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Results for “single nucleotide polymorphisms”

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At least 757 records · Page 42Linked to original sources
PubMed2005

RANTES gene single nucleotide polymorphisms and expression in patients with chronic hepatitis B virus infection.

BACKGROUND: Regulated on activation, normal T-cell expressed and secreted (RANTES) plays a critical role in T-lymphocyte activation and proliferation. The process is involved in both acute and chronic phases of inflammation. The present study was to ascertain the possible correlations between chronic hepatitis B virus (HBV) infection and the RANTES gene polymorphisms and their expression. METHODS: The study included 130 HBV negative healthy donors and 152 patients with chronic hepatitis B (CHB) virus infection. The polymerase chain reaction (PCR) and restriction fragment length polymorphisms (RFLPs) were used to detect RANTES gene single nucleotide polymorphisms (SNPs). RANTES levels in the platelet depleted plasma were detected by enzyme linked immunosorbent assay (ELISA). RESULTS: RANTES alleles -403G, -28C and In1.1T were the predominant alleles in the subjects studied. No significant correlation was found between CHB infection and the RANTES alleles, while a significant correlation was found between CHB infection and increased RANTES expression in platelet depleted plasma (P < 0.05). CONCLUSIONS: SNPs in RANTES gene do not affect chronic HBV infection or the outcome of interferon-alpha treatment in patients positive for HBV "e" antigen (HBeAg+). However, patients with CHB infection express the higher levels of plasma RANTES, which is thus associated with CHB infection.

Alleles↗
PubMed2004

[Linkage disequilibrium analysis of -31, -511, -1470 single nucleotide polymorphisms in the promoter of IL-1 beta in Chongqing population].

OBJECTIVE: To investigate the frequencies of -31, -511 and -1470 single nucleotide polymorphisms (SNPs) in the promoter of IL-1 beta in Chongqing population and address the question whether they are in linkage disequilibrium (LD). METHODS: One hundred and twelve healthy Chongqing people were enrolled in this study. Polymorphisms at -31 (C>T), -511 (T>C) and -1470 (G>C) of IL-1 beta were genotyped with the method of restriction fragment length polymorphism (RFLP). Haplotype frequencies were evaluated with Arlequine software. Two-point LD analyses were done with the software TransposerV1-0. The P values were determined by Pearson chi square test analysis. RESULTS: Allelic frequencies of IL-1 beta -31, -511 and -1470 were 45.33%, 50.00% and 41.67%, respectively. The dominant haplotypes comprising the three loci were T-C-G (44.1%), C-T-C(40.3%) and C-T-G(8.8%), LD analyses revealed that none of the LD parameters(delta value) was 0. Meanwhile, chi square test showed P<0.005. CONCLUSION: -31, -511 and -1470 loci in the promoter region of IL-1 beta are in strong linkage disequilibrium. And this study provides a basis for searching disease-related IL-1 beta haplotye.

Adult↗
PubMed2004

Novel hairpin-shaped primer assay to study the association of the -44 single-nucleotide polymorphism of the DEFB1 gene with early-onset periodontal disease.

A powerful, cost-effective new method for studying single-nucleotide polymorphisms (SNPs) is described. This method is based on the use of hairpin-shaped primers (HP), which give a sensitive and specific PCR amplification of each specific allele, without the use of costly fluorophore-labeled probes and any post-PCR manipulation. The amplification is monitored in real-time using SYBR Green I dye and takes only 2 h to yield results. The HP assay has a simple design and utilizes a conventional real-time PCR apparatus. The -44 C-->G transversion in the DEFB1 gene (which encodes human beta-defensin 1) has been previously associated with Candida carriage in oral epithelia. In this study, we analyzed the association between early-onset periodontal disease (EOP) and the -44 SNP. We used an HP assay to study the distribution of the -44 SNP in 264 human DNAs obtained from two cohorts of EOP patients and healthy controls from different ethnic backgrounds. The results indicate that the -44 SNP has a similar distribution between EOP and healthy patients, suggesting that it is not associated with the disease.

Alleles↗
PubMed2005

Influence of endothelial nitric oxide synthase T-786C single nucleotide polymorphism on aneurysm size.

OBJECT: Among patients with aneurysms, those with heterozygous (T/C) endothelial nitric oxide synthase (eNOS) T-786C single nucleotide polymorphism (SNP), a mutation reducing endothelial nitric oxide synthesis, are reported to have larger ruptured intracranial aneurysms (IAs) than those with homozygous (C/C or T/T) genotype. The authors tested patients harboring aneurysms for eNOS T-786C SNP in two populations--Japanese and Korean. METHODS: The eNOS T-786C SNP was genotyped through direct sequencing in genomic DNA obtained from 336 Japanese and 191 Korean patients with lAs and 214 Japanese and 191 Korean control volunteers. Differences in genotype frequencies among the various aneurysm sizes were evaluated using the Fisher exact test. There was no significant difference in heterozygous (T/C) eNOS T-786C SNP between aneurysms 5 mm or smaller and those from 6 to 9 mm, and between lesions 5 mm or smaller and those 10 mm or larger in 336 Japanese patients harboring aneurysms--220 with ruptured and 116 with unruptured lesions--and in 191 Korean patients with ruptured aneurysms. CONCLUSION: The eNOS T-786C SNP genotype does not influence the size of aneurysms.

Aged↗
PubMed2005

Single-nucleotide polymorphisms in the promoter region influence the expression of the human follicle-stimulating hormone receptor.

OBJECTIVE: To characterize novel single-nucleotide polymorphisms (SNPs) in the human FSH receptor (FSHR) promoter region. DESIGN: Retrospective and basic research study. SETTING: University hospital. PATIENTS: Women (202 from Germany and 55 from Indonesia) with male or tubal factor infertility undergoing controlled ovarian stimulation for IVF treatment. INTERVENTIONS: None. MAIN OUTCOME MEASURE(S): Frequency, distribution, and correlation with clinical data of the SNPs. Dual luciferase assays and electrophoretic mobility shift assays (EMSA). RESULT(S): We identified two SNPs and three mutations in the promoter region of the human FSHR which could be allocated to positions -29, -37, -114, -123, and -138 upstream of the translational initiation codon. One SNP showed a high incidence (-29: 44%, n = 202), but no correlation with basal FSH serum levels or ovarian response with the SNP at position -29 was found. Luciferase reporter assays, using pGL3 vector constructs, showed that mutations at positions -37 and -138 lead to significantly higher promoter activity. EMSA indicate that putative binding sites for transcription factors are affected by the SNPs. CONCLUSIONS: The newly identified SNPs do not seem to influence clinical parameters substantially, but modulate expression of the FSHR via changes in transcription factor binding sites.

Analysis of Variance↗
PubMed2005

[SNaPshot technique for detection of single-nucleotide polymorphisms (SNPs) in HBV polymerase gene region of HBV gene].

OBJECTIVE: To establish a rapid specific method to identify the single-nucleotide polymorphisms (SNPs) of HBV polymerase gene region which are the methionine residue of the conserved YMDD motif. METHODS: Two specific primers were designed to amplify interested gene region involved in SNPs which were also used as HBV DNA identification. Specific primers of SNaPshot were designed to detect 741A-G (YVDD), 743G-T (YIDD). The different fluorescent dye labeled ddNTP was used to further extend the strand of PCR product and was detected by ABI PRISM 310 Genetic Analyzer. Sera from 13 patients with chronic hepatitis B after lamivudine treatment were analyzed. RESULTS: Aside from mutation of YMDD, there were mutations of 514C-A, 523C-A, 562T-A, 667C-A. The 13 samples were simultaneously tested with SNaPshot and DNA sequencing, the same results were obtained. The method of SNaPshot showed high specificity. CONCLUSION: Mutation of YMDD results in the changes of ATG codon, and there are new ATG codon in the upper strand of YMDD. SNaPshot technique is rapid, specific and accurate for the SNPs monitoring of HBV DNA mutation during lamivudine therapy. Two samples were determined by SnaPshot technique, identifying the co-existence of the mixed wild type and mutant type HBV infection.

Antiviral Agents↗
PubMed2004

Interleukin-10 promoter single-nucleotide polymorphisms as markers for disease susceptibility and disease severity in leprosy.

We have determined IL-10 promoter genotypes of five single-nucleotide polymorphisms (SNPs): T-3575A, A-2849G, C-2763A, -A-1082G and C-819T. The haplotype frequencies were defined in healthy subjects compared to leprosy patients, and analyzed for their occurrence in multi- (MB) vs paucibacillary (PB) as severe and mild forms of leprosy, respectively. Haplotypes defined by three SNP positions (-3575, -2849 and -2763) captured significant differences between controls and patients (P=0.04). The haplotype carrying -3575A, -2849G and -2763C was associated with resistance to leprosy and to the development of severe forms of the disease using either a binomial (controls vs cases, P=0.005, OR=0.35, CI=0.13-0.91) or ordinal (controls vs PB vs MB, P=0.006, OR=0.32, CI=0.12-0.83) model. By contrast, the IL-10 haplotype -3575T/-2849A/-2763C was found to be associated with susceptibility to leprosy per se (P=0.027, OR=2.37, CI=1.04-5.39), but not leprosy type. The data suggest that the IL-10 locus contributes to the outcome of leprosy.

Confidence Intervals↗
PubMed2004

Sub-picomole colorimetric single nucleotide polymorphism discrimination using oligonucleotide-nanoparticle conjugates.

Oligonucleotide-gold nanoparticle conjugates are employed to demonstrate selective colorimetric discrimination of a cystic fibrosis-related genetic mutation in a model oligonucleotide system. Specifically, three strand oligonucleotide complexes are employed, wherein two probe oligonucleotide-gold nanoparticle conjugates are linked together by a third target oligonucleotide strand bearing the chosen CF-related mutation. By monitoring the solution optical absorption behaviour of the complexes as a function of temperature, melting profiles may be accurately acquired and reproducibly compared. Following this method, fully complementary sequences are successfully distinguished from mismatched sequences, with single base mismatch resolution, for the V232D mutation. To extend the detection sensitivity of this oligonucleotide-nanoparticle conjugate assay, a novel and compact LED-based optical monitoring system capable of sub-picomole level colorimetric SNP discrimination is also demonstrated.

Colorimetry↗
PubMed2002

The common single nucleotide polymorphism E23K in K(IR)6.2 sensitizes pancreatic beta-cell ATP-sensitive potassium channels toward activation through nucleoside diphosphates.

E23K, a common polymorphism in the pore-forming subunit K(IR)6.2 of pancreatic beta-cell ATP-sensitive K(+) (K(ATP)) channels, is functionally relevant and thus might play a major role in the pathophysiology of common type 2 diabetes. In this study, we show that in the simultaneous presence of activatory and inhibitory nucleotides, the polymorphism exerts opposite effects on the potencies of these modulators: channel opening through nucleoside diphosphates is facilitated, whereas sensitivity toward inhibition through ATP is slightly decreased. The results support the conclusion that E23K predisposes to type 2 diabetes by changing the channel's response to physiological variation of cytosolic nucleotides, resulting in K(ATP) overactivity and discrete inhibition of insulin release.

Adenosine Diphosphate↗
PubMed2004

Hairpin primers for simplified single-nucleotide polymorphism analysis of Mycobacterium tuberculosis and other organisms.

We describe a novel, simple, rapid, and highly sensitive method to detect single-nucleotide polymorphisms (SNPs) in Mycobacterium tuberculosis and other organisms. Amplification refractory mutation (ARMS) SNP assays were modified by converting the SNP-detecting linear primers in the ARMS assay to hairpin-shaped primers (HPs) through the addition of a 5' tail complementary to the 3' end of the linear primer. The improved ability of these primers to detect SNPs in M. tuberculosis was compared in a real-time PCR with SYBR-I green dye. Linear primers resulted in incorrect or indeterminate allele designation for 6 of the 13 SNP alleles tested in seven different SNP assays, while HPs determined the correct SNP in all cases. We compared the cycle threshold differences (DeltaC(t)) between the reactions containing primer-template matches and the reactions containing primer-template mismatches (where a larger DeltaC(t) indicates a more robust assay). The use of HPs dramatically improved the mean DeltaC(t) values for the SNP assays (7.6 for linear primers and 11.2 for HPs). We designed 98 different HP assays for SNPs previously associated with resistance to the antibiotic isoniazid to test the large-scale utility of the HP approach. Assay design was successful in 72.4%, 83.7%, 88.8%, and 92.9% of the assays after one to four rounds of assay design, respectively. HP SNP assays are simple, sensitive, robust, and inexpensive. These advantages favor the application of this technique for SNP assays of M. tuberculosis and other organisms.

Base Sequence↗
PubMed2000

Identification of single nucleotide polymorphisms in human DNA repair genes.

Variation in gene coding sequence represents a significant factor in predisposition to disease, including cancer. Variants of some DNA repair genes (e.g. MLH1, MSH2 and MSH6) are known to predispose to cancer. We identified single nucleotide polymorphisms (SNPs) in five DNA repair genes in 142 healthy individuals using a DNA sequencing protocol optimized for the direct detection of single nucleotide polymorphisms. This approach, called the heterozygote sequencing protocol (HSP), enables moderate-scale population surveys of SNPs. HSP uses fluorescently tagged primers and exploits the large dynamic range and low background of automated fluorescent sequencing. HSP may be used for any sequence that can be amplified by PCR. A total of 12 SNP variants in MGMT, ERCC1, CDK7, CCNH and XRCC4 were identified, 11 at polymorphic frequencies, with an average frequency of 0.22 (95% confidence interval 0.20-0.24). Among the 82 individuals for whom complete SNP profiles were available, no one person carried the GenBank reference sequence for all five genes. The extensive heterogeneity observed in these five genes is intriguing. All variants are in Hardy-Weinberg equilibrium, although the meaning of this equilibrium is unclear. Using this approach, possible associations of sequence variation, and hence of variation in DNA repair, with disease risk can be assessed.

Adolescent↗