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https://www.readbyqxmd.com/read/28225792/the-adamts9-gene-is-associated-with-cognitive-aging-in-the-elderly-in-a-taiwanese-population
#1
Eugene Lin, Shih-Jen Tsai, Po-Hsiu Kuo, Yu-Li Liu, Albert C Yang, Chung-Feng Kao, Cheng-Hung Yang
Evidence indicates that the pathophysiologic mechanisms associated with insulin resistance may contribute to cognitive aging and Alzheimer's diseases. In this study, we hypothesize that single nucleotide polymorphisms (SNPs) within insulin resistance-associated genes, such as the ADAM metallopeptidase with thrombospondin type 1 motif 9 (ADAMTS9), glucokinase regulator (GCKR), and peroxisome proliferator activated receptor gamma (PPARG) genes, may be linked with cognitive aging independently and/or through complex interactions in an older Taiwanese population...
2017: PloS One
https://www.readbyqxmd.com/read/28220155/specificity-of-snp-detection-with-molecular-beacons-is-improved-by-stem-and-loop-separation-with-spacers
#2
Valentina M Farzan, Mikhail L Markelov, Alexander Yu Skoblov, German A Shipulin, Timofei S Zatsepin
Molecular beacons (MBs) are valuable tools in molecular biology, clinical diagnostics and analytical chemistry. Here we describe a novel approach for the design of MBs with nucleotide or non-nucleotide linkers between the stem and loop regions. Such modified MBs have significantly improved specificity and performance for single nucleotide polymorphism (SNP) detection. These advantages are especially distinct, when compared to the classic MBs, in the case of possible interactions between the stem and loop regions...
February 21, 2017: Analyst
https://www.readbyqxmd.com/read/28216333/vitamin-d-receptor-gene-polymorphisms-smoking-and-risk-of-sporadic-parkinson-s-disease-in-japan
#3
Keiko Tanaka, Yoshihiro Miyake, Wakaba Fukushima, Chikako Kiyohara, Satoshi Sasaki, Yoshio Tsuboi, Tomoko Oeda, Hiroyuki Shimada, Nobutoshi Kawamura, Nobutaka Sakae, Hidenao Fukuyama, Yoshio Hirota, Masaki Nagai, Yoshikazu Nakamura
Epidemiological evidence on the relationships between the vitamin D receptor (VDR) single nucleotide polymorphisms (SNPs) rs731236 (TaqI), rs7975232 (ApaI), rs1544410 (BsmI), and rs2228570 (FokI) and Parkinson's disease (PD) is inconsistent. We investigated these relationships in 229 sporadic PD patients within six years of onset in Japan. Controls were 357 patients without neurodegenerative disease. Adjustment was made for sex, age, region of residence, and smoking. A significant inverse association was found between SNP rs2228570 and the risk of sporadic PD under the additive but not the co-dominant or dominant model (P=0...
February 16, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28213371/polygenic-risk-scores-in-familial-alzheimer-disease
#4
Giuseppe Tosto, Thomas D Bird, Debby Tsuang, David A Bennett, Bradley F Boeve, Carlos Cruchaga, Kelley Faber, Tatiana M Foroud, Martin Farlow, Alison M Goate, Sarah Bertlesen, Neill R Graff-Radford, Martin Medrano, Rafael Lantigua, Jennifer Manly, Ruth Ottman, Roger Rosenberg, Daniel J Schaid, Nicole Schupf, Yaakov Stern, Robert A Sweet, Richard Mayeux
OBJECTIVE: To investigate the association between a genetic risk score (GRS) and familial late-onset Alzheimer disease (LOAD) and its predictive value in families multiply affected by the disease. METHODS: Using data from the National Institute on Aging Genetics Initiative for Late-Onset Alzheimer Disease (National Institute on Aging-Late-Onset Alzheimer's Disease Family Study), mixed regression models tested the association of familial LOAD with a GRS based on single nucleotide polymorphisms (SNPs) previously associated with LOAD...
February 17, 2017: Neurology
https://www.readbyqxmd.com/read/28211474/dissection-of-genomic-features-and-variations-of-three-pathotypes-of-puccinia-striiformis-through-whole-genome-sequencing
#5
Kanti Kiran, Hukam C Rawal, Himanshu Dubey, R Jaswal, Subhash C Bhardwaj, P Prasad, Dharam Pal, B N Devanna, Tilak R Sharma
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the important diseases of wheat. We used NGS technologies to generate a draft genome sequence of two highly virulent (46S 119 and 31) and a least virulent (K) pathotypes of P. striiformis from the Indian subcontinent. We generated ~24,000-32,000 sequence contigs (N50;7.4-9.2 kb), which accounted for ~86X-105X sequence depth coverage with an estimated genome size of these pathotypes ranging from 66.2-70.2 Mb. A genome-wide analysis revealed that pathotype 46S 119 might be highly evolved among the three pathotypes in terms of year of detection and prevalence...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28202046/highly-predictive-snp-markers-for-efficient-selection-of-the-wheat-leaf-rust-resistance-gene-lr16
#6
Mulualem T Kassa, Frank M You, Colin W Hiebert, Curtis J Pozniak, Pierre R Fobert, Andrew G Sharpe, James G Menzies, D Gavin Humphreys, Nicole Rezac Harrison, John P Fellers, Brent D McCallum, Curt A McCartney
BACKGROUND: Lr16 is a widely deployed leaf rust resistance gene in wheat (Triticum aestivum L.) that is highly effective against the North American Puccinia triticina population when pyramided with the gene Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the uredinium. Lr16 was previously mapped to the telomeric region of the short arm of wheat chromosome 2B. The goals of this study were to develop numerous single nucleotide polymorphism (SNP) markers for the Lr16 region and identify diagnostic gene-specific SNP marker assays for marker-assisted selection (MAS)...
February 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28193307/heritability-and-gwas-studies-for-monocyte-lymphocyte-ratio
#7
Bochao D Lin, Gonneke Willemsen, Iryna O Fedko, Rick Jansen, Brenda Penninx, E de Geus, C Kluft, JoukeJan Hottenga, Dorret I Boomsma
The monocyte-lymphocyte ratio (MLR) is a useful biomarker for disease development, but little is known about the extent to which genetic and environmental factors influence MLR variation. Here, we study the genetic architecture of MLR and determine the influence of demographic and lifestyle factors on MLR in data from a Dutch non-patient twin-family population. Data were obtained in 9,501 individuals from the Netherlands Twin Register. We used regression analyses to determine the effects of age, sex, smoking, and body mass index (BMI) on MLR and its subcomponents...
February 14, 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28192798/identification-of-angpt2-as-a-new-gene-for-neovascular-age-related-macular-degeneration-and-polypoidal-choroidal-vasculopathy-in-the-chinese-and-japanese-populations
#8
Li Ma, Marten E Brelen, Motokazu Tsujikawa, Haoyu Chen, Wai Kit Chu, Timothy Y Y Lai, Danny S C Ng, Kaori Sayanagi, Chicako Hara, Noriyasu Hashida, Vesta C K Chan, Pancy O S Tam, Alvin L Young, Weiqi Chen, Kohji Nishida, Chi Pui Pang, Li Jia Chen
Purpose: We determine the angiopoietin 2 (ANGPT2) gene as a new susceptibility gene for neovascular age-related macular degeneration (nAMD) and polypoidal choroidal vasculopathy (PCV). Methods: A total of 34 haplotype-tagging single-nucleotide polymorphisms (SNPs) were first genotyped in an exploratory Hong Kong Chinese cohort. Suggestive SNPs were replicated in a Shantou Chinese cohort and an Osaka Japanese cohort, with a total of 2343 subjects. The SNP rs800292 in the complement factor H (CFH) gene was genotyped in all the subjects...
February 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28191858/impact-of-the-pde4d-gene-polymorphism-and-additional-snp-snp-and-gene-smoking-interaction-on-ischemic-stroke-risk-in-chinese-han-population
#9
Xianxiang Wang, Zhongwu Sun, Yiquan Zhang, Xuefeng Tian, Qingxin Li, Jing Luo
AIMS: To investigate the association between phosphodiesterase 4D gene (PDE4D) gene single nucleotide polymorphisms (SNPs) and ischemic stroke (IS) risk, and impact of additional SNP- SNP and gene- smoking interaction on IS risk in Chinese population. METHODS: A total of 1228 subjects (666 males, 562 females) were selected, including 610 IS patients and 618 control subjects. Logistic regression model was used to examine the association between SNPs in PDE4D gene and IS risk...
February 13, 2017: Neurological Research
https://www.readbyqxmd.com/read/28183528/transethnic-genome-wide-scan-identifies-novel-alzheimer-s-disease-loci
#10
Gyungah R Jun, Jaeyoon Chung, Jesse Mez, Robert Barber, Gary W Beecham, David A Bennett, Joseph D Buxbaum, Goldie S Byrd, Minerva M Carrasquillo, Paul K Crane, Carlos Cruchaga, Philip De Jager, Nilufer Ertekin-Taner, Denis Evans, M Danielle Fallin, Tatiana M Foroud, Robert P Friedland, Alison M Goate, Neill R Graff-Radford, Hugh Hendrie, Kathleen S Hall, Kara L Hamilton-Nelson, Rivka Inzelberg, M Ilyas Kamboh, John S K Kauwe, Walter A Kukull, Brian W Kunkle, Ryozo Kuwano, Eric B Larson, Mark W Logue, Jennifer J Manly, Eden R Martin, Thomas J Montine, Shubhabrata Mukherjee, Adam Naj, Eric M Reiman, Christiane Reitz, Richard Sherva, Peter H St George-Hyslop, Timothy Thornton, Steven G Younkin, Badri N Vardarajan, Li-San Wang, Jens R Wendlund, Ashley R Winslow, Jonathan Haines, Richard Mayeux, Margaret A Pericak-Vance, Gerard Schellenberg, Kathryn L Lunetta, Lindsay A Farrer
BACKGROUND: Genetic loci for Alzheimer's disease (AD) have been identified in whites of European ancestry, but the genetic architecture of AD among other populations is less understood. METHODS: We conducted a transethnic genome-wide association study (GWAS) for late-onset AD in Stage 1 sample including whites of European Ancestry, African-Americans, Japanese, and Israeli-Arabs assembled by the Alzheimer's Disease Genetics Consortium. Suggestive results from Stage 1 from novel loci were followed up using summarized results in the International Genomics Alzheimer's Project GWAS dataset...
February 6, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28183353/endothelial-injury-in-rheumatoid-arthritis-a-crosstalk-between-dimethylarginines-and-systemic-inflammation
#11
Theodoros Dimitroulas, James Hodson, Aamer Sandoo, Jacqueline Smith, George D Kitas
BACKGROUND: Symmetric (SDMA) and asymmetric (ADMA) dimethylarginines have emerged as novel biomarkers of cardiovascular disease (CVD) in several disease settings associated with atherosclerosis. Rheumatoid arthritis (RA) is a chronic systemic inflammatory disease characterized by high CVD mortality and morbidity. ADMA and SDMA levels are abnormal in RA patients, but their correlation with assessments of endothelial function and structure remains unknown. We aimed to investigate whether SDMA and ADMA are associated with carotid intima media thickness (cIMT) and arterial stiffness as well as non-invasive assessments of in vivo micro- and macrovascular endothelial function in RA patients with high systemic inflammatory load...
February 10, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28183167/detection-of-superior-genotype-of-fatty-acid-synthase-fasn-in-korean-native-cattle-by-an-environment-adjusted-statistical-model
#12
Jeayoung Lee, Dongyep Oh, Hyunji Kim, Gabsue Jang, Seunguk Lee
Objective: This study examines the genetic factors influencing the phenotypes (four economic traits: oleic acid (C18:1), monounsaturated fatty acids (MUFAs), carcass weight (CWT), and marbling score (MS)) of Hanwoo. Methods: To enhance the accuracy of the genetic analysis, the study proposes a new statistical model that excludes environmental factors. A statistically adjusted, analysis of covariance (ANCOVA) model of environmental and genetic factors was developed, and estimated environmental effects (covariate effects of age and effects of calving farms) were excluded from the model...
February 1, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28179588/tp53-based-interaction-analysis-identifies-cis-eqtl-variants-for-tp53bp2-fbxo28-and-fam53a-that-associate-with-survival-and-treatment-outcome-in-breast-cancer
#13
Rainer Fagerholm, Sofia Khan, Marjanka K Schmidt, Montserrat García-Closas, Päivi Heikkilä, Jani Saarela, Jonathan Beesley, Maral Jamshidi, Kristiina Aittomäki, Jianjun Liu, H Raza Ali, Irene L Andrulis, Matthias W Beckmann, Sabine Behrens, Fiona M Blows, Hermann Brenner, Jenny Chang-Claude, Fergus J Couch, Kamila Czene, Peter A Fasching, Jonine Figueroa, Giuseppe Floris, Gord Glendon, Qi Guo, Per Hall, Emily Hallberg, Ute Hamann, Bernd Holleczek, Maartje J Hooning, John L Hopper, Agnes Jager, Maria Kabisch, Renske Keeman, Veli-Matti Kosma, Diether Lambrechts, Annika Lindblom, Arto Mannermaa, Sara Margolin, Elena Provenzano, Mitul Shah, Melissa C Southey, Joe Dennis, Michael Lush, Kyriaki Michailidou, Qin Wang, Manjeet K Bolla, Alison M Dunning, Douglas F Easton, Paul D P Pharoah, Georgia Chenevix-Trench, Carl Blomqvist, Heli Nevanlinna
TP53 overexpression is indicative of somatic TP53 mutations and associates with aggressive tumors and poor prognosis in breast cancer. We utilized a two-stage SNP association study to detect variants associated with breast cancer survival in a TP53-dependent manner. Initially, a genome-wide study (n = 575 cases) was conducted to discover candidate SNPs for genotyping and validation in the Breast Cancer Association Consortium (BCAC). The SNPs were then tested for interaction with tumor TP53 status (n = 4,610) and anthracycline treatment (n = 17,828)...
February 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28178311/an-integrative-study-on-the-impact-of-highly-differentially-methylated-genes-on-expression-and-cancer-etiology
#14
Bugra Ozer, Ugur Sezerman
DNA methylation is an important epigenetic phenomenon that plays a key role in the regulation of expression. Most of the studies on the topic of methylation's role in cancer mechanisms include analyses based on differential methylation, with the integration of expression information as supporting evidence. In the present study, we sought to identify methylation-driven patterns by also integrating protein-protein interaction information. We performed integrative analyses of DNA methylation, expression, SNP and copy number data on paired samples from six different cancer types...
2017: PloS One
https://www.readbyqxmd.com/read/28177360/genomewide-association-of-piglet-responses-to-infection-with-one-of-two-porcine-reproductive-and-respiratory-syndrome-virus-isolates
#15
E H Waide, C K Tuggle, N V L Serão, M Schroyen, A Hess, R R R Rowland, J K Lunney, G Plastow, J C M Dekkers
Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease in the swine industry. Identification of host genetic factors that enable selection for improved performance during PRRS virus (PRRSV) infection would reduce the impact of this disease on animal welfare and production efficiency. We conducted genomewide association study (GWAS) analyses of data from 13 trials of approximately 200 commercial crossbred nursery-age piglets that were experimentally infected with 1 of 2 type 2 isolates of PRRSV (NVSL 97-7985 [NVSL] and KS2006-72109 [KS06])...
January 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28168354/the-endophytic-fungus-phomopsis-liquidambari-increases-nodulation-and-n2-fixation-in-arachis-hypogaea-by-enhancing-hydrogen-peroxide-and-nitric-oxide-signalling
#16
Xing-Guang Xie, Wan-Qiu Fu, Feng-Min Zhang, Xiao-Min Shi, Ying-Ting Zeng, Hui Li, Wei Zhang, Chuan-Chao Dai
The continuous cropping obstacles in monoculture fields are a major production constraint for peanuts. Application of the endophytic fungus Phomopsis liquidambari has increased peanut yields, and nodulation and N2 fixation increases have been considered as important factors for P. liquidambari infection-improved peanut yield. However, the mechanisms involved in this process remain unknown. This work showed that compared with only Bradyrhizobium inoculation, co-inoculation with P. liquidambari significantly elevated endogenous H2O2 and NO levels in peanut roots...
February 6, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28167095/genome-wide-interaction-study-of-dust-mite-allergen-on-lung-function-in-children-with-asthma
#17
Erick Forno, Joanne Sordillo, John Brehm, Wei Chen, Takis Benos, Qi Yan, Lydiana Avila, Manuel Soto-Quirós, Michelle M Cloutier, Angel Colón-Semidey, Maria Alvarez, Edna Acosta-Pérez, Scott T Weiss, Augusto A Litonjua, Glorisa Canino, Juan C Celedón
BACKGROUND: Childhood asthma is likely the result of gene-by-environment (GxE) interactions. Dust mite is a known risk factor for asthma morbidity. Yet, there have been no genome-wide GxE studies of dust mite allergen on asthma-related phenotypes. OBJECTIVE: To identify genetic variants whose effects on lung function in children with asthma are modified by level of dust mite allergen exposure. METHODS: A genome-wide interaction analysis of dust mite allergen level and lung function was performed in a cohort of Puerto Rican children with asthma (PRGOAL)...
February 3, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28167041/phenotypic-characterization-and-genetic-dissection-of-nine-agronomic-traits-in-tokachi-nagaha-and-its-derived-cultivars-in-soybean-glycine-max-l-merr
#18
Zhangxiong Liu, Huihui Li, Xuhong Fan, Wen Huang, Jiyu Yang, Zixiang Wen, Yinghui Li, Rongxia Guan, Yong Guo, Ruzhen Chang, Dechun Wang, Pengyin Chen, Shuming Wang, Li-Juan Qiu
By using the soybean founder parent Tokachi nagaha and its 137 derived cultivars as materials, a genome-wide association analysis was performed to identify the single nucleotide polymorphisms (SNPs) underlying soybean yield and quality related traits at two planting densities. Results of ANOVA showed that genotype, environment, and genotype by environment interaction effects were all significant for each trait. The Tokachi nagaha-derived soybean population could be divided into two subpopulations based on molecular data, and accessions in each subpopulation were almost all from the same Chinese province...
March 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28166716/pyhla-tests-for-the-association-between-hla-alleles-and-diseases
#19
Yanhui Fan, You-Qiang Song
BACKGROUND: Recently, several tools have been designed for human leukocyte antigen (HLA) typing using single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) data. These tools provide high-throughput and cost-effective approaches for identifying HLA types. Therefore, tools for downstream association analysis are highly desirable. Although several tools have been designed for multi-allelic marker association analysis, they were designed only for microsatellite markers and do not scale well with increasing data volumes, or they were designed for large-scale data but provided a limited number of tests...
February 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28162103/a-study-of-associations-between-early-dha-status-and-fatty-acid-desaturase-fads-snp-and-developmental-outcomes-in-children-of-obese-mothers
#20
Karina R Andersen, Laurine B S Harsløf, Theresia M Schnurr, Torben Hansen, Lars I Hellgren, Kim F Michaelsen, Lotte Lauritzen
DHA from diet or endogenous synthesis has been proposed to affect infant development, however, results are inconclusive. In this study, we aim to verify previously observed fatty acid desaturase gene cluster (FADS) SNP-specific associations with erythrocyte DHA status in 9-month-old children and sex-specific association with developmental outcomes. The study was performed in 166 children (55 % boys) of obese mothers. Erythrocyte fatty acid composition was analysed in blood-samples obtained at 9 months of age, and developmental outcomes assessed by the Ages and Stages Questionnaire at 3 years...
February 6, 2017: British Journal of Nutrition
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