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https://www.readbyqxmd.com/read/28636232/a-genetic-stochastic-process-model-for-genome-wide-joint-analysis-of-biomarker-dynamics-and-disease-susceptibility-with-longitudinal-data
#1
Liang He, Ilya Zhbannikov, Konstantin G Arbeev, Anatoliy I Yashin, Alexander M Kulminski
Unraveling the underlying biological mechanisms or pathways behind the effects of genetic variations on complex diseases remains one of the major challenges in the post-GWAS (where GWAS is genome-wide association study) era. To further explore the relationship between genetic variations, biomarkers, and diseases for elucidating underlying pathological mechanism, a huge effort has been placed on examining pleiotropic and gene-environmental interaction effects. We propose a novel genetic stochastic process model (GSPM) that can be applied to GWAS and jointly investigate the genetic effects on longitudinally measured biomarkers and risks of diseases...
June 21, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28635630/development-of-a-high-density-snp-based-linkage-map-and-detection-of-qtl-for-%C3%AE-glucans-protein-content-grain-yield-per-spike-and-heading-time-in-durum-wheat
#2
Ilaria Marcotuli, Agata Gadaleta, Giacomo Mangini, Antonio Massimo Signorile, Silvana Addolorata Zacheo, Antonio Blanco, Rosanna Simeone, Pasqualina Colasuonno
High-density genetic linkage maps of crop species are particularly useful in detecting qualitative and quantitative trait loci for important agronomic traits and in improving the power of classical approaches to identify candidate genes. The aim of this study was to develop a high-density genetic linkage map in a durum wheat recombinant inbred lines population (RIL) derived from two elite wheat cultivars and to identify, characterize and correlate Quantitative Trait Loci (QTL) for β-glucan, protein content, grain yield per spike and heading time...
June 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28635556/executive-control-in-schizophrenia-a-preliminary-study-on-the-moderating-role-of-comt-val158met-for-comorbid-alcohol-and-substance-use-disorders
#3
Giuseppe Carrà, Gabriella Nicolini, Cristina Crocamo, Annamaria Lax, Francesca Amidani, Francesco Bartoli, Filippo Castellano, Alessia Chiorazzi, Giulia Gamba, Costanza Papagno, Massimo Clerici
BACKGROUND: A functional polymorphism in the catechol-O-methyltransferase (COMT) gene (Val158Met) appears to influence cognition in people with alcohol/substance use disorders (AUD/SUD) and in those with psychosis. METHODS: To explore the potential moderating effect of these factors, a cross-sectional study was conducted, randomly recruiting subjects with DSM-IV diagnosis of schizophrenia. AUD/SUD was rigorously assessed, as well as COMT Val158Met polymorphism. Executive control functioning was measured using the Intra-Extra Dimensional Set Shift (IED)...
February 14, 2017: Nordic Journal of Psychiatry
https://www.readbyqxmd.com/read/28635422/metallothionein-polymorphisms-in-a-northern-spanish-population-with-neovascular-and-dry-forms-of-age-related-macular-degeneration
#4
Montserrat García, Lydia Álvarez, Ángela Fernández, Héctor González-Iglesias, Julio Escribano, Beatriz Fernández-Vega, Eva Villota, Luis Fernández-Vega Cueto, Álvaro Fernández-Vega, Miguel Coca-Prados
BACKGROUND: To elucidate the potential role of single nucleotide polymorphisms (SNPs) in the metallothionein (MT) genes in Northern Spanish patients with age-related macular degeneration (AMD). METHODS: A total of 130 unrelated Northern Spanish natives diagnosed with AMD (46 dry, 35 neovascular, and 49 mixed) and 96 healthy controls, matched by age and ethnicity, were enrolled in a case-control study. DNA was isolated from peripheral blood and genotyped for 14 SNPs located at 5 MT genes (MT1A: rs11076161, rs 11640851, rs8052394, and rs7196890; MT1B: rs8052334, rs964372, and rs7191779; MT1M: rs2270836 and rs9936741; MT2A: rs28366003, rs1610216, rs10636, and rs1580833; MT3: rs45570941) using TaqMan probes...
March 1, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28634255/population-genetic-structure-of-bromus-tectorum-in-the-mountains-of-western-north-america
#5
Spencer Arnesen, Craig E Coleman, Susan E Meyer
PREMISE OF THE STUDY: Invasive species are often initially restricted to a narrow range and may then expand through any of multiple mechanisms including phenotypic plasticity, in situ evolution, or selection on traits preadapted for new habitats. Our study used population genetics to explore possible processes by which the highly selfing invasive annual grass Bromus tectorum has expanded into montane environments. METHODS: We used 69 single nucleotide polymorphic (SNP) markers to genotype ca...
June 20, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28633917/polymorphic-variants-of-caspase-genes-8-3-in-the-risk-prediction-of-coronary-artery-disease
#6
Kishore Kumar Gundapaneni, Nivas Shyamala, Rajesh Kumar Galimudi, Keerthi Kupsal, Srilatha Reddy Gantala, Chiranjeevi Padala, Padma Gunda, Mohini Aiyengar Tupurani, Kaushik Puranam, Sanjib Kumar Sahu, Surekha Rani Hanumanth
Apoptosis has been involved in a number of pathological conditions including coronary artery disease (CAD). Caspases (CASP) are important regulators and executioners in both extrinsic and intrinsic apoptotic pathways and play a crucial role in the development and progression of CAD. The aim of the present study is to examine the role of Caspase 8 and 3 polymorphisms in the pathogenesis of CAD. 300 CAD patients and 300 healthy controls were genotyped for polymorphisms in CASP8 (-652 6N del/ins, IVS12-19G>A), CASP3 (rs4647601;G>T) by PCR-RFLP...
June 17, 2017: Gene
https://www.readbyqxmd.com/read/28633686/polymorphisms-of-the-tnf-%C3%AE-gene-interact-with-plasma-fatty-acids-on-inflammatory-biomarker-profile-a-population-based-cross-sectional-study-in-s%C3%A3-o-paulo-brazil
#7
Erica Oki, Marina N Norde, Antônio A F Carioca, José M P Souza, Inar A Castro, Dirce M L Marchioni, Regina M Fisberg, Marcelo M Rogero
The aim of the present study was to investigate the relationship of four TNF-α SNP with inflammatory biomarkers and plasma fatty acids (FA), and the interaction among them in a population-based, cross-sectional study in São Paulo, Brazil. A total of 281 subjects, aged >19 and <60 years, participated in a cross-sectional, population-based study performed in Brazil. The following SNP spanning the TNF-α gene were genotyped: -238G/A (rs361525), -308G/A (rs1800629), -857C/T (rs1799724) and -1031T/C (rs1799964)...
June 21, 2017: British Journal of Nutrition
https://www.readbyqxmd.com/read/28633642/prediction-and-analysis-of-three-gene-families-related-to-leaf-rust-puccinia-triticina-resistance-in-wheat-triticum-aestivum-l
#8
Fred Y Peng, Rong-Cai Yang
BACKGROUND: The resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens...
June 20, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28633446/genetic-indicators-of-drug-resistance-in-the-highly-repetitive-genome-of-trichomonas-vaginalis
#9
Martina Bradic, Sally D Warring, Grace E Tooley, Paul Scheid, William E Secor, Kirkwood M Land, Po-Jung Huang, Ting-Wen Chen, Chi-Ching Lee, Petrus Tang, Steven A Sullivan, Jane M Carlton
Trichomonas vaginalis, the most common non-viral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications and increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole is used for treatment, but in a fraction of clinical cases, the parasites can become resistant to this drug. We undertook sequencing of multiple clinical isolates and lab derived lines to identify genetic markers and mechanisms of metronidazole resistance...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28632940/characterization-of-the-i4399m-variant-of-apolipoprotein-a-implications-for-altered-prothrombotic-properties-of-lipoprotein-a
#10
Corey A Scipione, Jackson T McAiney, Daniel J Simard, Zainab A Bazzi, Matthew Gemin, Rocco Romagnuolo, Fraser L Macrae, Robert A Ariëns, Robert A Hegele, Janeen Auld, James W Gauld, Michael B Boffa, Marlys L Koschinsky
BACKGROUND: Lipoprotein(a) (Lp(a)) is a causal risk factor for a variety of cardiovascular diseases. Apolipoprotein(a) (apo(a)), the distinguishing component of Lp(a), is homologous to plasminogen, suggesting that Lp(a) can interfere with the normal fibrinolytic functions of plasminogen. This has implications for the persistence of fibrin clots in the vasculature and hence to atherothrombotic diseases. A single nucleotide polymorphism (rs3798220) in the gene encoding apo(a) has been reported that results in an Ile to Met substitution in the protease-like domain (I4399M variant)...
June 20, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28632302/sequentially-responsive-shell-stacked-nanoparticles-for-deep-penetration-into-solid-tumors
#11
Jinjin Chen, Jianxun Ding, Yucai Wang, Jianjun Cheng, Shengxiang Ji, Xiuli Zhuang, Xuesi Chen
Nanomedicine to overcome both systemic and tumor tissue barriers ideally should have a transformable size and surface, maintaining a certain size and negative surface charge for prolonged circulation, while reducing to a smaller size and switching to a positive surface charge for efficient penetration to and retention in the interstitial space throughout the tumor tissue. However, the design of such size and charge dual-transformable nanomedicine is rarely reported. Here, the design of a shell-stacked nanoparticle (SNP) is reported, which can undergo remarkable size reduction from about 145 to 40 nm, and surface charge reversal from -7...
June 20, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28630650/a-maternally-inherited-8-05%C3%A2-mb-xq21-deletion-associated-with-choroideremia-deafness-and-mental-retardation-syndrome-in-a-male-patient
#12
Siying Liang, Nan Jiang, Shuo Li, Xiaohu Jiang, Dongyi Yu
BACKGROUND: Deletions in Xq21 cause various congenital defects in males including choroideremia, deafness and mental retardation, depending on their size and gene content. Until now only a limited number of patients with Xq21 deletions has been reported. CASE PRESENTATION: Here we describe a 17-year-old male with choroideremia, deafness, and mental retardation syndrome. Using SNP arrays, an 8.05 Mb deletion in Xq21 was identified inherited from the apparently healthy mother...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28630621/development-of-snp-genotyping-assays-for-seed-composition-traits-in-soybean
#13
Gunvant Patil, Juhi Chaudhary, Tri D Vuong, Brian Jenkins, Dan Qiu, Suhas Kadam, Grover J Shannon, Henry T Nguyen
Seed composition is one of the most important determinants of the economic values in soybean. The quality and quantity of different seed components, such as oil, protein, and carbohydrates, are crucial ingredients in food, feed, and numerous industrial products. Soybean researchers have successfully developed and utilized a diverse set of molecular markers for seed trait improvement in soybean breeding programs. It is imperative to design and develop molecular assays that are accurate, robust, high-throughput, cost-effective, and available on a common genotyping platform...
2017: International Journal of Plant Genomics
https://www.readbyqxmd.com/read/28630475/utilization-of-a-wheat660k-snp-array-derived-high-density-genetic-map-for-high-resolution-mapping-of-a-major-qtl-for-kernel-number
#14
Fa Cui, Na Zhang, Xiao-Li Fan, Wei Zhang, Chun-Hua Zhao, Li-Juan Yang, Rui-Qing Pan, Mei Chen, Jie Han, Xue-Qiang Zhao, Jun Ji, Yi-Ping Tong, Hong-Xia Zhang, Ji-Zeng Jia, Guang-Yao Zhao, Jun-Ming Li
In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630081/calcium-sensing-receptor-genotype-and-response-to-cinacalcet-in-patients-undergoing-hemodialysis
#15
Sharon M Moe, Leah Wetherill, Brian Scott Decker, Dongbing Lai, Safa Abdalla, Jin Long, Matteo Vatta, Tatiana M Foroud, Glenn M Chertow
BACKGROUND AND OBJECTIVES: We tested the hypothesis that single nucleotide polymorphisms (SNPs) in the calcium-sensing receptor (CASR) alter the response to the calcimimetic cinacalcet. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: We analyzed DNA samples in the Evaluation of Cinacalcet HCl Therapy to Lower Cardiovascular Events (EVOLVE) trial, a randomized trial comparing cinacalcet to placebo on a background of usual care. Of the 3883 patients randomized, 1919 (49%) consented to DNA collection, and samples from 1852 participants were genotyped for 18 CASR polymorphisms...
June 19, 2017: Clinical Journal of the American Society of Nephrology: CJASN
https://www.readbyqxmd.com/read/28629864/structure-function-relationships-in-human-d-aspartate-oxidase-characterisation-of-variants-corresponding-to-known-single-nucleotide-polymorphisms
#16
Masumi Katane, Ryo Kanazawa, Risa Kobayashi, Megumi Oishi, Kazuki Nakayama, Yasuaki Saitoh, Tetsuya Miyamoto, Masae Sekine, Hiroshi Homma
D-Aspartate oxidase (DDO) is a degradative enzyme that is stereospecific for the acidic amino acid D-aspartate, an endogenous agonist of the N-methyl-D-aspartate (NMDA) receptor. Dysregulation of NMDA receptor-mediated neurotransmission has been implicated in the onset of various neuropsychiatric disorders including schizophrenia and in chronic pain. Thus, appropriate regulation of the amount of D-aspartate is believed to be important for maintaining proper neural activity in the nervous system. Herein, the effects of the non-synonymous single nucleotide polymorphisms (SNPs) R216Q and S308N on several properties of human DDO were examined...
June 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28629370/pharmacogenetic-testing-through-the-direct-to-consumer-genetic-testing-company-23andme
#17
Mengfei Lu, Cathryn M Lewis, Matthew Traylor
BACKGROUND: Rapid advances in scientific research have led to an increase in public awareness of genetic testing and pharmacogenetics. Direct-to-consumer (DTC) genetic testing companies, such as 23andMe, allow consumers to access their genetic information directly through an online service without the involvement of healthcare professionals. Here, we evaluate the clinical relevance of pharmacogenetic tests reported by 23andMe in their UK tests. METHODS: The research papers listed under each 23andMe report were evaluated, extracting information on effect size, sample size and ethnicity...
June 19, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28628859/structural-and-functional-effects-of-nucleotide-variation-on-the-human-tb-drug-metabolizing-enzyme-arylamine-n-acetyltransferase-1
#18
Ruben Cloete, Wisdom A Akurugu, Cedric J Werely, Paul D van Helden, Alan Christoffels
The human arylamine N-acetyltransferase 1 (NAT1) enzyme plays a vital role in determining the duration of action of amine-containing drugs such as para-aminobenzoic acid (PABA) by influencing the balance between detoxification and metabolic activation of these drugs. Recently, four novel single nucleotide polymorphisms (SNPs) were identified within a South African mixed ancestry population. Modeling the effects of these SNPs within the structural protein was done to assess possible structure and function changes in the enzyme...
June 10, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28628480/kernel-based-measure-of-variable-importance-for-genetic-association-studies
#19
Vicente Gallego, M Luz Calle, Ramon Oller
The identification of genetic variants that are associated with disease risk is an important goal of genetic association studies. Standard approaches perform univariate analysis where each genetic variant, usually Single Nucleotide Polymorphisms (SNPs), is tested for association with disease status. Though many genetic variants have been identified and validated so far using this univariate approach, for most complex diseases a large part of their genetic component is still unknown, the so called missing heritability...
June 17, 2017: International Journal of Biostatistics
https://www.readbyqxmd.com/read/28627804/the-effect-of-genetic-polymorphisms-in-slco2b1-on-the-lipid-lowering-efficacy-of-rosuvastatin-in-healthy-adults-with-elevated-low-density-lipoprotein
#20
Tae-Eun Kim, Dong-Seong Shin, Namyi Gu, Byung Hwa Jung, Jayoun Kim, Young Min Cho, Kyung-Sang Yu, Joo-Youn Cho
Rosuvastatin is an HMG-CoA reductase inhibitor widely used for treating hypercholesterolaemia. We investigated whether genetic polymorphisms in solute carrier organic anion transporter 2B1 (SLCO2B1) affect the lipid-lowering effect of rosuvastatin in healthy adults with elevated low-density lipoprotein (LDL). This study included 18 volunteers with LDL levels above 130 mg/dL. Rosuvastatin (20 mg) was administered once a day for 8 weeks. Blood samples were drawn before and after the 8-week treatment to measure changes in lipid levels...
June 19, 2017: Basic & Clinical Pharmacology & Toxicology
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