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Single nucleotide polymorphism

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https://www.readbyqxmd.com/read/28535114/association-of-pd-1-5-c-t-but-not-pd-1-3-g-a-with-malignant-and-benign-brain-tumors-in-iranian-patients
#1
Fatemeh Namavar Jahromi, Morteza Samadi, Zahra Mojtahedi, Mohammad Reza Haghshenas, Mosa Taghipour, Nasrollah Erfani
Programmed death-1 (PD-1) negatively regulates the immune response. The aims of this study were to assess the association of two single nucleotide polymorphisms in the PD-1 gene, PD-1.5 (+7785 C/T-rs2227981) and PD-1.3 (+7146 G/A- rs11568821), with benign and malignant brain tumors. Patients with brain tumors (96 patients with benign and 56 with malignant brain tumors) and 150 healthy control individuals were included. PCR-RFLP was performed for genotyping. It was revealed that the genotype and allele frequencies of PD-1...
May 23, 2017: Immunological Investigations
https://www.readbyqxmd.com/read/28534892/minimizing-next-generation-sequencing-errors-for-hiv-drug-resistance-testing
#2
José A Fernández-Caballero, Natalia Chueca, Eva Poveda, Federico García
Next-generation sequencing prototypes for the routine diagnosis of resistance to antiretrovirals approved for the treatment of HIV infection are now being used in many clinical diagnostic laboratories. As some of the next-generation sequencing platforms may be a source of errors, it is necessary to improve the currently available protocols and implement bioinformatic tools that may help to correctly identify the presence of resistance mutations with clinical impact. Several studies have addressed these issues in recent years...
May 23, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28534704/associations-of-cyp4a11-gene-gene-and-gene-smoking-interactions-with-essential-hypertension-in-the-male-eastern-chinese-han-population
#3
Huimin Zhang, Limin Jin, Tonglu Mu, Yingying Fan, Haiyang Zhang, Yuhua Zhu, Xujie Mao, Rong Li, Siyuan Tang
OBJECTIVES: The aim of this study was to investigate the impact of CYP4A11 single-nucleotide polymorphisms (SNP), additional gene-gene and gene-environment interactions on essential hypertension (EH) risk. METHODS: A total of 1648 participants (788 males, 860 females), with a mean age of 56.1 ± 14.1 years old, were selected, including 820 EH patients and 828 normotension subjects. Logistic regression was performed to investigate association of SNPs within CYP4A11 gene with high DBP, high SBP and EH risk, and generalized multifactor dimensionality reduction (GMDR) was used to analyze the gene-gene interaction and gene-smoking interaction...
May 23, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/28534442/genotype-and-haplotype-analysis-of-abcb1-at-1236-2677-and-3435-among-systemic-sclerosis-patients
#4
Małgorzata Barańska, Mariola Rychlik-Sych, Jadwiga Skrętkowicz, Michał Dudarewicz, Bożena Dziankowska-Bartkowiak, Jacek Owczarek, Elżbieta Waszczykowska
Systemic sclerosis (SSc) belongs to the group of systemic diseases of the connective tissue, which are characterized by a chronic autoimmune inflammatory process. P-glycoprotein, initially associated with the drug resistance in patients with cancer, becomes more and more often a subject of considerations in terms of its significance in the development of illnesses, including autoimmune diseases. The aim of the study was an attempt to answer the question whether there was a relationship between ABCB1 polymorphisms and morbidity of systemic sclerosis in a Polish population...
May 23, 2017: Autoimmunity
https://www.readbyqxmd.com/read/28534360/association-of-microrna-933-variant-with-the-susceptibility-to-gastric-cancer
#5
Yitong Zhang, Yanyun Ma, Weihong Xu, Wenshuai Li, Pei Min, Jigang Qiu, Min Li, Feng Tang, Mingqing Zhang, Dongqin Yang, Jun Zhang
PURPOSE: Common single-nucleotide polymorphisms (SNPs) in microRNAs (miRs) have been shown to be associated with susceptibility to several types of human cancer. However, the association of miR-933 rs79402775 with gastric cancer (GC) has not been explored. METHODS: The association between rs79402775 in miR- 933 and the risk of GC was explored in Chinese population based on MassARRAY technology. A total 374 GC patients and 999 cancer-free controls were enrolled in this study...
March 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/28534238/a-fast-algorithm-for-bayesian-multi-locus-model-in-genome-wide-association-studies
#6
Weiwei Duan, Yang Zhao, Yongyue Wei, Sheng Yang, Jianling Bai, Sipeng Shen, Mulong Du, Lihong Huang, Zhibin Hu, Feng Chen
Genome-wide association studies (GWAS) have identified a large amount of single-nucleotide polymorphisms (SNPs) associated with complex traits. A recently developed linear mixed model for estimating heritability by simultaneously fitting all SNPs suggests that common variants can explain a substantial fraction of heritability, which hints at the low power of single variant analysis typically used in GWAS. Consequently, many multi-locus shrinkage models have been proposed under a Bayesian framework. However, most use Markov Chain Monte Carlo (MCMC) algorithm, which are time-consuming and challenging to apply to GWAS data...
May 22, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28533558/investigating-the-causal-effect-of-smoking-on-hay-fever-and-asthma-a-mendelian-randomization-meta-analysis-in-the-carta-consortium
#7
Tea Skaaby, Amy E Taylor, Rikke K Jacobsen, Lavinia Paternoster, Betina H Thuesen, Tarunveer S Ahluwalia, Sofus C Larsen, Ang Zhou, Andrew Wong, Maiken E Gabrielsen, Johan H Bjørngaard, Claudia Flexeder, Satu Männistö, Rebecca Hardy, Diana Kuh, Sarah J Barry, Line Tang Møllehave, Charlotte Cerqueira, Nele Friedrich, Tobias N Bonten, Raymond Noordam, Dennis O Mook-Kanamori, Christian Taube, Leon E Jessen, Alex McConnachie, Naveed Sattar, Mark N Upton, Charles McSharry, Klaus Bønnelykke, Hans Bisgaard, Holger Schulz, Konstantin Strauch, Thomas Meitinger, Annette Peters, Harald Grallert, Ellen A Nohr, Mika Kivimaki, Meena Kumari, Uwe Völker, Matthias Nauck, Henry Völzke, Chris Power, Elina Hyppönen, Torben Hansen, Torben Jørgensen, Oluf Pedersen, Veikko Salomaa, Niels Grarup, Arnulf Langhammer, Pål R Romundstad, Frank Skorpen, Jaakko Kaprio, Marcus R Munafò, Allan Linneberg
Observational studies on smoking and risk of hay fever and asthma have shown inconsistent results. However, observational studies may be biased by confounding and reverse causation. Mendelian randomization uses genetic variants as markers of exposures to examine causal effects. We examined the causal effect of smoking on hay fever and asthma by using the smoking-associated single nucleotide polymorphism (SNP) rs16969968/rs1051730. We included 231,020 participants from 22 population-based studies. Observational analyses showed that current vs never smokers had lower risk of hay fever (odds ratio (OR) = 0·68, 95% confidence interval (CI): 0·61, 0·76; P < 0·001) and allergic sensitization (OR = 0·74, 95% CI: 0·64, 0·86; P < 0·001), but similar asthma risk (OR = 1·00, 95% CI: 0·91, 1·09; P = 0·967)...
May 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28533516/asd-restricted-and-repetitive-behaviors-associated-at-17q21-33-genes-prioritized-by-expression-in-fetal-brains
#8
R M Cantor, L Navarro, H Won, R L Walker, J K Lowe, D H Geschwind
Autism spectrum disorder (ASD) is a behaviorally defined condition that manifests in infancy or early childhood as deficits in communication skills and social interactions. Often, restricted and repetitive behaviors (RRBs) accompany this disorder. ASD is polygenic and genetically complex, so we hypothesized that focusing analyses on intermediate core component phenotypes, such as RRBs, can reduce genetic heterogeneity and improve statistical power. Applying this approach, we mined Caucasian genome-wide association studies (GWAS) data from two of the largest ASD family cohorts, the Autism Genetics Resource Exchange and Autism Genome Project (AGP)...
May 23, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28532787/evolution-of-avian-encephalomyelitis-virus-during-embryo-adaptation
#9
Rüdiger Hauck, C Gabriel Sentíes-Cué, Ying Wang, Colin Kern, H L Shivaprasad, Huaijun Zhou, Rodrigo A Gallardo
Wild-type avian encephalomyelitis virus (AEV) causes neurological signs in young chicks but no disease in pullets after oral or intracutaneous infection. However, if the virus gets embryo-adapted by serial passaging in chicken embryos, it will cause AE after intracutaneous infection in chickens of all ages. Recently, several cases of AE in layer pullets occurring shortly after intracutaneous vaccination were described. The present investigation was initiated to determine if vaccines that had inadvertently been embryo-adapted were responsible for these outbreaks...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28532626/single-nucleotide-polymorphisms-of-abcc2-modulate-renal-secretion-of-endogenous-organic-anions
#10
Kienana Muhrez, Bérenger Largeau, Patrick Emond, Montigny Frédéric, Jean-Michel Halimi, Patrick Trouillas, Chantal Barin-LE Guellec
The ATP-binding cassette family transporter MRP2 (multidrug resistance-associated protein 2), encoded by the ABCC2 gene, is involved in the renal excretion of numerous xenobiotics and it is likely that it also transports many endogenous molecules arising from not only normal essential metabolic processes but also from environmental toxins or food intake. We used a targeted gas chromatography-mass spectrometry metabolomics analysis to study whether endogenous organic anions are differentially excreted in urines of healthy volunteers according to their genotype for three functional single nucleotide polymorphisms (SNPs) in ABCC2...
May 19, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28531893/association-study-of-serotonin-3-receptor-subunit-gene-variants-in-antipsychotic-induced-weight-gain
#11
Clement C Zai, Arun K Tiwari, Nabilah I Chowdhury, Eva J Brandl, Sajid A Shaikh, Natalie Freeman, Jeffrey A Lieberman, Herbert Y Meltzer, James L Kennedy, Daniel J Müller
BACKGROUND: Schizophrenia (SCZ) is a chronic severe neuropsychiatric disorder, where pharmacological treatment has been hindered by adverse effects, including antipsychotic-induced weight gain (AIWG) and related complications. Genetic studies have been exploring the appetite regulation and energy homeostasis pathways in AIWG with some promising leads. The serotonin system has been shown to participate in these pathways. METHODS: In the current study, we examined single nucleotide polymorphisms across the serotonin receptor genes HTR3A and HTR3B...
May 23, 2017: Neuropsychobiology
https://www.readbyqxmd.com/read/28531104/stumbling-across-the-same-phage-comparative-genomics-of-widespread-temperate-phages-infecting-the-fish-pathogen-vibrio-anguillarum
#12
Panos G Kalatzis, Nanna Iben Rørbo, Daniel Castillo, Jesper Juel Mauritzen, Jóhanna Jørgensen, Constantina Kokkari, Faxing Zhang, Pantelis Katharios, Mathias Middelboe
Nineteen Vibrio anguillarum-specific temperate bacteriophages isolated across Europe and Chile from aquaculture and environmental sites were genome sequenced and analyzed for host range, morphology and life cycle characteristics. The phages were classified as Siphoviridae with genome sizes between 46,006 and 54,201 bp. All 19 phages showed high genetic similarity, and 13 phages were genetically identical. Apart from sporadically distributed single nucleotide polymorphisms (SNPs), genetic diversifications were located in three variable regions (VR1, VR2 and VR3) in six of the phage genomes...
May 20, 2017: Viruses
https://www.readbyqxmd.com/read/28530680/the-effect-of-glucose-dependent-insulinotropic-polypeptide-gip-variants-on-visceral-fat-accumulation-in-han-chinese-populations
#13
T Wang, X Ma, T Tang, K Higuchi, D Peng, R Zhang, M Chen, J Yan, S Wang, D Yan, Z He, F Jiang, Y Bao, W Jia, K Ishida, C Hu
OBJECTIVES: We aim to validate the effects of glucose-dependent insulinotropic polypeptide (GIP) on fat distribution and glucose metabolism in Han Chinese populations. METHODS: We genotyped six tag single-nucleotide polymorphisms (SNPs) of GIP and four tag SNPs of glucose-dependent insulinotropic polypeptide receptor (GIPR) among 2884 community-based individuals from Han Chinese populations. Linear analysis was applied to test the associations of these variants with visceral fat area (VFA) and subcutaneous fat area (SFA) quantified by magnetic resonance imaging as well as glucose-related traits...
May 22, 2017: Nutrition & Diabetes
https://www.readbyqxmd.com/read/28530679/polymorphisms-of-the-oxytocin-receptor-gene-and-overeating-the-intermediary-role-of-endophenotypic-risk-factors
#14
C Davis, K Patte, C Zai, J L Kennedy
BACKGROUND/OBJECTIVES: Oxytocin (OXT) is an evolutionarily ancient neuropeptide with strong links to affiliative and prosocial behaviors, and the management of stress. Increases in OXT also tend to decrease food intake, especially of sweet carbohydrates. The social correlates of low OXT levels mesh with the social deficits and stress proneness identified in interpersonal models of overeating, as well as the increased appetite for highly palatable foods typically seen in chronic overeaters...
May 22, 2017: Nutrition & Diabetes
https://www.readbyqxmd.com/read/28530466/angiotensin-type-1-receptor-a1166c-polymorphism-and-systemic-lupus-erythematosus-correlation-with-cellular-immunity-and-oxidative-stress-markers
#15
H Baniamerian, F Bahrehmand, A Vaisi-Raygani, Z Rahimi, T Pourmotabbed
Angiotensin II, one of the rennin-angiotensin system components, is important in the cardiovascular hemodynamic and plays an important role in the development of cardiovascular disease in systemic lupus erythematosus (SLE) patients. The angiotensin II, through interaction with angiotensin II type 1 receptor (AGTR1), promotes proliferation, inflammation and fibrosis. The single nucleotide polymorphism of the AGTR1 (dbSNP: rs5186) gene can be associated with development and progression of SLE disease. The aims of this study were to compare the frequency of AGTR1 rs5186 in SLE patients with healthy individuals and to evaluate possible association between AGTR1 A1166C gene polymorphism and serum level of lipids, neopterin and malondialdehyde in SLE patients from a population of West Iran...
January 1, 2017: Lupus
https://www.readbyqxmd.com/read/28530443/association-of-single-nucleotide-polymorphism-in-the-hepcidin-promoter-gene-with-susceptibility-to-extrapulmonary-tuberculosis
#16
Li Liang, Huijuan Liu, Jun Yue, Li-Rong Liu, Min Han, Liu-Lin Luo, Yan-Lin Zhao, Heping Xiao
BACKGROUND: Hepcidin is a 25-amino acid peptide produced by the liver in response to inflammation and iron overload. It is encoded by the hepcidin antimicrobial peptide (HAMP) gene and plays a key role in innate immunity. Previous studies have reported that a -582 A>G polymorphism in the HAMP promoter (HAMP-P) affects hepcidin expression, causing susceptibility to various bacterial and viral pathogens. However, it is not known whether the HAMP-P -582 A>G polymorphism is associated with tuberculosis (TB) susceptibility...
May 22, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28528403/assessing-the-causal-relationship-between-obesity-and-venous-thromboembolism-through-a-mendelian-randomization-study
#17
Sara Lindström, Marine Germain, Marta Crous-Bou, Erin N Smith, Pierre-Emmanuel Morange, Astrid van Hylckama Vlieg, Hugoline G de Haan, Daniel Chasman, Paul Ridker, Jennifer Brody, Mariza de Andrade, John A Heit, Weihong Tang, Immaculata DeVivo, Francine Grodstein, Nicholas L Smith, David Tregouet, Christopher Kabrhel
Observational studies have shown an association between obesity and venous thromboembolism (VTE) but it is not known if observed associations are causal, due to reverse causation or confounding bias. We conducted a Mendelian Randomization study of body mass index (BMI) and VTE. We identified 95 single nucleotide polymorphisms (SNPs) that have been previously associated with BMI and assessed the association between genetically predicted high BMI and VTE leveraging data from a previously conducted GWAS within the INVENT consortium comprising a total of 7507 VTE cases and 52,632 controls of European ancestry...
May 20, 2017: Human Genetics
https://www.readbyqxmd.com/read/28527809/accuracy-of-genomic-predictions-in-gyr-bos-indicus-dairy-cattle
#18
S A Boison, A T H Utsunomiya, D J A Santos, H H R Neves, R Carvalheiro, G Mészáros, Y T Utsunomiya, A S do Carmo, R S Verneque, M A Machado, J C C Panetto, J F Garcia, J Sölkner, M V G B da Silva
Genomic selection may accelerate genetic progress in breeding programs of indicine breeds when compared with traditional selection methods. We present results of genomic predictions in Gyr (Bos indicus) dairy cattle of Brazil for milk yield (MY), fat yield (FY), protein yield (PY), and age at first calving using information from bulls and cows. Four different single nucleotide polymorphism (SNP) chips were studied. Additionally, the effect of the use of imputed data on genomic prediction accuracy was studied...
May 17, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28527365/variation-in-the-ovine-myf5-gene-and-its-effect-on-carcass-lean-meat-yield-in-new-zealand-romney-sheep
#19
Jiqing Wang, Huitong Zhou, Rachel H J Forrest, Jiang Hu, Xiu Liu, Shaobin Li, Yuzhu Luo, Jon G H Hickford
Myogenic factor 5 (MYF5) plays an important role in regulating skeletal muscle, but to date there have been no reports on whether the gene is variable and whether this variation is associated with meat yield in sheep. In this study, four variants (A to D) of ovine MYF5 containing two Single Nucleotide Polymorphisms (SNPs) and one basepair (bp) insertion/deletion were detected by Polymerase Chain Reaction - Single Stranded Conformational Polymorphism (PCR-SSCP) analysis. Breed differences in variant frequencies were observed...
May 11, 2017: Meat Science
https://www.readbyqxmd.com/read/28527151/association-of-the-mir-196a2-mir-146a-and-mir-499-polymorphisms-with-asthma-phenotypes-in-a-korean-population
#20
Hoang Kim Tu Trinh, Duy Le Pham, Su-Chin Kim, Ri-Yeon Kim, Hae-Sim Park, Seung-Hyun Kim
BACKGROUND: MicroRNAs (miRNAs) modulate expressions of inflammatory genes, thereby regulating inflammatory responses. Single nucleotide polymorphisms (SNPs) in miRNAs could affect their efficiency in binding to messenger RNAs (mRNAs). OBJECTIVE: We investigated the associations of miRNA SNPs with asthma phenotypes. miR-196a2 (rs11614913 T>C), miR-146a (rs2910164 C>G), and miR-499 (rs3746444 A>G) were genotyped in 347 asthma patients and 172 normal healthy controls (NCs)...
May 19, 2017: Molecular Diagnosis & Therapy
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