were heavy-drinking college students. Analyses using a structural equation modeling framework suggested that the significant direct path between DRD4 VNTR genotype and problematic alcohol use was reduced to a trend level in the context of a model that included novelty seeking as a mediator, thereby suggesting that the effects of DRD4 VNTR genotype on problematic alcohol use among heavy-drinking young adults were partially mediated by novelty seeking. Cross-group comparisons indicated that the relationships among the model variables were not significantly different in models for men versus women. These results extend recent findings of the association between this polymorphism of the DRD4 receptor gene, problematic alcohol use and novelty seeking. These findings may also help elucidate the specific pathways of risk associated with genetic influences on alcohol use and abuse phenotypes. [source] GENETIC STUDY: Polymorphisms of the dopamine D4 receptor gene (DRD4 VNTR) and cannabinoid CB1 receptor gene (CNR1) are not strongly related to cue-reactivity after alcohol exposureADDICTION BIOLOGY, Issue 2 2007Esther Van Den Wildenberg ABSTRACT Polymorphisms in the D4 dopamine receptor gene (DRD4) and the CB1 cannabinoid receptor gene (CNR1) have been associated with a differential response to alcohol after consumption. The goal of the present study was to investigate whether heavy drinkers with these polymorphisms would respond with enhanced cue-reactivity after alcohol exposure. Eighty-eight male heavy drinkers were genotyped for the DRD4 variable number of tandem repeats (VNTR) [either DRD4 long (L) or short (S)] and the CNR1 rs2023239 polymorphism (either CT/CC or TT). Participants were exposed to water and beer in 3-minute trials. Dependent variables of main interest were subjective craving for alcohol, subjective arousal and salivary reactivity. Overall, no strong evidence was found for stronger cue-reactivity (= outcome difference between beer and water trial) in the DRD4 L and CNR1 C allele groups. The DRD4 VNTR polymorphism tended to moderate salivary reactivity such that DRD4 L participants showed a larger beverage effect than the DRD4 S participants. Unexpectedly, the DRD4 L participants reported, on average, less craving for alcohol and more subjective arousal during cue exposure, compared with the DRD4 S participants. As weekly alcohol consumption increased, the CNR1 C allele group tended to report more craving for alcohol during the alcohol exposure than the T allele group. The DRD4 and CNR1 polymorphisms do not appear to strongly moderate cue-reactivity after alcohol cue exposure, in male heavy drinkers. [source] GENETIC STUDY: Association between dopamine transporter genotypes and smoking cessation: a meta-analysisADDICTION BIOLOGY, Issue 2 2007John A. Stapleton ABSTRACT This review assessed the evidence of an association between genotypes of the dopamine transporter (DAT1, SLC6A3) 3, untranslated region (3,UTR) variable number of tandem repeats (VNTR) and smoking cessation. Five studies (seven cohorts) comprising 2155 subjects were included in the meta-analysis. All gave data on the number of smokers who had stopped smoking and the number still smoking for those with one or more variant 9-repeat alleles and other genotypes. Three studies (comprising five cohorts) were cross-sectional population surveys and two were smoking cessation treatment programs with follow-up. Four of the five studies (six of the seven cohorts) showed a trend in favor of cessation when the variant 9-repeat allele was present, although only one study showed a statistically significant effect. The pooled odds ratio in favor of a greater likelihood of cessation for the variant 9-repeat allele was 1.15 [95% confidence interval (CI) = 0.97,1.37]. In a more refined analysis where cohorts within studies were treated as separate samples and adjusted odds ratios were used, the overall pooled odds ratio in favor of cessation with the 9-repeat alleles was 1.20 (95% CI = 1.01,1.43). These results support the hypothesis that the DAT1 3,UTR VNTR polymorphism is associated with smoking cessation. One or more variant 9-repeat alleles relative to the more common 10-repeat allele confers a greater likelihood of cessation, indicative of lower dependence on tobacco. The effect was a 20% increase in the odds of cessation for those with a variant allele. [source] Molecular heterogeneity in Yersinia enterocolitica and ,Y. enterocolitica -like' species , Implications for epidemiology, typing and taxonomyFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 1 2005Jugsharan S. Virdi Abstract Yersinia enterocolitica is an extremely heterogeneous species. Serotyping and biotyping have been used extensively, in the past, to study its heterogeneity and epidemiology. Application of methods like ribotyping, pulsed-field gel electrophoresis and a host of other genomic techniques have further revealed molecular heterogeneity in this species. Furthermore, these methods may be used effectively to supplement serotyping and biotyping schema for studying epidemiology of Y. enterocolitica. This is evident from the ability of some of these methods to subtype strains belonging to serogroups O:3, O:9 and O:8 , which are most commonly encountered in human Yersiniosis. Multilocus enzyme electrophoresis and nucleotide sequencing have reiterated the taxonomic relationships of this organism. However there is paucity of information about the molecular heterogeneity of ,Y. enterocolitica -like' species, which need to be addressed in the future. Also, newer techniques such as amplified fragment length polymorphism, VNTR-based typing and multilocus sequence typing should be applied to further understand epidemiology, population structure and evolutionary genetics of Y. enterocolitica and ,Y. enterocolitica -like' species. [source] Additive effect of BDNF and REST polymorphisms is associated with improved general cognitive abilityGENES, BRAIN AND BEHAVIOR, Issue 7 2008F. Miyajima Brain-derived neurotrophic factor (BDNF) is a pleiotropic protein involved in neuronal proliferation, differentiation, synaptic plasticity and survival. Independent studies investigating association between the functional BDNF Val66Met polymorphism and cognitive abilities have reported some conflicting findings, which may reflect inadequate sample size, variation in testing methods, population stratification or the confounding effects of other genes. To test the latter hypothesis, we screened and genotyped polymorphisms in the RE1-silencing transcription factor (REST) gene whose function includes the downregulation of BDNF expression. We identified an exon 4 hexadecapeptide variable number tandem repeat (VNTR) with either four or five copies that was located within a proline-rich domain and investigated a further five single nucleotide polymorphisms (SNPs). Using a cohort of 746 community-dwelling older volunteers, we analysed REST genotype data both independently and in combination with the BDNF Val66Met polymorphism. A haplotype within the REST gene containing the four copy VNTR and a non-synonymous SNP showed a weak but significant association with a higher score of general intelligence (P = 0.05). Analysis of this haplotype and the BDNF Val66Met polymorphism in combination showed a significant interaction (global P -value = 0.0003) with an additive increase in cognitive performance for those possessing the BDNF Val66 allele and the REST haplotype containing the four copy repeat (P = 0.004). The REST haplotypes in combination with the BDNF Met66 polymorphism did not reduce cognitive performance more than the independent influence of the Met66 allele. Our results suggest that investigation of a common REST polymorphism may be necessary to help reduce contrasting reports based around BDNF Val66Met and cognition. [source] Serotonin Transporter Protein Polymorphism and Harm Avoidance Personality in Migraine without AuraHEADACHE, Issue 6 2006Jeong Wook Park MD Objective.,To investigate polymorphisms in the serotonin transporter protein gene and harm avoidance personality dimension in patients with migraine without aura (MWOA). Background.,The serotonin transporter protein is a key modulator of serotonergic synaptic neurotransmission. Two polymorphic regions of the gene for serotonin transporter protein have been found, and are associated with variations in the functional activity of serotonin caused by differing transcriptional efficiency. The harm avoidance (HA) personality trait may also be heritable and associated with altered serotonergic neurotransmitter activity. Design.,We amplified the polymorphism in the promoter of serotonin transporter protein (5-HTTLPR) and the variable number of tandem repeats polymorphism within intron 2 (VNTR) using the polymerase chain reaction and performed genotype polymorphism analyses in 97 patients with MWOA and 100 healthy controls. We investigated serotonin-related personality traits by evaluating the HA personality dimension using a tridimensional questionnaire. Results.,The genotype frequencies and allele distributions of 5-HTTLPR did not differ between patients with MWOA and controls. The VNTR genotype STin2.12/STin2.12 was significantly more common in patients with MWOA (90%) than in controls (77%; P= .017). Patients with MWOA also had HA scores (21.9 ± 6.4) significantly higher than those of controls (16.3 ± 6.1; P < .001). Conclusions.,Serotonergic activity might be involved in the development of MWOA and VNTR of serotonin transporter gene might be one of the genetically contributing factors. [source] Short rare MUC6 minisatellites-5 alleles influence susceptibility to gastric carcinoma by regulating gene,HUMAN MUTATION, Issue 8 2010Jeong-Ah Kwon Abstract The human MUC6 gene, which is reported to be expressed in the stomach and gall bladder, is clustered on chromosome 11p15.5 with other secreted mucins. In this study, the genomic structure of MUC6 has been analyzed and five VNTR (minisatellites; MS1,MS5) were identified. These minisatellites were analyzed in genomic DNA extracted from 1,103 controls, 470 gastric cancer patients, and multigenerational families. Five novel minisatellites were found to be polymorphic and transmitted through meiosis by Mendelian inheritance in families. We evaluated allelic variation in these minisatellites to determine if such variation affected the susceptibility to gastric cancer. A significant association (odds ratio [OR]=7.08) between short rare MUC6,MS5 alleles and relative risks were observed for gastric cancer (95% confidence interval [CI], 1.43,35.19; P=0.005). To investigate the function of minisatellite alleles of MUC6,MS5, we examined the effects on gene expression from luciferase reporters when inserted with minisatellites. Interestingly, when the shortest allele (7TR) was inserted in the promoter, the expression level decreased over 20-fold (P<0.001) in normal and cancer cell lines. Furthermore, the cancer-specific rare allele (TR8) also showed decreased expression levels in cancer cells. Therefore, we suggest that the short rare MUC6,MS5 alleles may be related to cancer development by the regulation of MUC6 expression. Hum Mutat 31:1,8, 2010. © 2010 Wiley-Liss, Inc. [source] A variable number of tandem repeats polymorphism influences the transcriptional activity of the neonatal Fc receptor ,-chain promoterIMMUNOLOGY, Issue 1 2006Ulrich J. H. Sachs Summary The neonatal Fc receptor, FcRn, plays a central role in immunoglobulin G (IgG) transport across placental barriers. Genetic variations of FcRn-dependent transport across the placenta may influence antibody-mediated pathologies of the fetus and the newborn. Sequencing analysis of 20 unrelated individuals demonstrated no missense mutation within the five exons of the FcRn gene. However, a variable number of tandem repeats (VNTR) region within the FcRn promoter was observed, consisting of five different alleles (VNTR1,VNTR5). Alleles with two (VNTR2) and three (VNTR3) repeats were found to be most common in Caucasians (7·5 and 92·0%, respectively). Real-time polymerase chain reaction revealed that monocytes from VNTR3 homozygous individuals express 1·66-fold more FcRn transcript than do monocytes from VNTR2/VNTR3 heterozygous individuals (P = 0·002). In reporter plasmid assays, the VNTR3 allele supported the transcription of a reporter gene twice as effectively as did the VNTR2 allele (P = 0·003). Finally, under acidic conditions, monocytes from VNTR3 homozygous individuals showed an increased binding to polyvalent human IgG when compared with monocytes from VNTR2/VNTR3 heterozygous individuals (P = 0·021). These data indicate that a VNTR promoter polymorphism influences the expression of the FcRn receptor, leading to different IgG-binding capacities. [source] An intron 4 VNTR polymorphism of the endothelial nitric oxide synthase gene is associated with early-onset colorectal cancerINTERNATIONAL JOURNAL OF CANCER, Issue 7 2009Chih-Ching Yeh Abstract Endothelial-derived nitric oxide, which is produced by endothelial nitric oxide synthase (eNOS), may play an important role in colorectal carcinogenesis. However, the putative contribution of common eNOS genetic polymorphisms to colorectal cancer risk remains unknown. We genotyped 3 polymorphisms of eNOS (T-786C, G894T, and intron4b/a) in 727 colorectal adenocarcinoma cases and 736 age- and sex-matched healthy controls in Taiwan. Genotypes of the T-786C and G894T polymorphisms were determined by fluorescence polarization assays and the 27-bp variable number of tandem repeat (VNTR) polymorphism in intron 4 (intron4b/a) was analyzed by PCR. Logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs). Among younger participants (,60 yrs), the intron4a variant genotype was associated with a significantly increased risk of colorectal cancer, compared with the intron4bb genotype (OR = 1.60, 95% CI = 1.04,2.46). In addition, those young individuals bearing a greater number of high-risk genotypes (OR > 1, i.e., CT+TT for T-786C, ba+aa for intron4b/a, and GG for G894T) of eNOS had a higher colorectal cancer risk (ptrend = 0.039). Compared with younger individuals without any putative high-risk genotypes, those with 3 high-risk genotypes had a significantly greater cancer risk (OR = 1.89, 95% CI = 1.04,3.43). Our results suggest that the eNOS intron4b/a polymorphism may contribute to early-onset colorectal cancer risk in the Taiwanese population. © 2008 Wiley-Liss, Inc. [source] Identification of a novel single nucleotide polymorphism in the first tandem repeat sequence of the thymidylate synthase 2R alleleINTERNATIONAL JOURNAL OF CANCER, Issue 9 2007Lisa F. Lincz Abstract Thymidylate synthase (TS) activity is an important determinant of response to chemotherapy with fluoropyrimidine prodrugs and its expression is largely determined by the number of functional upstream stimulatory factor (USF) E-box consensus elements present in the 5,regulatory region of the TYMS gene. Two known polymorphisms in this area, a variable number of tandem repeat (VNTR) consisting of 2 or 3 repeats (2R/3R) of a 28-bp sequence and a further G > C single nucleotide substitution within the second repeat of the 3R, result in genotypes with between 2 and 4 functional repeats in most humans. Here, we identify a further G > C SNP in the first repeat of the TYMS 2R allele, which effectively abolishes the only functional USF protein binding site in this promoter. The frequency of the new allele was found to be 4.2% (95% CI = 1.4,9.6%), accounting for 8.8% (95% CI = 2.9,19.3%) of all 2R alleles in our patient cohort. Thus, we observed that the lowest number of inherited functional binding sites is 1 instead of 2 as previously thought, and could potentially be 0 in a homozygous individual. This would severely decrease TS expression and may have implications for predicting efficacy and toxicity of therapy with commonly used fluorouracil-based therapy regimes. © 2007 Wiley-Liss, Inc. [source] Association of serotonin transporter gene-linked polymorphic region and variable number of tandem repeat polymorphism of the serotonin transporter gene in lichen simplex chronicus patients with psychiatric statusINTERNATIONAL JOURNAL OF DERMATOLOGY, Issue 10 2008Necmettin Kirtak MD Background, The serotonin (5-hydroxytryptamine; 5-HT) is a key neurotransmitter in the central nervous system and a responsible mediator for the itch. Dysregulation of serotonergic pathways has been implicated in the pathogenesis of many complex neuropsychiatric diseases. Objectives, The purpose of this study was to evaluate the relationship between lichen simplex chronicus and dysfunction and serotonin transporter (5-HTT) gene polymorphism. Methods, Thirty-nine patients with lichen simplex chronicus and 61 healthy control subjects were examined. Results, The results for the patients and control subjects were not significantly different (P > 0.05) in long/long (L/L) and long/short (L/S) genotypes of 5-HTT gene-linked polymorphic region (HTTLPR) polymorphism, but short/short S/S genotype was lower in lichen simplex chronicus patients (17.9%) than in controls (42.6%). This difference was statistically significant (P = 0.028). The results for the patients and control subjects were not significantly different in 12/12, 10/12 and 10/10 genotypes of variable number of tandem repeat (VNTR) polymorphism (P > 0.05). Beck depression inventory (BDI) scores and symptom checklist-90-revised (SCL-90) psychotic subscale were overrepresented significantly in the 12/12 genotypes than 10/12 genotypes. State and Trait Anxiety Inventory tests (STAI-I and -II) point averages were not statistically significant (P > 0.05) Conclusion, S/S genotypes of HTTLPR polymorphism in the 5-HTT gene may be related to lichen simplex chronicus and that patients who have 12/12 genotypes of VNTR polymorphism may be affected psychiatrically. [source] Investigation of dopamine receptors in susceptibility to behavioural and psychological symptoms in Alzheimer's diseaseINTERNATIONAL JOURNAL OF GERIATRIC PSYCHIATRY, Issue 9 2009Antonia L. Pritchard Abstract Objective Alzheimer's disease (AD) patients commonly suffer from behavioural and psychological symptoms of dementia (BPSD). A genetic component to the development of BPSD in AD has been supported. Polymorphisms within dopamine receptors DRD1, DRD2, DRD3 and DRD4 have previously been investigated in a few interesting studies that are reviewed here and extended using our patient cohort. Methods Our large cohort of 395 probable AD patients had longitudinal information on the BPSD (Neuropsychiatric Inventory), which was used to dichotomise patients into whether they had ever suffered from a given symptom within the study period, or not. These measures were related to the DRD1 (A-48G), DRD2 (ser311cys; C-ins/del), DRD3 (ser9gly) and DRD4 (VNTR) genotype and allele frequencies. Results Associations were revealed between DRD3 and elation, and between DRD4 with agitation/aggression and with depression; however, these findings do not remain significant after correction for multiple testing. No associations were found with the other genetic variants and these symptoms and no associations were observed between any of the polymorphic variants examined and delusions, hallucinations, psychosis and aberrant motor behaviour. Conclusion Our data, in combination with a review of the literature, reveal a potential role for the VNTR variant of DRD4 in the development of depression in AD patients. The findings presented here need to be replicated in large, well characterised longitudinal cohorts. Copyright © 2009 John Wiley & Sons, Ltd. [source] IL-1 receptor antagonist gene polymorphism in idiopathic recurrent spontaneous abortion in a Chinese Han populationINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 5 2010M. Z. Dai Summary Interleukin-1 receptor antagonist (IL-1Ra) has been supposed to play important roles in pregnancy. The purpose of this study was to evaluate the association between the polymorphisms of IL-1Ra gene (IL1RN) variable number tandem repeat (VNTR) in intron 2 with idiopathic recurrent spontaneous abortion (RSA). Ninety-two RSA patients and hundred normal women with at least one live birth and no history of miscarriage were included in the study. Frequencies of the IL1RN alleles and genotypes were determined. Data revealed that the prevalence of IL1RN allele and genotype was not significant between the RSA and control group (all P > 0.05). Our finding indicated that the polymorphism VNTR of IL1RN gene in intron 2 may not be a risk factor for RSA in the Chinese Han population. [source] Study on VNTR polymorphism of gene IL-1RA in 19 Chinese populationsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2010J. Jiang Summary Earlier studies suggested that a variable number tandem repeat (VNTR) polymorphism in intron 2 of the interleukin-1 receptor antagonist (IL-1RA) gene might be associated with some chronic inflammatory diseases, autoimmune diseases and solid tumours. To study the distribution of this polymorphism in China, 1352 samples were collected from 19 widely distributed Chinese populations. PCR was used to genotype the VNTR. The overall frequencies of allele 1 and allele 2 were 0.913 and 0.064 respectively. The frequency of the allele 2 was significantly different between the northeastern and the northwestern populations. Moreover, the allele frequencies at this locus in three Chinese Han populations were different from that in minority populations. When compared with other populations worldwide, the frequencies of the two alleles in China were not significantly different from those in the Asian and Pacific Islands. However, the prevalence of allele 1 in China was significantly higher, and the prevalence of allele 2 was significantly lower, than those in American and European Caucasians, and the pairwise Fst values reinforced this observation. The differences of the allele frequencies between different regions and within the same region showed that geography and race have important roles in the population differentiation for the IL-1RA gene. In summary, our results provide a valuable reference for population genetic information and future disease association studies in Chinese populations. [source] Molecular analysis of HumDN1 VNTR polymorphism of the human deoxyribonuclease I in systemic lupus erythematosusINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2010Suad AlFadhli Summary Deoxyribonuclease I (DNASE1) may be responsible for the removal of DNA from nuclear antigens at sites of high cell turnover, thus preventing the onset of systemic lupus erythematosus (SLE). The purpose of this study was to screen DNASE1 gene for mutations that may have an effect on susceptibility to develop SLE. DNA was extracted from 76 Kuwaiti SLE patients and 92 race-matched controls. PCR-direct sequencing was used to screen DNASE1 promoter, coding sequence and exon,intron boundaries for mutation. Association of genomic variations was assessed using a Chi-square test. Molecular analysis of the DNASE1 gene did not reveal any mutation. However, a 56-bp repeat was detected in intron4 which was previously reported and named HumDN1. The allelic and genotypic distributions of the HumDN1 VNTR were compared between SLE patients and healthy subjects. Alleles were denoted as 2, 3, 4, 5 and 6 corresponding to the number of repeats of the 56 bp unit. Alleles 4, 5, and 6 showed significant association with SLE. Allele 5 showed the highest association [,2 = 32.57; P , 0.001; OR = 4.16; 95% CI: (2.55,6.79)]. Association of allele 5 was also found at the genotypic level, where genotype 5/5 is more prevalent in SLE subjects as compared with controls (17% versus 9%). We report a significant association of HumDN1 VNTR polymorphism in DNASE1 gene with SLE. Further functional assays needed to assess the effect of this VNTR on DNASE1 activity and its association with SLE. [source] C-reactive protein levels and common polymorphisms of the interleukin-1 gene cluster and interleukin-6 gene in patients with coronary heart diseaseINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 5 2004G. Latkovskis Summary C-reactive protein (CRP) is an inflammatory marker associated with increased cardiovascular risk. Production of CRP is regulated by interleukin (IL)-1,, IL-1 receptor antagonist and IL-6. In 160 patients with coronary heart disease (CHD) confirmed by angiography, we examined the relationship between CRP level and five polymorphisms in genes coding for these cytokines: IL-1B(,511), IL-1B(+3954), a variable number tandem repeat (VNTR) polymorphism in intron 2 of IL-1RN [IL-1RN(VNTR)], IL-6(,174) and IL-6(,572). CRP values were logarithmically normalized (log-CRP) for statistical calculations. In univariate analysis, carrier status for the IL-1B(+3954)T allele and IL-1RN(VNTR) allele 2 [IL-1RN(VNTR)*2] correlated with higher (P < 0.01) and lower (P < 0.05) log-CRP values, respectively. Among the potential confounding factors analysed, smoking, body mass index, total cholesterol (P < 0.05 for all) and diabetes (P = 0.056) were positively correlated with CRP level. After adjustment for non-genetic covariates, CRP levels remained significantly (P < 0.01) higher in carriers of IL-1B(+3954)T than in non-carriers: mean log-CRP (with 95% confidence interval) was 0.443 (0.311,0.574) for CT or TT genotypes compared with 0.240 (0.107,0.373) for the CC genotype, which corresponded to back-transformed CRP levels of 2.77 and 1.74 mg l,1, respectively. Adjusted association was also significant for IL-1RN(VNTR)*2 (P < 0.01), with lower CRP levels in the presence of allele 2: the mean log-CRP value was 0.252 (0.115,0.388) for carriers and 0.421 (0.290,0.552) for non-carriers (CRP 1.79 and 2.64 mg l,1, respectively). When alleles of both polymorphisms were entered into the model simultaneously, the association remained significant for IL-1B(+3954)T (P < 0.05), but not for IL-1RN(VNTR)*2. We conclude that IL-1B(+3954)T is associated with higher CRP levels in patients with CHD, and we found that this association was significant after adjustment for major risk factors. Our data also suggest a possible relationship of IL-1RN(VNTR)*2 with lower CRP levels in the same patients. [source] Recovery of normal autologous myelopoiesis after graft rejection following allogeneic bone marrow transplant for agnogenic myeloid metaplasiaINTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 2 2006S. ALKINDI Summary Allogeneic hematopoietic transplantation is the only currently available therapy that has the potential to cure agnogenic myeloid metaplasia (AMM) or primary myelofibrosis (PMF). Amelioration of fibrosis and eradication of the abnormal clone is thought to occur through the repopulation of marrow by donor-derived hematopoiesis and graft- vs. -host reaction leading to graft vs. tumor effect. We report here a 50-year-old female with AMM/PMF, conditioned with busulfan and cyclophosphamide, who rejected a single locus (HLA-B) mismatched bone marrow transplant from her daughter, but recovered normal autologous hematopoiesis with disappearance of marrow fibrosis and extramedullary hematopoiesis. Variable number tandem repeats (VNTR) analysis showed a gradual loss of donor-derived hematopoietic cells with recovery of autologous hematopoiesis. This case therefore illustrates that eradication of AMM/PMF in this patient with myeloablative chemotherapy combined with a transient allogeneic effect was sufficient to suppress the abnormal stem cell clone associated with AMM/PMF with subsequent cure. [source] Association of interleukin-1 receptor antagonist gene polymorphisms with early onset periodontitis in JapaneseJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 10 2002Hideaki Tai Abstract Background/Aims: Early onset periodontitis (EOP), newly ,aggressive periodontitis', is considered to have genetic basis, which have not been clearly defined. The interleukin-1 (IL-1) gene cluster polymorphism as one of genetic factors may influence the expression of several chronic inflammatory diseases. The aim of this study is to investigate the frequency of single nucleotide polymorphisms (SNPs) in the genes encoding IL-1,, IL-1, and a variable number of tandem repeat (VNTR) polymorphisms in the IL-1 receptor antagonist gene (IL-1RN) in 47 generalized EOP (G-EOP) patients and 97 periodontally healthy controls. Material and methods: All subjects were of Japanese descent and systemically healthy. They were identified according to established clinical criteria. SNPs in the IL-1, (+ 4845) and IL-1, (, 511, + 3954) genes were analyzed by amplifying the polymorphic region using polymerase chain reaction (PCR), followed by restriction-enzyme digestion and agarose gel electrophoresis. IL-1RN (VNTR) polymorphisms were then detected by PCR amplification and fragment size analysis. Results: There was no significant difference in the IL-, (+ 4845) and IL-1, (, 511, +,3954) genotypes and allele frequencies between G-EOP patients and healthy controls. However, the frequency of IL-1RN (VNTR) polymorphic alleles was found to be significantly increased in G-EOP patients (,2 test, P = 0.007; odds ratio = 3.40). Additionally, the carriage rate of IL-1RN (VNTR) polymorphisms was significantly higher in G-EOP patients than in healthy controls (,2 test, P = 0.005; odds ratio = 3.81). Conclusion: These findings suggest that IL-1RN (VNTR) polymorphisms are associated with G-EOP in Japanese. [source] Variable number of tandem repeats polymorphism of platelet glycoprotein Ib , in Chinese people and CC genotype with aspirin sensitivity in patients with cerebral infarctionJOURNAL OF CLINICAL PHARMACY & THERAPEUTICS, Issue 2 2009Y.-Y. Jin MM Summary Background and objective:, To study the prevalence of variable number of tandem repeats (VNTR) polymorphism in platelet membrane glycoprotein (GP) Ib , in a Chinese Han population and to determine the relationship between VNTR polymorphisms and aspirin resistance. Methods:, Three hundred healthy individuals and 110 patients with cerebral infarction volunteered to participate in this study. The genotype status of all participants was determined by polymerase chain reaction-restriction fragment length polymorphism analysis. Platelet aggregation in patients with cerebral infarction receiving aspirin (100 mg/day) for at least 7 days, was measured by optical transmission aggregometry. Results and discussion:, Only three alleles of GP Ib ,, namely, B, C and D, were found. Type A was not found in the Chinese Han participants. Aspirin-sensitive patients were significantly more often of CC genotype than aspirin-semi-responders. Conclusions:, Only three types of alleles B, C and D were detected in the north-eastern region of China. The CC genotype of the VTNR polymorphism in GPIb appears to be more sensitive to the inhibitory action of low-dose aspirin. [source] Variable number of tandem repeats in the growth hormone gene of Sparus aurata: association with growth and effect on gene transcriptionJOURNAL OF FISH BIOLOGY, Issue 2004R. Almuly The GH gene of Sparus aurata(saGH) contains variable number of tandem repeats (VNTR). The hyper-variable minisatellites in the first and third introns segregate in a Mendelian manner and exhibit numerous alleles. Analysis by PCR and sequencing of the two introns in several wild Sparidae species revealed comparable minisatellites with some variations. ,Zoo blot' with the first intron unit as a probe showed this sequence to be characteristic of several families from the Perciformes order. Unexpectedly, a similar minisatellite was found in the first intron of the GH gene in flounder, which belongs to a different order. Transfection of constructs containing a reporter gene and first intron of different length to four cell lines resulted in an inhibitory effect of the longer intron relative to the short intron. A (CA)n microsatellite (saGHpCA) is found in the GH promoter. A similar repeat at the same location is present in GH promoters of several other fish species. High variability (11 alleles) of the saGHpCA was found in a hatchery population. Full-sib family genotyping showed a Mendelian inheritance of these alleles. A significant association was found between allele distribution and body mass in large and average size fishes from a hatchery population. The intron minisatellites may serve as markers for hybrid population and parental assignment. Its presence in families and orders of the higher teleosts may help solving classification uncertainties. Their conservation and inhibitory effect suggest a biological role. The saGHpCA is correlated with growth and may be a good candidate for predicting growth performance. [source] The 3, Part of the Dopamine Transporter Gene DAT1/SLC6A3 Is Associated With Withdrawal Seizures in Patients With Alcohol DependenceALCOHOLISM, Issue 1 2008Yann Le Strat Background: Some studies have reported that the A9 allele of the variable nucleotide tandem repeat (VNTR) of the gene which encodes the dopamine transporter (DAT1/SLC6A3) is associated with alcoholism withdrawal symptoms such as alcohol withdrawal seizures (WSs), whereas others did not. We investigated whether polymorphisms within the DAT1 gene are associated with WS taking into account some of the confounding factors such as the severity of alcohol dependence. Methods: To further assess the role of this gene in WS, we genotyped the VNTR and 7 single nucleotide polymorphisms (SNPs) encompassing the DAT1 gene in a sample of 250 alcohol-dependent subjects (175 men and 75 women), of whom 24% exhibited WSs, taking into account the severity of alcohol dependence. Results: The VNTR is associated with an increased risk of WSs (odd ratio = 3.5; p = 0.019), even when controlling for confounding factors (p = 0.031). As 2 SNPs, in roughly the same location of the gene (namely rs27072 and rs27048), are also associated with WSs, it is possible that the initial association of the VNTR polymorphism was tagging a specific haplotype of this gene. Indeed, in our sample of alcohol-dependent patients, 2 haplotypes were associated with a significantly different risk of WSs. Conclusions: The present study adds evidence for a significant role of the 3, part of the DAT1 gene in WS of alcohol-dependent patients, not only because it is in accordance with previous work, but also because of larger statistical power (as relying on a sample over sampled with the studied phenotype), as it gives a more precise analysis of different SNPs within the DAT1 gene, and as it confirms the association when major potentially confounding factors are taken into account in a logistical regression analysis. [source] Age-related change in the association between a polymorphism in the PER3 gene and preferred timing of sleep and waking activitiesJOURNAL OF SLEEP RESEARCH, Issue 1 2007KAY H. S. JONES Summary The objective of this study was to investigate the effect of age on the association between preferred timing of sleep and waking activities and a coding-region variable number tandem repeat (VNTR) polymorphism in the clock gene PER3. We have previously reported this polymorphism to associate with diurnal preference and delayed sleep phase syndrome (DSPS). Participants (n = 1590; 707 males and 883 females) completed the Horne,Östberg (HÖ) questionnaire for diurnal preference and provided a DNA sample. Overall HÖ scores were plotted against age. The 5% extremes and intermediates were selected for genotyping. Frequencies of the PER3 4- and 5-repeat alleles were examined in separate age groups (18,29, 30,39, 40,49 and 50+ years of age). The 4-repeat allele was significantly more frequent in evening types, and the 5-repeat allele more frequent in morning types (Fisher's exact test, P = 0.016). Analysis in the four age groupings revealed that the strength of this association attenuated with age and was significant only in the youngest group (18,29 years). These results extend our previous finding of an association between the PER3 VNTR and diurnal preference. They also demonstrate that diurnal preference in young people is more closely associated with this polymorphism than it is in other age groups. [source] Genetic structure of avian populations , allozymes revisitedMOLECULAR ECOLOGY, Issue 10 2000P.-A. Crochet Abstract Selection on allozymes has sometimes been advanced as one explanation for the low levels of population differentiation detected in avian populations by the use of enzymatic markers. Comparisons of the amount of population subdivision (estimated by FST values or analogous indices) measured by enzymatic and mitochondrial DNA (mtDNA) markers in birds were seen as evidence for this because mtDNA typically produces a more structured picture of population subdivisions. In fact, when taking into account the smaller effective population size of mtDNA, nuclear and mitochondrial markers give concordant results. Some discrepancies still exist, but I suggest that some might originate from different amounts of nuclear vs. mitochondrial gene flow due to partial reproductive isolation. Variable number of tandem repeat (VNTR) loci do not provide a dramatically different picture of population structures in birds compared to allozymes. Although more tests are needed, such as comparing the amount of genetic structure detected in the same populations with allozymes and microsatellites, the low levels of population subdivision measured with allozymes in birds seem to reflect historical and demographic processes and would not appear to result from any peculiarities of bird enzymatic loci. [source] Polymorphic variable number of tandem repeat (VNTR) loci in the ommastrephid squid, Illex coindetii and Todaropsis eblanaeMOLECULAR ECOLOGY, Issue 7 2000E. Dillane [source] C677T polymorphism of methylenetetrahydrofolate reductase gene affects plasma homocysteine level and is a genetic factor of late-onset Alzheimer's diseasePSYCHOGERIATRICS, Issue 1 2004Tomoyuki KIDA Abstract Background:, Elevated plasma homocysteine levels are known as a risk for atherosclerotic vascular disease and venous thrombosis and have been shown as a risk for late-onset Alzheimer's disease (LOAD). Method:, To examine the effect of genetic factors predisposing to elevated plasma homocysteine levels on the occurrence of LOAD, we determined the genotype of a C677T polymorphism of methylenetetrahydrofolate reductase (MTHFR) gene and a variable number tandem repeat (VNTR) spanning exon 13,intron 13 boundary of cystathionine ,-synthase (CBS) gene in patients with LOAD and community-based control subjects. Results:, Logistic regression indicated that the MTHFR-T allele was a risk for LOAD (P < 0.05), independently from apolipoprotein E-,4 (APOE-,4) allele. Kaplan,Meier tests showed that in APOE-,4 non-carriers, individuals with the MTHFR-TT genotype have occurences of LOAD earlier than those with the MTHFR-CC genotype (P < 0.05). Multiple regression analysis indicates that MTHFR-T allele increases plasma homocysteine levels (P = 0.0002), while the number of X chromosomes decreases (P = 0.01). Plasma homocysteine level was not correlated with age, plasma albumin reflecting nutritional condition, and the dose of APOE-,4 allele. The CBS-20 VNTR allele showed the same trend to increase plasma homocysteine level as the MTHFR-T allele, but a risk effect for LOAD was not evident. Conclusion:, A genetic propensity for elevated plasma homocysteine levels, explained by the MTHFR-T allele encoding defective enzymatic function, is involved in the development of LOAD, particularly in APOE-,4 non-carriers, and that homocysteine metabolism could be a preventive target to LOAD in the elderly. [source] Polymorphism of the promoter region of prostacyclin synthase gene in chronic thromboembolic pulmonary hypertensionRESPIROLOGY, Issue 2 2004Shinya AMANO Objective: Decreased expression of prostacyclin synthase (PGIS) is observed in the lung vasculature of patients with pulmonary arterial hypertension and the biosynthesis of prostacyclin (PGI2) may be impaired in chronic thromboembolic pulmonary hypertension (CTEPH). Whether it is genetically determined or develops as the disease progresses is unclear. A variable-number tandem repeat (VNTR) polymorphism has been detected in the 5,-upstream promoter region of the PGIS gene. It has been demonstrated that the alleles vary in size from three to seven repeats of nine base pairs, and transcriptional activity increased with the number of repeats. The purpose of the present study was to elucidate the association between the VNTR polymorphisms of the PGIS gene and CTEPH in Japanese subjects. Methodology: Ninety patients with CTEPH and 144 control subjects were investigated for the presence of VNTR polymorphisms. Sixty-two blood samples were obtained from CTEPH patients and the plasma concentrations of prostacyclin and thromboxane A2 metabolites were measured. Results: VNTR polymorphisms in the prostacyclin synthase gene were grouped into L alleles (five, six and seven repeats) and S alleles (three and four repeats). The overall distribution of the alleles and genotypes were not significantly different between CTEPH patients and the control subjects. The patients with the LL genotype had higher plasma concentrations of 6-keto-prostaglandin F1, than patients with the LS and SS genotypes. Conclusions: Our results suggested that the specific VNTR polymorphism in the 5,-upstream promoter region of the PGIS gene regulated prostacyclin production, but did not seem to be associated with the development of CTEPH in this patient population. [source] | |||||||||||||||||||||||||||||||