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Results for “Single nucleotide polymorphisms (SNPs)”

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At least 181 records · Page 10Linked to original sources
PubMed2006

Quencher extension for single nucleotide polymorphism quantification in bacterial typing and microbial community analyses.

Quencher extension is a novel single-step closed tube real-time method to quantify single nucleotide polymorphisms (SNPs) in combination with primer extension. A probe with a 5'-reporter is single-base extended with a dideoxy nucleotide containing a quencher if the target SNP allele is present. The reaction is measured from the quenching (reduced fluorescence) of the reporter. The relative amount of a specific SNP allele is determined from the nucleotide incorporation rate in a thermocycling reaction. The quencher extension protocol presented was developed for SNP allele quantification in Listeria monocytogenes and for microbial community analyses.

Bacterial Typing Techniques↗
PubMed2003

Digital genotyping and haplotyping with polymerase colonies.

Polymerase colony (polony) technology amplifies multiple individual DNA molecules within a thin acrylamide gel attached to a microscope slide. Each DNA molecule included in the reaction produces an immobilized colony of double-stranded DNA. We genotype these polonies by performing single base extensions with dye-labeled nucleotides, and we demonstrate the accurate quantitation of two allelic variants. We also show that polony technology can determine the phase, or haplotype, of two single- nucleotide polymorphisms (SNPs) by coamplifying distally located targets on a single chromosomal fragment. We correctly determine the genotype and phase of three different pairs of SNPs. In one case, the distance between the two SNPs is 45 kb, the largest distance achieved to date without separating the chromosomes by cloning or somatic cell fusion. The results indicate that polony genotyping and haplotyping may play an important role in understanding the structure of genetic variation.

DNA↗
PubMed2005

Large-scale characterization of public database SNPs causing non-synonymous changes in three ethnic groups.

Single nucleotide polymorphisms (SNPs) that lead to non-synonymous changes in proteins may have functional effects and be subject to selection. Hence they are of particular interest in the study of genetic diseases. We have genotyped approximately 28,000 such SNPs in three ethnic populations (the HapMap plates) and ten primate species and analyzed these data for evidence of selection. We find SNPs predicted by PolyPhen to be damaging, have lower allele frequencies, and are particularly likely to be population-specific. We have also grouped SNPs by molecular function or biological process of the associated genes and find evidence that selection may be acting in concert on classes of genes.

Animals↗
PubMed2002

Characterization of DNA polymorphisms in the E-cadherin gene (CDH1) promoter region.

E-cadherin is a tumor suppressor involved in epithelial cell-cell interactions. Some of the nucleotide variation in the 5'-promoter region of the gene influences transcriptional efficiency. We investigated single nucleotide polymorphisms (SNPs) in the promoter-exon 1 region of the E-cadherin gene (CDH1) using fluorescence-based PCR-single-strand conformation polymorphism (PCR-SSCP) analysis. We detected four kinds of polymorphisms between nucleotides -516 and +12, numbering from the translation initiation site. SNPs were localized at -472G-->GA, -288T-->deltaT, -285C-->A, and -54G-->C. Variants -472GA and -285A were frequently found in controls, but the -288deltaT and -54C are rare variants. We examined the effects of these variants on transcription. The activity of promoters containing the variants -288deltaT, -285A, or -54C was lower than the activity of promoters with the major variants, as assayed by a luciferase reporter gene. Variants -472G and -472GA displayed the same promoter activity. The decreased transcriptional activity from variant promoters affects the expression of E-cadherin.

Alleles↗
PubMed2003

DNA enrichment by allele-specific hybridization (DEASH): a novel method for haplotyping and for detecting low-frequency base substitutional variants and recombinant DNA molecules.

Detecting rare sequence variants in genomic DNA is central to the analysis of de novo mutation and recombination events and the detection of rare pathological mutations in mixed cell populations. Current PCR techniques suffer from noise that limits detection to variants present at a frequency of at least 10(-4)-10(-5) per cell. We now describe an alternative approach that recovers genomic DNA molecules containing a known single-nucleotide variant by hybridization selection using a biotinylated allele-specific oligonucleotide, followed by hybrid capture on streptavidin-coated paramagnetic beads and subsequent analysis by PCR. This technique of DNA enrichment by allele-specific hybridization (DEASH) is fast, effective for all tested single-nucleotide polymorphisms (SNPs), and can recover large (>10 kb) single-stranded molecules. A single round of DEASH is effective in separating haplotypes from genomic DNA and can not only readily detect and validate DNA molecules containing a single base change at a frequency of 10(-5) per cell, but can also place these changes within the context of an extended haplotype. This technique offers a new approach to the analysis of mutation and recombination, and has the potential to detect very rare de novo base substitutions.

Alleles↗
PubMed2001

Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms.

Haplotypes have gained increasing attention in the mapping of complex-disease genes, because of the abundance of single-nucleotide polymorphisms (SNPs) and the limited power of conventional single-locus analyses. It has been shown that haplotype-inference methods such as Clark's algorithm, the expectation-maximization algorithm, and a coalescence-based iterative-sampling algorithm are fairly effective and economical alternatives to molecular-haplotyping methods. To contend with some weaknesses of the existing algorithms, we propose a new Monte Carlo approach. In particular, we first partition the whole haplotype into smaller segments. Then, we use the Gibbs sampler both to construct the partial haplotypes of each segment and to assemble all the segments together. Our algorithm can accurately and rapidly infer haplotypes for a large number of linked SNPs. By using a wide variety of real and simulated data sets, we demonstrate the advantages of our Bayesian algorithm, and we show that it is robust to the violation of Hardy-Weinberg equilibrium, to the presence of missing data, and to occurrences of recombination hotspots.

Algorithms↗
PubMed2006

No pathogenic mutations identified in the COL8A1 and COL8A2 genes in familial Fuchs corneal dystrophy.

PURPOSE: To investigate the genetic basis of late-onset, familial Fuchs endothelial corneal dystrophy (FECD) through screening of the COL8A1 and COL8A2 genes, in which mutations have been associated with both early and late-onset, familial and sporadic FECD. METHODS: DNA extraction, PCR amplification, and direct sequencing of the COL8A1 and COL8A2 genes was performed in affected and unaffected members of 15 unrelated families with two or more members with late-onset FECD. RESULTS: Screening of the COL8A1 gene did not reveal sequence variants in any affected individuals from the 15 FECD families. In the COL8A2 gene, the previously identified mutations presumed to play a pathogenic role in cases of familial FECD (Arg155Gln, Leu450Trp, and Gln455Lys) were not discovered in any of the affected patients. A mutation previously considered causative of FECD (Arg434His) was shown not to segregate with the disease in the one family in which it was identified. Two previously identified single-nucleotide polymorphisms (SNPs), Pro575Leu and Pro586Pro, were identified in a single affected individual and three affected individuals (two families), respectively. CONCLUSIONS: The Arg434His mutation in the COL8A2 gene, previously associated with FECD, has been shown not to segregate with the disease phenotype, and thus may not be considered a disease-causing mutation. The absence of pathogenic mutations identified in the COL8A1 or COL8A2 genes in affected members of 15 pedigrees with familial FECD indicates that other genetic factors are involved in the development of this autosomal dominant corneal dystrophy.

Adult↗
PubMed2005

A genetic screen for dominant modifiers of a small-wing phenotype in Drosophila melanogaster identifies proteins involved in splicing and translation.

Studies in the fly, Drosophila melanogaster, have revealed that several signaling pathways are important for the regulation of growth. Among these, the insulin receptor/phosphoinositide 3-kinase (PI3K) pathway is remarkable in that it affects growth and final size without disturbing pattern formation. We have used a small-wing phenotype, generated by misexpression of kinase-dead PI3K, to screen for novel mutations that specifically disrupt organ growth in vivo. We identified several complementation groups that dominantly enhance this small-wing phenotype. Meiotic recombination in conjunction with visible markers and single-nucleotide polymorphisms (SNPs) was used to map five enhancers to single genes. Two of these, nucampholin and prp8, encode pre-mRNA splicing factors. The three other enhancers encode factors required for mRNA translation: pixie encodes the Drosophila ortholog of yeast RLI1, and RpL5 and RpL38 encode proteins of the large ribosomal subunit. Interestingly, mutations in several other ribosomal protein-encoding genes also enhance the small-wing phenotype used in the original screen. Our work has therefore identified mutations in five previously uncharacterized Drosophila genes and provides in vivo evidence that normal organ growth requires optimal regulation of both pre-mRNA splicing and mRNA translation.

Amino Acid Sequence↗
PubMed2003

Polycation-accelerated strand exchange (PASE) for SNPs typing.

In the previous study (Chem. Eur. J., 7, 176 (2001), J. Am. Chem. Soc., 124, 12676 (2002)), we demonstrated that the cationic comb-type copolymer (PLL-g-Dex, CCC) composed of a cationic poly(L-lysine) backbone and water-soluble side chains of dextran accelerated the DNA strand exchange reaction between double helical DNA and its homologous single strand. In this study, Polycation-Accelerated Strand Exchange (PASE) assay was applied to discriminate single-base mismatch in DNA sequence such as single nucleotide polymorphisms (SNPs). We could discriminate the 20mer DNA with a single-base mismatch from the full matched DNA with high efficacy by PASE.

Base Pair Mismatch↗
PubMed2006

VEGF polymorphisms are associated with neovascular age-related macular degeneration.

Age-related macular degeneration (AMD) is the most common cause of blindness in the elderly. Linkage has been shown to the vascular endothelial growth factor (VEGF) gene and ocular levels of VEGF are raised in individuals with the neovascular form of disease. To examine the role of VEGF further, we conducted a case-control study where 45 individuals with neovascular AMD and 94 age-matched controls were genotyped for 14 single nucleotide polymorphisms (SNPs) in the VEGF promoter and gene. The single SNP +674 CC genotype was significantly associated with AMD (OR=2.40, 95%CI 1.09-5.26, P=0.027). Haplotype analysis of SNPs +674, +4618, +5092, +9162 and +9512 revealed that CTCCT and TCACC were associated with AMD (OR=15.77, 95% CI 1.91-130.24, P=0.0161 and OR=9.95, 95%CI 3.22-30.74, P=0.000053, respectively). The haplotype TCACT was associated with the control group (P=0.0001832). Furthermore, haplotype analysis of promoter SNPs revealed that possession of the -460T, -417T, -172C, -165C, -160C, -152G, -141A, -116A, +405C haplotype was strongly associated with AMD (OR=18.24, 95%CI 2.25-148.25, P=0.0074). This is the most extensive analysis of the VEGF gene in AMD, demonstrating a clear association with the exudative form of disease, thereby creating the possibility for predictive testing. Smoking, high fat intake and hypertension are negative environmental risk factors in AMD, whereas increased consumption of dietary antioxidants can have a protective effect. Identification of those at risk in the population would allow individual counselling with lifestyle advice to reduce the risks of blindness. (Genbank accession nos M63971 and AF437895).

5' Untranslated Regions↗
PubMed2026

Upper airway microbiome interacts with GSDMB and ORMDL3 asthma risk SNPs to influence early-life wheeze risk.

BACKGROUND: Single-nucleotide polymorphisms (SNPs) in the chromosome 17q12-q21 region and, independently, early-life nasal microbiota dominated by Moraxella, Streptococcus, or Haemophilus (MSH) increase risk of chronic wheeze and asthma development. OBJECTIVE: We sought to determine whether 17q12-q21 risk SNPs and nasal microbiota interact to modulate childhood wheeze risk. METHODS: Nasal wash samples from 12-month-old infants in 2 birth cohorts, COAST (Childhood Origins of Asthma; n = 180) and URECA (Urban Environment and Childhood Asthma; n = 139), underwent 16S ribosomal RNA variable region 4 sequencing. Nasal microbiota dominated by MSH or Corynebacterium, Dolosigranulum, Staphylococcus, or Bacillus (CDSB) were assessed. Paired blood was genotyped for 9 17q12-q21 risk SNPs. Logistic regression tested interactions between 17q12-q21 SNPs and MSH or CDSB on wheeze risk in the first 3 years of life. A549 lung epithelial cells, CRISPR-edited to encode the rs7216389 risk genotype (rs7216389TT) were compared to the heterozygous (rs7216389CT) line using bulk RNA sequencing. RESULTS: SNPs, particularly those in the ORMDL3 (rs8076131; odds ratio [OR]: 1.72; 95% CI: 1.09-2.71; Pint = .031) and GSDMB (rs2305480; OR: 1.72; 95% CI: 1.09-2.71; Pint = 0.042; and rs7216389; OR: 1.73; 95% CI: 1.09-2.70; Pint = .047) genes, interact with MSH microbiota to increase early-life wheeze risk (false discovery rate Pint = .016 for all), while interactions with CDSB reduce risk. A549 airway epithelial cells homozygous for rs7216389TT exhibited decreased expression of genes involved in antimicrobial responses and neutrophil recruitment and evidence increased microbial adherence compared with the heterozygous cell line. CONCLUSION: Airway microbiota interact with SNPs at the 17q12-q21 locus in genes involved in sphingolipid metabolism and intracellular antimicrobial responses, to modulate wheeze risk.

Humans↗
PubMed2006

High-throughput single-nucleotide polymorphisms genotyping: TaqMan assay and pyrosequencing assay.

Single-nucleotide polymorphisms (SNPs) are DNA sequence variations that occur at a single base in the genome sequence. SNPs are valuable markers for identifying genes responsible for susceptibility to common diseases, and in some cases, they are the causes of human diseases. A genetic study of a complex disease usually involves a case-control association study that requires genotyping of a large number of SNPs in hundreds of patients (cases) and matched controls. A significant difference of the allele frequency or genotypic frequency of a SNP between the two populations is considered to be the evidence for the association between the SNP and disease. A key to a fast and effective case-control association study requires high-throughput genotyping of SNPs. Two assays-the TaqMan SNP genotyping assay and the pyrosequencing assay-have been developed for this purpose and proven to be particularly useful. Here, we present the operative protocol, clarify the key technical issues, and highlight certain cautionary notes for high throughput SNP genotyping using TaqMan and pyrosequencing assays.

Gene Frequency↗
PubMed2002

SNP typing by apyrase-mediated allele-specific primer extension on DNA microarrays.

This study reports the development of a microarray-based allele-specific extension method for typing of single nucleotide polymorphisms (SNPs). The use of allele-specific primers has been employed previously to identify single base variations but it is acknowledged that certain mismatches are not refractory to extension. Here we have overcome this limitation by introducing apyrase, a nucleotide-degrading enzyme, to the extension reaction. We have shown previously that DNA polymerases exhibit slower reaction kinetics when extending a mismatched primer compared with a matched primer. This kinetic difference is exploited in the apyrase-mediated allele-specific extension (AMASE) assay, allowing incorporation of nucleotides when the reaction kinetics are fast but degrading the nucleotides before extension when the reaction kinetics are slow. Here we show that five homozygous variants (14% of the total number of variants) that were incorrectly scored in the absence of apyrase were correctly typed when apyrase was included in the extension reaction. AMASE was performed in situ on the oligonucleotide microarrays using fluorescent nucleotides to type 10 SNPs and two indels in 17 individuals generating approximately 200 genotypes. Cluster analysis of these data shows three distinct clusters with clear-cut boundaries. We conclude that SNP typing on oligonucleotide microarrays by AMASE is an efficient, rapid and accurate technique for large-scale genotyping.

Alleles↗
PubMed2005

Human SNPs reveal no evidence of frequent positive selection.

We compared the single-nucleotide polymorphisms (SNPs) in humans in 182 housekeeping and 148 tissue-specific genes. SNPs were divided into rare and common polymorphisms based on their frequencies. We found that housekeeping genes tend to be less polymorphic than tissue-specific genes for both rare and common SNPs. Using mouse as a second species for computing sequence divergences, we found no evidence of positive selection: for both housekeeping and tissue-specific genes, the ratio of nonsynonymous to synonymous common SNPs per site showed no significant difference from that of divergence. Similarly, we observed no evidence of positive selection for the 289 and 149 genes that have orthologs available for divergence calculation between humans and chimpanzees and between humans and Old World monkeys, respectively. A comparison with previous SNP studies suggests that approximately 20% of the nonsynonymous SNPs in the human population are nearly neutral and that positive selection in the human genome might not be as frequent as previously thought.

Animals↗
PubMed2004

The role of MDR1 genetic polymorphisms in interindividual variability in P-glycoprotein expression and function.

The human multidrug resistance gene (MDR1), spanning greater than 200 kb, encodes for the ATP-dependent membrane efflux transporter, P-glycoprotein (Pgp). Significant progress has been made in the discovery of MDR1 polymorphisms and the assessment of allelic frequencies. The search for key genetic determinants that predispose individuals to drugs that are substrates or inhibitors of Pgp has just begun. Reports in the literature, particularly focusing on the C3435T polymorphism, have provided discordant results with respect to functional modification in vitro, and Pgp expression and disposition of probe drugs in vivo. Due to the large size of the MDR1 gene, genotyping based on individual single nucleotide polymorphism (SNPs) analysis is not sufficient to predict functional consequences. Strong linkage disequilibrium has been detected between several MDR1 polymorphisms, and discrepancies in the literature may be due to the focus on the influence of single nucleotide variations instead of on linked nucleotide variations. Multiple SNPs found on the same chromosome are assigned to a specific haplotype, and some attempts have been made to determine the role of MDR1 haplotypes in Pgp variability. Most of the data for MDR1 haplotype have been predicted based on computational or mathematical models. However, molecular haplotyping techniques, analysis of linkages on the same chromosome directly by biophysical and biochemical means, may be needed to characterize haplotypes in individuals with a highly polymorphic and large gene like MDR1. Haplotype identification may prove to be vital in identifying the functional significance of MDR1 polymorphisms on disease susceptibility and drug disposition.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1999

Single nucleotide polymorphisms of the N-formyl peptide receptor in localized juvenile periodontitis.

BACKGROUND: Neutrophils from patients with localized juvenile periodontitis (LJP) exhibit decreased binding and responsiveness to various chemotactic agents, including N-formyl-1-methionyl-1-leucyl-1-phenylalanine (FMLP). This altered reaction of neutrophils is thought to account in part for the increased susceptibility of LJP patients to infections by periodontal organisms. Receptors for FMLP are involved in the activation and the subsequent response to certain chemotactic stimuli. METHODS: In order to determine if this decreased response is due to a genetic variation in the receptor, we directly compared DNA encoding the FMLP receptor from controls matched for gender and race and LJP patients by single-strand conformation polymorphism analysis (SSCP). RESULTS: Using this technique, we observed a characteristic SSCP pattern in 29 out of 30 patient samples in the FMLP receptor DNA. This pattern differed from those obtained from the 20 control subjects as well as 31 patients with adult periodontitis. DNA sequencing of 30 patients indicated single nucleotide polymorphisms (SNPs) in the FMLP receptor DNA from the LJP patients when compared to 20 controls (P = 0.0005). Two single nucleotide base alterations were consistently seen: either a thymine to cytosine substitution at base 329 in 17 LJP patients or a cytosine to guanine substitution at base 378 in 5 LJP patients. A combination of both alterations were seen in 7 LJP patients. Both alterations resulted in amino acid changes in the second intracellular loop of the receptor, specifically phenylalanine to serine at residue 110 and cysteine to tryptophan at residue 126. This region of the FMLP receptor has recently been shown to play a role in ligand binding and G-protein activation. CONCLUSIONS: This study suggests that a molecular alteration in the second intracellular loop of the FMLP receptor molecules in LP patients may play a role in the decreased chemotactic activity reported for some LJP patients.

Adult↗
PubMed2005

Capillary electrophoretic discrimination of single nucleotide polymorphisms using an oligodeoxyribonucleotidepolyacrylamide conjugate as a pseudo-immobilized affinity ligand: optimum ligand length predicted by the melting temperature values.

We developed a weak-affinity separation system for single-nucleotide polymorphisms (SNPs) based on capillary electrophoresis. In this approach, single-stranded DNA (ssDNA)-polyacrylamide (polyAAm) conjugate was used as a pseudo-immobilized affinity ligand to separate the target DNA, cytochrome P450 2C9 (CYP2C9), and its point mutant. The ligand DNA was designed to be complementary to the normal DNA, and the target DNA was electrophoretically separated by the difference in the affinity with the pseudo-immobilized ligand in the capillary. We showed that the separation efficiency was closely associated with the Tm value of double-stranded DNA (dsDNA) consisting of the target and ligand DNA, which depends on the measurement conditions, such as the base number of the ligand DNA and the concentration of Mg2+ in the buffer solution.

Acrylic Resins↗
PubMed2006

A greedier approach for finding tag SNPs.

MOTIVATION: Recent studies have shown that a small subset of Single Nucleotide Polymorphisms (SNPs) (called tag SNPs) is sufficient to capture the haplotype patterns in a high linkage disequilibrium region. To find the minimum set of tag SNPs, exact algorithms for finding the optimal solution could take exponential time. On the other hand, approximation algorithms are more efficient but may fail to find the optimal solution. RESULTS: We propose a hybrid method that combines the ideas of the branch-and-bound method and the greedy algorithm. This method explores larger solution space to obtain a better solution than a traditional greedy algorithm. It also allows the user to adjust the efficiency of the program and quality of solutions. This algorithm has been implemented and tested on a variety of simulated and biological data. The experimental results indicate that our program can find better solutions than previous methods. This approach is quite general since it can be used to adapt other greedy algorithms to solve their corresponding problems. AVAILABILITY: The program is available upon request.

Algorithms↗