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Single nucleotide polymorphism

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https://www.readbyqxmd.com/read/28350819/development-and-application-of-a-taqman-single-nucleotide-polymorphism-genotyping-assay-to-study-infectious-laryngotracheitis-virus-recombination-in-the-natural-host
#1
Carlos A Loncoman, Carol A Hartley, Mauricio J C Coppo, Paola K Vaz, Andrés Diaz-Méndez, Glenn F Browning, Sang-Won Lee, Joanne M Devlin
To date, recombination between different strains of the avian alphaherpesvirus infectious laryngotracheitis virus (ILTV) has only been detected in field samples using full genome sequencing and sequence analysis. These previous studies have revealed that natural recombination is widespread in ILTV and have demonstrated that recombination between two attenuated ILTV vaccine strains generated highly virulent viruses that produced widespread disease within poultry flocks in Australia. In order to better understand ILTV recombination, this study developed a TaqMan single nucleotide polymorphism (SNP) genotyping assay to detect recombination between two field strains of ILTV (CSW-1 and V1-99 ILTV) under experimental conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28350742/short-article-impact-of-genetic-variation-in-the-vasopressin-1a-receptor-on-the-development-of-organ-failure-in-patients-admitted-for-acute-decompensation-of-liver-cirrhosis
#2
Annarein J C Kerbert, Jelte J Schaapman, Johan J van der Reijden, Àlex Amorós Navarro, Aiden McCormick, Bart van Hoek, Vicente Arroyo, Pere Ginès, Rajiv Jalan, Victor Vargas, Rudolf Stauber, Hein W Verspaget, Minneke J Coenraad
BACKGROUND: Vasopressin receptor-mediated vasoconstriction is considered to be involved in the pathogenesis of organ failure in acute-on-chronic liver failure (ACLF). PATIENTS AND METHODS: We studied the association between six single nucleotide polymorphisms (SNPs) of the vasopressin 1a receptor gene and the development of organ failure in 826 patients admitted for acute decompensation of liver cirrhosis (n=641) or ACLF (n=185). RESULTS: No associations were found for SNPs with the presence of circulatory or renal failure...
May 2017: European Journal of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28350619/genetic-determinants-of-essential-hypertension-in-the-population-of-tatars-from-russia
#3
Yanina Timasheva, Timur Nasibullin, Elvira Imaeva, Vera Erdman, Ilsiyar Tuktarova, Olga Mustafina
OBJECTIVE: Systemic inflammation and impaired function of endothelium play an important role in the development of hypertension. Our study aimed to analyze an association between essential hypertension and polymorphic markers in candidate genes in the group of 530 Tatars from the Republic of Bashkortostan, Russia. METHODS: The study group consisted of 216 male patients with essential hypertension (mean age 48.92 ± 8.8 years) and 314 healthy individuals of corresponding sex and age without history of cardiovascular disease...
May 2017: Journal of Hypertension
https://www.readbyqxmd.com/read/28350535/relationship-between-polymorphisms-in-the-crp-lep-and-lepr-genes-and-high-sensitivity-c-reactive-protein-levels-in-spanish-children
#4
Pilar Navarro, Olaya de Dios, Teresa Gavela-Pérez, Leandro Soriano-Guillen, Carmen Garcés
BACKGROUND: We investigated the association of single nucleotide polymorphisms (SNPs) in the C-reactive protein (CRP), leptin (LEP) and leptin receptor (LEPR) genes with high sensitivity CRP (hs-CRP) levels in two independent cohorts of healthy Spanish children. METHODS: We measured hs-CRP levels in 646 6-8-year-old and 707 12-16-year-old children using a high-sensitivity C-Reactive Protein ELISA kit. Four SNPs in the CRP gene (rs1205, rs1130864, rs2794521 and rs1800947), one SNP in the LEP gene (rs7799039) and two SNPs in the LEPR (rs1137100 and rs1137101) gene were determined by TaqMan® allelic discrimination assays...
March 28, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28346829/polymorphisms-in-the-glucocorticoid-receptor-gene-and-associations-with-glucocorticoid-induced-avascular-osteonecrosis-of-the-femoral-head
#5
Zhanqin Zhao, Yun Xue, Dun Hong, Hongjun Zhang, Zhigang Hu, Shunwu Fan, Haixiao Chen
AIMS: Individual sensitivity to glucocorticoid (GC) therapy might play a pivotal role in the development of GC-induced avascular necrosis of the femoral head (GANFH). In a growing number of studies, common polymorphisms of the glucocorticoid receptor gene (nuclear receptor subfamily 3 group C member 1 [NR3C1]) have been associated with variability in the individual sensitivity to GCs. However, whether the NR3C1 gene polymorphisms actually influence the susceptibility of GANFH remains unknown...
March 27, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28346566/gene-gene-interaction-between-pparg-and-apoe-gene-on-late-onset-alzheimer-s-disease-a-case-control-study-in-chinese-han-population
#6
S Wang, L Guan, D Luo, J Liu, H Lin, X Li, X Liu
AIMS: The aim was to investigate the impact of PPARG and APOE gene single nucleotide polymorphisms (SNPs) and additional gene- gene interaction on late-onset Alzheimer's disease (LOAD) risk based on Chinese Han population. METHODS: A total of 928 participants (466 males, 462 females), with a mean age of 81.3 ± 16.4 years old, were included in the study, including 460 LOAD patients and 468 normal controls participants. Logistic regression was performed to investigate association between SNP and LOAD risk and generalized multifactor dimensionality reduction (GMDR) was used to analysis the gene-gene interaction...
2017: Journal of Nutrition, Health & Aging
https://www.readbyqxmd.com/read/28346410/quality-of-tcr-signaling-determined-by-differential-affinities-of-enhancers-for-the-composite-batf-irf4-transcription-factor-complex
#7
Arifumi Iwata, Vivek Durai, Roxane Tussiwand, Carlos G Briseño, Xiaodi Wu, Gary E Grajales-Reyes, Takeshi Egawa, Theresa L Murphy, Kenneth M Murphy
Variable strengths of signaling via the T cell antigen receptor (TCR) can produce divergent outcomes, but the mechanism of this remains obscure. The abundance of the transcription factor IRF4 increases with TCR signal strength, but how this would induce distinct types of responses is unclear. We compared the expression of genes in the TH2 subset of helper T cells to enhancer occupancy by the BATF-IRF4 transcription factor complex at varying strengths of TCR stimulation. Genes dependent on BATF-IRF4 clustered into groups with distinct TCR sensitivities...
March 27, 2017: Nature Immunology
https://www.readbyqxmd.com/read/28346387/oprm1-c-118a-g-polymorphism-and-duration-of-morphine-treatment-associated-with-morphine-doses-and-quality-of-life-in-palliative-cancer-pain-settings
#8
Aline Hajj, Lucine Halepian, Nada El Osta, Georges Chahine, Joseph Kattan, Lydia Rabbaa Khabbaz
Despite increased attention on assessment and management, pain remains the most persistent symptom in patients with cancer, in particular in end-of-life settings, with detrimental impact on their quality-of-life (QOL). We conducted this study to evaluate the added value of determining some genetic and non-genetic factors to optimize cancer pain treatment. Eighty-nine patients were included in the study for the evaluation of palliative cancer pain management. The regression analysis showed that age, OPRM1 single nucleotide polymorphism (SNP), as well as the duration of morphine treatment were significantly associated with morphine doses at 24 h (given by infusion pump; p = 0...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346370/de-novo-assembly-annotation-and-characterization-of-root-transcriptomes-of-three-caladium-cultivars-with-a-focus-on-necrotrophic-pathogen-resistance-defense-related-genes
#9
Zhe Cao, Zhanao Deng
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium × hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to Pythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346242/genetic-variation-in-gabr%C3%AE-1-and-the-risk-for-developing-alcohol-dependence
#10
William A McCabe, Michael J Way, Kush Ruparelia, Susanne Knapp, M Adam Ali, Quentin M Anstee, Howard C Thomas, Andrew McQuillin, Marsha Y Morgan
Associations between the γ-aminobutyric acid type-A receptors (GABAA) and alcohol dependence risk have been reported, although the receptor subunit driving the association is unclear. Recent work in mice has highlighted a possible role for variants in the Gabr β1 subunit (Gabrβ1) in alcohol dependence risk, although this gene does not contain any common nonsynonymous variants in humans. However, the GABAA receptor is a heteropentamer so multiple potential variants within the gene complex could generate the alcohol dependence phenotype...
March 24, 2017: Psychiatric Genetics
https://www.readbyqxmd.com/read/28346054/genomic-regions-in-local-endangered-sheep-encode-potentially-favorable-genes
#11
Bianca Moioli, Roberto Steri, Gennaro Catillo
The economic evaluation of farm animal genetic resources plays a key role in developing conservation programs. However, to date, the link between diversity as assessed by neutral genetic markers and the functional diversity is not yet understood. Two genome-wide comparisons, using over 44,000 Single Nucleotide Polymorphisms, identified the markers with the highest difference in allele frequency between the Alpago endangered breed and two clusters, composed of four specialized dairy sheep, and four meat breeds respectively...
March 27, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/28345837/association-of-the-asp1312gly-thyroglobulin-gene-polymorphism-with-susceptibility-to-differentiated-thyroid-cancer-in-an-iranian-population
#12
Maryam Abidi, Shima Fayaz, Pezhman Fard Esfahani
Background and aim: While the causes of thyroid cancer in most patients remain largely unknown, it has recently been reported that there may be links to particular chromosome regions. In particular, polymorphisms (SNPs) in the thyroglobulin (TG) gene could be susceptibility factors. Methods: In this case-control study, any association of the Asp1312Gly single nucleotide polymorphism (SNP) in the TG gene (rs2069556) with susceptibility to differentiated thyroid cancer (DTC) was investigated among 103 Iranian patients and 100 controls who had no history of any type of cancer...
February 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28345816/germline-variation-in-the-3-untranslated-region-of-the-pou2af1-gene-is-associated-with-susceptibility-to-lymphoma
#13
Kan Zhai, Jiang Chang, Jinlong Hu, Chen Wu, Dongxin Lin
Genetic variations in certain genes may alter the susceptibility to lymphoma. We searched electronic databases and selected candidate single-nucleotide polymorphisms (SNPs) located within 3'-untranslated regions (3'-UTRs) that might affect miRNA-binding ability in the 50 most dysregulated genes in lymphoma for further study. We found that rs1042752-located in the 3'-UTR of POU2AF1, which plays a vital role in lymphomagenesis-was significantly associated with lymphoma risk in a case-control study with 793 patients and 939 controls...
March 27, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28345264/blood-transcriptomes-and-de-novo-identification-of-candidate-loci-for-mating-success-in-lekking-great-snipe-gallinago-media
#14
Jacob Höglund, Biao Wang, Stein Are Saether, Mozes Pil Kyu Blom, Peder Fiske, Peter Halvarsson, Gavin J Horsburgh, Terry Burke, John Atle Kålås, Robert Ekblom
We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called Single Nucleotide Polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking...
March 27, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28345042/human-genetic-and-metabolite-variation-reveals-that-methylthioadenosine-is-a-prognostic-biomarker-and-an-inflammatory-regulator-in-sepsis
#15
Liuyang Wang, Emily R Ko, James J Gilchrist, Kelly J Pittman, Anna Rautanen, Matti Pirinen, J Will Thompson, Laura G Dubois, Raymond J Langley, Sarah L Jaslow, Raul E Salinas, D Clayburn Rouse, M Arthur Moseley, Salim Mwarumba, Patricia Njuguna, Neema Mturi, Thomas N Williams, J Anthony G Scott, Adrian V S Hill, Christopher W Woods, Geoffrey S Ginsburg, Ephraim L Tsalik, Dennis C Ko
Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine measurements, and testing in a mouse model demonstrate that the methionine salvage pathway is a regulator of sepsis that can accurately predict prognosis in patients. Pathway-based genome-wide association analysis of nontyphoidal Salmonella bacteremia showed a strong enrichment for single-nucleotide polymorphisms near the components of the methionine salvage pathway...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28344492/cyp2c9-cypc19-and-cyp2d6-gene-profiles-and-gene-susceptibility-to-drug-response-and-toxicity-in-turkish-population
#16
Merve Arici, Gül Özhan
Pharmacogenetics is a vast field covering drug discovery research, the genetic basis of pharmacokinetics and dynamics, genetic testing and clinical management in diseases. Pharmacogenetic approach usually focuses on variations of drug transporters, drug targets, drug metabolizing enzymes and other biomarker genes. Cytochrome P450 (CYP) enzymes, an essential source of variability in drug-response, play role in not only phase I-dependent metabolism of xenobiotics but also metabolism of endogenous compounds such as steroids, vitamins and fatty acids...
March 2017: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
https://www.readbyqxmd.com/read/28344482/the-genetic-profiles-of-cyp1a1-cyp1a2-and-cyp2e1-enzymes-as-susceptibility-factor-in-xenobiotic-toxicity-in-turkish-population
#17
Merve Arici, Gül Özhan
Evaluation and sequencing of heritable alterations in the human genome and the large-scale identification of gene polymorphism for understanding the genetic background of individuals in response to potential toxicants are provided by toxicogenetics. Cytochrome P450 (CYP) enzymes play role not only phase I-dependent metabolism of xenobiotics but also metabolism of endogenous compounds. CYP1A1, CYP1A2 and CYP2E1 enzymes, which are in phase I enzymes, are responsible for metabolic activation and detoxification of several chemical compounds...
February 2017: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
https://www.readbyqxmd.com/read/28344410/identification-of-single-nucleotide-polymorphism-in-protein-phosphatase-1-regulatory-subunit-11-gene-in-murrah-bulls
#18
Varsha Jain, Brijesh Patel, Farhat Paul Umar, H M Ajithakumar, Suraj K Gurjar, I D Gupta, Archana Verma
AIM: This study was conducted with the objective to identify single nucleotide polymorphism (SNP) in protein phosphatase 1 regulatory subunit 11 (PPP1R11) gene in Murrah bulls. MATERIALS AND METHODS: Genomic DNA was isolated by phenol-chloroform extraction method from the frozen semen samples of 65 Murrah bulls maintained at Artificial Breeding Research Centre, ICAR-National Dairy Research Institute, Karnal. The quality and concentration of DNA was checked by spectrophotometer reading and agarose gel electrophoresis...
February 2017: Veterinary World
https://www.readbyqxmd.com/read/28344162/identification-of-genetic-markers-of-resistance-to-echinocandins-azoles-and-5-fluorocytosine-in-candida-glabrata-by-next-generation-sequencing-a-feasibility-study
#19
Chayanika Biswas, Sharon C-A Chen, Catriona Halliday, Karina Kennedy, E Geoffrey Playford, Deborah J Marriott, Monica A Slavin, Tania C Sorrell, Vitali Sintchenko
OBJECTIVES: Multi-antifungal drug resistance in Candida glabrata is increasing. We examined the feasibility of next generation sequencing (NGS) to investigate the presence of antifungal drug resistance markers in C. glabrata. METHODS: The antifungal susceptibility of 12 clinical isolates and one ATCC strain of C. glabrata was determined using the Sensititre YeastOne® YO10 assay. These included three isolate pairs where the second isolate of each pair had developed a rise in drug MICs...
March 23, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28343731/endoplasmic-reticulum-aminopeptidase-2-a-common-immunological-link-to-adverse-pregnancy-outcomes-and-cancer-clearance
#20
Eun D Lee
Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) trims HLA class I-binding peptides, determining the peptide repertoire presented for immune recognition. Variation in the ERAP2 amino acid sequence could affect the ability of some fetuses and tumors to achieve immune evasion. For example, homozygosity for an ERAP2 variant that has increased trimming efficiency for hydrophobic molecules has never been detected in mothers and fetuses. Thus, it is possible that this single nucleotide polymorphism (SNP) in the ERAP2 gene has been selected against in order to prevent alteration of the immune privileged uterine environment, and to allow tumors to escape immune recognition...
March 18, 2017: Placenta
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