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At least 469 records · Page 26Linked to original sources
PubMed2004

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.

Alleles↗
PubMed2004

Self-assembly DNA-conjugated polymer for detection of single nucleotide polymorphism.

We developed a self-assembly DNA-conjugated polymer based on polyacrylic acid (PAA) for DNA chip fabrication. A 20-mer single-stranded DNA (ssDNA, probe-1), and 3-(2-pyridyldithio)propionyl hydrazide (PDPH), for promoting self-assembled immobilization, were both covalently attached to PAA as sidechains. This DNA-conjugated PAA was then spontaneously immobilized on a gold substrate. Probe-1 on the immobilized polymer was hybridized to a 34-mer ssDNA (probe-2), which had the sequence desired for analyzing the target DNA. The fluorescence intensity after incubating the P-1 DNA-conjugated polymer with probe-2 DNA was much higher than with control sequence in the first hybridization. The interactions between target DNA and the DNA-conjugated PAA were investigated by fluorescence measurement. The interaction of fully matched target DNA with this immobilized DNA conjugated polymer has been studied at different ion strength conditions. SNP sequences as targets showed less than 15% the intensity of fully matched target DNA in the second hybridization, indicating that the gold surfaces coated with the DNA-conjugated PAA was highly specific to fully matched DNA. The DNA-conjugated PAA immobilized on a gold substrate is characterized by reduced nonspecific adsorption, due to less electrostatic repulsion as well as the polymer coating. Therefore, DNA-conjugated PAA can be used for probe DNA immobilization method.

Base Sequence↗
PubMed2006

[Distribution of MIF -173 single nucleotide polymorphism checked by tetra-primer amplification refractory mutation system].

OBJECTIVE: To study the distribution of macrophagemigration inhibitory factor gene (MIF) -173 single nucleotide polymorphism (SNP) of Chinese Han population in Zhejiang province. METHODS: The DNA samples were extracted from EDTA blood of 142 unrelated healthy individuals. Alleles of MIF -173 SNP were genotyped by using the techniques of tetra-primer amplification refractory mutation system (ARMS) and restriction fragment length polymorphisms (RFLP)-PCR Meantime the PCR products were cloned and sequenced. RESULTS: The authors detected three kinds of genotypes at the MIF -173 locus, and no deviation was observed from Hardy-Weinberg equilibrium. The final results were the same completely, whatever either tetra-primer ARMS or RFLP-PCR was used to check the MIF -173 single nucleotide polymorphism. Statistical analysis showed that the distributions of MIF -173 SNP alleles and genotype frequencies were significantly different between Chinese Han population and European Caucasian(P< 0.01), but no significant difference demonstrated to happen between Chinese and Japanese(P> 0.05). CONCLUSION: Tetra-primer ARMS is an accurate, rapid and economical method for SNP genotyping.There exists ethnic difference in the distribution of MIF -173 SNP alleles.

Adult↗
PubMed2002

Rapid genotyping of single nucleotide polymorphisms using novel minor groove binding DNA oligonucleotides (MGB probes).

Novel fluorescent oligonucleotides that contain a 3' minor groove binding group (MGB) hybridize to single-stranded targets with increased sequence-specificity compared to ordinary DNA probes. This reduces non-specific probe hybridization and results in low background fluorescence during the 5' nuclease PCR assay (TaqMan, Applied Biosystems, Foster City, CA). We developed a method for closed-tube genotyping using two allele-specific MGB probes labeled with different fluorophores in one reaction. After PCR, tubes were transported to a fluorescence plate-reader for analysis of fluorescence. Common spreadsheet software was used for automated genotype assignment. As an example, DNA samples from 172 hemochromatosis patients were selected and tested for molecular defects in the HFE gene, i.e., mutations in codon 63 and 282. Tight genotype clusters were observed for both codons and results with MGB probes were identical to conventional genotyping (PCR + restriction-fragment-length-polymorphism). We show that this fast and easy method can be used for large-scale (high-throughput) genetic studies but also for routine molecular diagnostics without post-PCR manipulation of amplicons or the need for real-time quantitative PCR machines. Hum Mutat 19:554-559, 2002.

Alleles↗
PubMed2005

Discrimination of single nucleotide polymorphisms by strand exchange assay using partially double-stranded probes.

Previously we designed the partially double-stranded (PDS) probes that have protruding single-stranded portion for a single-base mismatch analysis. The single-stranded portion is engineered to sense existences of mismatches in the counterparts and to transduce it in strand exchange rates. Here we report the influence of probe length and operating conditions, such as temperature and buffer conditions, on the mismatch resolution using the PDS probes. Reliable detection of single-base mismatches was achieved even with a 45mer-long probe. By lowering operating temperature, the higher and faster discrimination of the mismatches was demonstrated. Addition of cationic comb-type copolymers (CCCs) in the buffer increased the reaction rate 3-4 orders without disordering the resolving power.

Base Pair Mismatch↗
PubMed2004

[Sequencing analysis on partial translated region of uncoupling protein-3 gene and single nucleotide polymorphism associations with the porcine carcass and meat quality traits].

Porcine uncoupling protein-3 gene was used to study its effect on carcass and meat quality traits. The UCP3 partial translated regions in skeletal muscle from four pig breeds were sequenced and the comparison of the fragment sequences among four pig breeds showed that there were three coding-region single nucleotide polymorphisms (cSNP), of which the mutation at 842 bp of the open reading frame can result in the amino acid chang between methionine and threonine, so we selected the mutation as polymorphic site. The detection of polymorphic fragment by the technique of single strand conformation polymorphism (SSCP) and chi2 analysis among three pig breeds indicated that the distribution of three genotypes(AA, AB and BB) was significantly different between Meishan and Large White or Meishan and Landrace( P < 0.01). In addition, association analysis of UCP3 polymorphism with carcass and meat quality traits was conducted in the F2 generation from the Large White x Meishan resource family, the results with GLM analysis showed that UCP3 polymorphism has significant effect on several carcass and meat quality traits and also additive effect on some carcass and meat quality traits predominated in the resource family. It implied that UCP3 gene could be a candidate gene locus or a linked marker to a major gene, which affects the porcine carcass traits and meat quality traits significantly.

Animals↗
PubMed2004

Novel nonsynonymous single nucleotide polymorphisms in the CYP2D6 gene.

Cytochrome P450 (CYP) 2D6 is an important drug-metabolizing enzyme, and its gene is known to be highly polymorphic. Here, we report five novel nonsynonymous single nucleotide polymorphisms (SNPs), and 65 other sequence variations detected from the gene coding for cytochrome P450 (CYP) 2D6 in 254 Japanese subjects. Two of the novel nonsynonymous SNPs were associated with the *10 key SNP, C100T. Among the 65 variations, 23 were novel, including 12 SNPs in 5'-flanking, 1 in 5'-untranslated, and 10 in intronic regions. The nonsynonymous SNPs in the CYP2D6 gene were as follows: 73 C>T (Arg25Trp, exon 1), 972 C>T (Ala90Val, exon 2), 1611 T>A (Phe120Ile, exon 3), 1720 A>C (Glu156Ala, exon 3), 3172 A>C (Glu334Ala, exon 7). The SNPs, 73C>T, 972 C>T, 1611 T>A, 1720 A>C and 3172 A>C were linked with *10, *1, *10, *1 and *2, respectively.

Amino Acid Substitution↗
PubMed2001

The birth and death of human single-nucleotide polymorphisms: new experimental evidence and implications for human history and medicine.

Extensive, new databases of single-nucleotide polymorphisms (SNPs) provide a powerful resource for disease gene discovery, and they will be even more useful as more frequency data become available. Interesting observed genomic patterns include SNP deserts (regions of low SNP incidence) and lengthy regions of linkage disequilibrium containing only a few haplotypes. A variety of genetic studies will benefit from SNP resources.

Gene Frequency↗
PubMed2005

Functional MASP2 single nucleotide polymorphism plays no role in psoriasis.

BACKGROUND: Psoriasis is a heritable disease and genome-wide scans have implicated several loci of susceptibility. The gene for MASP-2, a protease involved in complement activation, is located within one of these loci on chromosome 1p. OBJECTIVES: To assess whether partial or total MASP-2 deficiency is a risk factor for developing psoriasis. METHODS: We screened a cohort of patients affected by plaque psoriasis and their parents by restriction fragment length polymorphism analyses. RESULTS: We detected a single nucleotide polymorphism that leads to an amino acid exchange, which results in dissociation of MASP-2 from a carbohydrate recognition complex. CONCLUSIONS: We show that this mutant allele is not associated with psoriasis. There was no favoured transmission from parents to affected offspring. The calculated allele frequency in this psoriasis group (Scottish and English) was 0.0326, and in the unaffected group 0.0379.

Alleles↗
PubMed2000

Identification of 142 single nucleotide polymorphisms in 41 candidate genes for rheumatoid arthritis in the Japanese population.

Single-nucleotide polymorphisms (SNPs) can make an important contribution to our understanding of genetic backgrounds that may influence medical conditions and ethnic diversity. We undertook a systematic survey of genomic DNA for SNPs located not only in coding sequences but also in non-coding regions (e.g., introns and 5' flanking regions) of selected genes. Using DNA samples from 48 Japanese patients with rheumatoid arthritis (RA) as templates, we surveyed 41 genes that represent candidates for RA, screening a total of 104 kb of DNA (30 kb of coding sequences and 74 kb of non-coding DNA). Within this 104 kb of genomic sequences we identified 163 polymorphisms (1 per 638 bases on average), of which 142 were single-nucleotide substitutions and the remainder, insertions or deletions. Of the coding SNPs, 52% were non-synonymous substitutions, and non-conservative amino acid changes were observed in a quarter of those. Sixty-nine polymorphisms showed high frequencies for minor alleles (more than 15%) and 20 revealed low frequencies (<5%). Our results indicated a greater average distance between SNPs than others have reported, but this disparity may reflect the type of genes surveyed and/or the relative ethnic homogeneity of our test population.

Alleles↗
PubMed1998

Identification of three new single nucleotide polymorphisms in the human tumor necrosis factor-alpha gene promoter.

We have identified three new human tumor necrosis factor-alpha (TNF-alpha) promoter polymorphisms with single nucleotide (nt) substitutions at -862, -856, and -574 nt relative to the TNF-alpha transcription start site. The -862 and -856 nt TNF-alpha promoter polymorphisms occur with high frequency in Caucasian and Cambodian individuals and are each non-randomly associated with three extended HLA haplotypes. This study, in which 61 independent TNF-alpha promoters were analyzed spanning from -977 to +93 nt relative to the TNF-alpha mRNA cap site, establishes a new canonical TNF-alpha promoter sequence. Furthermore, we show that none of the three novel polymorphisms at -862, -856 and -574 nt or polymorphisms previously described at positions -238, -308 and +70 have an effect upon TNF-alpha gene expression in activated lymphocytes. Thus, these TNF-alpha promoter polymorphisms likely serve as markers for neighboring genes encoding HLA or other undefined molecules in the MHC that may influence disease susceptibility.

Animals↗
PubMed2004

[Single nucleotide polymorphism analysis in sow mu opioid receptor gene].

Mu opioid receptor (MOR) is a member of G protein-coupled receptor family, distributed in the pain transduction region in the brain and related to emotion and behaviour. This study was designed to investigate the Single Nucleotide Polymorphism (SNP) of Mu opioid receptor gene in various breeds,including duroc, landrace and Yorkshire. 5' UTR (untranslate region), coding region and 3' UTR of Mu opioid receptor gene were amplified by eight pairs of primers, and the Single Nucleotide Polymorphism (SNP) were detected by SSCP. Five polymorphisms were found (Genebank Accession number: AF521309). The results of chi(2) test showed that the frequencies of genotypes in different breeds were significantly different (P<0.01). The frequencies of mutation genotypes in Yorkshire were significantly higher than Duroc and Landrace. According to the above results, we can speculate the difference of the frequencies of genotypes may be the results of long term choice pressure.

3' Untranslated Regions↗
PubMed2002

Single-nucleotide polymorphisms in the lipoprotein lipase gene associated with coronary heart disease in Chinese.

Coronary heart disease is a complex disease reflecting the interaction of multiple genes with the environment (e.g. diet, life style). Lipoprotein lipase (LPL) plays an important role in lipid metabolism and the pathogenesis of coronary atherosclerosis. Recent associations between single-nucleotide polymorphisms in the LPL gene and heart disease have been reported, but little is known in Chinese. The LPL gene spans >26 kb, with an mRNA of 3549 bp. In the present study, we screened 5155 bp (565 bp of 5' flanking region, nine exons and donor- and acceptor-splice sites, and some intronic bases) in 160 Chinese patients with confirmed coronary heart disease and 150 age- and gender-matched controls. Thirteen of the sixteen single-nucleotide polymorphisms that we found have not been previously reported. In males, significant (P<0.05) differences between the coronary heart disease patients and controls were found for five single-nucleotide polymorphisms: -421G>A (5' flanking region); +13,577C>A (intron 2); +16,052G>A, R192Q (exon 5); +16,173C>G and +16,177T>C (intron 5). In females, significant differences between the patients with coronary heart disease and controls were found for only the -421G>A and +16,052G>A (R192Q) mutations. Among the coronary heart disease males, significant (P<0.05) associations were found between the low-HDL high-triglyceride (LHDL/HTG) phenotype and the non-LHDL/HTG trait for the 5' flanking-421G, the intron 2+13,577C, and the exon 5+16,052G mutations, with odds-ratios (ORs)[confidence intervals] of 3.90[1.12-13.66], 3.38[1.22-9.40], and 3.22[1.04-10.01], respectively; no corresponding associations were found in females. There were 69, 51, 57 and 41 unphased haplotype patterns in male coronary heart disease, male control, female coronary heart disease and female control groups, respectively; the computer program PM-Plus found the heterogeneity model by far the best fit (P<0.0001 in males, >0.01 in females). These data show that some single-nucleotide polymorphisms in the LPL gene among Chinese are associated with abnormal lipid and lipoprotein profiles and predisposition to coronary heart disease, a genetically heterogeneous complex disease, and that they are gender-specific.

Adult↗
PubMed2006

Multiplex real-time single nucleotide polymorphism detection and quantification by quencher extension.

Multiplex quencher extension (multiplex-QEXT) is a novel closed tube single-step method for detection and quantification of several single nucleotide polymorphisms (SNPs) simultaneously. The principle of multiplex-QEXT is that 5' reporter-labeled probes are 3' single-base-extended with TAMRA dideoxy nucleotides if the respective SNP alleles are present. TAMRA can serve as either an energy acceptor (quencher-based detection) or donor [fluorescence resonance energy transfer (FRET)-based detection] for a wide range of different reporter fluorochromes. The extension can therefore be recorded by the respective reporter fluorescence change. We evaluated multiplex-QEXT, analyzing four different SNP loci in the Listeria monocytogenes inlA gene. Probes labeled with the reporters 6-FAM, TET, VIC, and Alexa Fluor 594 were used. Responses for the fluorochromes 6-FAM, TET, and VIC were detected by quenching (decreased fluorescence), while the response for Alexa Fluor 594 was detected by FRET (increased fluorescence). We evaluated the SNP-allele pattern in 252 different L. monocytogenes strains. Multiplex-QEXT gave a good resolution, detecting seven major and five minor groups of L. monocytogenes. Comparison with serotyping showed that multiplex-QEXT gave better resolution. We also evaluated the quantitative aspects of multiplex-QEXT. Quantitative information was obtained for all the fluorochrome/probe combinations in the sample pools. The detection limits for 6-FAM, TET and Alexa Fluor 594 were the presence of the 10% target SNP alleles (P < 0.05), while the detection limit for VIC was the presence of the 5% target SNP alleles (P < 0.05). Currently, overlap in the fluorescence emission spectra is the limiting factor for the multiplexing potential of QEXT. With the emergence of new fluorochromes with narrow emission spectra, we foresee great potential for increasing the multiplex level in the future.

Chromosome Mapping↗
PubMed2004

Novel single nucleotide polymorphisms and haplotypes within the bovine CXCR2 gene.

The objectives of this study were to identify single nucleotide polymorphisms (SNPs) and resulting haplotypes in the bovine CXCR2 gene. A 311-bp segment of the bovine CXCR2 gene was amplified and sequenced. Five SNPs at positions 612, 684, 777, 858, and 861 were expressed in both Holstein and Jersey dairy cattle. Four SNPs resulted in synonymous substitutions, while a non-synonymous switch at position 777 (G-->C) resulted in a glutamine to histidine substitution at amino acid residue 245. Strong linkage disequilibrium was exhibited for both breeds among all five loci (P<0.001). Both allele and genotype frequencies differed significantly with respect to breed at four of the five loci (P<0.001). The five polymorphisms generated ten distinct haplotypes. Six haplotypes were common between the two breeds, while Holsteins and Jerseys each uniquely expressed two haplotypes. Of the six common haplotypes, two represented 83% of the Jersey population; whereas four of these haplotypes represented 95% of the Holstein population.

Animals↗
PubMed2004

Large-scale validation of single nucleotide polymorphisms in gene regions.

Genome-wide association studies using large numbers of bi-allelic single nucleotide polymorphisms (SNPs) have been proposed as a potentially powerful method for identifying genes involved in common diseases. To assemble a SNP collection appropriate for large-scale association, we designed assays for 226,099 publicly available SNPs located primarily within known and predicted gene regions. Allele frequencies were estimated in a sample of 92 CEPH Caucasians using chip-based MALDI-TOF mass spectrometry with pooled DNA. Of the 204,200 designed assays that were functional, 125,799 SNPs were determined to be polymorphic (minor allele frequency > 0.02), of which 101,729 map uniquely to the human genome. Many of the commonly available RefSNP annotations were predictive of polymorphic status and could be used to improve the selection of SNPs from the public domain for genetic research. The set of uniquely mapping, polymorphic SNPs is located within 10 kb of 66% of known and predicted genes annotated in LocusLink, which could prove useful for large-scale disease association studies.

Databases, Genetic↗