Table_2_Single Nucleotide Polymorphism Analysis Indicates Genetic Distinction and Reduced Diversity of Swine-Associated Methicillin Resistant Staphylococcus aureus (MRSA) ST5 Isolates Compared to Clinical MRSA ST5 Isolates.xlsx
TY - JOUR. T1 - Characterization of chromosome arm 20q abnormalities in myeloid malignancies using genome-wide single nucleotide polymorphism array analysis. AU - Huh, Jungwon. AU - Tiu, Ramon V.. AU - Gondek, Lukasz P.. AU - OKeefe, Christine L.. AU - Jasek, Monika. AU - Makishima, Hideki. AU - Jankowska, Ania M.. AU - Jiang, Ying. AU - Verma, Amit. AU - Theil, Karl S.. AU - McDevitt, Michael A.. AU - Maciejewski, Jaroslaw P.. PY - 2010/4. Y1 - 2010/4. N2 - Deletion of the long arm of chromosome 20 is a common abnormality associated with myeloid malignancies. We characterized abnormalities of chromosome 20 as defined by metaphase cytogenetics (MC) in patients with myeloid neoplasms to define commonly deleted regions (CDR) and commonly retained regions (CRR) using genome-wide, high resolution single nucleotide polymorphism array (SNP-A) analysis. We reviewed the MC results of a cohort of 1,162 patients with myeloid malignancies, including myelodysplastic syndromes (MDS), MDS/myeloproliferative ...
The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes - especially southern Swedes - were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of
Henry, RJ, Bundock, PC, Pacey-Miller, T, Kennedy, BG, Ablett, GA, Waters, DLE & Jin,QS 2003, Single nucleotide polymorphism analysis in support of plant breeding, paper presented to the 12th Australasian Plant Breeding Conference, Perth, WA, 15-20 September.. ...
The identification of copy number aberration in the human genome is an important area in cancer research. We develop a model for determining genomic copy numbers using high-density single nucleotide polymorphism genotyping microarrays. The method is based on a Bayesian spatial normal mixture model with an unknown number of components corresponding to true copy numbers. A reversible jump Markov chain Monte Carlo algorithm is used to implement the model and perform posterior inference. The performance of the algorithm is examined on both simulated and real cancer data, and it is compared with the popular CNAG algorithm for copy number detection. We demonstrate that our Bayesian mixture model performs at least as well as the hidden Markov model based CNAG algorithm and in certain cases does better. One of the added advantages of our method is the flexibility of modeling normal cell contamination in tumor samples.
YAKUBU, A.; DE DONATO, M. e IMUMORIN, I. G.. Modelling functional and structural impact of non-synonymous single nucleotide polymorphisms of the DQA1 gene of three Nigerian goat breeds. S. Afr. j. anim. sci. [online]. 2017, vol.47, n.2, pp.146-156. ISSN 2221-4062. http://dx.doi.org/10.4314/sajas.v47i2.6.. The DQA1 gene is a member of the highly polymorphic MHC class II locus that is responsible for the differences among individuals in immune response to infectious agents. In this study, the authors performed a comprehensive computational analysis of the functional and structural impact of non-synonymous or amino acid-changing single nucleotide polymorphisms (SNPs) (nsSNPs) that are deleterious to the DQA1 protein in Nigerian goats. A 310-bp fragment of exon 2 of the DQA1 gene was amplified and sequenced in 27 unrelated animals that are representative of three major Nigerian goat breeds (nine each of West African Dwarf, Red Sokoto, and Sahel of both sexes) using genomic DNA. Forty-two nsSNPs were ...
Single nucleotide polymorphisms (SNPs) are single base variations among groups of individuals. In order to study their properties in fine gene mapping, I considered their occurrence as transitions and transversions. The aim of the study was to classify each polymorphism depending upon whether it was a transition or transversion and to calculate the proportions of transitions and transversions in the SNP data from the public databases. This ratio was found to be 2.35 for data from the Whitehead Institute for Genome Research database, 2.003 from the Genome Database, and 2.086 from the SNP Consortium database. These results indicate that the ratio of the numbers of transitions to transversions was very different than the expected ratio of 0.5. To study the effect of different transition to transversion ratios in fine gene mapping, a simulation study was performed to generate nucleotide sequence data. The study investigated the effect of different transition to transversion ratios on linkage ...
Early detection of karyotype abnormalities, including aneuploidy, could aid producers in identifying animals which, for example, would not be suitable candidate parents. Genome-wide genetic marker data in the form of single nucleotide polymorphisms (SNPs) are now being routinely generated on animals. The objective of the present study was to describe the statistics that could be generated from the allele intensity values from such SNP data to diagnose karyotype abnormalities; of particular interest was whether detection of aneuploidy was possible with both commonly used genotyping platforms in agricultural species, namely the Applied BiosystemsTM AxiomTM and the Illumina platform. The hypothesis was tested using a case study of a set of dizygotic X-chromosome monosomy 53,X sheep twins. Genome-wide SNP data were available from the Illumina platform (11 082 autosomal and 191 X-chromosome SNPs) on 1848 male and 8954 female sheep and available from the AxiomTM platform (11 128 autosomal and 68 ...
Read Associations between three common single nucleotide polymorphisms (rs266729, rs2241766, and rs1501299) of ADIPOQ and cardiovascular disease: a meta-analysis, Lipids in Health and Disease on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
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Recent technological progress has permitted the efficient performance of genome-wide association studies (GWAS) to map genetic variants associated with common diseases. Here, we analyzed 2,893 single nucleotide polymorphisms (SNPs) that have been identified in 593 published GWAS as associated with a disease phenotype with respect to their genomic location. In absolute numbers, most significant SNPs are located in intergenic regions and introns. When compared to their representation on the chips, there is essentially overrepresentation of nonsynonymous coding SNPs (nsSNPs), synonymous coding SNPs, and SNPs in untranscribed regions upstream of genes among the disease associated SNPs. A Gene Ontology term analysis showed that genes putatively causing a phenotype often code for membrane associated proteins or signal transduction genes.. ...
Novel association of a functional single nucleotide polymorphism in the BTNL2 gene with susceptibility to rheumatoid arthritis and baseline radiographic severity in African-Americans independent of HLA DRB1: Results from the CLEAR registry ...
BNP assays are widely used in the diagnosis and prognosis of left ventricular (LV) dysfunction and heart failure. The functional single nucleotide polymorphism rs198389 in the promoter region of the BNP gene has been associated with higher BNP levels [1-3]. The prevalence of rs198389 in the general US population is unknown. The impact on common assay test characteristics, and cardiovascular and clinical phenotypes is also unknown. The goal of this study was to determine for the first time the prevalence of rs198389 in a US general adult population and its impact on (a) three commonly used BNP assays (BNP levels, diagnostic test performance), and (b) clinical phenotype and disease prevalence. ...
Pharmacological potency, side effect, and kinetics in body are influenced by single nucleotide polymorphisms of genes encoding key proteins controlling drugs
In regions where malaria is endemic, individuals are often infected with multiple distinct parasite genotypes, a situation that may impact on evolution of parasite virulence and drug resistance. Most approaches to studying genotypic diversity have involved analysis of a modest number of polymorphic loci, although whole genome sequencing enables a broader characterisation of samples. PCR-based microsatellite typing of a panel of ten loci was performed on Plasmodium falciparum in 95 clinical isolates from a highly endemic area in the Republic of Guinea, to characterize within-isolate genetic diversity. Separately, single nucleotide polymorphism (SNP) data from genome-wide short-read sequences of the same samples were used to derive within-isolate fixation indices (F ws), an inverse measure of diversity within each isolate compared to overall local genetic diversity. The latter indices were compared with the microsatellite results, and also with indices derived by randomly sampling modest numbers ...
Coronary Heart Disease (CHD) is one of the leading causes of death in the world with a projected global 82 million DALYs by 2020. Genetic and environmental factors contribute to CHD development. Here, the authors investigate the association between CHD risk and three Single Nucleotide Polymorphisms (SNPs) in the AdipoQ gene (rs3774261, rs1063537 and rs2082940); and the interaction of this association with environmental factors, in Northeast Han Chinese population. Using a case-control study design, 1514 participants (754 cases and 760 controls) were investigated. Three variants in the AdipoQ gene (rs3774261, rs1063537 and rs2082940) were selected and genotyped. The online SNPstats program and SPSS 21.0 software were used for data analyses. The authors found that the rs3774261G allele is associated with the risk of CHD but that the rs2082940T allele protects against CHD. No significant association was found between rs1063537 and CHD risk. The study also found significant interactions between triglyceride
We questioned the significance of haplotype structure in gene regulation by testing whether individual single nucleotide polymorphisms (SNPs) within a gene promoter region [interleukin-1-beta (IL1B)] might affect promoter function and, if so, whether function was dependent on haplotype context. We sequenced genomic DNA from 25 individuals of diverse ethnicity, focusing on exons and upstream flanking regions of genes of the cluster. We identified four IL1B promoter region SNPs that were active in transient transfection reporter gene assays. To substantiate allelic differences found in reporter gene assays, we also examined nuclear protein binding to promoter sequence oligonucleotides containing different alleles of the SNPs. The effect of individual SNPs on reporter gene transcription varied according to which alleles of the three other SNPs were present in the promoter construct. The SNP patterns that influenced function reflected common haplotypes that occur in the population, suggesting ...
Association of carriers of single nucleotide polymorphisms rs1143634 and rs16944 of the Il-1B gene and rs6265 of the BDNF gene with temporal lobe epilepsy
Genome‐wide association studies have successfullyidentified many novel genetic loci for various human complex diseases and quantitative traits
TABLE-US-00003 TABLE 3 SNPs associated with adolescent idiopathic scoliosis Case Control Allele1/2 Genotype count Genotype count Odds ratiob dbSNP ID Risk Study 11 12 22 RAF 11 12 22 RAF P valuea (95% CI) Pheic rs11190870 T/C GWAS 449 470 114 0.662 479 728 266 0.572 1.27.E-10 1.46 (1.30-1.65) T Replication 152 148 26 0.693 3129 4809 1883 0.563 5.13.E-11 1.75 (1.48-2.07) Combinedd 601 618 140 0.670 3608 5537 2149 0.565 1.24.E-19 1.56 (1.41-1.71) 0.0881 rs625039 G/A GWAS 533 424 76 0.721 600 695 178 0.643 4.75.E-09 1.43 (1.27-1.62) G Replication 172 135 19 0.735 1297 4579 3947 0.635 1.69.E-07 1.59 (1.34-1.90) Combinedd 705 559 95 0.724 1475 5274 4547 0.636 4.30.E-15 1.49 (1.35-1.65) 0.341 rs11598564 A/G GWAS 297 508 228 0.533 310 724 439 0.456 9.40.E-08 1.36 (1.22-1.53) G Replication 107 156 63 0.567 2107 4837 2879 0.461 8.82.E-08 1.54 (1.31-1.80) Combinedd 404 664 291 0.542 2417 5531 3318 0.46 5.98.E-14 1.42 (1.30-1.56) 0.226 Allele 1 represents major allele. Allele 1/2 is shown according to (+) ...
Miller, R. D., Phillips, M. S., Jo, I., Donaldson, M. A., Studebaker, J. F., Addleman, N., Alfisi, S. V., Ankener, W. M., Bhatti, H. A., Callahan, C. E., Carey, B. J., Conley, C. L., Cyr, J. M., Derohannessian, V., Donaldson, R. A., Elosua, C., Ford, S. E., Forman, A. M., Gelfand, C. A., Grecco, N. M., Gutendorf, S. M., Hock, C. R., Hozza, M. J., Hur, S., In, S. M., Jackson, D. L., Jo, S. A., Jung, S. C., Kim, S., Kimm, K., Kloss, E. F., Koboldt, D. C., Kuebler, J. M., Kuo, F. S., Lathrop, J. A., Lee, J. K., Leis, K. L., Livingston, S. A., Lovins, E. G., Lundy, M. L., Maggan, S., Minton, M., Mockler, M. A., Morris, D. W., Nachtman, E. P., Oh, B., Park, C., Park, C. W., Pavelka, N., Perkins, A. B., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Restine, S. L., Sachidanandam, R., Reinhart, A. J., Scott, K. E., Shah, G. J., Tate, J. M., Varde, S. A., Walters, A., White, J. R., Yoo, Y. K., Lee, J. E., Boyce-Jacino, M. T., Kwok, P. Y. (August 2005) High-density single-nucleotide ...
The single nucleotide polymorphism (SNP) rs1053004 in Signal transducer and activator of transcription 3(STAT3) was recently reported to be associated with chronic hepatitis B (CHB)-related hepatocellular carcinoma(HCC) in a Chinese cohort. This study was aimed at investigating whether the SNP might also contribute toHCC susceptibility in the Thai population. Study subjects were enrolled and divided into 3 groups includingCHB-related HCC (n=211), CHB without HCC (n=233) and healthy controls (n=206). The SNP was genotypedusing allelic discrimination assays based on TaqMan real-time PCR. Data analysis revealed that the distributionof different genotypes was in Hardy-Weinberg equilibrium (P|0.05). The frequencies of allele T (major allele)in HCC patients, CHB patients and healthy controls were 51.4%, 58.6% and 61.4%, respectively, whereas thefrequencies of C allele (minor allele) were 48.6%, 41.4% and 38.6%. The C allele frequency was higher in HCCwhen compared with CHB patients (odds ratio (OR)=1.34, 95%
Adiponectin gene (ADIPOQ) polymorphisms have been shown to affect adiponectin serum concentration and some have been associated with breast cancer (BC) risk. The aims of this study were to describe the frequency of single nucleotide polymorphisms (SNPs) of ADIPOQ in Mexican women with BC and to determine if they show an association with it. DNA samples from 397 patients and 355 controls were tested for the ADIPOQ gene SNPs: rs2241766 (GT) and rs1501299 (GT) by TaqMan allelic discrimination assay. Hardy-Weinberg equilibrium (HWE) was tested. Multiple SNP inheritance models adjusted by age and body mass index (BMI) were examined for the SNP rs1501299. We found that in the frequency analysis of rs1501299 without adjusting the BMI and age, the genotype distribution had a statistically significant difference (P = 0.003). The T allele was associated with a BC risk (OR, 1.99; 95% CI 1.13-3.51, TT vs. GG; OR, 1.53; 95% CI 1.12-2.09, GT vs. GG). The SNP rs2241766 was in HW disequilibrium in controls. In
Novel Single Nucleotide Polymorphisms and Combinations of Novel and Known Polymorphisms for Determining the Allele-Specific Expression of the IGF2 Gene - diagram, schematic, and image 42 ...
Introduction: Inherited susceptibility to lung cancer risk in never-smokers is poorly understood. The major reason for this gap in knowledge is that this disease is relatively uncommon (except in Asians), making it difficult to assemble an adequate study sample. In this study we conducted a genome-wide association study on the largest, to date, set of European-descent never-smokers with lung cancer. Methods: We conducted a two-phase (discovery and replication) genome-wide association study in never-smokers of European descent. We further augmented the sample by performing a meta-analysis with never-smokers from the recent OncoArray study, which resulted in a total of 3636 cases and 6295 controls. We also compare our findings with those in smokers with lung cancer. Results: We detected three genome-wide statistically significant single nucleotide polymorphisms rs31490 (odds ratio [OR]: 0.769, 95% confidence interval [CI]: 0.722-0.820; p value 5.31 x 10(-16)), rs380286 (OR: 0.770, 95% CI: ...
BACKGROUND Non-synonymous single nucleotide polymorphisms (SNPs) within vital DNA repair genes may cause reduction of activity leaving the genome unrepaired resulting in genomic instability and cancer. MATERIALS AND METHODS The present endeavour involved study on the association of the SNP rs13181 (Lys751Gln/A18911C) in the Nucleotide Excision Repair (NER) pathway gene ERCC2 (excision repair cross-complementing rodent repair deficiency, complementation group 2) with the risks of Squamous Cell Carcinomas of the Head and Neck (SCCHN) and Breast cancer using a case-control based association study among 685 (400 controls and 285 SCCHN-affected cases) and 395 (227 normal healthy female controls and 168 breast cancer cases) ethnically-matched samples, respectively from north India using Polymerase Chain Reaction followed by Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. RESULTS Results showed significant association of rs13181 homozygous mutant (CC) [Odds Ratio (OR) 4.412, 95% Confidence
This paper introduces and applies a genome wide predictive study to learn a model that predicts whether a new subject will develop breast cancer or not, based on her SNP profile. We first genotyped 696 female subjects (348 breast cancer cases and 348 apparently healthy controls), predominantly of Caucasian origin from Alberta, Canada using Affymetrix Human SNP 6.0 arrays. Then, we applied EIGENSTRAT population stratification correction method to remove 73 subjects not belonging to the Caucasian population. Then, we filtered any SNP that had any missing calls, whose genotype frequency was deviated from Hardy-Weinberg equilibrium, or whose minor allele frequency was less than 5%. Finally, we applied a combination of MeanDiff feature selection method and KNN learning method to this filtered dataset to produce a breast cancer prediction model. LOOCV accuracy of this classifier is 59.55%. Random permutation tests show that this result is significantly better than the baseline accuracy of 51.52%. Sensitivity
Single nucleotide polymorphism at exon 7 splice acceptor site of OAS1 gene determines response of hepatitis C virus patients to interferon therapy.: Response to
TY - CHAP. T1 - Development of single nucleotide polymorphism (SNP) markers for cereal breeding and crop research. T2 - current methods and future prospects. AU - Schramm, Carly. AU - Shavrukov, Yuri. AU - Anderson, Peter. AU - Kurishbaev, Akhylbek. AU - Jatayev, Satyvaldy. PY - 2019/6/27. Y1 - 2019/6/27. N2 - Modern cereal breeding and research increasingly relies upon the application of molecular genetics. This chapter provides an overview of the development of single nucleotide polymorphism (SNP) markers for use in such breeding and research. Fluorescence detection methods are fully reviewed as this field is experiencing an explosion of interest among plant biologists and crop breeders. More than 20 modern fluorescence-based methods for SNP identification and discrimination are included and the specific advantages and disadvantages of each covered. This variety of approaches gives researchers and industry the freedom to adapt and improve upon existing methods and develop novel techniques to ...
Objective: The objective of this study is to determine the associations among genetic variations in the P2X7 receptor gene, decreased bone mineral density (BMD), and the risk of osteoporosis in patients aged older than 50 years with ankle fractures. Methods: Patients were genotyped for 15 nonsynonymous single-nucleotide polymorphisms (SNPs) in the P2X7 gene. The sample was divided into two groups according to the bone densitometry results: an intervention group with osteopenia (T scores between -1.0 and -2.5) or osteoporosis (T scores ≤ -2.5) and a control group with values within the normal range (T scores ≥ -1). A total of 121 patients were evaluated: 65 in the intervention group and 56 in the control group. Results: The results suggested that SNPs 1, 4, 11, 13, 14, and 15 were loss-of-function (LOF) variants. SNP 12 was also associated with LOF in our population, but its RNA expression has not been analyzed to date. Conclusions: In conclusion, we demonstrate that functional polymorphisms ...
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Detecting causal single nucleotide polymorphisms (SNPs) from genome-wide association studies (GWASs) has been focusing on measuring the statistical power of single SNPs, which have a relatively small effect on predicting disease susceptibility and ignore prior biological information about the target disease. Especially in complex diseases such as type 2 diabetes (T2D), the effect of each single SNP is too small to explain the disease association significantly.. To enhance the statistical power, we propose considering combinations of SNPs. Yang et al. discovered that estimates of variance explained by genome-wide SNPs are unbiased with the proportion of SNPs used to estimate genetic relationships in human height [1]. Although SNPs with relatively low statistical power are considered together, the statistical power is not significantly affected. In addition, Park et al. compared the discriminatory power of the risk models in Crohns disease and prostate and colorectal (BPC) cancer and found that a ...
The prognoses of head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC) are poor, especially when both tumors occur at the same time. We examined the clonal relatedness of HNSCCs with synchronous ESCCs to confirm whether the second tumors were metastasis or separate second primary malignancies (SPMs) using loss of heterozygosity (LOH) analysis. Twenty-one pairs of formalin-fixed paraffin-embedded tissue from HNSCC patients with synchronous esophageal cancer were analyzed by single nucleotide polymorphism (SNP) array using the Illumina HumanCytoSNP FFPE-12 BeadChip (San Diego, CA), which contains approximately 300,000 probes. LOH was identified using Nexus Copy Number software (El Segundo, CA). Comparing the LOH pattern between HNSCC and paired ESCC, we found that 20 out of 21 paired tissues had a high number of discordant LOHs (LOH identified solely in the primary HNSCC but not in synchronous ESCC at the same genomic location) and a low number of concordant LOHs (LOH
TY - JOUR. T1 - An investigation of modifying effects of single nucleotide polymorphisms in metabolism-related genes on the relationship between peripheral nerve function and mercury levels in urine and hair. AU - ​Wang, ​Yi AU - Goodrich, Jaclyn M.. AU - Werner, Robert. AU - Gillespie, Brenda. AU - Basu, Niladri. AU - Franzblau, Alfred. PY - 2012/2/15. Y1 - 2012/2/15. N2 - Mercury (Hg) is a potent neurotoxicant. We hypothesized that single nucleotide polymorphisms (SNPs) in genes coding glutathione-related proteins, selenoproteins and metallothioneins may modify the relationship of mercury biomarkers with changes in peripheral nerve function. Dental professionals (n = 515) were recruited in 2009 and 2010. Sensory nerve function (onset latency, peak latency and amplitude) of the median, ulnar and sural nerves was recorded. Samples of urine, hair and DNA were collected. Covariates related to demographics, nerve function and elemental and methyl-mercury exposure were also collected. Subjects ...
Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire. All single nucleotide polymorphisms were segregating in this sample population and none deviated (P | 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P | 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P | 0.1). The G allele of LEP-1238 was associated (P | 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer
A number of previous studies suggested the presence of deleterious amino acid altering nonsynonymous single-nucleotide polymorphisms (nSNPs) in human populations. However, the proportions of deleterious nSNPs among rare and common variants are not known. To estimate these, ,77?000 SNPs from human protein-coding genes were analyzed. Based on two independent methods, this study reveals that up to 53% of rare nSNPs (minor allele frequency (MAF),0.002) could be deleterious in nature. The fraction of deleterious nSNPs declines with the increase in their allele frequencies and only 12% of the common nSNPs (MAF,0.4) were found to be harmful. This shows that even at high frequencies significant fractions of deleterious polymorphisms are present in human populations. These results could be useful for genome-wide association studies in understanding the relative contributions of rare and common variants in causing human genetic diseases ...
Mechanisms involved in metabolic syndrome (MetS) development include insulin resistance, weight regulation, inflammation and lipid metabolism. Aim of this study is to investigate the association of single nucleotide polymorphisms (SNPs) involved in these mechanisms with MetS. In a random sample of the EPIC-NL study (n = 1886), 38 SNPs associated with waist circumference, insulin resistance, triglycerides, HDL cholesterol and inflammation in genome wide association studies (GWAS) were selected from the 50K IBC array and one additional SNP was measured with KASPar chemistry. The five groups of SNPs, each belonging to one of the metabolic endpoints mentioned above, were associated with MetS and MetS-score using Goemans global test. For groups of SNPs significantly associated with the presence of MetS or MetS-score, further analyses were conducted. The group of waist circumference SNPs was associated with waist circumference (P=0.03) and presence of MetS (P=0.03). Furthermore, the group of SNPs related to
The vast majority of drugs act through binding to their protein targets. Prediction of the interaction between small molecules and these receptors is a key elem...
Researchers believe there are some 10 million common SNPs in the human genome. Scanning the genomes of large numbers of patients for such a large number of variants would be prohibitively expensive. Fortunately, a major shortcut has been discovered that reduces the workload about 30-fold. When the International HapMap Project was completed in October 2005, the researchers demonstrated that the 10 million variants cluster into local neighborhoods, called haplotypes, and that they can be accurately sampled by as few as 300,000 carefully chosen SNPs. New technological systems allow these SNPs to be systematically studied in high-throughput facilities that dramatically lower the cost.. In genome-wide association studies, researchers compare the genomes of people with an illness, who are referred to as cases, to unaffected people, who are referred to as controls. Through this comparison, it becomes possible to identify the genetic differences between sick and healthy people, even when the genetic ...
TY - JOUR. T1 - Association of single nucleotide polymorphisms in SOD2, XRCC1 and XRCC3 with susceptibility for the development of adverse effects resulting from radiotherapy for prostate cancer. AU - Burri, Ryan J.. AU - Stock, Richard G.. AU - Cesaretti, Jamie A.. AU - Atencio, David P.. AU - Peters, Sheila. AU - Peters, Christopher A.. AU - Fan, Grace. AU - Stone, Nelson N.. AU - Ostrer, Harry. AU - Rosenstein, Barry S.. PY - 2008/7. Y1 - 2008/7. N2 - The objective of this study was to determine whether an association exists between certain single nucleotide polymorphisms (SNPs), which have previously been linked with adverse normal tissue effects resulting from radiotherapy, and the development of radiation injury resulting from radiotherapy for prostate cancer. A total of 135 consecutive patients with clinically localized prostate cancer and a minimum of 1 year of follow-up who had been treated with radiation therapy, either brachytherapy alone or in combination with external-beam ...
To the Editors:. Asthma is a complex disease characterised by inflammation and remodelling of the airways. Over the past few decades enormous progress has been made to understand which genes are associated with asthma development and several interactions between genes and environmental factors have been elucidated. Investigations into genetic and gene expression profiling, as well as single nucleotide polymorphism analyses, have helped to better understand the underlying molecular mechanisms of asthma. However, the recent identification of novel regulatory functions for transposable and transposed genetic elements (TEs) may be an important and new key to help understand the genetics that cause the heterogeneous manifestations of the asthma pathology.. Approximately 45% of the human genome is made of TEs [1]. The vast majority of TEs originate from retrotransposition of genetic elements known as short and long interspersed nuclear elements, long terminal repeat-superfamilies and direct ...
Articular cartilage functions in withstanding mechanical loads and provides a lubricating surface for frictionless movement of joints. Osteoarthritis, characterised by cartilage degeneration, develops due to the progressive erosion of structural integrity and eventual loss of functional performance. Osteoarthritis is a multi-factorial disorder; two important risk factors are abnormal mechanical load and genetic predisposition. A single nucleotide polymorphism analysis demonstrated an association of hip osteoarthritis with an Arg324Gly substitution mutation in FrzB, a Wnt antagonist. The purpose of this study was two-fold: to assess whether mechanical stimulation modulates β-catenin signalling and catabolic gene expression in articular chondrocytes, and further to investigate whether there is an interplay of mechanical load and Wnt signalling in mediating a catabolic response. Chondrocytes were pre-stimulated with recombinant Wnt3A for 24 hours prior to the application of tensile strain (7.5%, 1 Hz) for
Single nucleotide polymorphisms One of the most significant outcomes of the Human Genome Project has been the iden- tification of large numbers of single nucleotide polymorphisms (SNPs) [1-3]. The ap-plication ...
Çfarë janë SNP-te - single nucleotide polymorphisms? Polimorfizmi i një nukleotidi te vetëm, te quajtur shpesh SNP (single nucleotide polymorphisms) janë lloji i variacionit me i shpeshte midis njerezve. Çdo SNP përfaqëson një diference ne një njësi te vetme te ADN-së, te quajtur nukleotid. Për shembull, një SNP mund te zevendesoje nukleotidin citozinë (C) me…
Beth Robb awarded the Stephen J. OBrien Award for the best student paper published in the Journal of Heredity for the paper Robb, E.A., C.L. Gitter, H. Cheng and M.E. Delany. 2011. Single nucleotide polymorphism analysis of chicken genetic resources: Variation within and among MHC-congenic lines and mapping of developmental mutations. J. Heredity 102:141-156. (cover art ...
BACKGROUND: Sustainable DNA resources and reliable high-throughput genotyping methods are required for large-scale, long-term genetic association studies. In the genetic dissection of common disease it is now recognised that thousands of samples and hundreds of thousands of markers, mostly single nucleotide polymorphisms (SNPs), will have to be analysed. In order to achieve these aims, both an ability to boost quantities of archived DNA and to genotype at low costs are highly desirable. We have investigated phi29 polymerase Multiple Displacement Amplification (MDA)-generated DNA product (MDA product), in combination with highly multiplexed BeadArray genotyping technology. As part of a large-scale BeadArray genotyping experiment we made a direct comparison of genotyping data generated from MDA product with that from genomic DNA (gDNA) templates. RESULTS: Eighty-six MDA product and the corresponding 86 gDNA samples were genotyped at 345 SNPs and a concordance rate of 98.8% was achieved. The BeadArray
Background: Sustainable DNA resources and reliable high-throughput genotyping methods are required for large-scale, long-term genetic association studies. In the genetic dissection of common disease it is now recognised that thousands of samples and hundreds of thousands of markers, mostly single nucleotide polymorphisms (SNPs), will have to be analysed. In order to achieve these aims, both an ability to boost quantities of archived DNA and to genotype at low costs are highly desirable. We have investigated Φ29 polymerase Multiple Displacement Amplification (MDA)-generated DNA product (MDA product), in combination with highly multiplexed BeadArray™ genotyping technology. As part of a large-scale BeadArray genotyping experiment we made a direct comparison of genotyping data generated from MDA product with that from genomic DNA (gDNA) templates. Results: Eighty-six MDA product and the corresponding 86 gDNA samples were genotyped at 345 SNPs and a concordance rate of 98.8% was achieved. The BeadArray
The MDR1 gene encodes the P-glycoprotein, an efflux transporter with broad substrate specificity. P-glycoprotein has raised great interest in pharmacogenetics because it transports a variety of structurally divergent drugs, including lipid-lowering drugs. The synonymous single-nucleotide polymorphism C3435T and the nonsynonymous single-nucleotide polymorphism G2677T/A in MDR1 have been indicated as potential determinants of variability in drug disposition and efficacy. In order to evaluate the effect of G2677T/A and C3435T MDR1 polymorphisms on serum levels of lipids before and after atorvastatin administration, 69 unrelated hypercholesterolemic individuals from São Paulo city, Brazil, were selected and treated with 10 mg atorvastatin orally once daily for ...
Single nucleotide polymorphisms, frequently called SNPs are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block called a nucleotide. SNPs occur normally throughout a persons DNA. They occur in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. Most commonly, these variations are found in the DNA between genes. They can act as biological markers, helping locate genes that are associated with disease. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in a disease by affecting the genes function. It has been proposed that SNPs may help predict an individuals response to certain drugs, susceptibility to environmental factors such as toxins and risk of developing particular diseases such as cancer.. SNPs, which are single base-pair variations in the DNA sequence of the genome, have been found to be associated with breast cancer ...
OLIVEIRA, Martha Maria de et al. Single Nucleotide Polymorphisms (SNPs) of the TNF-a (-238/-308) gene among TB and nom TB patients: susceptibility markers of TB occurrence?. J. bras. pneumol. [online]. 2004, vol.30, n.4, pp.371-377. ISSN 1806-3713. https://doi.org/10.1590/S1806-37132004000400012.. BACKGROUND: Host genetic factors may play a role in the susceptibility to active tuberculosis (TB), and several polymorphisms in different cytokine coding genes have been described and associated with diseases to date. OBJECTIVES: To investigate whether polymorphisms within the promoter region of the TNF-a (-238/-308) coding genes are associated to the occurrence of active TB. METHODS: SNPs within the TNF-a gene were analyzed by PCR-RFLP among two groups of individuals: patients with TB (n = 234, and patients non TB (n = 113). RESULTS: In this study, the presence of the -238A allele was associated with susceptibility to TB disease occurrence and severity (p = 0,00002; OR = 0,15; IC = 0,06-0,36. On the ...