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Results for “Single nucleotide polymorphisms”

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At least 271 records · Page 15Linked to original sources

PubMed2001

Two novel single-nucleotide polymorphisms of the Caspase-9 (CASP9) gene in the Japanese population.

We identified two single-nucleotide polymorphisms (SNPs) in the human Caspase-9 (CASP9) gene (1p36.3), which encodes an apoptosis-related cysteine protease, by screening all exons and exon-intron boundaries. These SNPs were present in coding regions. One of coding SNPs reflected an amino-acid substitution; an A to G transition at codon 221 in exon 5 would encode arginine instead of glutamine. As the gene is implicated in apoptotic cascade, the polymorphic sites will serve as useful markers for genetic studying of disorders affecting immune response and cancer susceptibility in humans.

Caspase 9↗

PubMed2001

Nine novel single-nucleotide polymorphisms in the integrin beta4 (ITGB4) gene in the Japanese population.

We identified nine single-nucleotide polymorphisms (SNPs) in the human integrin beta4 (ITGB4) gene (17q24-q25), which encodes a cell-surface receptor, by screening all exons and exon-intron boundaries. Seven of these SNPs were present in coding regions and two in intronic sequences; four of the coding SNPs involved amino-acid substitutions. As the gene is implicated in the tumorigenesis of breast cancers, the polymorphic sites will serve as useful markers not only for distinguishing alleles in loss of heterozygosity (LOH) analyses but also for studying genetic susceptibility to malignancies in humans.

Antigens, CD↗

PubMed2005

A new PCR-SSP typing method for six single-nucleotide polymorphisms impairing the blood-clotting cascade as well as T-cell stimulation.

Single-nucleotide polymorphisms (SNPs) within the genes of factor V (FV) (G1691A; exon 10), prothrombin (FII) (G20210A; 3'untranslated - region) and methylenetetrahydrofolate reductase (MTHFR) (C677T; exon 4) are associated with hypercoagulability, and systematic screening of individuals being at higher risk of thrombosis has been suggested. SNPs in the 2q33 region within the genes of CD28 (+17T/C; intron 3) and CTLA4 (-318C/T; promoter and +49A/G; exon 1) are likely to affect T-cell proliferation and antigen presentation signaling, which may lead to altered sensitivity of allograft or self-tissue recognition and affect the incidence of autoimmune diseases. We developed primers that allow specific amplification of these six SNPs at test conditions identical with those used for HLA typing with the CTS PCR-SSP reagents. One hundred ninety-six healthy German Caucasian individuals were tested for the six SNPs. The genotype frequencies for all SNPs were in Hardy-Weinberg equilibrium. There was no significant difference in the distribution of genotypes when compared to other published studies in which these SNPs were tested. The described PCR-SSP method can be used to screen large numbers of patients for these SNPs.

Antigens, CD↗

PubMed2002

A novel procedure for simple and efficient genotyping of single nucleotide polymorphisms by using the Zn2+-cyclen complex.

The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilized in the study of various genetic determinants. Here, we introduce a simple, rapid, low-cost and accurate procedure for the detection of SNPs by polyacrylamide gel electrophoresis (PAGE) with a novel additive, the Zn2+- cyclen complex (cyclen = 1,4,7,10-tetraazacyclododecane). The method is based on the difference in mobility of mutant DNA (in the same length) in PAGE, which is due to Zn2+-cyclen binding to thymine bases accompanying a total charge decrease and a local conformation change of target DNA. Various nucleotide substitutions (e.g. AT to GC) in DNA fragments (up to 150 bp) can be visualized with ethidium bromide staining. Furthermore, heteroduplex and homoduplex DNAs are clearly separated as different bands in the gel. We demonstrate the analysis of single- and multiple-nucleotide substitutions in a voltage-dependent sodium channel gene by using this novel procedure (Zn2+-cyclen-PAGE).

Base Sequence↗

PubMed2003

[Single nucleotide polymorphism and its use in chicken QTL mapping].

Single nucleotide polymorphism (SNP) refers to the change of single nucleotide in DNA sequence. Because of its high density in genomes and easy in detection and analysis statistically,SNP can be used in genetic linkage map construction and QTL mapping.Here,the characters and detecting technology of SNP,as well as the status and foreground of the use of candidate gene SNP in chicken QTL mapping are introduced.

English Abstract↗

PubMed2001

Single nucleotide polymorphisms and recombination rate in humans.

Levels of heterozygosity for single nucleotide polymorphisms vary by more than one order of magnitude in different regions of the human genome. Regional differences in the rate of recombination explain a substantial fraction of the variation in levels of nucleotide polymorphism, consistent with the widespread action of natural selection at the molecular level.

Evolution, Molecular↗

PubMed2004

Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS-PCR.

Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism. These polymorphisms can be used in plants as simple genetic markers for many breeding applications, for population studies, and for germplasm fingerprinting. The great increase in the available DNA sequences in the databases has made it possible to identify SNPs by "database mining", and the single most important factor preventing their widespread use appears to be the genotyping cost. Many genotyping platforms rely on the use of sophisticated, automated equipment coupled to costly chemistry and detection systems. A simple and economical method involving a single PCR is reported here for barley SNP genotyping. Using the tetra-primer ARMS-PCR procedure, we have been able to assay unambiguously five SNPs in a set of 132 varieties of cultivated barley. The results show the reliability of this technique and its potential for use in low- to moderate-throughput situations; the association of agronomically important traits is discussed.

Alleles↗

PubMed2004

Three single-nucleotide polymorphisms of the angiotensinogen gene and susceptibility to hypertension: single locus genotype vs. haplotype analysis.

Although some single polymorphism analyses of the angiotensinogen (AGT) gene have been found to be associated with hypertension, the results are still inconsistent. The objectives of this study are to evaluate the association of the genotype and haplotype distributions of three single-nucleotide polymorphisms (SNPs) (G-217A, A-6G, and M235T) in the AGT gene with hypertension. In a sample of 461 hypertensive and 327 normotensive patients in Taiwan, we found that -217AA and -6GG homozygotes conferred independently an increased risk to hypertension (P = 0.008 and P = 0.037, respectively), as illustrated by their significant associations with hypertension in both single SNP and pair-wise SNPs analyses. Meanwhile, a very weak linkage disequilibrium was found between the G-217A and the A-6G polymorphisms in terms of r2 (<0.05). On the basis of likelihood ratio test, only the set of haplotypes that constituted the A-6G and the M235T polymorphisms was associated with hypertension (chi2 = 20.91, P = 0.0008), which was mainly due to the increased frequency of the recombinant haplotypes (-6A identical with 235M and -6G identical with 235T), and a pathophysiological role in the predisposition to hypertension was hence indicated. In functional assays, the promoter activities of the haplotypes -217A identical with -6A and -217G identical with -6G were significantly higher than the most common haplotype -217G identical with -6A. These results highlight the necessity of a thorough analysis of all reported variants of a candidate gene in the elucidation of genetic susceptibility to a complex disease like hypertension, even when the variants are in the same haplotype block.

Angiotensinogen↗

PubMed2005

SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs).

UNLABELLED: SNPNB is a user-friendly and platform-independent application for analyzing Single Nucleotide Polymorphism NeighBoring sequence context and nucleotide bias patterns, and subsequently evaluating the effective SNP size for the bias patterns observed from the whole data. It was implemented by Java and Perl. SNPNB can efficiently handle genome-wide or chromosome-wide SNP data analysis in a PC or a workstation. It provides visualizations of the bias patterns for SNPs or each type of SNPs. AVAILABILITY: SNPNB and its full description are freely available at http://bioinfo.vipbg.vcu.edu/SNPNB/

Algorithms↗

PubMed2005

Identification of a single nucleotide polymorphism in porcine testis cytochrome P450-c17 (CYP17) and its effect on steroidogenesis.

Raising uncastrated male pigs could have significant economic benefits for pig production. Uncastrated male pigs can accumulate high levels of 16-androstene steroids, however, resulting in boar taint, which is highly objectionable to consumers. Cytochrome P450-c17 (CYP17) interacts with cytochrome b5 in the biosynthesis of the 16-androstene steroids and the sex steroids from pregnenolone. Amino acid substitutions in CYP17 could therefore affect the ability of this enzyme to catalyze the reactions leading to the production of androstenone and the sex steroids. In this study, we established a sensitive and flexible single-stranded conformational polymorphism technique capable of detecting a single nucleotide polymorphism. We then used this method to identify a substitution from T to A at nucleotide 1317 of CYP17, which caused a change in the amino acid sequence from Leu(439) to His(439). This mutation, however, did not alter the enzyme activity of CYP17 in the biosynthesis of androstenone or sex steroids. Other polymorphisms previously suggested for CYP17, which are vital for the functional interaction of CYP17 with CYB5 in human, were not observed. This study suggests that the synthesis of androstenone in pig testis is not directly affected by any polymorphisms in the coding region of the porcine CYP17 gene.

Amino Acid Substitution↗

PubMed2000

Association between single nucleotide polymorphisms in the hMSH3 gene and sporadic colon cancer with microsatellite instability.

The association between three single nucleotide polymorphisms (SNPs) in the hMSH3 gene and sporadic colon cancer with microsatellite instability (MSI) was analyzed. Of the three SNPs observed in this population, SNPs at residues 235 and 693 were novel, while that at residue 3133 was previously described. The SNPs at residues 235 and 3133 caused amino acid substitutions, V79I and T1045A, respectively. We analyzed the allele frequencies of the three SNPs in samples from 19 patients with sporadic colon cancer with MSI and 90 healthy controls. We found that the V79 allele frequency was significantly higher in the tumor samples than in controls. In addition, the frequency of the G693 allele showed a higher trend in the tumor samples than in controls. These results indicated that some SNPs in the hMSH3 gene were associated with colon cancer with MSI.

Alleles↗

PubMed2004

The expected performance of single nucleotide polymorphism loci in paternity testing.

We discuss the utility of single nucleotide polymorphism loci for full trio and mother-unavailable paternity testing cases, in the presence of population substructure and relatedness of putative and actual fathers. We focus primarily on the expected number of loci required to gain specified probabilities of mismatches, and report the expected proportion of paternity indices greater than three threshold values for these loci.

Female↗

PubMed1999

Identification of two single nucleotide polymorphisms in exon 8 of PAX2.

We estimate the allele frequencies of two single nucleotide polymorphisms (1410 C --> T) and (1521 A --> C) in the coding region of PAX2. The coding region single nucleotide polymorphisms (cSNPs) were identified by sequencing of amplimers of PAX2 exon 8 exhibiting variant migration patterns in the course of genomic DNA mutation screening from patients with renal-coloboma syndrome. Allele frequencies of the two polymorphisms were 0.94 for 1410C and 0.72 for 1521A. Cosegregation analyses of both alleles suggest that they are each in Hardy-Weinberg equilibrium and jointly in linkage equilibrium and may represent ancient polymorphisms. Characterization of PAX2 exon 8 cSNPs will serve as useful tools for mapping at the PAX2 locus.

Abnormalities, Multiple↗

PubMed2000

Single nucleotide polymorphisms as tools in human genetics.

The development of detailed single nucleotide polymorphism (SNP) maps of the human genome coupled with high-throughput genotyping technologies may allow us to unravel complex genetic traits, such as multifactorial disease or drug response, over the next few years. Here we describe the current efforts to identify and characterize the large numbers of SNPs required and discuss the practicalities of association studies for the identification of genes involved in complex traits.

Genetics, Medical↗

PubMed2004

Allele-specific binding to the -308 single nucleotide polymorphism site in the tumour necrosis factor-alpha promoter.

Single nucleotide polymorphisms in the tumour necrosis factor alpha (TNF-alpha) promoter region may modulate TNF-alpha gene transcriptional activity by modifying the binding of transcription factors. Here we confirm that a specific DNA complex binds preferentially the variant TNF2 allele in various cell types and demonstrate that activating protein (AP)-2, myeloid zinc finger gene 1 (MZF-1) and Sp1 are not involved in this complex.

Alleles↗

PubMed2005

Clinical genotyping: the need for interrogation of single nucleotide polymorphisms and mutations in the clinical laboratory.

BACKGROUND: Detection of single nucleotide polymorphisms (SNPs) and gene mutations is becoming more routine to the clinical laboratory. METHODS: Completion of the Human Genome Project has led to new scientific knowledge of human disease processes that has revealed the most fundamental of abnormalities in nucleic acids while at the same time bringing some of the most sophisticated diagnostic tools to the clinical laboratory. In addition, public awareness (both lay persons and healthcare providers) and sensitivity to human genetics has increased tremendously. Together, this rapidly evolving science and increased public education has led to an increasing demand for genotypic testing. CONCLUSIONS: There are several clinical applications of human genotyping that are available using these newer technologies.

Base Sequence↗

PubMed2001

Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation.

A method for identifying and validating single nucleotide polymorphisms (SNPs) with high-density oligonucleotide arrays without the need for locus-specific polymerase chain reactions (PCR) is described in this report. Genomic DNAs were divided into subsets with complexity of ~10 Mb by restriction enzyme digestion and gel-based fragment size resolution, ligated to a common adaptor, and amplified with one primer in a single PCR reaction. As a demonstration of this approach, a total of 124 SNPs were located in 190 kb of genomic sequences distributed across the entire human genome by hybridizing to high-density variant detection arrays (VDA). A set of independent validation experiments was conducted for these SNPs employing bead-based affinity selection followed by hybridization of the affinity-selected SNP-containing fragments to the same VDA that was used to identify the SNPs. A total of 98.7% (74/75) of these SNPs were confirmed using both DNA dideoxynucleotide sequencing and the VDA methodologies. With flexible sample preparation, high-density oligonucleotide arrays can be tailored for even larger scale genome-wide SNP discovery as well as validation.

Cell Line↗

PubMed2001

Alkaline-mediated differential interaction (AMDI): a simple automatable single-nucleotide polymorphism assay.

The key requirements for high-throughput single-nucleotide polymorphism (SNP) typing of DNA samples in large-scale disease case-control studies are automatability, simplicity, and robustness, coupled with minimal cost. In this paper we describe a fluorescence technique for the detection of SNPs that have been amplified by using the amplification refractory mutation system (ARMS)-PCR procedure. Its performance was evaluated using 32 sequence-specific primer mixes to assign the HLA-DRB alleles to 80 lymphoblastoid cell line DNAs chosen from our database for their diversity. All had been typed previously by alternative methods, either direct sequencing or gel electrophoresis. We believe the detection system that we call AMDI (alkaline-mediated differential interaction) satisfies the above criteria and is suitable for general high-throughput SNP typing.

Alkalies↗