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At least 559 records · Page 31Linked to original sources
PubMed2003

Identification and functional analysis of single nucleotide polymorphism in the tandem repeat sequence of thymidylate synthase gene.

The variable number of tandem repeat (VNTR) of thymidylate synthase (TS) gene, mainly 2 repeat (2R) and 3 repeat (3R), is one of the genetic variations that can potentially predict the effectiveness of 5-fluorouracil-based chemotherapy. In this study we identified an additional single nucleotide polymorphism (SNP) in the VNTR of TS, followed by functional and clinical analysis of the SNP. Two-hundred fifty eight tumor samples were obtained from patients with primary colorectal adenocarcinoma. We observed three different patterns of electrophoresis by analysis of the VNTR with 2R/3R heterozygote. The sequencing results revealed a SNP, G/C polymorphism, within the 28-bp repeat component of TS VNTR. Each polymorphic allele was assigned as 2G, 2C, 3G, or 3C according to the combination of SNP and VNTR. Functional analysis showed that the plasmid construct with 3G sequence had three to four times greater efficiency of translation than other polymorphic sequences. 3R allele in colorectal cancer was subdivided into around half by the SNP, indicating its commonness among Japanese. TS genotypes of the patients with colorectal cancer were classified into high expression type (2R/3G, 3C/3G, and 3G/3G) and low expression type (2R/2R, 2R/3C, and 3C/3C). The patients who received oral fluoropyrimedines survived longer than the patients with no treatment in the group of low expression type. No benefit of oral fluoropyrimedines was observed in the group of high expression type. These results suggest that the double polymorphism in the TS tandem repeat sequence, the SNP and the VNTR, may provide a potential for more effective prediction of the clinical outcome of 5-fluorouracil-based chemotherapy.

Adenocarcinoma↗
PubMed2026

[Genetic diversity analysis of Forsythia suspensa germplasm resources in Shanxi based on phenotypic traits and SNP molecular markers].

This study aimed to clarify the degree of fruit phenotypic variation and the characteristics of genetic diversity, population structure, and genetic differentiation of Forsythia suspensa resources in Shanxi, providing an important basis for germplasm conservation and breeding of superior varieties. A total of 46 F. suspensa fruits were collected, and 12 agronomic traits were measured and analyzed. The population genetic structure and genetic diversity of F. suspensa germplasm were evaluated using simplified genome sequencing technology. For the five quality traits of the 46 fruits, the Shannon-Wiener index ranged from 0.631 to 1.074, and the Simpson index ranged from 0.379 to 0.560. The seven quantitative traits exhibited abundant genetic variation, with coefficients of variation ranging from 9.764%(fruit shape index) to 45.494%(forsythin content). Principal component analysis reduced the 12 phenotypic traits to four factors, with a cumulative variance contribution of 74.547%. Sequencing data showed mean Q20 and Q30 values of 98.13% and 94.33%, respectively, with an average GC content of 35.95%. After filtering, a total of 12 347 327 high-quality single nucleotide polymorphism(SNP) loci were obtained. Based on these high-quality SNPs, principal component analysis, population structure analysis, and phylogenetic tree construction were carried out. The 46 germplasm resources were divided into four groups; however, grouping showed little relationship with geographic origin, and intermixing occurred among regions. Mantel test revealed a significant but weak positive correlation between phenotypic and genetic distances(r=0.159, P=0.001). At the molecular level, the four groups exhibited moderate genetic diversity overall, and the genetic differentiation index among populations ranged from 0.027 to 0.084, indicating low to moderate differentiation. The rich genetic diversity of the main phenotypic traits provides a solid material basis for screening superior germplasm and genetic breeding of F. suspensa.

Forsythia↗
PubMed2005

Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers.

Single-nucleotide polymorphisms (SNPs) are rapidly replacing microsatellites as the markers of choice for genetic linkage studies and many other studies of human pedigrees. Here, we describe an efficient approach for modeling linkage disequilibrium (LD) between markers during multipoint analysis of human pedigrees. Using a gene-counting algorithm suitable for pedigree data, our approach enables rapid estimation of allele and haplotype frequencies within clusters of tightly linked markers. In addition, with the use of a hidden Markov model, our approach allows for multipoint pedigree analysis with large numbers of SNP markers organized into clusters of markers in LD. Simulation results show that our approach resolves previously described biases in multipoint linkage analysis with SNPs that are in LD. An updated version of the freely available Merlin software package uses the approach described here to perform many common pedigree analyses, including haplotyping and haplotype frequency estimation, parametric and nonparametric multipoint linkage analysis of discrete traits, variance-components and regression-based analysis of quantitative traits, calculation of identity-by-descent or kinship coefficients, and case selection for follow-up association studies. To illustrate the possibilities, we examine a data set that provides evidence of linkage of psoriasis to chromosome 17.

Algorithms↗
PubMed2001

Application of denaturing high-performance liquid chromatography for mapping of single nucleotide polymorphisms in barley (Hordeum vulgare L.).

Recent advances in DNA sequence analysis and the establishment of high-throughput assays have provided the framework for large-scale discovery and analysis of DNA sequence variation. In this context, single nucleotide polymorphisms (SNPs) are of particular interest. To initiate a systematic approach to develop an SNP map of barley (Hordeum vulgare L.), we have employed denaturing high-performance liquid chromatography (DHPLC) to analyse segregating SNP patterns in a doubled-haploid (DH) mapping population. To this end, SNPs between the parental genotypes were identified using a direct sequencing approach. Once a SNP was established between the parents, the optimal melting temperature of the PCR fragment containing the SNP was predicted for its analysis by DHPLC. Following the detection of the optimal temperature, the DH lines were analysed for the presence of either of the alleles. To test the utility of the analysis, data from previously mapped RFLP markers from which these SNPs were derived were compared. Results from these experiments indicate that DHPLC can be efficiently employed in analysing SNPs on a high-throughput scale.

Chromatography, High Pressure Liquid↗
PubMed2003

Amino acid substitutions in the thyroglobulin gene are associated with susceptibility to human and murine autoimmune thyroid disease.

The 8q24 locus, which contains the thyroglobulin (Tg) gene, was previously shown to be strongly linked with autoimmune thyroid disease (AITD). We sequenced all 48 exons of the Tg gene and identified 14 single-nucleotide polymorphisms (SNPs). Case control association studies demonstrated that an exon 10-12 SNP cluster and an exon 33 SNP were significantly associated with AITD (P < 0.01). Haplotype analysis demonstrated that the combination of these two SNP groups was more significantly associated with AITD (P < 0.001). Gene-gene interaction studies provided evidence for an interaction between HLA-DR3 and the exon 33 SNP, giving an odds ratio of 6.1 for Graves' disease. We then sequenced exons 10,12, and 33 of the mouse Tg gene in 19 strains of mice. Fifty percent of the strains susceptible to thyroiditis had a unique SNP haplotype at exons 10 and 12, whereas none of the mouse strains that were resistant to thyroiditis had this SNP haplotype (P = 0.01). We concluded that Tg is a susceptibility gene for AITD, both in humans in and in mice. A combination of at least two Tg SNPs conferred susceptibility to human AITD. Moreover, the exon 33 SNP showed evidence for interaction with HLA-DR3 in conferring susceptibility to Graves' disease.

Alleles↗
PubMed2025

Amplicon-based analyses of single-nucleotide polymorphisms reveal the genetic structure of a forest insect baculovirus.

Amplicon-based next-generation sequencing (aNGS) is a powerful tool in diagnostics and genetic studies. We developed an aNGS approach to study the population structure of the Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV), a specific pathogen of the spongy moth Lymantria dispar, a devastating lepidopteran pest in European, Asian, and American deciduous forests. Naturally occurring pathogens, such as LdMNPV, are frequently reported to cause epizootics and a rapid decline of insect pest populations. DNA samples of pooled LdMNPV-infected larvae from forest regions in Northern Bavaria (Germany) were subjected to whole genome sequencing (WGS) and aNGS optimization. Then, five marker regions were identified in the genome of LdMNPV for PCR amplification, covering 21 highly specific single-nucleotide polymorphism (SNP) positions that enabled comprehensive analysis at the intra- and intersample levels. These markers were used in aNGS analyses of 70 single larvae collected in 12 forest sites, followed by SNP-based hierarchical clustering on principal components (HCPC). This approach identified three LdMNPV population clusters consisting of homogenous (pure) and heterogeneous (mixed) LdMNPV samples. To explain the genetic variability within each sample, a model based on linear optimization was developed and validated by comparing the predictions from aNGS and WGS data. The analyses showed that LdMNPV from Bavarian forests carried genetic variants highly similar to those present in the commercial product Gypchek&#xae;, developed for biocontrol. The distribution of genetic characteristics showed some trends of geographic and temporal prevalence, which are indicative of short-distance and long-distance transmission. The aNGS approach offers a fast, cost-effective, and comprehensive insight into the natural population structure of LdMNPV.

insects↗
PubMed2001

Statistical estimation and pedigree analysis of CCR2-CCR5 haplotypes.

As more SNP marker data becomes available, researchers have used haplotypes of markers, rather than individual polymorphisms, for association analysis of candidate genes. In order to perform haplotype analysis in a population-based case-control study, haplotypes must be determined by estimation in the absence of family information or laboratory methods for establishing phase. Here, we test the accuracy of the Expectation-Maximization (EM) algorithm for estimating haplotype state and frequency in the CCR2-CCR5 gene region by comparison with haplotype state and frequency determined by pedigree analysis. To do this, we have characterized haplotypes comprising alleles at seven biallelic loci in the CCR2-CCR5 chemokine receptor gene region, a span of 20 kb on chromosome 3p21. Three-generation CEPH families (n=40), totaling 489 individuals, were genotyped by the 5'nuclease assay (TaqMan). Haplotype states and frequencies were compared in 103 grandparents who were assumed to have mated at random. Both pedigree analysis and the EM algorithm yielded the same small number of haplotypes for which linkage disequilibrium was nearly maximal. The haplotype frequencies generated by the two methods were nearly identical. These results suggest that the EM algorithm estimation of haplotype states, frequency, and linkage disequilibrium analysis will be an effective strategy in the CCR2-CCR5 gene region. For genetic epidemiology studies, CCR2-CCR5 allele and haplotype frequencies were determined in African-American (n=30), Hispanic (n=24) and European-American (n=34) populations.

Alleles↗
PubMed2004

SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data.

UNLABELLED: SNP Chart is a Java application for the visualization and interpretation of microarray genotyping data primarily derived from arrayed primer extension-based chemistries. Spot intensity output files from microarray analysis tools are imported into SNP Chart, together with a multi-channel TIFF image of the original array experiment and a list of the actual single nucleotide polymorphisms (SNPs) being tested. Data from different and/or replicate probes that interrogate the same SNP, but that are scattered across the array grid, can be reassembled into a single chart format, specific for the SNP. This allows a quick and very effective 'visualization'/'quality control' of the data from multiple probes for the same SNP that can be easily interpreted and manually scored as a genotype. AVAILABILITY: http://www.snpchart.ca.

Computer Graphics↗
PubMed2005

Single-nucleotide polymorphism versus microsatellite markers in a combined linkage and segregation analysis of a quantitative trait.

Increasingly, single-nucleotide polymorphism (SNP) markers are being used in preference to microsatellite markers. However, methods developed for microsatellites may be problematic when applied to SNP markers. We evaluated the results of using SNPs vs. microsatellites in Monte Carlo Markov chain (MCMC) oligogenic combined segregation and linkage analysis methods. These methods were developed with microsatellite markers in mind. We selected chromosome 7 from the Collaborative Study on the Genetics of Alcoholism dataset for analysis because linkage to an electrophysiological trait had been reported there. We found linkage in the same region of chromosome 7 with the Affymetrix SNP data, the Illumina SNP data, and the microsatellite marker data. The MCMC sampler appears to mix with both types of data. The sampler implemented in this MCMC oligogenic combined segregation and linkage analysis appears to handle SNP data as well as microsatellite data and it is possible that the localizations with the SNP data are better.

Chromosome Mapping↗
PubMed2005

Microsatellites versus single-nucleotide polymorphisms in linkage analysis for quantitative and qualitative measures.

BACKGROUND: Genetic maps based on single-nucleotide polymorphisms (SNP) are increasingly being used as an alternative to microsatellite maps. This study compares linkage results for both types of maps for a neurophysiology phenotype and for an alcohol dependence phenotype. Our analysis used two SNP maps on the Illumina and Affymetrix platforms. We also considered the effect of high linkage disequilibrium (LD) in regions near the linkage peaks by analysing a "sparse" SNP map obtained by dropping some markers in high LD with other markers in those regions. RESULTS: The neurophysiology phenotype at the main linkage peak near 130 MB gave LOD scores of 2.76, 2.53, 3.22, and 2.68 for the microsatellite, Affymetrix, Illumina, and Illumina-sparse maps, respectively. The alcohol dependence phenotype at the main linkage peak near 101 MB gave LOD scores of 3.09, 3.69, 4.08, and 4.11 for the microsatellite, Affymetrix, Illumina, and Illumina-sparse maps, respectively. CONCLUSION: The linkage results were stronger overall for SNPs than for microsatellites for both phenotypes. However, LOD scores may be artificially elevated in regions of high LD. Our analysis indicates that appropriately thinning a SNP map in regions of high LD should give more accurate LOD scores. These results suggest that SNPs can be an efficient substitute for microsatellites for linkage analysis of both quantitative and qualitative phenotypes.

Alcoholism↗
PubMed2004

The -514 C->T hepatic lipase promoter region polymorphism and plasma lipids: a meta-analysis.

Investigations of the -514 C-->T single nucleotide polymorphism (SNP) in the hepatic lipase (HL) gene promoter region (LIPC) have yielded contradictory results regarding its association with changes in plasma lipids. The current study is a meta-analysis of 25 publications on this SNP, comprising over 24,000 individuals, and its relationship with total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol (HDL), triglycerides, and HL activity. Significant decreases were observed in HL activity for both the CT and TT genotypes compared with the CC genotype [weighted mean difference (WMD), -5.83 mmol/liter.h (95% confidence interval, -8.48, -3.17) and -11.05 mmol/liter.h (95% confidence interval, -14.74, -7.36), respectively]. Moreover, significant increases in HDL were found; the CT to CC comparison showed an increase in WMD of 0.04 mmol/liter (95% confidence interval, 0.02, 0.05) mmol/liter, and the increase in the TT vs. CC difference was WMD of 0.09 mmol/liter (95% confidence interval, 0.07, 0.12). These changes appear to be stepwise, implying an allele dosage effect. All P values for these associations were less than 0.001. This meta-analysis demonstrates the importance of the -514C-->T SNP in determining HL activity and plasma HDL concentration and helps quantify the role that hepatic lipase plays in the metabolism of HDL.

Cytosine↗
PubMedDate not supplied

Relevance of frequent mu-opioid receptor polymorphisms for opioid activity in healthy volunteers.

Polymorphisms in the mu-opioid receptor gene (OPRM1) are primary candidate sources of clinical variability in opioid therapy. Apart from the 118A>G single nucleotide polymorphism, nothing is known about the role of OPRM1 mutations in opioid therapy. The influence of the OPRM1 mutations on opioid pharmacodynamics was assessed in pooled data from 31 healthy volunteers obtained in previous studies with available plasma concentrations and pupil diameters after intravenous administration of morphine or morphine-6-glucuronide (M6G). A total of 24 candidate ORPM1 mutations were screened for and those found at an allelic frequency of at least 5% in the 31 subjects were analyzed for functional consequences, using population pharmacokinetic-pharmacodynamic modeling of the miotic effects of the opioids as a reliable and sensitive surrogate parameter of the central nervous opioid effects. Polymorphisms at an allelic frequency of > or =5% (n=310) were 118A>G in exon 1 (11.5%), the IVS2-31G>A (8.9%) and IVS2-691C>G (44.5%) SNPs in intron 2. The 118A>G SNP significantly increased the values of EC50 by a factor of more than 2 (non-mutated: EC50,morphine=30 nmol/l, EC50,M6G=750 nmol/l, 118G carriers: EC50,morphine=66 nmol/l, EC50,M6G=1650 nmol/l), whereas the IVS2-691C>G SNP had no effect. Based on morphine and M6G, the present analysis encourages focusing on the 118A>G SNP when investigating the role of OPRM1 mutations for the activity of opioid analgesics. Other OPRM1 mutations are probably less important either owing to low allelic frequency or due to poor indications for functional consequences. This applies to opioid potency in the context of opioid therapy but not to pain processing or substance addiction, in which opioid receptors are involved but other or additional OPRM1 mutations may be important.

Alleles↗
PubMed2002

[Identification of common disease related genes by means of genome-wide SNP typing].

Determination of the human genome sequence will enable analysis of one entire set of genes (genome). Single nucleotide polymorphism (SNP) is now increasingly a focus of attention because of its important role in the genetic background of common disease. In Japan, we have identified 190,000 SNPs in two years and also established high-throughput genotyping system as part of SNP projects started in 2000. Using such infrastructure, we are now advancing to the next phase: identification of common disease-related genes by genome-wide association studies.

Crohn Disease↗
PubMed2002

Nitric oxide induces osteoblast apoptosis through the de novo synthesis of Bax protein.

Nitric oxide (NO) plays a crucial role in the physiological and pathophysiological regulations of osteoblast functions. This study is designed to evaluate the toxic effects of NO released by sodium nitroprusside (SNP), an NO donor, on neonatal Wistar rat calvarial osteoblasts from the analyses of cell viability, alkaline phosphatase (ALP) activity, cell morphology, apoptotic cells, terminal deoxynucleotidyl transferase-mediated dUTP nick end-label (TUNEL) assay, DNA ladder, and immunocytochemistry and Western blot for proapoptotic Bax protein. SNP increased the levels of nitrite, an oxidative product of NO, in the culture medium of osteoblasts in concentration- and time-dependent manners, and altered cell morphologies to round and shrinkage shapes. Administration of osteoblasts with SNP resulted in concentration- and time-dependent decreases of cell viability and ALP activity. Analysis of apoptotic cells revealed that SNP increased the percentages of osteoblasts processing apoptosis. Analyses of TUNEL and DNA ladder showed that SNP caused DNA fragmentation. Pretreatment with cycloheximide, an inhibitor of protein synthesis, partially blocked SNP-induced osteoblast apoptosis. Imunocytochemical and immunoblotting analyses revealed that SNP increased Bax protein in osteoblasts. This study suggests that SNP could increase the levels of NO in osteoblasts, and cause osteoblast apoptosis possibly through the de novo synthesis of proapoptotic Bax protein.

Alkaline Phosphatase↗
PubMed2002

Analysis of six SNPs of NAT2 in Ngawbe and Embera Amerindians of Panama and determination of the Embera acetylation phenotype using caffeine.

Six NAT2 single-nucleotide polymorphisms (SNPs) were analysed in 105 unrelated Ngawbe and 136 unrelated Embera Amerindians (482 chromosomes) by SNP-specific polymerase chain reaction analysis. 282C>T was the most common synonymous mutation, while 857G>A was the most frequent nonsynonymous inactivating exchange. The allelic frequency of the NAT2*5 series (containing the 341T>C exchange) was 2.4% and 9.9% for Ngawbe and Embera, respectively, five- to 20-times lower than that in Caucasians. The NAT2*6 series (590G>A) showed allelic frequencies of 0% and 3.7%, eight- to 30-times lower than in Caucasians. On the other hand, the NAT2*7 series, characterized by mutation 857G>A, had allelic frequencies (23.3% and 22.8%) that were 10-20-times higher in Amerindians than in Caucasians. Amerindians are characterized by decreased genetic diversity because they display a low number of mutated alleles (four and five for Ngawbe and Embera, respectively) that are present at low proportions (27.6% and 39%), reduced genotypic variability (seven out of 15 and 12 out of 21 possible genotypes) and low heterozygosity (40% and 55.1%) at the NAT2 locus. The NAT2 phenotype was evaluated with caffeine in a subset of 72 Embera. There were no disagreements between genotype and phenotype among rapid and slow acetylators (13/72, 18%). We conclude that, in the Embera, the analysis of three inactivating mutations was sufficient in predicting the phenotype in more than 99.5% of these subjects. NAT2 would appear to be of a selectively neutral character given that there is no evidence of adaptation to the prevailing ecology in Amerindians.

Acetylation↗
PubMed2005

Association analysis of common variants of STAT6, GATA3, and STAT4 to asthma and high serum IgE phenotypes.

BACKGROUND: Immune responses characterized by T H 2 type cells and IgE are important for the development of asthma and atopy. The transcription factors STAT6, GATA3, and STAT4 mediate the cytokine-induced development of naive CD4 + T cells into either T H 1 or T H 2 type. OBJECTIVE: We studied genetic variation of the STAT6, GATA3, and STAT4 genes and examined whether single nucleotide polymorphisms (SNPs) in these loci were associated with asthma or serum high IgE levels in the Finnish asthmatic families. METHODS: With denaturing high-performance liquid chromatography we screened all exons and exon-intron boundaries of the genes in 14 to 22 patients. All identified SNPs were genotyped in 120 nuclear families, and the haplotypes were analyzed by Haplotype Pattern Mining based statistical analysis. When potential association was observed, the analysis was replicated among 245 asthmatic patients and 405 population-based control subjects. RESULTS: A total of 23 SNPs were identified, of which 8 were not previously listed in the SNP database. Interestingly, a haplotype analysis of GATA3 showed 3 related haplotypes that associated with different asthma and atopy related phenotypes among both the family and case-control data sets. For STAT6 and STAT4, no significant association to asthma or serum total IgE levels was observed. CONCLUSIONS: We identified a panel of novel SNPs in genes coding for proteins important in the T H 1/T H 2 cell differentiation. SNPs of the GATA3 gene showed an initial association to asthma-related phenotypes. Elucidation of the importance of the identified panel of SNPs in other T H 1/T H 2 mediated diseases will be of great interest.

Adult↗
PubMed2002

Single nucleotide polymorphisms derived from ancestral populations show no evidence for biased diversity estimates in Drosophila melanogaster.

Single nucleotide polymorphisms (SNPs) are about to become one of the most popular genetic markers for genetic model organisms. To test the usefulness of SNPs for estimating genetic diversity, we surveyed three genomic regions in two Drosophila melanogaster populations, one from Africa and one European, collected in Austria. Diversity estimates based on the full SNP set indicated higher levels of variability in the African than in the European flies. When the analysis was based on the European SNP set, European and African flies had similar levels of variability. Interestingly, this bias was not observed for diversity estimates using SNPs derived from the ancestral African population. This result suggests that diversity estimates based on SNPs from ancestral populations could provide a general strategy to avoid biased SNP diversity estimates. Finally, the potential of SNPs for nonmodel organisms is discussed.

Animals↗
PubMed2006

BNTagger: improved tagging SNP selection using Bayesian networks.

Genetic variation analysis holds much promise as a basis for disease-gene association. However, due to the tremendous number of candidate single nucleotide polymorphisms (SNPs), there is a clear need to expedite genotyping by selecting and considering only a subset of all SNPs. This process is known as tagging SNP selection. Several methods for tagging SNP selection have been proposed, and have shown promising results. However, most of them rely on strong assumptions such as prior block-partitioning, bi-allelic SNPs, or a fixed number or location of tagging SNPs. We introduce BNTagger, a new method for tagging SNP selection, based on conditional independence among SNPs. Using the formalism of Bayesian networks (BNs), our system aims to select a subset of independent and highly predictive SNPs. Similar to previous prediction-based methods, we aim to maximize the prediction accuracy of tagging SNPs, but unlike them, we neither fix the number nor the location of predictive tagging SNPs, nor require SNPs to be bi-allelic. In addition, for newly-genotyped samples, BNTagger directly uses genotype data as input, while producing as output haplotype data of all SNPs. Using three public data sets, we compare the prediction performance of our method to that of three state-of-the-art tagging SNP selection methods. The results demonstrate that our method consistently improves upon previous methods in terms of prediction accuracy. Moreover, our method retains its good performance even when a very small number of tagging SNPs are used.

Algorithms↗