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Snp interaction

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https://www.readbyqxmd.com/read/28646072/genetic-and-environmental-interactions-modify-the-risk-of-diabetes-related-autoimmunity-by-6-years-of-age-the-teddy-study
#1
Jeffrey P Krischer, Kristian F Lynch, Åke Lernmark, William A Hagopian, Marian J Rewers, Jin-Xiong She, Jorma Toppari, Anette-G Ziegler, Beena Akolkar
OBJECTIVE: We tested the associations between genetic background and selected environmental exposures with respect to islet autoantibodies and type 1 diabetes. RESEARCH DESIGN AND METHODS: Infants with HLA-DR high-risk genotypes were prospectively followed for diabetes-related autoantibodies. SNPs came from the Illumina ImmunoChip and environmental exposure data were by parental report. Children were followed to age 6 years. RESULTS: Insulin autoantibodies occurred earlier than GAD antibody (GADA) and then declined, while GADA incidence rose and remained constant (significant in HLA-DR4 but not in the DR3/3 children)...
June 23, 2017: Diabetes Care
https://www.readbyqxmd.com/read/28642860/ataxia-telangiectasia-mutated-atm-polymorphisms-and-risk-of-lung-cancer-in-a-chinese-population
#2
Ajay A Myneni, Shen-Chih Chang, Rungui Niu, Li Liu, Baoxing Zhao, Jianping Shi, Xiaoyou Han, Jiawei Li, Jia Su, Shunzhang Yu, Zuo-Feng Zhang, Lina Mu
BACKGROUND: The ataxia telangiectasia-mutated (ATM) gene has a key role in DNA repair including activation and stabilization of p53, which implicates the importance of ATM polymorphisms in the development of cancer. This study aims to investigate the association of two ATM single-nucleotide polymorphisms (SNPs) with lung cancer, as well as their potential interaction with p53 gene and other known risk factors of lung cancer. METHODS: A population-based case-control study was conducted in Taiyuan city, China with 399 cases and 466 controls matched on the distribution of age and sex of cases...
2017: Frontiers in Public Health
https://www.readbyqxmd.com/read/28641921/genome-wide-association-and-interaction-studies-of-csf-t-tau-a%C3%AE-42-ratio-in-adni-cohort
#3
Jin Li, Qiushi Zhang, Feng Chen, Xianglian Meng, Wenjie Liu, Dandan Chen, Jingwen Yan, Sungeun Kim, Lei Wang, Weixing Feng, Andrew J Saykin, Hong Liang, Li Shen
The pathogenic relevance in Alzheimer's disease (AD) presents a decrease of cerebrospinal fluid amyloid-ß42 (Aß42) burden and an increase in cerebrospinal fluid total tau (T-tau) levels. In this work, we performed genome-wide association study (GWAS) and genome-wide interaction study of T-tau/Aß42 ratio as an AD imaging quantitative trait on 843 subjects and 563,980 single-nucleotide polymorphisms (SNPs) in ADNI cohort. We aim to identify not only SNPs with significant main effects but also SNPs with interaction effects to help explain "missing heritability"...
May 15, 2017: Neurobiology of Aging
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
#4
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/28635556/executive-control-in-schizophrenia-a-preliminary-study-on-the-moderating-role-of-comt-val158met-for-comorbid-alcohol-and-substance-use-disorders
#5
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/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/28628480/kernel-based-measure-of-variable-importance-for-genetic-association-studies
#8
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/28622115/ppar%C3%AE-2-c1431t-polymorphism-interacts-with-the-antiobesogenic-effects-of-kochujang-a-korean-fermented-soybean-based-red-pepper-paste-in-overweight-obese-subjects-a-12-week-double-blind-randomized-clinical-trial
#9
Yunkyoung Lee, Youn-Soo Cha, Yongsoon Park, Myoungsook Lee
Kochujang, a Korean fermented soybean-based red pepper paste, has been reported to have beneficial health effects. The aim of this study was to examine the antiobesity effects of Kochujang as a supplement in overweight/obese subjects according polymorphisms in the obesity-linked gene, peroxisome proliferator activator receptor γ (PPARγ2). Sixty overweight/obese subjects, who had body mass indexes (BMI, kg/m(2)) ≥23 or waist/hip ratios (WHR) ≥0.90 for males or ≥0.85 for females, were randomly assigned to either taking 32 g/day of placebo or Kochujang for 12 weeks...
June 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28620303/effect-of-genetic-variability-in-the-cyp4f2-cyp4f11-and-cyp4f12-genes-on-liver-mrna-levels-and-warfarin-response
#10
J E Zhang, Kathrin Klein, Andrea L Jorgensen, Ben Francis, Ana Alfirevic, Stephane Bourgeois, Panagiotis Deloukas, Ulrich M Zanger, Munir Pirmohamed
Genetic polymorphisms in the gene encoding cytochrome P450 (CYP) 4F2, a vitamin K oxidase, affect stable warfarin dose requirements and time to therapeutic INR. CYP4F2 is part of the CYP4F gene cluster, which is highly polymorphic and exhibits a high degree of linkage disequilibrium, making it difficult to define causal variants. Our objective was to examine the effect of genetic variability in the CYP4F gene cluster on expression of the individual CYP4F genes and warfarin response. mRNA levels of the CYP4F gene cluster were quantified in human liver samples (n = 149) obtained from a well-characterized liver bank and fine mapping of the CYP4F gene cluster encompassing CYP4F2, CYP4F11, and CYP4F12 was performed...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28620222/nitric-oxide-mediated-transcriptional-modulation-enhances-plant-adaptive-responses-to-arsenic-stress
#11
Pradyumna Kumar Singh, Yuvraj Indoliya, Abhisekh Singh Chauhan, Surendra Pratap Singh, Amit Pal Singh, Sanjay Dwivedi, Rudra Deo Tripathi, Debasis Chakrabarty
Arsenic (As) contamination in rice leads to yield decline and causes carcinogenic risk to human health. Although the role of nitric oxide (NO) in reducing As toxicity is known, NO-mediated genetic modulation in the plant during arsenic toxicity has not yet been established. We analyzed the key components of NO metabolism and the correlations between NO interaction and arsenic stress using rice as a relevant model plant. Illumina sequencing was used to investigate the NO-mediated genome-wide temporal transcriptomic modulation in rice root upon AsIII exposure during 12 days (d) of the growth period...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28616916/-relationship-between-lep-g2548a-polymorphism-and-cholesterol-gallstone
#12
Jing Chen, Jie He, Jiang-Hui Chen, Zhen-Bin Lai, Qi-Jun Cheng, Xiao-Shan Yu, Hui-Fen Liu, Yan-Hua Su, Ben-Hua Zhao
OBJECTIVES: To determine the associations of single nucleotide polymorphism (SNP) in leptin (LEP) genes and environmental factors with cholesterol gallstone in southeast Han populations. METHODS: A 1:2 matched case-control study was conducted involving 200 patients with cholesterol gallstone. Genotyping of the SNP was examined on the LightCycler480 PCR platform using in-house high resolution melting (HRM) approaches. Detection correctness was validated through direct sequencing...
May 2017: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
https://www.readbyqxmd.com/read/28615674/meta-analysis-of-genome-wide-snp-and-pathway-based-associations-for-facets-of-neuroticism
#13
Song E Kim, Han-Na Kim, Yeo-Jun Yun, Seong Gu Heo, Juhee Cho, Min-Jung Kwon, Yoosoo Chang, Seungho Ryu, Hocheol Shin, Chol Shin, Nam H Cho, Yeon Ah Sung, Hyung-Lae Kim
Neuroticism is a heritable personality trait that is comprised of distinct sub-factors, or facets. Sub-factors of neuroticism are linked to different emotional states or psychiatric symptoms and studying the genetic variants associated with these facets may help reveal the biological mechanisms underlying psychiatric disorders. In the present study, a meta-analysis of genome-wide association studies for six facets of neuroticism was performed in 5584 participants from three cohorts. Additionally, a Gene Set Enrichment Analysis was conducted to find biological pathways associated with each facet...
June 15, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28615284/tcl1a-snps-and-estrogen-mediated-toll-like-receptor-myd88-dependent-nf-%C3%AE%C2%BAb-activation-snp-and-serm-dependent-modification-of-inflammation-and-immune-response
#14
Ming-Fen Ho, James N Ingle, Tim Bongartz, Krishna R Kalari, Paul E Goss, Lois E Shepherd, Taisei Mushiroda, Michiaki Kubo, Liewei Wang, Richard M Weinshilboum
In a previous genome-wide association study (GWAS) for musculoskeletal adverse events during aromatase inhibitor therapy of breast cancer, we reported that single nucleotide polymorphisms (SNPs) near the TCL1A gene were associated with this adverse drug reaction. Functional genomic studies showed that TCL1A expression was induced by estradiol (E2), but only in cells with the variant sequence for the top GWAS SNP (rs11849538), a SNP that created a functional estrogen response element. In addition, TCL1A genotype influenced the "downstream" expression of a series of cytokines and chemokines and had a striking effect on NF-κB transcriptional activity...
June 14, 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/28614350/ranking-and-characterization-of-established-bmi-and-lipid-associated-loci-as-candidates-for-gene-environment-interactions
#15
Dmitry Shungin, Wei Q Deng, Tibor V Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P Morris, Nita G Forouhi, Cecilia Lindgren, Patrik K E Magnusson, Nancy L Pedersen, Göran Hallmans, Audrey Y Chu, Anne E Justice, Mariaelisa Graff, Thomas W Winkler, Lynda M Rose, Claudia Langenberg, L Adrienne Cupples, Paul M Ridker, Nicholas J Wareham, Ken K Ong, Ruth J F Loos, Daniel I Chasman, Erik Ingelsson, Tuomas O Kilpeläinen, Robert A Scott, Reedik Mägi, Guillaume Paré, Paul W Franks
Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G×E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G×E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's ρ = 0...
June 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28612708/contribution-of-matrix-metalloproteinases-1-genotypes-to-gastric-cancer-susceptibility-in-taiwan
#16
Mei-Due Yang, Kuo-Cheng Lin, Meng-Chun Lu, Long-Bin Jeng, Chieh-Lun Hsiao, Te-Cheng Yueh, Chun-Kai Fu, Hsin-Ting Li, Shiou-Ting Yen, Chia-Wen Lin, Cin-Wun Wu, Su-Yi Pang, Da-Tian Bau, Fuu-Jen Tsai
Expression of matrix metalloproteinase-1 (MMP1), an interstitial collagenase regulating the extracellular matrix, plays a major role in carcinogenesis of gastric cancer, a leading cause of death worldwide. In literature, the single-nucleotide polymorphism (SNP) promoter -1607 1G/2G (rs1799750) at the MMP1 gene promoter has been reported to alter its own transcription level. While the importance's of the genotype of MMP1 promoter -1607 has not yet been studied in gastric cancer in Taiwan, our aim was to investigate MMP1 promoter -1607 genotypes and gastric cancer (GC) susceptibility in central Taiwan population...
June 2017: BioMedicine
https://www.readbyqxmd.com/read/28611364/association-of-polymorphisms-in-pharmacogenetic-candidate-genes-with-propofol-susceptibility
#17
Qi Zhong, Xiangdong Chen, Yan Zhao, Ru Liu, Shanglong Yao
Significant individual susceptibility to intravenous anesthetic propofol exists. The etiology of individual variability in the response to propofol may be influenced by genetic polymorphisms in metabolic and functional pathways. With current pharmacogenetics and modern molecular biology technologies, it is possible to study the influence of genetic polymorphisms on susceptibility to propofol. When inducing general anesthesia with intravenous propofol, high individual susceptibility to propofol was found. Using Sequenom MassARRAY single-nucleotide polymorphism (SNP) genotyping, we identified a mutation (rs6313) in the 5HT2A gene that was correlated to individual susceptibility to propofol effect-site concentration (Cep) and onset time of propofol induction...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28610615/quantitative-trait-loci-at-the-11q23-3-chromosomal-region-related-to-dyslipidemia-in-the-population-of-andhra-pradesh-india
#18
Rayabarapu Pranavchand, Battini Mohan Reddy
BACKGROUND: Given the characteristic atherogenic dyslipidemia of south Indian population and crucial role of APOA1, APOC3, APOA4 and APOA5 genes clustered in 11q23.3 chromosomal region in regulating lipoprotein metabolism and cholesterol homeostasis, a large number of recently identified variants are to be explored for their role in regulating the serum lipid parameters among south Indians. METHODS: Using fluidigm SNP genotyping platform, a prioritized set of 96 SNPs of the 11q23...
June 13, 2017: Lipids in Health and Disease
https://www.readbyqxmd.com/read/28602359/predictive-and-prognostic-factors-influencing-outcomes-of-rituximab-therapy-in-systemic-lupus-erythematosus-sle-a-systematic-review
#19
Carmelo Pirone, Claudia Mendoza-Pinto, Daniëlle A van der Windt, Ben Parker, Miriam O Sullivan, Ian N Bruce
BACKGROUND: The clinical outcomes following rituximab (RTX) treatment in patients with systemic lupus erythematosus (SLE) is highly variable. We aimed to identify predictive and prognostic factors associated with RTX therapy outcomes in patients with SLE. METHODS: Studies in adults and paediatric patients with SLE were included. We included randomized clinical trials (RCTs) for predictors of differential treatment effect and cohort studies for potential prognostic factors in patients treated with RTX (global clinical, cutaneous and renal either response or relapse, and side effects)...
May 5, 2017: Seminars in Arthritis and Rheumatism
https://www.readbyqxmd.com/read/28597135/glis3-rs7020673-and-rs10758593-polymorphisms-interact-in-the-susceptibility-for-type-1-diabetes-mellitus
#20
Guilherme C K Duarte, Tais S Assmann, Cristine Dieter, Bianca M de Souza, Daisy Crispim
AIMS: The transcription factor Gli-similar 3 (GLIS3) plays a key role in the development and maintenance of pancreatic beta cells as well as in the regulation of Insulin gene expression in adults. Accordingly, genome-wide association studies identified GLIS3 as a susceptibility locus for type 1 diabetes mellitus (T1DM) and glucose metabolism traits. Therefore, the aim of this study was to replicate the association of the rs10758593 and rs7020673 single nucleotide polymorphisms (SNPs) in the GLIS3 gene with T1DM in a Brazilian population...
June 9, 2017: Acta Diabetologica
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