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Allelic Frequencies (allelic + frequency)
Selected AbstractsAllelic frequencies of HPA-1 to 5 human platelet antigens in patients infected with hepatitis C virusJOURNAL OF MEDICAL VIROLOGY, Issue 4 2009Camila Fernanda Verdichio-Moraes Abstract Studies have suggested that hepatitis C virus (HCV) may infect not only hepatocytes but may also be carried by platelets. Platelets express more than 20 polymorphic antigenic determinants on their surface, which are called human platelet antigens (HPA). To determine the allele frequency of the HPA-1 to -5 in patients infected with HCV, blood samples were collected from 257 blood donors for the control group and from 191 patients infected with HCV. DNA was isolated and amplified for genes HPA-1 to -4 using PCR Sequence Specific Primers (PCR-SSP) and HPA-5 using PCR-Restriction Fragment Length Polymorphism (PCR-RFLP). The allelic and genotypic frequency of HPA-5a in patients infected with HCV was found to be significantly lower (P,<,0.05) than in the controls, and HPA-5b from patients infected with HCV was significantly higher (P,<,0.05) than in controls. The increase in HPA-5b allelic frequency in HCV infection may indicate a possible association between HCV infection and HPAs. J. Med. Virol. 81:757,759, 2009 © 2009 Wiley-Liss, Inc. [source] Angiotensin-converting enzyme gene insertion/deletion polymorphism frequency in normotensive children with a positive family history of essential hypertensionJOURNAL OF PAEDIATRICS AND CHILD HEALTH, Issue 12 2009Lale Camci Aim: To evaluate the possible relationship between blood pressure (BP) and angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism in normotensive children with a positive family history of essential hypertension (EHT). Material and Methods: Three hundred seventy-six randomly selected normotensive schoolchildren (147 boys, 229 girls) between the ages of seven and 17 years were enrolled. Children were subdivided into a ,first-degree relative group' and a ,second-degree relative group' according to the presence of EHT in parents or grandparents, respectively. BP was measured twice from the right arm and the systolic BP, diastolic BP and mean BP were recorded. ACE gene I/D polymorphism was performed from all studied children and frequency od DD, ID and ID allele were analysed in each study group. Results: Allelic frequencies of the DD genotype of the ACE gene were higher in children with a positive history in the first- (36.2%) and second-degree (38.3%) relatives for EHT than the controls (30.7%) (P < 0.05 for both). Children with a positive family history of EHT and a DD genotype, had significantly higher SBP, DBP and MBP levels (P < 0.05) than the children with ID or II genotypes. Conclusion: We found that the ACE gene DD genotype was common and that BP levels were higher in Turkish children with a positive family history of EHT and DD genotype. Because the presence of DD allele might be the one of the potential contributor of EHT pathogenesis, further studies needed in large cohort for long term follow-up for EHT in children with DD allele. [source] Genetic variation among populations of Pythium irregulare in southern AustraliaPLANT PATHOLOGY, Issue 5 2000P. R. Harvey Isolates of Pythium irregulare were sampled from seven cereal crops throughout South Australia to determine the extent of genetic diversity within this pathogen and the scale of genetic differentiation among populations. Data derived from 29 individual restriction fragment length polymorphism (RFLP) loci differentiated 54 DNA fingerprints among the 92 isolates analysed. Some isolates had two alleles at several RFLP loci and were scored as heterozygous. One such isolate was selfed in vitro and segregation ratios in the progeny were not significantly different from those expected for allelic variation in a diploid. These data provided evidence that outcrossing occurs within P. irregulare and may contribute to the high level of genetic variation within the species (DT = 0·502). Allelic frequencies were significantly different among all seven populations and GST values showed significant genetic differentiation between populations. The average genetic identity among populations was low and hierarchical cluster analysis provided no clear evidence that populations formed geographically related groups. These analyses indicate low levels of interpopulation gene flow within P. irregulare and imply that population differentiation results from genetic drift. [source] An INSIG2 Polymorphism Affects Glucose Homeostasis in Sardinian Obese Children and AdolescentsANNALS OF HUMAN GENETICS, Issue 5 2010Patrizia Zavattari Summary Allelic variants of a single nucleotide polymorphism (SNP), rs7566605, located approximately 10 kb upstream of the INSIG2 gene have been found in association with body weight and with other clinical features related to obesity in some populations but not in others. Our objective was to test the association of this SNP in obese children and adolescents from the genetically isolated population of Sardinia. We tested the association of rs7566605 with body mass index (BMI) and with serum glucose and insulin concentrations and a surrogate measure of insulin resistance (HOMA-IR) in a cohort of 747 Sardinian obese children and adolescents. A case control analysis was performed using 548 ethnically-matched healthy controls. Allelic frequencies of the SNP were similar between patients and controls. Mean glucose and insulin concentration and mean HOMA-IR values were significantly higher in patients carrying the CC genotype than in the CG and GG carriers. In the patients with impaired fasting glucose (IFG) and/or impaired glucose tolerance (IGT), allele C was significantly more frequent than in controls. Although INSIG2 polymorphisms do not consistently associate with BMI, the observation of an association with glucose concentration would support a role for this gene in the metabolic complications of obesity. [source] CTG repeats at the myotonic protein kinase gene in a healthy Chilean population sampleACTA NEUROLOGICA SCANDINAVICA, Issue 5 2009F. Amenabar Objectives,,, To study the variability at the myotonic dystrophy protein kinase (DMPK) gene in a Chilean sample of healthy people. DM1 is an autosomal dominant disorder caused by an expansion of a (CTG) repeat at the 3,-UTR of the gene DMPK. Healthy individuals have alleles under 35 repeats and diseased individuals have over 50. Methods,,, Genotyping the number of (CTG) repeats at this gene in a sample of healthy Chilean people. Results,,, Allele frequencies were significantly different from those of other populations. The most frequent allele was with five repeats. The frequency of larger alleles (>18 CTG repeats) was 11%, close to the European frequency (12%) and higher than the Japanese (8%) and Aboriginal Pehuenche samples (8%). Conclusions,,, Allelic frequencies in the Chilean sample studied were intermediate between those of the two ancestral populations (European and Pehuenche). [source] Caucasian patients with type 2 diabetes mellitus have elevated levels of monocyte chemoattractant protein-1 that are not influenced by the ,2518 A,G promoter polymorphismDIABETES OBESITY & METABOLISM, Issue 5 2005B. Zietz Aim:, To investigate the association of serum levels and the ,2518 A,G promoter polymorphism of the gene for chemokine monocyte chemoattractant protein-1 (MCP-1), a major chemoattractant of monocytes and activated lymphocytes, with metabolic parameters as well as insulin, leptin and the cytokines tumour necrosis factor-, (TNF-,) and interleukin-6 (IL-6) in 534 Caucasian patients with type 2 diabetes mellitus. Methods:, MCP-1 concentrations were measured by enzyme-linked immunosorbent assay. MCP-1 genotyping was performed by RFLP analysis in a subset of 426 patients. Results:, Two hundred and thirty-one (54.2%) patients were homozygous for the wildtype allele (AA), 156 (36.6%) were heterozygous (AG) and 39 (9.2%) were homozygous for the mutated allele (GG). Allelic frequency was similar to non-diabetic populations (wildtype allele A: 0.73; mutated allele G: 0.27). MCP-1 mean concentrations and percentiles were substantially higher in non-diabetic populations but were not influenced by the genotype (AA: 662.0 ± 323.0 pg/ml; AG: 730.6 ± 491.4 pg/ml; GG: 641.2 ± 323.8 pg/ml). MCP-1 serum levels and genotypes were only marginally related to hormones (insulin and leptin) and cytokines (TNF-, and IL-6). Conclusions:, This is the first study providing MCP-1 levels, percentiles and genotype frequency in a large and representative cohort of patients with type 2 diabetes mellitus. Compared to the literature, MCP-1 levels were found to be substantially higher in patients with type 2 diabetes mellitus. In contrast, genotype frequencies were similar compared to those in non-diabetic patients and were not related to MCP-1 levels. The mechanisms behind these elevated MCP-1 serum levels in type 2 diabetes are not to be explained by simple associations with hormones, cytokines or genotypes. [source] Association of HLA-DRB1*07 and DRB1*04 to citrus red mite (Panonychus citri) and house dust mite sensitive asthmaCLINICAL & EXPERIMENTAL ALLERGY, Issue 11 2000S.-H. Cho Background Specific IgE responses to allergens provide useful models for evaluating the genetic factors that control human immune responses. A recent survey demonstrated that the citrus red mite (Panonychus citri, CRM) is the most important allergen in the development of asthma in citrus farmers. Objective The aim of this study was to evaluate whether susceptibility or resistance to CRM-induced asthma was associated with HLA-DRB1 gene. Methods DNAs were extracted from two groups of unrelated Korean adults living around citrus farms: (1) Ninety-one adults with CRM-sensitive asthma; and (2) 98 exposed, healthy nonatopic controls. Genotypes of HLA-DRB1 alleles were carried out using PCR-based methods. Results Allelic frequency of HLA-DRB1*07 was higher in the CRM-sensitive asthmatics compared to the controls (17.6% vs 4.1%, Pc = 0.01). Conversely, the frequency of DRB1*04 was lower in the CRM-sensitive asthmatics compared to the controls (19.8% vs 40.8%, Pc = 0.01). No significant difference was found in the distributions of the other HLA-DRB1 gene-encoded antigens between the two groups. Conclusion HLA-DRB1 genes may be involved in the development of CRM-induced asthma. In addition, HLA-DR7 may increase, and DR4 decrease, the risk of developing the asthma in CRM-exposed adults. [source] Patterns of isozyme variation as indicators of biogeographic history in Pilgerodendron uviferum (D. Don) FlorínDIVERSITY AND DISTRIBUTIONS, Issue 2 2002A. C. Premoli Abstract. The effects of Pleistocene glaciations on the genetic characteristics of the most austral conifer in the world, Pilgerodendron uviferum, were analysed with specific reference to the hypothesis that the species persisted locally in ice-free areas in temperate South America. It was expected that genetic variation would decrease with latitude, given that ice fields were larger in southern Patagonia and thus refugia were probably located towards the northern distributional limit of the species as suggested by the fossil record. In addition, an increase in among-population genetic divergence was expected with increasing distance to putative glacial refugia. We examined the relationship between location and within-population variability indices of 20 Pilgerodendron populations derived from isozyme analyses. We analysed possible refugia hypotheses by the distribution of allele frequencies using multivariate discriminant analysis. The degree of genetic differentiation with geographical distance between all population pairs was investigated by Mantel tests. Results indicated that Pilgerodendron populations are highly monomorphic, probably reflecting past population bottlenecks and reduced gene flow. Southernmost populations tend to be the least genetically variable and were therefore probably more affected by glacial activity than northern ones. Populations located outside ice limits seem to have been isolated during the glacial period. The presence of centres of genetic diversity, together with the lack of a significant correlation between genetic and geographical distances and the absence of geographical patterns of allelic frequencies at most analysed alleles, may indicate that Pilgerodendron did not advance southward after the last glaciation from a unique northern refugium, but spread from several surviving populations in ice-free areas in Patagonia instead. [source] HETEROZYGOTE EXCESS IN SMALL POPULATIONS AND THE HETEROZYGOTE-EXCESS EFFECTIVE POPULATION SIZEEVOLUTION, Issue 9 2004Franclois Balloux Abstract It has been proposed that effective size could be estimated in small dioecious population by considering the heterozygote excess observed at neutral markers. When the number of breeders is small, allelic frequencies in males and females will slightly differ due to binomial sampling error. However, this excess of heterozygotes is not generated by dioecy but by the absence of individuals produced through selfing. Consequently, the approach can also be applied to self-incompatible monoecious species. Some inaccuracies in earlier equations expressing effective size as function of the heterozygote excess are also corrected in this paper. The approach is then extended to subdivided populations, where time of sampling becomes crucial. When adults are sampled, the effective size of the entire population can be estimated, whereas when juveniles are sampled, the average effective number of breeders per subpopulations can be estimated. The main limitation of the heterozygote excess method is that it will only perform satisfactorily for populations with a small number of reproducing individuals. While this situation is unlikely to happen frequently at the scale of the entire population, structured populations with small subpopulations are likely to be common. The estimation of the average number of breeders per subpopulations is thus expected to be applicable to many natural populations. The approach is straightforward to compute and independent of equilibrium assumptions. Applications to simulated data suggest the estimation of the number of breeders to be robust to mutation and migration rates, and to specificities of the mating system. [source] Genetic polymorphisms of drug-metabolizing enzymes CYP2D6, CYP2C9, CYP2C19 and CYP3A5 in the Greek populationFUNDAMENTAL & CLINICAL PHARMACOLOGY, Issue 4 2007Kostas Arvanitidis Abstract The aim of the present study was to determine the prevalence of the most common allelic variants of the polymorphic cytochrome P450 (CYP) enzymes CYP2D6, CYP2C9, CYP2C19 and CYP3A5 and to predict the genotype frequency for each polymorphism in the Greek population. DNA isolated from peripheral blood samples derived from 283 non-related Greek ethnic subjects was used to determine the frequency of CYP2D6*3, CYP2D6*4, CYP2C9*2, CYP2C9*3 and CYP3A5*3 allelic variants by the polymerase chain reaction (PCR)-restriction fragment length polymorphism method, CYP2C19*2 and CYP2C19*3 with allelic specific amplification (PCR-ASA), and CYP2D6*2 (gene duplications) by long PCR analysis. The allelic frequencies (out of a total of 566 alleles) for CYP2D6*3 and CYP2D6*4, were 2.3% and 17.8%, respectively, while gene duplications (CYP2D6*2) were found in 7.4% of the subjects tested. For CYP2C9*2 and CYP2C9*3 polymorphisms the allelic frequencies were 12.9% and 8.13% respectively. For CYP2C19, the *2 polymorphism was present at an allelic frequency of 13.1%, while no subjects were found carrying the CYP2C19*3 allele. Finally, the CYP3A5*3 allele was abundantly present in the Greek population with an allelic frequency of 94.4%. Overall our results show that the frequencies of the common defective allelic variants of CYP2C9, CYP2C19 and CYP3A5 in Greek subjects are similar to those reported for several other Caucasian populations. Finally, a high prevalence of CYP2D6 gene duplication among Greeks was found, a finding that strengthens the idea that a South/North gradient exists in the occurrence of CYP2D6 ultrarapid metabolizers in European populations. [source] H intragenic polymorphisms and haplotype analysis in the ornithine transcarbamylase (OTC) gene and their relevance for tracking the inheritance of OTC deficiency,,HUMAN MUTATION, Issue 5 2002Consuelo Climent Abstract The "private" nature of most mutations causing ornithine transcarbamylase (OTC) deficiency makes mutation identification in the patients difficult. Further, the PCR-amplification technology generally used for the genetic diagnosis of the deficiency misses large deletions in carrier females. Intragenic OTC polymorphisms may allow detection of these deletions and may represent an alternative to mutation detection for prenatal diagnosis and carrier identification in families with a history of inherited OTC deficiency. A new highly informative polymorphism (allele frequencies, 0.66/0.34) in intron 3 of the OTC gene (IVS3-39_40insT) is reported here, and allelic frequencies of 16 additional intragenic OTC polymorphisms are determined in 133-35 (average per polymorphism, 72) unrelated chromosomes. In addition to the novel polymorphism, only three of the studied polymorphisms (Lys46Arg, allelic frequency 0.68/0.32; IVS3-8A>T, 0.34/0.66; Gln270Arg, 0.97/0.03) are confirmed to be informative. These provide, together with another reported polymorphism (IVS4-7A>G; reported allelic frequency 0.71/0.29; Plante and Tuchman, 1998), a set of highly valuable markers of the OTC gene. Nevertheless, the combined informativity of the studied polymorphisms is limited by their distribution in only four haplotypes with one of them predominating (65% of the sampled chromosomes). Although this haplotype composition may be restricted to the Iberian peninsula (the origin of the samples), more informative polymorphisms are required to increase the diagnostic potential and, particularly, to identify large deletions affecting OTC gene exons 5-10, where only one polymorphism of weak diagnostic value is known. © 2002 Wiley-Liss, Inc. [source] Susceptibility to refractory ulcerative colitis is associated with polymorphism in the hMLH1 mismatch repair geneINFLAMMATORY BOWEL DISEASES, Issue 6 2004Siro Bagnoli MD Abstract The hMLH1 gene lies in the linkage susceptibility region to inflammatory bowel disease (IBD) on 3p21. A single nucleotide polymorphism, 655A>G, in exon 8 of the gene causes an I219V change in the MLH1 protein. To test whether hMLH1 may confer susceptibility to ulcerative colitis (UC), we investigated an association between the 655A>G polymorphism and the disease. DNA-based technologies were used to analyze the 655A>G polymorphism in 201 UC patients and 126 healthy ethnically matched controls. The comparison of the allelic frequencies of the 655A>G polymorphism in UC patients and healthy controls did not show significant differences. However, genotype frequencies at the hMLH1 655 position were found to be significantly different when patients with and without refractory UC were compared. This was mainly attributable to a higher level of homozygosity for the G allele in refractory UC patients. Almost 5 times as many (4.9 times) refractory UC patients carried the GG genotype compared with nonrefractory patients (P < 0.0001). The present study provides evidence that the hMLH1 gene is involved in genetic susceptibility to refractory UC. If confirmed by other studies, the GG genotype at position 655 of the hMLH1 gene may represent a useful predictive factor for the clinical management of UC patients. [source] The effects of RANTES/CCR5 promoter polymorphisms on HIV disease progression in HIV-infected KoreansINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2008D. H. Jang Summary Recent studies have reported that two single nucleotide polymorphisms (SNPs) in the RANTES gene promoter region, ,403G/A and ,28C/G, are associated with a slower rate of decline in CD4+ T-cell number, whereas genetic polymorphisms within the CCR5 promoter are linked to acceleration of AIDS progression. In this study, we investigated the distribution of SNPs in the RANTES and CCR5 promoters and the association between these SNPs and HIV-1 disease progression in HIV-infected Koreans. Twenty-seven long-term non-progressors (LTNPs), 29 AIDS patients and 39 HIV-uninfected persons were enrolled in this study. SNPs for the RANTES and CCR5 promoters were determined by polymerase chain reaction,restriction fragment length polymorphism (PCR-RFLP) and a direct sequencing method. In the analysis of RANTES promoter polymorphisms, the genotypic and allelic frequencies of the RANTES ,28G mutation were significantly lower in HIV-infected patients than in HIV-uninfected persons (P = 0.005 and P = 0.001, respectively). The genotypic frequencies of RANTES ,28G and ,403A mutations did not differ significantly between LTNPs and AIDS patients. The frequencies of three CCR5 promoter polymorphisms, designated 59029 G/A, 59353T/C, and 59402G/A, did not differ significantly between HIV-uninfected and HIV-infected patients. However, the allelic frequency of CCR559353C was significantly higher in AIDS patients than in LTNPs (P = 0.003). These results suggest that RANTES-28G and CCR5 59353C mutations might be associated with HIV infection or pathogenesis in the Korean population. [source] Lack of association between HLA-A, -B and -DRB1 alleles and the development of SARS: a cohort of 95 SARS-recovered individuals in a population of Guangdong, southern ChinaINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2008P. Xiong Summary Severe acute respiratory syndrome (SARS), caused by infection with a novel coronavirus (SARS-CoV), was the first major novel infectious disease at the beginning of the 21st century, with China especially affected. SARS was characterized by high infectivity, morbidity and mortality, and the confined pattern of the disease spreading among the countries of South-East and East Asia suggested the existence of susceptible factor(s) in these populations. Studies in the populations of Hong Kong and Taiwan showed an association of human leucocyte antigen (HLA) polymorphisms with the development and/or severity of SARS, respectively. The aim of the present study was to define the genotypic patterns of HLA-A, -B and -DRB1 loci in SARS patients and a co-resident population of Guangdong province, southern China, where the first SARS case was reported. The samples comprised 95 cases of recovered SARS patients and 403 unrelated healthy controls. HLA -A, -B and -DRB1 alleles were genotyped using polymerase chain reaction with sequence-specific primers. The severity of the disease was assessed according to the history of lung infiltration, usage of assisted ventilation and occurrence of lymphocytopenia. Although the allelic frequencies of A23, A34, B60, DRB1*12 in the SARS group were slightly higher, and A33, -B58 and -B61 were lower than in the controls, no statistical significance was found when the Pc value was considered. Similarly, no association of HLA alleles with the severity of the disease was detected. Thus, variations in the major histocompatibility complex are unlikely to have contributed significantly to either the susceptibility or the severity of SARS in the population of Guangdong. [source] No relationship observed between human p53 codon-72 genotype and HPV-associated cervical cancer in a population group with a low arginine-72 allele frequencyINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 3 2007V. A. Govan Summary Infection with high-risk human papillomavirus (HR-HPV) is a necessary but not a sufficient event in the development of cervical cancer, as most infections regress without intervention. Thus, genetic host factors and cellular immune responses could be potential modifiers for the risk of developing cervical cancer. In particular, p53 is considered as the most critical tumour suppressor gene and is involved in regulating cell division. The polymorphism on p53, which encodes either a proline or an arginine amino acid residue at codon 72, has been reported as a possible risk factor for cervical disease. This polymorphism has been shown to differentially affect the efficiency of degradation of p53 protein mediated by HR-HPV E6 oncoprotein. Women with histologically proven cancer of the cervix (n = 111) and hospital-based controls (n = 143) were included in this study. The patients and controls were from the Western Cape Province in South Africa. Genotyping of the p53 polymorphism was conducted using polymerase chain reaction and restriction fragment-length polymorphism method. The distributions of the allelic frequencies were stratified in both patients and controls into two South African ethnic population groups. In this study, we observed no association between the distribution of p53 polymorphism and susceptibility to cervical cancer in the Western Cape Province populations (P = 0.466). However, the frequency of the Pro/Pro residue at codon 72 was increased in the South African population when compared to Caucasians, Indians and Portuguese population groups. Notably, as the distribution of the Pro/Pro at codon 72 of p53 gene was significantly different (P < 0.05) between the control groups of South Africa and other population groups. This result suggests that ethnic disparity may influence the levels of p53 produced. [source] No association of SUMO4 M55V with autoimmune diabetes in Asian-Indian patientsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2007S. K. Sedimbi Summary Autoimmune diabetes [type 1 diabetes mellitus (T1DM), latent autoimmune diabetes in adults (LADA) and part of malnutrition-related diabetes] has been shown to have genetic predisposition. Studies in IDDM 5 have lead to the discovery of a novel polymorphism 163 A,G, of SUMO4 (small ubiquitin-related modifier) gene, associated with risk to T1DM in Asians, but not in Caucasians. We studied patients with T1DM (n = 134), patients with LADA (n = 101), patients with malnutrition-modulated diabetes mellitus (n = 66) and patients with fibrocalculous pancreatic diabetes (n = 43) and healthy controls subjects (n = 114) from Cuttack, India. Polymerase chain reaction,sequence-specific primer (PCR-SSP) was used to amplify the 163 A,G sequences. Restriction fragment length polymorphism (RFLP) was performed using restriction enzyme Taq I (PCR-RFLP). Differences in the allelic frequencies of the A and the G alleles were tested statistically using Fisher's exact test or chi-squared test wherever appropriate. P -values were considered significant when equal to or less than 0.05. No significant association was detected between SUMO4 M55V and T1DM susceptibility in Asian-Indians. Comparison of the A and G alleles with HLA DR3-DR4 did not result in any significant P -values. No significant association was found between SUMO4 M55V and LADA or malnutrition-related diabetes mellitus (MRDM). Our results show that Asian-Indians with T1DM are different from other Asian populations. Asian-Indians show more similarity to Caucasians with respect to the association of SUMO4 M55V variant in T1DM. Association studies on Asian-Indian patients with LADA and MRDM showed no significant difference in the presence of the A and the G alleles when compared to healthy controls. [source] TCRBV3S1 and TCRBV18 gene segment polymorphisms in Brazilian Caucasoid and Black populationsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2002C. Dresch Summary The T-cell receptor (TCR) repertoire plays an important role in shaping specific immune responses. Genetic polymorphisms at the TCR locus, in both constant and variable regions, seem to represent an important mechanism for generating inter-individual and inter-population differences. Considering the scarcity of immune parameters characterized for normal human populations, we decided to determine the frequency of two TCRBV polymorphisms (located in the TCRBV3S1 and TCRBV18 gene segments) in two ethnically distinct groups of the general Brazilian population. Both polymorphisms are related to the expression of these segments at the T-cell surface and can consequently modulate the T-cell repertoire, potentially modifying the capacity of a given individual to develop an immune response. These DNA polymorphisms were analysed in material obtained from adult, normal South-American Caucasoid and Black individuals. A total of 139 individuals were analysed for the TCRBV3S1 and 141 for the TCRBV18 gene segment polymorphisms. The data indicated statistically significant differences in allelic frequencies for the two ethnic groups analysed, suggesting that any correlation between TCR usage or T-cell repertoire and development of a given disease should take in account the ethnic origin of the population studied. [source] Association of vitamin D receptor genotypes with early onset rheumatoid arthritisINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2001J. R. Garcia-Lozano The presence of certain vitamin D receptor (VDR) genotypes has been associated with low bone mineral density (BMD) in elderly populations as well as with accelerated bone loss in patients with rheumatoid arthritis (RA). In the present study, VDR genotypes from 120 Spanish patients with RA were investigated. Three VDR gene polymorphisms (BsmI, ApaI and TaqI) were investigated using polymerase chain reaction followed by enzymatic digestion. The distributions of VDR allelic frequencies were similar in patients and controls and therefore no influence of VDR polymorphisms on rheumatoid arthritis susceptibility could be demonstrated. However, in an analysis of the clinical features of the different VDR-related genetic subgroups, the BB/tt genotype, defined by the BsmI and TaqI restriction site polymorphisms, was identified to be weakly associated with an early onset RA in female patients. This VDR genotype has been associated with a low BMD level in various studies. When patients were stratified according to the presence of the shared HLA epitope SE, it was found that SE + female patients bearing the BB/tt genotype showed the earliest disease onset. The mechanisms by which the VDR polymorphism is associated with RA is unknown, but they could be related to the immunoregulatory properties of vitamin D. [source] Isozyme variation and recent biogeographical history of the long-lived conifer Fitzroya cupressoidesJOURNAL OF BIOGEOGRAPHY, Issue 2 2000A. C. Premoli Abstract Aim Palaeoenvironmental records of Pleistocene glaciation and associated vegetation changes in Patagonia have led to the hypothesis that during the last glacial maximum (LGM) tree species survived locally in favourable habitats. If present populations originated from spread from only one refugium, such as an ice-free area of coastal Chile (Single Refugium hypothesis), we would expect that eastern populations would be genetically depauperate and highly similar to western populations. In contrast, if the ice cap was not complete and tree species persisted in forest patches on both slopes of the Andes (Multiple Refugia hypothesis), we would expect a greater degree of genetic divergence between populations either on opposite sides of the Cordillera (Cordillera Effect scenario) or towards its present-day southern distributional limit where the ice sheet reached its maximum coverage (Extent-of-the-Ice scenario). Location We tested this refugia hypothesis using patterns of isozyme variation in populations sampled over the entire modern range of the endemic conifer Fitzroya cupressoides (Mol.) Johnst. (Cupressaceae) in temperate South America. Methods Fresh foliage was collected from twenty-four populations and analysed by horizontal electrophoresis on starch gels. Results Twenty-one putative loci were reliably scored and 52% were polymorphic in at least one population. Populations from the eastern slope of the Andes were genetically more variable than those from the western slope; the former had a greater mean number of alleles per locus, a larger total number of alleles and rare alleles, and higher polymorphism. Genetic identities within western populations were greater than within eastern populations. Discriminant analyses using allelic frequencies of different grouping schedules of populations were non significant when testing for the Single Refugium hypothesis whereas significant results were obtained for the Multiple Refugia hypothesis. Main conclusions Our results indicate that present Fitzroya populations are the result of spreading from at least two, but possibly more, glacial refugia located in Coastal Chile and on the southern flanks of the Andes in Argentina. [source] Association of idiopathic generalized epilepsy with polymorphisms in the neuronal nicotinic acetylcholine receptor subunitsJOURNAL OF CLINICAL LABORATORY ANALYSIS, Issue 2 2007Cheng-Chun Lee Abstract Idiopathic generalized epilepsy (IGE) refers to a common group of epilepsies, and genetic factors play an important role in the pathogenesis of these disorders. Mutations in CHRNA4 and CHRNB2 are associated with some cases of familial epilepsies classified as autosomal-dominant nocturnal frontal lobe epilepsies. We aimed to evaluate whether polymorphisms of CHRNA4 and CHRNB2are associated with IGE. A total of 75 children with IGE and 80 normal control subjects were included in the study. Each genetic polymorphism was typed by polymerase chain reaction (PCR)-based restriction analysis. The genotypes and allelic frequencies of each polymorphism were compared between the IGE patients and controls. The results showed that genotype and allelic frequency for CHRNB2 did not differ significantly between the groups. However, the genotype proportion of the CHRNA4 (Ser543Ser) gene in both groups was significantly different (P<0.0001). The T allele frequency was significantly higher (P=0.0126) in patients with IGE compared to healthy controls. The odds ratio (OR) for developing IGE in individuals with the CHRNA4 (Ser543Ser)-T homozygote was 4.9 (95% confidence interval (CI), 1.71,14.04) compared to individuals with two copies of the CHRNA4 (Ser543Ser)-C allele. This study demonstrates that the CHRNA4 gene may be one of the susceptibility factors for IGE. J. Clin. Lab. Anal. 21:67,70, 2007. © 2007 Wiley-Liss, Inc. [source] Molecular analysis of thiopurine S -methyltransferase alleles in Taiwan aborigines and TaiwaneseJOURNAL OF CLINICAL PHARMACY & THERAPEUTICS, Issue 1 2006H-F. Lu MS Summary Background:, Thiopurine S -methyltransferase (TPMT) is a cytosolic enzyme involved in the metabolism of these thiopurine drugs. Methylation of thiopurine drugs by TPMT competes with the formation of their active 6-thioguanine nucleotide metabolite, thereby potentially modulating the therapeutic and toxic effects of these drugs. Objective:, To analyze the thiopurine S -methyltransferase allelic frequencies in Taiwan aborigines and Taiwanese. Methods:, We used polymerase chain reaction,restriction fragment length polymorphism method to determine the allelic frequencies of TPMT variants (TPMT*1,TPMT*8) in 409 Taiwan aborigines and 117 Taiwanese. Results and discussion:, The results showed that the allelic frequencies of TPMT*1 were 99·88% and 98·72% for Taiwan aborigines and Taiwanese respectively. The allelic frequencies of TPMT*3C were 0·12% and 1·28% for Taiwan aborigines and Taiwanese respectively. No TPMT*2, 3A, 3B, 3D and 4,8 were found in these populations. Conclusion:, Our results provide useful information for using thiopurine drugs in these populations. [source] Molecular analysis of the thiopurine S-methyltransferase alleles in Bolivians and TibetansJOURNAL OF CLINICAL PHARMACY & THERAPEUTICS, Issue 5 2005H.-F. Lu MT Summary Background:, Thiopurine drugs are used as immunosuppressant or cytotoxic drugs. Thiopurine S-methyltransferase (TPMT) methylates and thereby modulates the therapeutic and toxic effects of these drugs. The activity of TPMT is affected by genetic polymorphism of TPMT alleles, and these alleles have not been studied in Tibetans and Bolivians. Objectives:, To analyse the TPMT allelic frequencies in Tibetans and Bolivians. Methods:, We developed an inexpensive method for collecting blood and extracting genomic DNA. Genomic DNA was extracted from blood spots of 50 Tibetans and 115 Bolivians. The frequencies of allelic variants of TPMT gene (TPMT*1 to TPMT*8) were determined using polymerase chain reaction-restriction fragment length polymorphism technique. Results:, The allelic frequencies of TPMT*1 were 99 and 93·48% for Tibetans and Bolivians, respectively. The corresponding allelic frequencies of TPMT*3A were 0 and 6·52% and those of TPMT*3C were 1·0 and 0%. No TPMT*2, 3B, 3D, 4,8 were found in these two populations. Conclusions:, As with Caucasian populations, TPMT*3A is the most prevalent mutant allele in Bolivians. Our results may be of value in helping to guide the prescription of thiopurine drugs in these populations. [source] Resolving Paternity Relationships Using X-Chromosome STRs and Bayesian NetworksJOURNAL OF FORENSIC SCIENCES, Issue 4 2007Didier Hatsch Ph.D. Abstract:, X-chromosomal short tandem repeats (X-STRs) are very useful in complex paternity cases because they are inherited by male and female offspring in different ways. They complement autosomal STRs (as-STRs) allowing higher paternity probabilities to be attained. These probabilities are expressed in a likelihood ratio (LR). The formulae needed to calculate LR depend on the genotype combinations of suspected pedigrees. LR can also be obtained by the use of Bayesian networks (BNs). These are graphical representations of real situations that can be used to easily calculate complex probabilities. In the present work, two BNs are presented, which are designed to derive LRs for half-sisters/half-sisters and mother/daughter/paternal grandmother relationships. These networks were validated against known formulae and show themselves to be useful in other suspect pedigree situations than those for which they were developed. The BNs were applied in two paternity cases. The application of the mother/daughter/paternal grandmother BN highlighted the complementary value of X-STRs to as-STRs. The same case evaluated without the mother underlined that missing information tends to be conservative if the alleged father is the biological father and otherwise nonconservative. The half-sisters case shows a limitation of statistical interpretations in regard to high allelic frequencies. [source] Interleukin-27 polymorphisms are associated with inflammatory bowel diseases in a Korean populationJOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, Issue 10 2009Chun-Shi Li Abstract Background and Aims:, The cytokine interleukin (IL)-27 is composed of two subunits, Epstein,Barr virus-induced gene 3 (EBI3) and p28, and IL-27 is a novel IL-12 family member that mediates between the innate and adaptive immune systems. We previously identified four polymorphisms in the human IL-27 gene and we suggested that the polymorphism of IL-27 is associated with the susceptibility to asthma. IL-27 transcripts are significantly elevated in active Crohn's disease (CD) but not in ulcerative colitis (UC). To determine whether these IL-27 single nucleotide polymorphisms are associated with the susceptibility to inflammatory bowel disease (IBD), the genotype and allelic frequencies of the IL-27 polymorphisms were analyzed between the IBD patients and the healthy controls. Methods:, Genotype analysis of the IL-27 gene was performed by the single-base extension (SBE) method. The haplotype frequencies of IL-27 for multiple loci were estimated using the expectation maximization (EM) algorithm. Results:, The genotype frequencies of the g.-964A > G polymorphism in the IBD patients were significantly different from those of the healthy control group (P = 0.001). In both the UC and CD patients, the genotype frequencies of the g.-964A > G polymorphism were also significantly different from the frequencies of the healthy control group (P = 0.009). The frequencies of the AGT and GGT haplotypes were significantly different between the healthy control group and the IBD patient group (P = 0.00004 and 0.021, respectively). Conclusion:, Our results suggest that the g.-964A > G polymorphism of the IL-27 gene located on the IBD1 locus might be associated with the susceptibility to IBD. [source] Association of vitamin D receptor gene polymorphisms in Chinese patients with generalized aggressive periodontitisJOURNAL OF PERIODONTAL RESEARCH, Issue 3 2008S. Li Background and Objective:, The clinical features suggest that genetic factors may have a strong influence on susceptibility to aggressive periodontitis. The aim of this study was to investigate the association of vitamin D receptor gene polymorphisms with generalized aggressive periodontitis in Chinese patients. Material and Methods:, A restriction fragment length polymorphism (RFLP) for 10,438,141 C to T (rs1544410, BsmI), 10,382,063 A to G (rs731236, TaqI), 10,382,143 C to A (rs7975232, ApaI) and 10,416,201 A to G (rs2228570, FokI) of vitamin D receptor gene was analysed by polymerase chain reaction, followed by digestion with restriction enzymes and gel electrophoresis. The genotypes of 51 generalized aggressive periodontitis patients and 53 periodontally healthy control subjects were analysed. The genotypic and allelic frequencies of each polymorphism site for the patients and control subjects were compared. Results:, The distribution of vitamin D receptor FokI genotypes and alleles between the two groups was significantly different (p = 0.043 and p = 0.012, respectively). The F allele seemed to increase the susceptibility of aggressive periodontitis (odds ratio = 2.02, 95% confidence interval = 1.16,3.50) in Chinese patients. There was no significant difference in the genotype distribution or the allele frequencies of vitamin D receptor BsmI, ApaI and TaqI between two groups. Conclusion:, The study indicates that FokI polymorphism of vitamin D receptor gene might be associated with generalized aggressive periodontitis in Chinese patients. In addition, the carriage of F allele increases the risk of developing generalized aggressive periodontitis. [source] The Relationship Between Serotonin Receptor 1B Polymorphisms A-161T and Alcohol DependenceALCOHOLISM, Issue 9 2009Sheng-Yu Lee Background:, Several studies have suggested that the serotonin receptor 1B gene (5HT1B) may be important in the pathogenesis of alcohol dependence (alcoholism; ALC; AD). We examined whether 5HT1B gene A-161T polymorphisms (rs130058) are a susceptibility factor for total AD and subgroups of AD. We further explored correlation of this 5HT1B gene variant between anxiety,depression alcoholism (ANX/DEP ALC) and antisocial alcoholism (antisocial ALC) subgroups because of the high comorbidity of anxiety,depression, antisocial personality disorder, and AD. Methods:, We recruited 522 Han Chinese in Taiwan for this study: 322 AD patients and 200 controls. The patient group was recruited primarily from medical teaching hospitals; patients with antisocial alcoholism were recruited from Taiwanese prisons. Individuals with AD were classified into 3 homogeneous clinical subgroups,pure alcoholism (pure ALC), ANX/DEP ALC, and antisocial ALC,using DSM-IV diagnosis. The 5HT1B gene A-161T polymorphism was determined using PCR,RFLP. Results:, No significant differences in genotypic and allelic frequencies were found between controls and the total AD group or between controls and the 3 AD subgroups. However, there were significant differences in the 5HT1B gene A-161T polymorphism at both the genotype and allelic levels between the ANX/DEP ALC and antisocial ALC subgroups. Conclusions:, This study suggests that the 5HT1B gene A-161T polymorphism alone is not a risk factor for increasing susceptibility to either AD or its subtypes. However, 5HT1B gene A-161T polymorphisms might be one of the common genetic factors between the ANX/DEP ALC and antisocial ALC subgroups. [source] Polymorphism in the Interleukin-1 Receptor Antagonist Gene Is Associated With Alcoholism in Spanish MenALCOHOLISM, Issue 10 2000Isabel J. Pastor Background: A polymorphism located in intron 2 of the interleukin-1 receptor antagonist (IL1RN) gene recently has been associated with the development of hepatic fibrosis in Japanese alcoholics. In the present study, we analyzed whether there is an association between this polymorphism, alcoholism, and alcoholic liver disease in a Spanish male population of alcoholics. Methods: The IL1RN genotype was assessed by polymerase chain reaction by using oligonucleotides that flank a variable nucleotide tandem repeat polymorphism located in intron 2 of this gene in 90 male alcoholic patients from Spain; 30 alcohol-dependent men, 30 alcohol abusers, and 30 alcoholics with liver cirrhosis. We also studied 40 healthy subjects. Results: The distribution of the IL1RN allelic frequencies in Spanish healthy subjects is similar to that previously reported in White subjects. However, the A1 allele is overrepresented in Spanish alcoholics when compared with healthy subjects. No significant differences in allelic frequencies were observed between alcoholics with liver cirrhosis and alcoholics without liver disease or between alcohol-dependent subjects and alcohol abusers. Conclusion: The presence of the A1 allele of the IL1RN gene is associated with a higher risk of alcoholism in Spanish men. [source] HLA DRB1*15-DPB1*05 haplotype: a susceptible gene marker for isocyanate-induced occupational asthma?ALLERGY, Issue 7 2006S.-H. Kim Background:, There has been no study for evaluating the associations of human leukocyte antigen (HLA) class I and II alleles with toluene diisocyanate (TDI)-induced asthma in an Asian population. Objective:, The aim of this study was to investigate a susceptible or protective marker of HLA class I and II alleles in TDI-induced asthma. Methods:, Fifty-five patients with TDI-induced asthma patients (group I) showing positive responses on TDI bronchoprovocation test, 47 asymptomatic exposed subjects (group II) and 95 unexposed healthy nonatopic controls (group III) were enrolled in our study. HLA class I and II genotyping was done by the direct DNA sequencing method. Results:, The allelic frequency of C*09 (15.5%) was significantly higher in group I than in group III (6.8%, P = 0.019), but this statistical significance disappeared after correction was made for multiple comparisons. On two-locus and three-locus haplotype analysis, the allelic frequency of HLA DRB1*15-DPB1*05 in group I (10.6%) was significantly higher than that of group II (0%, P = 0.001) and group III (2.5%, P = 0.003). The allelic frequencies of HLA A*02-DRB1*15, A*02-DQB1*06, B*62-C*09 and A*02-DRB1*15-DQB1*06 were significantly higher in group I (8.5%, 10.3%, 8.2% and 6.8%, respectively) than those allelic frequencies of group III (1.3%, P = 0.002; 1.6%, P = 0.001; 0.6%, P < 0.0001; 0%, P < 0.0001, respectively). The allelic frequencies of HLA DQB1*06-DPB1*05 and DRB1*15-DQB1*06-DPB1*05 were significantly higher in group I (16.0% and 10.5%) than those in group II (2.5%, P = 0.001; 0%, P = 0.001), while the frequencies of DRB1*09-DPB1*05 and DRB1*09-DQB1*0303-DPB1*05 were significantly lower in group I (0% and 0%) than those of group II (7.4%, P = 0.004; 7.5%, P = 0.004). These differences remained statistically significant even after the correction for multiple comparisons. Conclusions:, The HLA haplotype DRB1*15-DPB1*05 can be a susceptibility gene marker for the development of TDI-induced asthma among the exposed workers in the Korean population. [source] Genetic structure and gene flow in French populations of two Ostrinia taxa: host races or sibling species?MOLECULAR ECOLOGY, Issue 20 2007T. MALAUSA Abstract Most models of ecological speciation concern phytophagous insects in which speciation is thought to be driven by host shifts and subsequent adaptations of populations. Despite the ever-increasing number of studies, the current evolutionary status of most models remains incompletely resolved, as estimates of gene flow between taxa remain extremely rare. We studied the population genetics of two taxa of the Ostrinia genus , one feeding mainly on maize and the other on mugwort and hop , occurring in sympatry throughout France. The actual level of divergence of these taxa was unknown because the genetic structure of populations had been investigated over a limited geographical area and the magnitude of gene flow between populations had not been estimated. We used 11 microsatellite markers to investigate the genetic structure of populations throughout France and the extent of gene flow between the two Ostrinia taxa at several sites at which they are sympatric. We observed clear genetic differentiation between most populations collected on the typical respective hosts of each taxon. However, populations displaying intermediate allelic frequencies were found on hop plants in southern France. Individual assignments revealed that this result could be accounted for by the presence of both taxa on the same host. Gene flow, estimated by determining the proportion of hybrids detected, was low: probably < 1% per generation, regardless of site. This indicates that the two Ostrinia taxa have reached a high level of genetic divergence and should be considered sibling species rather than host races. [source] Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionistsMOLECULAR ECOLOGY, Issue 18 2007A. Bonin Abstract Recently, the amplified fragment length polymorphism (AFLP) technique has gained a lot of popularity, and is now frequently applied to a wide variety of organisms. Technical specificities of the AFLP procedure have been well documented over the years, but there is on the contrary little or scattered information about the statistical analysis of AFLPs. In this review, we describe the various methods available to handle AFLP data, focusing on four research topics at the population or individual level of analysis: (i) assessment of genetic diversity; (ii) identification of population structure; (iii) identification of hybrid individuals; and (iv) detection of markers associated with phenotypes. Two kinds of analysis methods can be distinguished, depending on whether they are based on the direct study of band presences or absences in AFLP profiles (,band-based' methods), or on allelic frequencies estimated at each locus from these profiles (,allele frequency-based' methods). We investigate the characteristics and limitations of these statistical tools; finally, we appeal for a wider adoption of methodologies borrowed from other research fields, like for example those especially designed to deal with binary data. [source] | |||||||||||||||||||||||||||||||||||||