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At least 523 records · Page 29Linked to original sources
PubMed2005

A single nucleotide polymorphism in the extracellular domain of TRAIL receptor DR4 at nucleotide 626 in gastric cancer patients in Japan.

Death receptor 4 (DR4) is a member of the tumor necrosis factor-related apoptosis-inducing ligand receptor genes. A single nucleotide polymorphism (Thr or Arg, C or G) in the extracellular domain was reported to be associated with a risk of lung cancer, head and neck cancer, and bladder cancer. In this study, we examined the association between the DR4 polymorphism and gastric cancer. The Thr/Thr, Thr/Arg and Arg/Arg genotypes were found in 250 (91.2%), 23 (8.4%) and 1 (0.4%) of 274 gastric cancer patients and in 317 (92.2%), 21 (6.1%) and 6 (1.7%) of 344 control subjects, respectively. The OR of Thr/Arg or Arg/Arg genotype did not reveal a significantly enhanced risk of 1.13 (95% CI, 0.63-2.00) compared to Thr/Thr genotype, suggesting that the DR4 polymorphism did not modify the risk of gastric cancer. In patients, no association between the genotype and clinicopathological characteristics (depth of invasion, lymph node metastasis, distant metastasis, stage and grade of differentiation) of gastric carcinoma was found. DR4 was constantly expressed in gastric carcinoma, but not in non-neoplastic gastric epithelium in immunohistochemistry. In conclusion, a Thr to Arg single nucleotide polymorphism in the extracellular domain of DR4 could not be associated with the development and progression of gastric cancer.

Adenocarcinoma↗
PubMed2004

Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis melo L.).

A search was performed for single-nucleotide polymorphisms (SNP) and short insertions-deletions (indels) in 34 melon (Cucumis melo L.) expressed sequence tag (EST) fragments between two distantly related melon genotypes, a group Inodorus 'Piel de sapo' market class breeding line T111 and the Korean accession PI 161375. In total, we studied 15 kb of melon sequence. The average frequency of SNPs between the two genotypes was one every 441 bp. One indel was also found every 1666 bp. Seventy-five percent of the polymorphisms were located in introns and the 3'untranslated regions. On average, there were 1.26 SNPs plus indels per amplicon. We explored three different SNP detection systems to position five of the SNPs in a melon genetic map. Three of the SNPs were mapped using cleaved amplified polymorphic sequence (CAPS) markers, one SNP was mapped using the single primer extension reaction with fluorescent-labelled dideoxynucleotides, and one indel was mapped using polyacrilamide gel electrophoresis separation. The discovery of SNPs based on ESTs and a suitable system for SNP detection has broad potential utility in melon genome mapping.

Chromosome Mapping↗
PubMed2003

[Detection of single-nucleotide polymorphisms in insulin receptor substrate-2 gene 3'-untranslated region by denaturing high-performance liquid chromatography].

OBJECTIVE: To explore the use of denaturing high-performance liquid chromatography (DHPLC) in detecting single-nucleotide polymorphisms(SNPs) of insulin receptor substrate-2(IRS-2) gene 3'-untranslated region (3'-UTR). METHODS: We detected the SNPs and mutation of IRS-2 gene 3'-UTR sequence, with polymerase chain reaction (PCR), DHPLC, single-strand conformation polymorphism (SSCP), and DNA sequence analysis respectively in 30 Type 2 diabetic subjects and 30 healthy controls. RESULTS: The SNPs of IRS-2 gene 3'-UTR in 4 patients with Type 2 diabetes mellitus were detected by PCR-DHPLC and were identified by DNA sequencing. CONCLUSION: DHPLC is a rapid and automated technology, which is simpler and more accurate for detecting longer fragment of DNA than SSCP. The present method lays a foundation for further studying the relationship between the mutation of IRS-2 gene 3'-UTR and Type 2 diabetes mellitus.

3' Untranslated Regions↗
PubMed2004

A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other.

In this report, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. This method provides a useful alternative to more computationally intensive permutation tests. A user-friendly interface (SNPSpD) for performing this correction is available online (http://genepi.qimr.edu.au/general/daleN/SNPSpD/). Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor "loadings" after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.

Gene Frequency↗
PubMed2005

Allelic diversity in the TGFB1 regulatory region: characterization of novel functional single nucleotide polymorphisms.

Altered TGF-beta1 expression due to polymorphisms affects a wide variety of normal cellular and disease processes such as T cell activation and proliferation, tumor progression, and asthma. In this study, a comprehensive examination of function and diversity was undertaken for the TGFB1 promoter region and exon 1 (-2,665 to +423). The known TGF-beta1 promoter was extended to encompass 463 bases by the identification of a strong enhancer activity for a distal segment (-2,665 to -2,204). Ten novel polymorphisms and 14 novel alleles were identified. Most single nucleotide polymorphisms (SNPs) appear to be randomly associated except c.-768_-769insC and c.+74G > C and a set of five novel polymorphisms present in a single allele in persons of African descent. The TGFB1 alleles clustered into three phylogenetic groups based on the common functional SNPs c.-1347C > T (commonly known as -509C-T) and c.+29T > C (commonly known as +869T-C) suggesting three phenotypic groups. Two SNPs unique to African-Americans affect the TGFB1 regulatory region. The c.-1287G > A SNP in the promoter alters the binding affinity of two unidentified transcription factor complexes which translates into a significant difference in reporter gene expression and the c.-387C > T SNP in the 5' UTR alters the binding of Stimulating protein 1 and 3. Thus, TGFB1 possesses a highly polymorphic, extensive regulatory region that likely impacts the pathogenesis of numerous TGF-beta1 related diseases.

Black or African American↗
PubMed2003

Application of fluorescence polarization to enzyme assays and single nucleotide polymorphism genotyping: some recent developments.

This article describes some recent developments in the field of fluorescence polarization (FP) as applied to enzyme assays and single nucleotide polymorphism (SNP) genotyping. First, we present our recent progress on the application of fluorescence polarization to high throughput screening (HTS). We show how the use of a 2-thiopyridinone-based, mixed disulfide biotinylation reagent can shorten the assay time of our recently reported kinase assay method based on thiophosphorylation and biotinylation from several hours to a few minutes. We also summarize our recent findings on a new approach for HTS of kinases, proteases and phosphatases based on the use of a cationic poly-amino acid such as polyarginine. We show how the careful selection of the polyarginine concentration and the ionic strength of the solution during the FP measurement allow one to expand the range of substrates that can be assayed. Both of these methods are valuable additions to the existing techniques for HTS. Most importantly, both of these methods can be applied to the assay of kinases without the need for any antibodies. In the area of genomics, we present some results from our studies on a new single nucleotide polymorphism typing approach based on the polymerase catalyzed extension of 3' fluorescein labeled primers. Contrary to our initial expectations, we observed that the enzymatic extension of these primers results in a significant decrease of the fluorescence polarization value. Possible explanations of this phenomenon are discussed.

Animals↗
PubMed2000

SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease.

There has been great interest in the prospects of using single-nucleotide polymorphisms (SNPs) in the search for complex disease genes, and several initiatives devoted to the identification and mapping of SNPs throughout the human genome are currently underway. However, actual data investigating the use of SNPs for identification of complex disease genes are scarce. To begin to look at issues surrounding the use of SNPs in complex disease studies, we have initiated a collaborative SNP mapping study around APOE, the well-established susceptibility gene for late-onset Alzheimer disease (AD). Sixty SNPs in a 1.5-Mb region surrounding APOE were genotyped in samples of unrelated cases of AD, in controls, and in families with AD. Standard tests were conducted to look for association of SNP alleles with AD, in cases and controls. We also used family-based association analyses, including recently developed methods to look for haplotype association. Evidence of association (P</=.05) was identified for 7 of 13 SNPs, including the APOE-4 polymorphism, spanning 40 kb on either side of APOE. As expected, very strong evidence for association with AD was seen for the APOE-4 polymorphism, as well as for two other SNPs that lie <16 kb from APOE. Haplotype analysis using family data increased significance over that seen in single-locus tests for some of the markers, and, for these data, improved localization of the gene. Our results demonstrate that associations can be detected at SNPs near a complex disease gene. We found that a high density of markers will be necessary in order to have a good chance of including SNPs with detectable levels of allelic association with the disease mutation, and statistical analysis based on haplotypes can provide additional information with respect to tests of significance and fine localization of complex disease genes.

Age of Onset↗
PubMed2004

Thyroid papillary carcinoma: preliminary evidence for a germ-line single nucleotide polymorphism in the Fas gene.

The expression of Fas in thyroid tumours and Graves' disease was analysed by mRNA transcript expression. As compared with unaffected thyroid tissue, Fas expression was enhanced in Graves' disease, adenomas, and papillary and follicular carcinomas. This pattern was also reflected in immunohistochemical studies. The PCR single-strand conformational polymorphism (SSCP) method and DNA sequencing were used to analyse Fas exons 1-9. The study was carried out on five different histotypes of thyroid tumours (n=93) and tissue from Graves' disease patients. As compared with a group of healthy blood donors (n=64), a significant association (P=0.006) emerged between papillary thyroid carcinoma and a silent single nucleotide polymorphism (SNP, 988C-->T) in exon 7 of the Fas gene. Other forms of thyroid pathology were not associated with the above polymorphism. Patients with neoplasia showed the same SNP in tumour tissue, in the unaffected contralateral thyroid lobe, and in peripheral blood cells. Thus, the 988C-->T polymorphism appeared to be of germ-line origin.

Adenoma↗
PubMed2005

SNPs (single nucleotide polymorphisms) detection based on the formation of cholic-acid binding DNA aptamer.

Simple and rapid methods for the detection of single nucleotide polymorphisms (SNPs) are required to analyze the genetic information. We have previously isolated DNA aptamers that bind to cholic acid by an in vitro selection method. A common feature of the sequences of the aptamers was that they included a secondary structure, a three-way junction, in which three stems were connected at the junction. It was also revealed that three-way junctions with fully matched three stems bind cholic acid whereas single-base substitutions at the junction lose binding affinity completely. Here we report a new method for the detection of single nucleotide mutations that is based on the formation of fully matched three-way junctions which bind to cholic acid.

Aptamers, Nucleotide↗
PubMed2005

Single-nucleotide polymorphisms in the p53 pathway.

A cell culture assay has been developed that detects and validates single-nucleotide polymorphisms (SNPs) in genes that populate the p53 pathway. One hundred thirteen EBV-transformed human B-lymphocyte cell lines obtained from a diverse population were employed to measure the apoptotic response to gamma radiation. Each cell line undergoes a reproducible, characteristic frequency of apoptosis, and the response of the population forms a normal distribution around a median of 35.5% apoptosis with a range from 12% to 58% apoptosis. Polymorphisms in the AKT1 and Perp genes significantly affect the frequency of apoptosis. The assay can detect both racial and sexual dimorphisms in these genes and has the ability to demonstrate epistatic relationships within the p53 pathway. The cell lines used in this assay provide biological materials to explore the molecular basis of the polymorphisms.

Black or African American↗
PubMed2006

Association of a non-synonymous single-nucleotide polymorphism of DNASEI with SLE susceptibility.

OBJECTIVES: To investigate the association of a non-synonymous single-nucleotide polymorphism (SNP) in DNASEI with susceptibility to systemic lupus erythematosus (SLE) and the production of autoantibodies to nuclear antigens. METHODS: The Gln244Arg (rs1053874) SNP was studied in 276 SLE patients and in 368 healthy controls of Spanish ancestry. Its relationship with SLE susceptibility, serum DNase I activity, anti-ribonucleoprotein (RNP), anti-double-stranded DNA (dsDNA), anti-nucleosome and anti-single-stranded DNA (ssDNA) antibodies was determined. RESULTS: An association of the Gln244Arg SNP with SLE susceptibility that followed a recessive genetic model (P=0.002) was found. The GG genotype was more common in SLE patients (59.8%) than in controls (47.3%). However, the Gln244Arg genotype did not correlate with DNase I activity in sera from SLE patients or from controls. In addition, the Gln244Arg SNP did not influence autoantibody titres significantly. CONCLUSION: The association of the Gln244Arg SNP with SLE susceptibility indicates that common polymorphisms in DNASEI play a role in the genetics of SLE. However, the lack of effect of the Gln244Arg SNP on serum DNase I activity calls into question the direct involvement of this specific SNP.

Antibodies, Antinuclear↗
PubMed2002

A single nucleotide polymorphism in the matrix metalloproteinase-3 promoter enhances breast cancer susceptibility.

PURPOSE: Matrix metalloproteinases (MMPs) are likely to be involved in invasion and metastasis of several tumors by degrading the extracellular matrix. A single adenine insertion/deletion polymorphism (5A/6A) in the MMP-3 promoter region causes the elevation of transcriptional level and local expression of MMP-3. The aim of this pilot study was to evaluate the impact of this 5A/6A polymorphism on susceptibility and metastasis in breast cancer. EXPERIMENTAL DESIGN: Genotyping for 5A/6A polymorphism was performed in 86 Italian women operated on for breast cancer and followed for 6-30 months (median follow-up, 21 months). A control population of 110 Italian age-matched tumor-free women was also genotyped for the same polymorphism. The 1G/2G gene promoter polymorphism for MMP-1 was additionally tested. RESULTS: The frequency of 5A allele was higher in the breast cancer group than in controls (P = 0.035; odds ratio, 1.53; 95% confidence interval, 1.02-2.29). The breast cancer group was divided into a group without metastasis (M-) and a group that had developed metastasis (M+). At the time of diagnosis, the 5A allele was more prevalent in the M+ group than in controls (P = 0.010; odds ratio, 1.96; 95% confidence interval, 1.16-3.30). The difference between M- patients and controls did not reach statistical significance (P = 0.37). This study was not able to demonstrate any statistical differences with respect to 1G/2G polymorphism between controls and cases and between M+ and M- subgroups. CONCLUSIONS: Although this should be considered only as a pilot study, our results suggest that the presence of 5A polymorphism at the MMP-3 promoter region may represent an unfavorable prognostic feature in breast cancer patients associated with more invasive disease.

Adenocarcinoma↗
PubMed2005

Single-nucleotide polymorphism versus microsatellite markers in a combined linkage and segregation analysis of a quantitative trait.

Increasingly, single-nucleotide polymorphism (SNP) markers are being used in preference to microsatellite markers. However, methods developed for microsatellites may be problematic when applied to SNP markers. We evaluated the results of using SNPs vs. microsatellites in Monte Carlo Markov chain (MCMC) oligogenic combined segregation and linkage analysis methods. These methods were developed with microsatellite markers in mind. We selected chromosome 7 from the Collaborative Study on the Genetics of Alcoholism dataset for analysis because linkage to an electrophysiological trait had been reported there. We found linkage in the same region of chromosome 7 with the Affymetrix SNP data, the Illumina SNP data, and the microsatellite marker data. The MCMC sampler appears to mix with both types of data. The sampler implemented in this MCMC oligogenic combined segregation and linkage analysis appears to handle SNP data as well as microsatellite data and it is possible that the localizations with the SNP data are better.

Chromosome Mapping↗
PubMed2004

Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population.

The tumor necrosis factor (TNF) and TNF receptor (TNF-TNFR) superfamily plays crucial roles in immune regulation and host immune responses. The superfamily has been also associated with many immune-mediated diseases such as asthma, rheumatoid arthritis, inflammatory bowel disease, and diabetes. In order to investigate genetic variants of the TNF-TNFR superfamily, a total of 63 known single nucleotide polymorphisms (SNPs) in the coding region (cSNPs) of the TNF-TNFR superfamily genes were selected from the public SNP database. Among 63 cSNPs tested in this study, only 24 SNPs (38%) were validated to be polymorphic in the Korean population by primer extension-based SNP genotyping. By means of the new enhanced single strand conformational polymorphism (SSCP) method, we also identified a total of 78 SNPs, including 48 known SNPs and 30 novel SNPs, in the 44 human TNF-TNFR superfamily genes. The newly discovered SNPs in the TNF-TNFR superfamily genes revealed that the Korean population had very different patterns of allele frequency compared with African or white populations, whereas Korean allele frequencies were highly similar to those of Asian (correlation coefficient r = 0.88, p < 0.046). A higher similarity of allele frequency was observed between Korean and Japanese populations (r = 0.90, p < 0.001). The validated SNPs in the TNF-TNFR superfamily would be valuable for association studies with several immune-mediated human diseases.

Adult↗
PubMed2004

[Single nucleotide polymorphisms of growth hormone receptor gene in Chinese Han ethnic population].

OBJECTIVE: To analyze the distribution of single nucleotide polymorphisms (SNP) of growth hormone receptor (GHR) gene in Chinese Han ethnic population. METHODS: The sample of 106 unrelated healthy Chinese Hans was studied by sequencing exons of the GHR gene to detect SNP. RESULTS: There were 6 SNP spots identified in exon 6 and exon 10. Five of them were found in exon 10, and one in exon 6. There were differences between the allele frequencies of the SNP we found and those in the NCBI database. The highest heterozygosity of the SNP was found at 1630 A > C (I526L), which was 47.6%. The SNP 1483 A > C (P477T), 1735 A > C (P561T) and 1319 G > T (C422F) had polarity change. The SNP 536 A > G in exon 6 from the NCBI database was not detected in this population. The allele distribution of SNP was in good unity with the Hardey-Weinberg equilibrium. CONCLUSION: It is suggested that the SNP of GHR are unevenly distributed and different in different ethnic populations.

Asian People↗
PubMed2004

[The haplotypes of three single nucleotide polymorphisms in caspase-3 gene in Han nationality of Zhejiang province in China].

OBJECTIVE: To investigate the single nucleotide polymorphisms (SNPs) and the distribution of their haplotypes in caspase-3 gene in Zhejiang Han nationality in China. METHODS: Denaturing high-performance liquid chromatography (DHPLC) and DNA sequencing were used to detect the SNPs in the regulatory region and the exons 2-7 and their flanking sequences in caspase-3 gene. Expectation maximization (EM) algorithm was used for haplotype frequencies analysis and pairwise linkage disequilibrium test. RESULTS: (1) Three SNPs were identified in caspase-3 gene; the three sites C829A, A17532C and C20541T were located in 5' regulatory region, intron 4 and 3' regulatory region, respectively. (2) Strong linkage disequilibrium was found among these SNPs; site A17532C and C20541T were in complete linkage disequilibrium. (3) C-829/A-17532/C-20541 (54.3%) was the main haplotype of Zhejiang Han nationality. CONCLUSION: The above findings indicated there is strong linkage disequilibrium among the three SNPs in caspase-3 gene in Han nationality of Zhejiang province and the main haplotype of Han nationality is obviously different from that of North American.

Asian People↗
PubMed2000

Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem.

There are great hopes that the most common form of human genetic variation, single nucleotide polymorphisms (SNPs), can be used to improve radically biological understanding and to advance medicine. However, considerable controversy exists over just how SNPs can be applied to gain these insights. The second international SNP meeting, held at Schloss Hohenkammer, Munich, Germany, brought together leading international scientists from academia and industry to look at these issues from a multidisciplinary perspective. Topics that were covered spanned SNP discovery, scoring technologies, population genetics, disease studies, commercial dimensions, pharmacogenomics, bioinformatics, and legal considerations. SNP discovery is picking up speed; The SNP Consortium (TSC) is set to produce 300,000 publicly available SNPs within 2 years. Improved technologies for scoring SNPs are reducing hands-on time and cost, although truly high-throughput methods are still lacking for genome-wide population-based studies. Large numbers of SNPs have already been analysed in diverse populations. The results emphasise the importance of considering population history when using SNPs to search for genetic risk factors. Opinions on the feasibility of extensive SNP-based analysis of complex disease vary. However, combining expertise from several fields will be key to achieving optimal utilization of SNPs.

Humans↗