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Snp-snp interaction

Zhong-Kai Lu, Zhi-Rong Chen, Jun-Yi Zhu, Ya Xu, Xian Hua
Inflammatory bowel disease (IBD) is a chronic, complex genetic disease with rapidly increasing prevalence in China. The interactions of genetic, environmental, and microbial factors contribute to the development of IBD, however, the precise etiologies of IBD are not well understood yet. Interleukin-23 receptor (IL-23R) encodes a subunit of receptor for IL-23, which is an important proinflammatory cytokine. In this study, we investigated the relationship between the single nucleotide polymorphism (SNP) of IL-23R gene and IBD in Chinese Han population...
September 27, 2016: Oncotarget
Karina Beatriz Acosta, Melina Noelia Lorenzini Campos, Susana Beatriz Etcheverry, Pedro Dario Zapata
The α6β4 integrin is composed of the α6 and β4 subunits that are encoded by the ITGα6 and the ITGβ4 genes, respectively. The α6β4 main function is to intervene in lamination and epithelia integrity maintenance by cell-matrix interactions. This integrin appears to have importance in breast cancer malignancy, as well as other epithelial carcinomas. The aim of this work was to investigate the potential role of ITGα6 (A380T) and ITGβ4 (R1281W) genetic variations in breast cancer susceptibility, in a female population from the northeast region of Argentina (Misiones)...
October 18, 2016: International Journal of Molecular Sciences
Bao-Zhu Yang, Shizhong Han, Henry R Kranzler, Abraham A Palmer, Joel Gelernter
Sex influences risk for opioid dependence (OD). We hypothesized that sex might interact with genetic loci that influence the risk for OD. Therefore we performed an analysis to identify sex-specific genomic susceptibility regions for OD using linkage. Over 6,000 single nucleotide polymorphism (SNP) markers were genotyped for 1,758 African- and European-American (AA and EA) individuals from 739 families, ascertained via affected sib-pairs with OD and/or cocaine dependence. Autosomewide non-parametric linkage scans, stratified by sex and population, were performed...
October 20, 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
Peter F Davies, Elisabetta Manduchi, Christian J Stoeckert, Yi-Zhou Jiang
Hemodynamics creates a constantly changing physical and chemical environment to which the arterial endothelium is exquisitely sensitive. Biomechanical stresses are intrinsic to blood flow characteristics and blood pressure and therefore are important considerations in hypertension. Near branching anatomical sites in arteries, blood flow separates from the main flow to undergo complex multi-directional characteristics for a part of each cardiac cycle (collectively referred to as disturbed flow). Atherosclerosis and aneurysmal pathology develop preferentially at disturbed flow locations, particularly when an additional cardiovascular risk factor such as hypercholesterolemia or high blood pressure are present...
September 2016: Journal of Hypertension
Stephen Harrap, Katrina Scurrah, Angela Lamantia, Justine Ellis
OBJECTIVE: Genes encoding key elements of the renin-angiotensin-aldosterone system (RAAS) cascade have been previously but inconsistently associated with blood pressure. Sex-dependency might be important here and functional genetic polymorphisms might exhibit epistatic effects. DESIGN AND METHOD: We assessed variation in the genes encoding renin (REN), angiotensinogen (AGT), angiotensin converting enzyme (ACE), angiotensin II type 1 receptor (AGTR1) and aldosterone synthase (CYP11B2)...
September 2016: Journal of Hypertension
Liang Li, Jian-Wei Zhang, Gregory Jenkins, Fang Xie, Erin E Carlson, Brooke L Fridley, William R Bamlet, Gloria M Petersen, Robert R McWilliams, Liewei Wang
BACKGROUND: Pancreatic cancer is a rapidly fatal disease with gemcitabine remaining the first-line therapy. We performed a genotype-phenotype association study to identify biomarkers for predicting gemcitabine treatment outcome. MATERIALS AND METHODS: We selected the top 200 single nucleotide polymorphisms (SNPs) identified from our previous genome-wide association study to associate with overall survival using 400 patients treated with/or without gemcitabine, followed by imputation analysis for regions around the identified SNPs and a replication study using an additional 537 patients by the TaqMan genotyping assay...
October 4, 2016: Pharmacogenetics and Genomics
Gnanasambandan Ramanathan, Santu Ghosh, Ramprasad Elumalai, Soundararajan Periyasamy, Bhaskar V K S Lakkakula
BACKGROUND & OBJECTIVES: Autosomal dominant polycystic kidney disease (ADPKD) is an inherited systemic disorder, characterized by the fluid filled cysts in the kidneys leading to end stage renal failure in later years of life. Hypertension is one of the major factors independently contributing to the chronic kidney disease (CKD) progression. The renin-angiotensin aldosterone system (RAAS) genes have been extensively studied as hypertension candidate genes. The aim of the present study was to investigate the role of angiotensin converting enzyme tagging - single nucleotide polymorphisms (ACE tag-SNPs) in progression of CKD in patients with ADPKD...
June 2016: Indian Journal of Medical Research
Gemma Amo, José A Cornejo-García, Jesus M García-Menaya, Concepcion Cordobes, M J Torres, Gara Esguevillas, Cristobalina Mayorga, Carmen Martinez, Natalia Blanca-Lopez, Gabriela Canto, Alfonso Ramos, Miguel Blanca, José A G Agúndez, Elena García-Martín
The high-affinity IgE receptor (Fcε RI) is a heterotetramer of three subunits: Fcε RIα, Fcε RIβ, and Fcε RIγ (αβγ2) encoded by three genes designated as FCER1A, FCER1B (MS4A2), and FCER1G, respectively. Recent evidence points to FCERI gene variability as a relevant factor in the risk of developing allergic diseases. Because Fcε RI plays a key role in the events downstream of the triggering factors in immunological response, we hypothesized that FCERI gene variants might be related with the risk of, or with the clinical response to, selective (IgE mediated) non-steroidal anti-inflammatory (NSAID) hypersensitivity...
2016: Frontiers in Pharmacology
Hyun-Jin Kim, Jin-Young Min, Kyoung-Bok Min
OBJECTIVES: Central obesity plays a major role in the development of many chronic diseases, including cardiovascular disease and cancer. Chronic stress may be involved in the pathophysiology of central obesity. Although several large-scale genome-wide association studies have reported susceptibility genes for central adiposity, the effects of interactions between genes and psychosocial stress on central adiposity have rarely been examined. A recent study focusing on Caucasians discovered the novel gene early B-cell factor 1 (EBF1), which was associated with central obesity-related traits via interactions with stress levels...
September 2016: Journal of Preventive Medicine and Public Health, Yebang Ŭihakhoe Chi
Sanjeev Budhathoki, Taiki Yamaji, Motoki Iwasaki, Norie Sawada, Taichi Shimazu, Shizuka Sasazuki, Teruhiko Yoshida, Shoichiro Tsugane
Epidemiological and experimental evidence suggest that vitamin D is protective against the risk of colorectal cancer. Polymorphisms in the gene encoding vitamin D receptor (VDR), which mediates most of the known cellular effects of vitamin D, have been suggested to alter this association. Here, using a tag SNP approach, we comprehensively evaluated the role of common genetic variants in VDR and their interaction with plasma vitamin D levels in relation to colorectal cancer risk in Japanese populations. A total of 356 colorectal cancer cases and 709 matched control subjects were selected from the participants of the Japan Public Health Center-based Prospective Cohort Study...
2016: PloS One
Jose M Colomina, Pere Cavallé-Busquets, Sílvia Fernàndez-Roig, Pol Solé-Navais, Joan D Fernandez-Ballart, Mónica Ballesteros, Per M Ueland, Klaus Meyer, Michelle M Murphy
: The effect of the betaine: homocysteine methyltransferase BHMT c.716G>A (G: guanosine; A: adenosine) single nucleotide polymorphism (SNP) on the BHMT pathway is unknown during pregnancy. We hypothesised that it impairs betaine to dimethylglycine conversion and that folate status modifies its effect. We studied 612 women from the Reus Tarragona Birth Cohort from ≤12 gestational weeks (GW) throughout pregnancy. The frequency of the variant BHMT c.716A allele was 30.8% (95% confidence interval (CI): 28...
October 9, 2016: Nutrients
Susanne Mommert, Lisanne Ratz, Kira Herwig, Maren Rost, Ralf Gutzmer, Thomas Werfel
Environmental triggers and genetic factors are supposed to lead to complex gene expression changes in psoriasis and interact in the manifestation of the disease. The histamine H4 receptor (HRH4) is functionally expressed on Th17 cells and plasmacytoid dendritic cells (pDCs) which play a prominent role in the pathogenesis of psoriasis. On pDCs a higher basal expression level of the HRH4 in psoriasis patients compared to healthy controls has been detected. The functional relationship between predisposing genetic variations in the HRH4 gene and psoriasis is yet not known...
October 7, 2016: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
John Gilbey, Eef Cauwelier, Mark W Coulson, Lee Stradmeyer, James N Sampayo, Anja Armstrong, Eric Verspoor, Laura Corrigan, Jonathan Shelley, Stuart Middlemas
Understanding the habitat use patterns of migratory fish, such as Atlantic salmon (Salmo salar L.), and the natural and anthropogenic impacts on them, is aided by the ability to identify individuals to their stock of origin. Presented here are the results of an analysis of informative single nucleotide polymorphic (SNP) markers for detecting genetic structuring in Atlantic salmon in Scotland and NE England and their ability to allow accurate genetic stock identification. 3,787 fish from 147 sites covering 27 rivers were screened at 5,568 SNP markers...
2016: PloS One
Jia Lin, Yanyan Zhang, Hongge Wang, Jiang Chang, Lixuan Wei, Lei Cao, Zhi Zhang, Xuemei Zhang
Caspase-3 (CASP3) plays a central role in executing cell apoptosis and thus in carcinogenesis. We previously investigated the relationship between functional polymorphisms in CAPS3 829 A>C and 20541 C>T and risk of esophageal squamous cell carcinoma. However little is known about the role of CASP3 variants in susceptibility to lung cancer. To figure out the contribution of CASP3 polymorphisms to lung cancer risk, genotypes of 1000 lung cancer patients and 1000 controls were conducted by RFLP-PCR (restriction fragment length polymorphism PCR)...
2016: PloS One
Daqing Nie, Hongbo Li, Guixiu Yan, Zhengyi Wang, Zhaomin He, Wenyu Zhou
The aim of the study is to investigate the impact of CD40 and CD226 gene single-nucleotide polymorphism (SNP) and additional gene-gene interaction on systemic lupus erythematosus (SLE) risk in Chinese Han populations. Three SNPs were selected for genotyping in the case-control study: rs4810485, rs763361, and rs3765456. Logistic regression was performed to investigate association between SNP within CD40 and CD226 and SLE. Generalized multifactor dimensionality reduction (GMDR) was used to analyze the interaction among three SNPs...
October 8, 2016: Rheumatology International
Chandra Prakash, S V Amitha Mithra, Praveen K Singh, T Mohapatra, N K Singh
BACKGROUND: Drought stress tolerance for crop improvement is an important goal worldwide. Drought is a complex trait, and it is vital to understand the complex physiological, biochemical, and molecular mechanisms of drought tolerance to tackle it effectively. Osmotic adjustment, oxidative stress management (OSM), and cell membrane stability (CMS) are major components of cellular tolerance under drought stress. In the current study, we explored the molecular basis of OSM in the drought tolerant rice variety, Nagina 22 and compared it with the popular drought sensitive rice variety, IR 64, under drought imposed at the reproductive stage, to understand how the parental polymorphisms correlate with the superiority of Nagina 22 and tolerant bulk populations under drought...
October 4, 2016: BMC Genomics
Theresa Dankowski, Torsten Schröder, Steffen Möller, Xinhua Yu, David Ellinghaus, Florian Bär, Klaus Fellermann, Hendrik Lehnert, Stefan Schreiber, Andre Franke, Christian Sina, Saleh M Ibrahim, Inke R König
BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory disorder of still unknown pathogenesis. Increasing evidence indicates that alterations in mitochondrial respiration and thus adenosine triphosphate (ATP) production are involved. This may contribute to mucosal energy deficiency and subsequently intestinal barrier malfunction, which is accepted to be a major hallmark of UC. Genetic alterations of the mitochondrial genome are one cause of mitochondrial dysfunction. However, less is known about mitochondrial gene polymorphisms in UC...
October 3, 2016: BMC Gastroenterology
Weizhao Yang, Yin Qi, Jinzhong Fu
BACKGROUND: High-altitude adaptation provides an excellent system for studying how organisms cope with multiple environmental stressors and interacting genetic modifications. To explore the genetic basis of high-altitude adaptation in poikilothermic animals, we acquired transcriptome sequences from a high-altitude population and a low-altitude population of the Asiatic toad (Bufo gargarizans). Transcriptome data from another high-altitude amphibian, Rana kukunoris and its low-altitude relative R...
October 3, 2016: BMC Genetics
Moses M Muraya, Jianting Chu, Yusheng Zhao, Astrid Junker, Christian Klukas, Jochen C Reif, Thomas Altmann
Hitherto, most quantitative trait loci (QTL) of maize growth and biomass yield have been identified for a single time point, usually the final harvest stage. Through this approach cumulative effects are detected, without considering genetic factors causing phase-specific differences in growth rates. To assess the genetics of growth dynamics, we employed automated non-invasive phenotyping to monitor the plant sizes of 252 diverse maize inbred lines at eleven different developmental time points. 50 k SNP array genotype data were used for genome wide association mapping and genomic selection...
October 6, 2016: Plant Journal: for Cell and Molecular Biology
Francisco Gomez-Delgado, Javier Delgado-Lista, Javier Lopez-Moreno, Oriol Alberto Rangel-Zuñiga, Juan Francisco Alcala-Diaz, Ana Leon-Acuña, Andreea Corina, Elena Yubero-Serrano, Jose David Torres-Peña, Antonio Camargo, Antonio Garcia-Rios, Javier Caballero, Justo Castaño, Jose M Ordovas, Jose Lopez-Miranda, Pablo Perez-Martinez
BACKGROUND: Leukocyte telomere length (LTL) attrition has been associated with age-related diseases. Telomerase RNA Component (TERC) genetic variants have been associated with LTL; whereas fatty acids (FAs) can interact with genetic factors and influence in aging. We explore whether variability at the TERC gene locus interacts with FA profile and two healthy diets (low-fat diet vs Mediterranean diet [MedDiet]) modulating LTL, glucose metabolism, and inflammation status in coronary heart disease (CHD) patients...
October 5, 2016: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
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