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Results for “single nucleotide polymorphisms”

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At least 865 records · Page 48Linked to original sources
PubMed2003

Frequencies of single nucleotide polymorphism in alcohol dehydrogenase7 gene in patients with multiple system atrophy and controls.

A polymerase chain reaction and direct sequencing of the ADH7 gene were carried out in 50 controls and 50 patients with probable multiple system atrophy (MSA). Seven SNPs, one insertion, and one mismatch were found in patients with MSA and controls. There was no significant difference in the frequencies of each SNP between the patients and the controls (P > 0.05). Interpretation of this negative finding should be cautious in view of the relatively small number of cases.

Alcohol Dehydrogenase↗
PubMed2000

dbSNP: a database of single nucleotide polymorphisms.

In response to a need for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, the National Cancer for Biotechnology Information (NCBI) has established the dbSNP database. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data. The complete contents of dbSNP are available to the public at website: http://www.ncbi.nlm.nih.gov/SNP. Submitted SNPs can also be downloaded via anonymous FTP at ftp://ncbi.nlm.nih.gov/snp/

Base Sequence↗
PubMed2000

New method for scanning of single-nucleotide polymorphisms (SNPs): recognition of guanine-guanine mismatches by dimeric naphthyridine.

Dimeric naphthyridine was designed and synthesized as a novel ligand that specifically binds to G-G mismatch, one of four SNP types. In the presence of dimeric naphthyridine, CD spectra of the G-G mismatch containing duplex noticeably changed, being accompanied by the induced CD at 300-350 nm, whereas no CD spectral change was observed for normal duplex. DNaseI footprinting titration indicated a selective binding of dimeric naphthyridine to the G-G mismatch with a dissociation constant of 53 nM.

Base Pair Mismatch↗
PubMedDate not supplied

Single nucleotide polymorphisms: early diagnosis and risk assessment in genitourinary malignancy.

Genetic screening for malignancy has been limited to high-risk individuals with a strong hereditary predisposition to cancer. With the cloning of the human genome, it has become apparent that genetic anomalies are not limited to high-risk individuals; more than 10 million genetic variants exist. Because the vast majority of these genetic variants have no functional significance, current efforts are focused on identification of which impact cancer development and/or progression. Here, we review the rationale for studying polymorphic variants in urologic malignancies, prior studies in the field, and future avenues of research.

DNA Primers↗
PubMed2001

Validation of a single nucleotide polymorphism genotyping assay for the human serum paraoxonase gene using electronically active customized microarrays.

OBJECTIVES: Develop a microarray based genotyping assay to detect SNPs in human paraoxonase (PON I) and compare its accuracy with DNA sequencing and RFLP based assays. DESIGN AND METHODS: Amplicons spanning the polymorphic regions of interest were genotyped by sequencing, RFLP, and microarray technology. Validation parameters included precision, linearity of signal response, and carryover between adjacent sites on the microarray. RESULTS: A 100% correlation in results obtained using DNA sequencing, RFLP and microarray technology was observed. CONCLUSIONS: The microarray technology provides an accurate and reliable assay platform with applicability in high throughput genotyping studies.

Aryldialkylphosphatase↗
PubMed2006

Estimating recombination rates from single-nucleotide polymorphisms using summary statistics.

We describe a novel method for jointly estimating crossing-over and gene-conversion rates from population genetic data using summary statistics. The performance of our method was tested on simulated data sets and compared with the composite-likelihood method of R. R. Hudson. For several realistic parameter values, the new method performed similarly to the composite-likelihood approach for estimating crossing-over rates and better when estimating gene-conversion rates. We used our method to analyze a human data set recently genotyped by Perlegen Sciences.

Computer Simulation↗
PubMed2001

Single nucleotide polymorphisms (SNPs) assay using reversible association and dispersion of DNA-linked colloidal nanoparticles.

The amphiphilic copolymer consisting of oligodeoxyribonucleotide (ODN; dT12) as the hydrophilic part and thermo-responsive poly(N-isopropylacrylamide) (polyNIPAAm) as the hydrophobic part was prepared. The copolymers formed DNA-linked colloidal nanoparticles above the phase transition temperature of polyNIPAAm part. The nanoparticles aggregated rapidly when the complementary ODN (dA12) was added into the dispersion. In contrast, they kept dispersed in the absence of the complementary ODN and in the presence of the point-mutated ODN ((dA6)dT(dA5)). These distinct phenomena may be applied for an oligonucleotides discrimination system in gene diagnosis.

Acrylic Resins↗
PubMed2003

Electrochemical DNA sensor for detection of single nucleotide polymorphisms.

In recent years there has been an increased interest in using biosensors for the recognition and monitoring of molecule interactions. DNA sensors and gene chips are particularly relevant for directly applying the information gathered from the genome projects. In this work electrochemical techniques are used to develop methodologies to detect DNA polymorphisms in human genes using cytochrome P450 3A4 (CYP3A4) as a model gene. CYP3A4*1B oligonucleotides were immobilized on the surface of a gold electrode and hybridized with fully complementary oligonucleotide sequences as well as with mismatched sequences corresponding to the CYP3A4*1A reference sequence. The methodology developed is based on double-stranded DNA's ability to transport charge along nucleotide stacking. The perturbation of the double helix pi-stack introduced by a mismatched nucleotide reduces electron flow and can be detected by measuring the attenuation of the charge transfer. The methodology developed could identify CYP3A4*1A homozygotes by the 5 microC charge attenuation observed when compared with DNA samples containing at least one CYP3A4*1B allele.

Biosensing Techniques↗
PubMed2006

Association of a single nucleotide polymorphism in SPP1 with growth traits and twinning in a cattle population selected for twinning rate.

Continued validation of genetic markers for economically important traits is crucial to establishing marker-assisted selection as a tool in the cattle industry. The objective of the current study was to evaluate the association of a SNP (T(9)/T(10)) in the osteopontin gene (SPP1) with growth rate in a large cattle population spanning multiple generations and representing alleles from 12 founding breeds. This population has been maintained at the US Meat Animal Research Center since 1981 and subjected to selection for twinning rate. Phenotypic records for this population included twinning rate and ovulation rate, providing an opportunity to examine the potential effects of SPP1 genotype on reproductive traits. A set of 2,701 animals was geno-typed for the T(9)/T(10) polymorphism at SPP1. The geno-typic data, including previously genotyped markers on chromosome 6 (BTA6), were used in conjunction with pedigree information to estimate genotypic probabilities for all 14,714 animals with phenotypic records. The genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fit as fixed effects in a mixed model analysis, in which each trait was analyzed in a 2-trait model where single births were treated as a separate trait from twin births. The association of the SPP1 marker with birth weight (P < 0.006), weaning weight (P < 0.007), and yearling weight (P < 0.003) was consistent with the previously reported effects of SPP1 genotype on yearling weight. Our data supports the conclusion that the SNP successfully tracks functional alleles affecting growth in cattle. The previously undetected effect of the SNP on birth and weaning weight suggests this particular SPP1 marker may explain a portion of the phenotypic variance explained by QTL for birth and HCW on BTA6.

Animals↗
PubMed2004

Genotyping of single nucleotide polymorphisms (SNPs) influencing drug response by competitive allele-specific short oligonucleotide hybridization (CASSOH) with immunochromatographic strip.

Using competitive allele-specific oligonucleotide hybridization with immunochromatographic strip (CASSOH), we have developed a simplified method for the detection of eight polymorphisms that are especially important in the identification of drug responders or non-responders and patients at increased risk of drug toxicity. The genotyping method is unambiguously determined by the presence or the absence of visible purple lines on the immunochromatographic strip, and results are obtained within 5 min after PCR. This method is rapid, highly sensitive, simplified, and should be suitable for point-of-care genotyping in clinical settings.

Alleles↗
PubMed2005

Association of habitual smoking and drinking with single nucleotide polymorphism (SNP) in 40 candidate genes: data from random population-based Japanese samples.

Basic information on the association between lifestyle factors and candidate genes is valuable for genetic-environmental study. We screened the association of habitual smoking or drinking with polymorphism in 40 candidate genes for a total of 153 single nucleotide polymorphisms (SNPs) using a sample of 339 middle-aged, randomly selected Japanese men. Smoking and drinking statuses were elicited during questionnaire-based interviews. Genes were selected based on their possible involvement in genetic-environmental, life-style interactions and constitute the genes expressing xenobiotic metabolism enzymes, DNA repair enzymes, and other stress-related proteins. The P values of odds ratios to habitual smoking for CYP17A1, ESR1, EPHX1, GSTT2, ALDH2, NOS2A, OGG1, and SLC6A4 and those of odds ratios to habitual drinking for CYP1B1, ESR1, HSD17B3, GSTM3, COMT, ADH1C, ALDH2, NOS3, and NUDT1 were under 0.05. These variables were included in a stepwise logistic analysis in order to develop a predictive model for smoking or drinking behavior. In the final model, the only significant variables selected for smoking were OGG1, SLC6A4, EPHX1, ESR1, and CYP17A1, and for drinking, ALDH2 and NUDT1. The findings of the present study suggest that polymorphism in associated candidate genes plays a role in the habitual use of tobacco and alcohol among Japanese men.

Adult↗
PubMed2005

Single nucleotide polymorphism in 5'-flanking region of BCL6 is not associated with increased risk of non-Hodgkin's lymphoma.

Mutations in the 5'-regulatory region of BCL6 were suggested to play a role in non-Hodgkin's lymphoma (NHL) progression and in the transformation of follicular lymphoma to more aggressive diffuse large B-cell type. The aim of this study was to explore association between polymorphism G397C in the 5'-region of BCL6 and both incidence and progression of NHL in 154 NHL cases and 362 controls. Neither frequencies of the rare BCL6 allele 397C nor particular genotypes differed significantly between NHL cases and controls. There was no significant association of histological type of NHL and clinical characteristics with this polymorphism.

5' Flanking Region↗
PubMed2006

A microarray system for genotyping 150 single nucleotide polymorphisms in the coding region of human mitochondrial DNA.

We established a genotyping system for a panel of 150 SNPs in the coding regions of mitochondrial DNA based on multiplex tag-array minisequencing. We show the feasibility of this system for simultaneous identification of individuals and prediction of the geographical origin of the mitochondrial DNA population lineage of the sample donors by genotyping the panel of SNPs in 265 samples representing nine different populations from Africa, Europe, and Asia. Nearly 40,000 genotypes were produced in the study, with an overall genotyping success rate of 95% and accuracy close to 100%. The gene diversity value of the panel of 150 SNPs was 0.991, compared to 0.995 for sequencing 500 nucleotides of the hypervariable regions I and II of mtDNA. For 17 individuals with identical sequences in the hypervariable regions of mtDNA, our panel of SNPs increased the power of discrimination. We observed 144 haplotypes that correspond to previously determined mitochondrial "haplogroups," and they allowed prediction of the origin of the maternal population lineage of 97% of the analyzed samples.

Asian People↗
PubMed2006

IFNGR1 single nucleotide polymorphisms in rheumatoid arthritis.

On the basis of their biological function, potential genetic candidates for susceptibility to rheumatoid arthritis can be postulated. IFNGR1, encoding the ligand-binding chain of the receptor for interferon gamma, IFNgammaR1, is one such gene because interferon gamma is involved in the pathogenesis of the disease. In the coding sequence of IFNGR1, two nucleotide positions have been described to be polymorphic in the Japanese population. We therefore investigated the association of those two IFNGR1 single nucleotide polymorphisms with rheumatoid arthritis in a case-control study in a central European population. Surprisingly, however, neither position was polymorphic in the 364 individuals examined, indicating that IFNGR1 does not contribute to susceptibility to rheumatoid arthritis, at least in Caucasians.

Adolescent↗
PubMed2006

Single nucleotide polymorphisms and breast cancer: not yet a success story.

Numerous studies have examined low penetrance susceptibility polymorphisms in candidate genes, with some reporting significant findings. However, for the most part these associations could not be replicated in subsequent studies, suggesting that the original observations were due to chance. The failure to identify meaningful common genetic variation in relation to breast cancer should give us pause for thought and make us reconsider our current research strategies. The most recent directions of pooling samples to increase statistical power and pursuing whole genome screens may overcome some obstacles while also creating new challenges. Future studies should perhaps also consider alternative designs such as using surrogate (preferably continuous) markers of breast cancer, focusing on high-risk populations, and defining pathologically distinct outcomes.

Breast Neoplasms↗
PubMed2002

Validation of single nucleotide polymorphism quantification in pooled DNA samples with SNaPIT. A glycosylase-mediated methods for polymorphism detection method.

Association studies using genome scans to identify quantitative trait loci for multifactorial disorders, with anything approaching reasonable power, have been compromised by the need for a very dense array of genetic markers and large numbers of affected individuals. These requirements impose enormous burdens on the genotyping capacity for most laboratories. DNA pooling has been proposed as a possible approach to reduce genotyping costs and effort. We report on the application of the SNaPIT technology to evaluate allele frequencies in pooled DNA samples and conclude that it offers a cost effective, efficient and accurate estimator and provides several advantages over competing technologies in this regard.

Chromosome Mapping↗
PubMed2003

Single nucleotide polymorphism--disease relationships: statistical issues for the performance of association studies.

There is increasing concern about the low reproducibility of findings of genetic association studies in complex diseases. In the present paper, we argue that it might be beneficial to learn from epidemiology and the methodology for clinical trials which address problems also crucial for genetic association studies. We propose a two-step sequential approach in order to (a) allow a study--internal control of reproducibility and (b) stop a study or lab analysis prematurely to save valuable specimen, time and costs. Additionally, minimal information is proposed which should be presented in publications about association studies in order to facilitate reproducibility studies by other authors.

Case-Control Studies↗
PubMed2002

The matrix coalescent and an application to human single-nucleotide polymorphisms.

The "matrix coalescent" is a reformulation of the familiar coalescent process of population genetics. It ignores the topology of the gene tree and treats the coalescent as a Markov process describing the decay in the number of ancestors of a sample of genes as one proceeds backward in time. The matrix formulation of this process is convenient when the population changes in size, because such changes affect only the eigenvalues of the transition matrix, not the eigenvectors. The model is used here to calculate the expectation of the site frequency spectrum under various assumptions about population history. To illustrate how this method can be used with data, we then use it in conjunction with a set of SNPs to test hypotheses about the history of human population size.

Data Interpretation, Statistical↗