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At least 145 records · Page 8Linked to original sources

PubMed2001

A high-throughput SNP typing system for genome-wide association studies.

One of the most difficult issues to be solved in genome-wide association studies is to reduce the amount of genomic DNA required for genotyping. Currently available technologies require too large a quantity of genomic DNA to genotype with hundreds or thousands of single-nucleotide polymorphisms (SNPs). To overcome this problem, we combined the Invader assay with multiplex polymerase chain reaction (PCR), carried out in the presence of antibody to Taq polymerase, as well as using a novel 384-well card system that can reduce the required reaction volume. We amplified 100 genomic DNA fragments, each containing one SNP, in a single tube, and analyzed each SNP with the Invader assay. This procedure correctly genotyped 98 of the 100 SNP loci examined in PCR-amplified samples from ten individuals: the genotypes were confirmed by direct sequencing. The reproducibility and universality of the method were confirmed with two additional sets of 100 SNPs. Because we used 40 ng of genomic DNA as a template for multiplex PCR, the amount needed to assay one SNP was only 0.4 ng; therefore, theoretically, more than 200,000 SNPs could be genotyped at once when 100 microg of genomic DNA is available. Our results indicate the feasibility of undertaking genome-wide association studies using blood samples of only 5-10 ml.

Alleles↗

PubMed2005

Resistin SNP-420 determines its monocyte mRNA and serum levels inducing type 2 diabetes.

Resistin, secreted from adipocytes, causes insulin resistance in rodents. Its roles and main source in humans remain unknown. The G/G genotype of resistin single nucleotide polymorphism, SNP-420, induces type 2 diabetes mellitus (T2DM) by increasing promoter activity. We elucidated factors correlated with serum resistin and effects of SNP-420 on monocyte resistin mRNA. In 198 T2DM and 157 controls, fasting serum resistin was higher in T2DM. Multiple regression analysis revealed that SNP-420 genotype was the strongest determinant of serum resistin. In T2DM, 1-year duration of T2DM and 1% HbA1c was also correlated with 0.19 and 0.54 ng/ml serum resistin, respectively. Logistic regression analysis revealed that serum resistin was an independent factor for T2DM. In 23 healthy volunteers, monocyte resistin mRNA was positively correlated with its simultaneous serum levels and was higher in G/G genotype. Thus, SNP-420 determines monocyte mRNA and serum levels of resistin, which could induce T2DM.

Adipocytes↗

PubMed2004

SNP typing strategies.

Single nucleotide polymorphism (SNP) typing is likely to be an adjunct forensic technology to be used when short tandem repeat (STR) typing fails to yield a result or when only a partial profile is obtained. It is anticipated that forensic SNP analyses will be applied to typing mtDNA, Y chromosome lineage analyses, characterizing highly degraded DNA samples, assessing biogeographical ancestry, and typing for determining physical characteristics. As examples, three SNP typing strategies are briefly described. They are SNaP shot, SNPstream Ultra High Throughput System, and electrospray ionization mass spectrometry. The latter approach offers certain advantages for SNP analyses, particularly so for mtDNA typing.

Chromosomes, Human, Y↗

PubMed2004

A DNA microarray system for forensic SNP analysis.

Forensic DNA analysis is routinely performed using polymorphic short tandem repeat (STR) markers. However, for degraded or minute DNA samples, analysis of autosomal single nucleotide polymorphisms (SNPs) in short fragments might be more successful. Furthermore, sequencing of mitochondrial DNA (mtDNA) is often performed on highly degraded or scarce samples due to the high copy number of mtDNA in each cell. Due to the increasing number of complete mtDNA genome sequences available, the limited discrimination power of an mtDNA analysis, may be increased by analysis of coding region polymorphisms in addition to the non-coding variation. Since sequence analysis of the coding region would require more material than generally present in forensic samples, an alternative SNP analysis approach is required. We have developed a one-colour microarray-based SNP detection system for limited forensic materials. The method is based on minisequencing in solution prior to hybridisation to universal tag-arrays. In a first outline of a forensic chip, a combination of 12 nuclear and 21 mitochondrial SNP markers are analysed simultaneously. The mitochondrial markers on the chip are polymorphisms within the hypervariable region as well as in the coding region. Even though the number of markers in the current system is limited, it can easily be extended to yield a greater power of discrimination. When fully developed, microarray analysis provides a promising system for efficient sensitive SNP analysis of forensic samples in the future.

Complementarity Determining Regions↗

PubMed2004

Characterization of a new SNP c767A/T (Arg222Trp) in the candidate TSG FUS2 on human chromosome 3p21.3: prevalence in Asian populations and analysis of association with nasopharyngeal cancer.

The FUS2 gene, encoding a novel cytoplasmic acetyltransferase, resides in the tumor suppressor gene region on human chromosome 3p21.3 and is considered a promising candidate tumor suppressor gene. We have identified a new single nucleotide polymorphism (SNP), c767A/T, in the coding region of the gene. The polymorphism leads to a non-conservative amino acid change (R222W) located between the acetyltransferase (GNAT) and the proline-rich domains of the protein. We have analyzed 254 subjects included in 14 sub-populations. The occurrence of the SNP varies with the ethnicity of the population, suggesting that this SNP could be a valuable biomarker for population genetics. It is most prevalent in various Asian populations (T allele frequency>0.54), followed by the Canadian polar Inuit (T allele frequency=0.3), African American (T allele frequency=0.17), and Caucasian population (T allele frequency=0.1). Since nasopharyngeal carcinoma (NPC) is frequent in Southern China, Taiwan, Borneo and polar Canada, we further tested for the possible association of the FUS2 SNP with this form of endemic cancer. Our analysis, albeit limited, suggests no likely association between NPC and the FUS2 gene polymorphism. Further large-scale case-control studies are necessary and warranted to prove the strength of this contention.

Acetyltransferases↗

PubMed2005

The Invader assay for SNP genotyping.

The Invader assay uses a structure-specific flap endonuclease (FEN) to cleave a three-dimensional complex formed by hybridization of allele-specific overlapping oligonucleotides to target DNA containing a single nucleotide polymorphism (SNP) site. Annealing of the oligonucleotide complementary to the SNP allele in the target molecule triggers the cleavage of the oligonucleotide by cleavase, a thermostable FEN. Cleavage can be detected by several different approaches. Most commonly, the cleavage product triggers a secondary cleavage reaction on a fluorescence resonance energy transfer (FRET) cassette to release a fluorescent signal. Alternatively, the cleavage can be detected directly by use of fluorescence polarization (FP) probes, or by mass spectrometry. The invasive cleavage reaction is highly specific, has a low failure rate, and can detect zeptomol quantities of target DNA. While the assay traditionally has been used to interrogate one SNP in one sample per reaction, novel chip- or bead-based approaches have been tested to make this efficient and accurate assay adaptable to multiplexing and high-throughput SNP genotyping.

Flap Endonucleases↗

PubMed2004

No association was found between a functional SNP in ZDHHC8 and schizophrenia in a Japanese case-control population.

ZDHHC8 is a new and attractive candidate for a schizophrenia-susceptibility factor. First, several lines of linkage studies showed that 22q11, on which ZDHHC8 is located, is a "hot" region. Second, fine linkage disequilibrium mapping revealed a significant association around ZDHHC8. Moreover, a very recent study reported that one single nucleotide polymorphism (SNP: rs175174) in ZDHHC8 might affect the splicing process, the ZDHHC8 knock-out mice showed the gender-specific phenotype, and the transmission disequilibrium test (TDT) using this SNP also showed significant association with human female schizophrenia. Thus, we attempted a replication study of this SNP using relatively large Japanese case-control samples (561 schizophrenics and 529 controls). No association was found between schizophrenia and controls even after dividing samples by gender. Because our sample size provided quite high power, ZDHHC8 may not play a major role in Japanese schizophrenia. And our results did not support the gender-specific effect of this SNP.

Acyltransferases↗

PubMed2005

Effects of SNP, GLU and GABA on the neuronal activity of striatum nucleus in rats.

This study investigated the activity of nitric oxide (NO) in the striatum (STR) for a further comprehension of the pathogenesis of Parkinson's disease (PD). Microiontophoresis was used to observe the effects of sodium nitroprusside (SNP), L-glutamic acid (GLU) and gamma-aminobutyric acid (GABA) on STR neurons' firing rates. It was observed that 77.27% (51/66) of the tested STR neurons were excited by SNP. This excitatory effect could be antagonized by the NO synthase (NOS) inhibitor, N(G)-nitro-L-arginine methyl ester (L-NAME). During the microiontophoresis of GLU, the excitatory firing of STR neurons was also attenuated by addition of L-NAME while SNP application could enhance the excitation of the neurons. On the other hand, in the presence of GABA, SNP still excited the tested STR neurons. These results demonstrated that NOergic, GLUergic and GABAergic co-existed in the same STR neurons. NOergic and GLUergic were excitatory whereas GABAergic was inhibitory on the firing activity in STR neurons.

Action Potentials↗

PubMed2004

Development of a SNP genotyping panel for genetic monitoring of the laboratory mouse.

We have developed a genotyping system for detecting genetic contamination in the laboratory mouse based on assaying single-nucleotide polymorphism (SNP) markers positioned on all autosomes and the X chromosome. This system provides a fast, reliable, and cost-effective way for genetic monitoring, while maintaining a very high degree of confidence. We describe the allelic distribution of 235 SNPs in 48 mouse strains, thereby creating a database of polymorphisms useful for genotyping purposes. The SNP markers used in this study were chosen from publicly available SNP databases. Four genotyping methods were evaluated, and dynamic two-tube allele-specific PCR assays were developed for each marker and tested on a set of 48 inbred mouse strains. The minimal number of assays sufficient to distinguish groups consisting of different numbers of mouse strains was estimated, and a panel of 28 SNPs sufficient to distinguish virtually all of the inbred strains tested was selected. Amplifluor SNP detection assays were developed for these markers and tested on an extended list of 96 strains. This panel was used as a genetic quality control approach to monitor the genotypes of nearly 300 inbred, wild-derived, congenic, consomic, and recombinant inbred strains maintained at The Jackson Laboratory. We have concluded that this marker panel is sufficient for genetic contamination monitoring in colonies containing a large number of genetically diverse mouse strains and that reduced versions of the panel could be implemented in facilities housing a lower number of strains.

Alleles↗

PubMed2000

A tryptophan-free diet markedly reduces frontocortical 5-HT release, but fails to modify ethanol preference in alcohol-preferring (sP) and non-preferring (sNP) rats.

It has been hypothesised that rat lines genetically selected for their alcohol preference consume large amounts of ethanol because they have a low 5-HT content. Since brain tryptophan (TRP) availability controls the rate at which neurons synthesise and release serotonin (5-HT), we assessed whether the administration of a TRP-supplemented or TRP-free diet for 3 consecutive days influenced alcohol intake in alcohol-preferring and non-preferring sP and sNP rats, respectively. In the same animals extracellular 5-HT concentration was monitored by microdialysis in the frontal cortex. A TRP-free diet progressively and markedly decreased cortical extracellular 5-HT in sP and sNP rats during the treatment period with respect to a balanced diet. However, the TRP-free diet failed to modify alcohol consumption and preference in sP and sNP rats. The TRP-supplemented diet also failed to alter the intake of alcohol in either group of rats. Therefore, these results do not support a specific role of 5-HT transmission in ethanol intake and preference in sP and sNP rats.

Animals↗

PubMed2003

Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution.

We investigated the single nucleotide polymorphism (SNP) density across the human genome and in different genic categories using two SNP databases: Celera's CgsSNP, which includes SNPs identified by comparing genomic sequences, and Celera's RefSNP, which includes SNPs from a variety of sources and is biased toward disease-associated genes. Based on CgsSNP, the average numbers of SNPs per 10 kb was 8.33, 8.44, and 8.09 in the human genome, in intergenic regions, and in genic regions, respectively. In genic regions, the SNP density in intronic, exonic and adjoining untranslated regions was 8.21, 5.28, and 7.51 SNPs per 10 kb, respectively. The pattern of SNP density based on RefSNP was different from that based on CgsSNP, emphasizing its utility for genotype-phenotype association studies but not for most population genetic studies. The number of SNPs per chromosome was correlated with chromosome length, but the density of SNPs estimated by CgsSNP was not significantly correlated with the GC content of the chromosome. Based on CgsSNP, the ratio of nonsense to missense mutations (0.027), the ratio of missense to silent mutations (1.15), and the ratio of non-synonymous to synonymous mutations (1.18) was less than half of that expected in a human protein coding sequence under the neutral mutation theory, reflecting a role for natural selection, especially purifying selection.

DNA, Intergenic↗

PubMed2001

Alcohol stimulates motor activity in selectively bred Sardinian alcohol-preferring (sP), but not in Sardinian alcohol-nonpreferring (sNP), rats.

The present study was conducted to evaluate the effect of low doses of ethanol on motor activity in selectively bred Sardinian alcohol-preferring (sP) and Sardinian alcohol-nonpreferring (sNP) rats. Ethanol was acutely administered at the doses of 0, 0.25, and 0.5 g/kg (i.p.) immediately before rat exposure to an open-field arena for 15 min. The number of square crossings, used as index of motor activity, was significantly lower in saline-treated sP than in saline-treated sNP rats, suggestive of a genetically determined higher emotional state in sP than in sNP rats. Ethanol administration resulted in a dose-dependent, significant increase in the number of square crossings in sP rats, whereas it was completely ineffective in sNP rats. These results suggest to us that a positive relationship exists between ethanol preference and ethanol-induced motor stimulation in sP/sNP rat lines.

Alcohol Drinking↗

PubMed2003

Long-term exposure to a sweetened alcoholic solution does not alter genetic aversion to ethanol in Sardinian alcohol-nonpreferring (sNP) rats.

Results of a recent investigation revealed that selectively bred Indiana ethanol-nonpreferring (NP) rats could be "environmentally" conditioned to consume high amounts of ethanol. Specifically, a long-term exposure to a sucrose-plus-ethanol solution resulted, when sucrose was faded out, in an ethanol intake that was equivalent to that recorded in the counterpart ethanol-preferring (P) rats. The current study was designed to extend the above investigation to the selectively bred Sardinian alcohol-nonpreferring (sNP) rats. To this aim, rats of the sNP and Sardinian alcohol-preferring (sP) lines were exposed to a 108-day sucrose-fading procedure, which was virtually identical to that previously used with NP and P rats. Results indicated that intake of the sucrose-plus-ethanol solution in sNP rats was maintained predominantly by sucrose, as negligible intakes of ethanol were observed when sucrose was faded out. In contrast, sP rats maintained high levels of ethanol intake both during and after the induction procedure. These results support the suggestion that an environmental manipulation such as a long-term exposure to a sucrose-fading procedure did not overcome the genetically determined predisposition to avoid ethanol in sNP rats.

Alcohol Drinking↗

PubMed2000

Use of single nucleotide polymorphisms (SNP) and real-time polymerase chain reaction for bone marrow engraftment analysis.

Allogeneic bone marrow transplant engraftment assays use polymorphisms in the human genome to determine the relative percentages of donor and recipient cells present in the recipient. We describe a novel posttransplant assay approach using single nucleotide polymorphisms (SNPs), the most common type of polymorphism in humans. Using samples of defined genotype, we used real-time polymerase chain reaction (PCR) and allele-specific fluorescent TaqMan probes to assay a SNP of the cytochrome P450 CYP2C9 gene. Standard curves of chimeric mixes showed a linear relationship between the ratio of two alleles and the ratio of their respective fluorophore emission, except for mixes with a low percentage (< 5%) of the less common allele. We validated the SNP real-time PCR assay by comparing it to Southern hybridization analysis, analyzing DNA mixes in a blinded fashion with both methods. The correlation between the two methods was high. We have produced a statistical model that varies allele frequency to predict how many SNPs would be required to produce a functional SNP panel. Additional development will be necessary to produce such a panel of highly informative SNPs for clinical use. A real-time PCR SNP assay may ultimately provide more accurate quantification and shortened turnaround time compared to current post-engraftment assays.

Alleles↗

PubMed2004

Pyrene-labeled base-discriminating fluorescent DNA probes for homogeneous SNP typing.

This paper describes the design of novel base-discriminating fluorescent (BDF) nucleobases and their application to single nucleotide polymorphism (SNP) typing. We devised novel BDF nucleosides, (Py)U and (Py)C, which contain a pyrenecarboxamide chromophore connected by a propargyl linker. The fluorescence spectrum of the duplex containing a (Py)U/A base pair showed a strong emission at 397 nm on 327 nm excitation. In contrast, the fluorescence of duplexes containing (Py)U/N base pairs (N = C, G, or T) was considerably weaker. The proposed structure of the duplex containing a matched (Py)U/A base pair suggests that the high polarity near the pyrenecarboxamide group is responsible for the strong A-selective fluorescence emission. Moreover, the fluorescence of the duplex containing a (Py)U/A base pair was not quenched by a flanking C/G base pair. The fluorescence properties are quite different from previous BDF nucleobases, where fluorescence is quenchable by flanking C/G base pairs. The duplex containing the C derivative, (Py)C, selectively emitted fluorescence when the base opposite (Py)C was G. The drastic change of fluorescence intensity by the nature of the complementary base is extremely useful for SNP typing. (Py)U- and (Py)C-containing oligodeoxynucleotides acted as effective reporter probes for homogeneous SNP typing of DNA samples containing c-Ha-ras and BRCA2 SNP sites.

Amides↗

PubMed2006

DNA hole transport on an electrode: application to effective photoelectrochemical SNP typing.

A useful feature of DNA is that long-range hole transport through DNA is readily achieved. Photostimulated long-range hole transport through DNA has prospective use in the development of a conceptually new electrochemical single-nucleotide polymorphism (SNP) typing method for use as a versatile platform for gene diagnostics and pharmacogenetics. We have applied artificial DNAs designed for photostimulated long-range hole transport through DNA to SNP typing. By hybridizing photosensitizer-equipped DNA probes, immobilized on gold working electrodes, with a target DNA strand containing an SNP site, we observed a cathodic photocurrent, which markedly changed depending on the nature of the base at the specific site. The use of a combination of hole-transporting bases constitutes a very powerful method for a single-step electrochemical assay applicable to SNP typing of all types of sequences.

Base Sequence↗

PubMed2000

An SNP map of the human genome generated by reduced representation shotgun sequencing.

Most genomic variation is attributable to single nucleotide polymorphisms (SNPs), which therefore offer the highest resolution for tracking disease genes and population history. It has been proposed that a dense map of 30,000-500,000 SNPs can be used to scan the human genome for haplotypes associated with common diseases. Here we describe a simple but powerful method, called reduced representation shotgun (RRS) sequencing, for creating SNP maps. RRS re-samples specific subsets of the genome from several individuals, and compares the resulting sequences using a highly accurate SNP detection algorithm. The method can be extended by alignment to available genome sequence, increasing the yield of SNPs and providing map positions. These methods are being used by The SNP Consortium, an international collaboration of academic centres, pharmaceutical companies and a private foundation, to discover and release at least 300,000 human SNPs. We have discovered 47,172 human SNPs by RRS, and in total the Consortium has identified 148,459 SNPs. More broadly, RRS facilitates the rapid, inexpensive construction of SNP maps in biomedically and agriculturally important species. SNPs discovered by RRS also offer unique advantages for large-scale genotyping.

Algorithms↗

PubMed2000

An SNP map of human chromosome 22.

The human genome sequence will provide a reference for measuring DNA sequence variation in human populations. Sequence variants are responsible for the genetic component of individuality, including complex characteristics such as disease susceptibility and drug response. Most sequence variants are single nucleotide polymorphisms (SNPs), where two alternate bases occur at one position. Comparison of any two genomes reveals around 1 SNP per kilobase. A sufficiently dense map of SNPs would allow the detection of sequence variants responsible for particular characteristics on the basis that they are associated with a specific SNP allele. Here we have evaluated large-scale sequencing approaches to obtaining SNPs, and have constructed a map of 2,730 SNPs on human chromosome 22. Most of the SNPs are within 25 kilobases of a transcribed exon, and are valuable for association studies. We have scaled up the process, detecting over 65,000 SNPs in the genome as part of The SNP Consortium programme, which is on target to build a map of 1 SNP every 5 kilobases that is integrated with the human genome sequence and that is freely available in the public domain.

Cell Line↗