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Snp-snp interaction

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https://www.readbyqxmd.com/read/28725234/major-novel-qtl-for-resistance-to-cassava-bacterial-blight-identified-through-a-multi-environmental-analysis
#1
Johana C Soto Sedano, Rubén E Mora Moreno, Boby Mathew, Jens Léon, Fabio A Gómez Cano, Agim Ballvora, Camilo E López Carrascal
Cassava, Manihot esculenta Crantz, has been positioned as one of the most promising crops world-wide representing the staple security for more than one billion people mainly in poor countries. Cassava production is constantly threatened by several diseases, including cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam), it is the most destructive disease causing heavy yield losses. Here, we report the detection and localization on the genetic map of cassava QTL (Quantitative Trait Loci) conferring resistance to CBB...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28724417/examining-the-role-of-unmeasured-confounding-in-mediation-analysis-with-genetic-and-genomic-applications
#2
Sharon M Lutz, Annie Thwing, Sarah Schmiege, Miranda Kroehl, Christopher D Baker, Anne P Starling, John E Hokanson, Debashis Ghosh
BACKGROUND: In mediation analysis if unmeasured confounding is present, the estimates for the direct and mediated effects may be over or under estimated. Most methods for the sensitivity analysis of unmeasured confounding in mediation have focused on the mediator-outcome relationship. RESULTS: The Umediation R package enables the user to simulate unmeasured confounding of the exposure-mediator, exposure-outcome, and mediator-outcome relationships in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding...
July 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28724063/evaluation-of-genetic-diversity-and-host-resistance-to-stem-rust-in-usda-nsgc-durum-wheat-accessions
#3
Shiaoman Chao, Matthew N Rouse, Maricelis Acevedo, Agnes Szabo-Hever, Harold Bockelman, J Michael Bonman, Elias Elias, Daryl Klindworth, Steven Xu
The USDA-ARS National Small Grains Collection (NSGC) maintains germplasm representing global diversity of small grains and their wild relatives. To evaluate the utility of the NSGC durum wheat ( L. ssp. ) accessions, we assessed genetic diversity and linkage disequilibrium (LD) patterns in a durum core subset containing 429 lines with spring growth habit originating from 64 countries worldwide. Genetic diversity estimated using wheat single-nucleotide polymorphism (SNP) markers showed considerable diversity captured in this collection...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28720099/association-between-genome-wide-copy-number-variation-and-arsenic-induced-skin-lesions-a-prospective-study
#4
Muhammad G Kibriya, Farzana Jasmine, Faruque Parvez, Maria Argos, Shantanu Roy, Rachelle Paul-Brutus, Tariqul Islam, Alauddin Ahmed, Muhammad Rakibuz-Zaman, Justin Shinkle, Vesna Slavkovich, Joseph H Graziano, Habibul Ahsan
BACKGROUND: Exposure to arsenic in drinking water is a global health problem and arsenic-induced skin lesions are hallmark of chronic arsenic toxicity. We and others have reported germline genetic variations as risk factors for such skin lesions. The role of copy number variation (CNV) in the germline DNA in this regard is unknown. METHODS: From a large prospectively followed-up cohort, exposed to arsenic, we randomly selected 2171 subjects without arsenic-induced skin lesions at enrollment and genotyped their whole blood DNA samples on Illumina Cyto12v2...
July 18, 2017: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/28719597/pharmacogenomics-study-of-thiazide-diuretics-and-qt-interval-in-multi-ethnic-populations-the-cohorts-for-heart-and-aging-research-in-genomic-epidemiology
#5
A A Seyerle, C M Sitlani, R Noordam, S M Gogarten, J Li, X Li, D S Evans, F Sun, M A Laaksonen, A Isaacs, K Kristiansson, H M Highland, J D Stewart, T B Harris, S Trompet, J C Bis, G M Peloso, J A Brody, L Broer, E L Busch, Q Duan, A M Stilp, C J O'Donnell, P W Macfarlane, J S Floyd, J A Kors, H J Lin, R Li-Gao, T Sofer, R Méndez-Giráldez, S R Cummings, S R Heckbert, A Hofman, I Ford, Y Li, L J Launer, K Porthan, C Newton-Cheh, M D Napier, K F Kerr, A P Reiner, K M Rice, J Roach, B M Buckley, E Z Soliman, R de Mutsert, N Sotoodehnia, A G Uitterlinden, K E North, C R Lee, V Gudnason, T Stürmer, F R Rosendaal, K D Taylor, K L Wiggins, J G Wilson, Y-DI Chen, R C Kaplan, K Wilhelmsen, L A Cupples, V Salomaa, C van Duijn, J W Jukema, Y Liu, D O Mook-Kanamori, L A Lange, R S Vasan, A V Smith, B H Stricker, C C Laurie, J I Rotter, E A Whitsel, B M Psaty, C L Avery
Thiazide diuretics, commonly used antihypertensives, may cause QT interval (QT) prolongation, a risk factor for highly fatal and difficult to predict ventricular arrhythmias. We examined whether common single-nucleotide polymorphisms (SNPs) modified the association between thiazide use and QT or its component parts (QRS interval, JT interval) by performing ancestry-specific, trans-ethnic and cross-phenotype genome-wide analyses of European (66%), African American (15%) and Hispanic (19%) populations (N=78 199), leveraging longitudinal data, incorporating corrected standard errors to account for underestimation of interaction estimate variances and evaluating evidence for pathway enrichment...
July 18, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28715704/oxytocin-receptor-gene-polymorphisms-attachment-and-ptsd-results-from-the-national-health-and-resilience-in-veterans-study
#6
Lauren M Sippel, Shizhong Han, Laura E Watkins, Ilan Harpaz-Rotem, Steven M Southwick, John H Krystal, Miranda Olff, Richard Sherva, Lindsay A Farrer, Henry R Kranzler, Joel Gelernter, Robert H Pietrzak
The human oxytocin system is implicated in social behavior and stress recovery. Polymorphisms in the oxytocin receptor gene (OXTR) may interact with attachment style to predict stress-related psychopathology like posttraumatic stress disorder (PTSD). The objective of this study was to examine independent and interactive effects of the OXTR single nucleotide polymorphism (SNP) rs53576, which has been associated with stress reactivity, support-seeking, and PTSD in prior studies, and attachment style on risk for PTSD in a nationally representative sample of 2163 European-American (EA) U...
July 8, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28713926/association-between-tnfsf4-and-blk-gene-polymorphisms-and-susceptibility-to-allergic-rhinitis
#7
Yang Shen, Yun Liu, Xiao-Qiang Wang, Xia Ke, Hou-Yong Kang, Su-Ling Hong
Allergic rhinitis (AR) is a common inflammatory disease of the upper airway. Recent evidence suggests that gene‑gene interactions between tumor necrosis factor receptor superfamily 4 (TNFSF4) and B cell lymphocyte kinase (BLK) may have a synergistic effect on T and B cells in determining immunologic aberration, via the nuclear factor‑κB pathway. The present study was performed to evaluate the potential association between specific single nucleotide polymorphisms (SNPs) in the TNFSF4 and BKL genes with susceptibility to AR in Chinese subjects...
July 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713270/evaluation-of-selected-cyp51a1-polymorphisms-in-view-of-interactions-with-substrate-and-redox-partner
#8
Tadeja Režen, Iza Ogris, Marko Sever, Franci Merzel, Simona Golic Grdadolnik, Damjana Rozman
Cholesterol is essential for development, growth, and maintenance of organisms. Mutations in cholesterol biosynthetic genes are embryonic lethal and few polymorphisms have been so far associated with pathologies in humans. Previous analyses show that lanosterol 14α-demethylase (CYP51A1) from the late part of cholesterol biosynthesis has only a few missense mutations with low minor allele frequencies and low association with pathologies in humans. The aim of this study is to evaluate the role of amino acid changes in the natural missense mutations of the hCYP51A1 protein...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28711952/polymorphic-variants-of-antioxidative-defense-enzymes-and-their-gene-gene-epistatic-interactions-in-systemic-lupus-erythematode-patients
#9
Tatjana Jevtovic Stoimenov, Milena Despotovic, Sonja Stojanovic, Jelena Basic, Dušica Pavlovic
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease in which pathogenesis oxidative stress has an important role. Single nucleotide polymorphisms (SNPs) in the genes that code enzymes involved in the antioxidative defense are possible factors that are responsible for their decreased activity of antioxidative defense enzymes. Thus, the aim of the study was to examine association of SNPs in these genes with SLE. A total of176 subjects were involved in this study. CAT A-21T (rs7943316), CAT C-262T (rs1001139) and manganese SOD (MnSOD) Ala16Val (rs4880) SNPs were determined using PCR-RFLP method, while GSTT1 and GSTM1 were determined using multiplex PCR...
July 15, 2017: Clinical Rheumatology
https://www.readbyqxmd.com/read/28710909/evaluation-of-the-interaction-between-genetic-variants-of-gad1-and-mirna-in-bipolar-disorders
#10
Yu-Chu Ella Chung, Shao-Chien Chen, Li-Chung Chuang, Wei-Liang Shih, Yi-Hang Chiu, Mong-Liang Lu, Hsi-Chung Chen, Po-Hsiu Kuo
BACKGROUND: Glutamic acid dehydrogenase 1 (GAD1) serves as the rate-limiting enzyme for synthesizing GABA, and is reported to be associated with several psychiatric disorders. The present study examined the effects of GAD1 genetic variants on bipolar disorder (BD) and its subtypes. Moreover, we investigated functional interactions between genetic variants and miRNAs via algorithm prediction and experimental validation. METHODS: A case-control study was conducted with 280 BD patients and 200 healthy controls...
July 10, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28707126/estrogen-receptor-alpha-gene-esr1-polymorphism-and-its-interaction-with-smoking-and-drinking-contribute-to-susceptibility-of-systemic-lupus-erythematosus
#11
Aihong Zhou, Xin Liu, Tao Xia, Fang Li, Jibo Wang, Jun Li
The aim of this study is to investigate the association of estrogen receptor alpha gene (ESR1) polymorphisms, additional gene-gene, and gene-environment interaction with systemic lupus erythematosus (SLE) risk. SNPStats (available online at http://bioinfo.iconcologia.net/SNPstats ) was used to investigate the Hardy-Weinberg equilibrium (HWE) in controls and association between SNP and SLE risk. Generalized multifactor dimensionality reduction (GMDR) was used to screen the interactions among SNPs and environmental risk factors; SLE risk was significantly higher in carriers of rs2234693 C allele than those with TT (TC + CC versus TT), adjusted OR (95%CI) = 1...
July 13, 2017: Immunologic Research
https://www.readbyqxmd.com/read/28706522/expressed-centromere-specific-histone-3-cenh3-variants-in-cultivated-triploid-and-wild-diploid-bananas-musa-spp
#12
Kariuki S Muiruri, Anne Britt, Nelson O Amugune, Edward K Nguu, Simon Chan, Leena Tripathi
Centromeres are specified by a centromere specific histone 3 (CENH3) protein, which exists in a complex environment, interacting with conserved proteins and rapidly evolving satellite DNA sequences. The interactions may become more challenging if multiple CENH3 versions are introduced into the zygote as this can affect post-zygotic mitosis and ultimately sexual reproduction. Here, we characterize CENH3 variant transcripts expressed in cultivated triploid and wild diploid progenitor bananas. We describe both splice- and allelic-[Single Nucleotide Polymorphisms (SNP)] variants and their effects on the predicted secondary structures of protein...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28701235/analyses-of-reaction-norms-reveal-new-chromosome-regions-associated-with-tick-resistance-in-cattle
#13
R R Mota, F F Silva, P S Lopes, R J Tempelman, B P Sollero, I Aguilar, F F Cardoso
Despite single nucleotide polymorphism (SNP) availability and frequent cost reduction has allowed genome-wide association studies even in complex traits as tick resistance, the use of this information source in SNP by environment interaction context is unknown for many economically important traits in cattle. We aimed at identifying putative genomic regions explaining differences in tick resistance in Hereford and Braford cattle under SNP by environment point of view as well as to identify candidate genes derived from outliers/significant markers...
July 13, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28700714/genome-wide-re-sequencing-of-newly-developed-rice-lines-from-common-wild-rice-oryza-rufipogon-griff-for-the-identification-of-nbs-lrr-genes
#14
Wen Liu, Fozia Ghouri, Hang Yu, Xiang Li, Shuhong Yu, Muhammad Qasim Shahid, Xiangdong Liu
Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89...
2017: PloS One
https://www.readbyqxmd.com/read/28698656/gene-gene-and-gene-environment-interactions-influence-platinum-based-chemotherapy-response-and-toxicity-in-non-small-cell-lung-cancer-patients
#15
Jia-Jia Cui, Lei-Yun Wang, Tao Zhu, Wei-Jing Gong, Hong-Hao Zhou, Zhao-Qian Liu, Ji-Ye Yin
Platinum-based chemotherapy is a major therapeutic regimen of lung cancer. Various single nucleotide polymorphisms (SNPs) reported were associated with platinum-based chemotherapy response and drug toxicity. However, neither of the studies explored this association from SNP-SNP interaction perspective nor taking into effects of SNP-environment consideration simultaneously. We genotyped 504 polymorphisms and explore the association of gene-gene and gene-environment interactions with platinum-based chemotherapy response and toxicity in 490 NSCLC patients...
July 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28694848/epiaco-a-method-for-identifying-epistasis-based-on-ant-colony-optimization-algorithm
#16
Yingxia Sun, Junliang Shang, Jin-Xing Liu, Shengjun Li, Chun-Hou Zheng
BACKGROUND: Identifying epistasis or epistatic interactions, which refer to nonlinear interaction effects of single nucleotide polymorphisms (SNPs), is essential to understand disease susceptibility and to detect genetic architectures underlying complex diseases. Though many works have been done for identifying epistatic interactions, due to their methodological and computational challenges, the algorithmic development is still ongoing. RESULTS: In this study, a method epiACO is proposed to identify epistatic interactions, which based on ant colony optimization algorithm...
2017: BioData Mining
https://www.readbyqxmd.com/read/28692066/genotype-covariate-interaction-effects-and-the-heritability-of-adult-body-mass-index
#17
Matthew R Robinson, Geoffrey English, Gerhard Moser, Luke R Lloyd-Jones, Marcus A Triplett, Zhihong Zhu, Ilja M Nolte, Jana V van Vliet-Ostaptchouk, Harold Snieder, Tonu Esko, Lili Milani, Reedik Mägi, Andres Metspalu, Patrik K E Magnusson, Nancy L Pedersen, Erik Ingelsson, Magnus Johannesson, Jian Yang, David Cesarini, Peter M Visscher
Obesity is a worldwide epidemic, with major health and economic costs. Here we estimate heritability for body mass index (BMI) in 172,000 sibling pairs and 150,832 unrelated individuals and explore the contribution of genotype-covariate interaction effects at common SNP loci. We find evidence for genotype-age interaction (likelihood ratio test (LRT) = 73.58, degrees of freedom (df) = 1, P = 4.83 × 10(-18)), which contributed 8.1% (1.4% s.e.) to BMI variation. Across eight self-reported lifestyle factors, including diet and exercise, we find genotype-environment interaction only for smoking behavior (LRT = 19...
July 10, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28687336/polymorphisms-of-cyp2c8-cyp2c9-and-cyp2c19-and-risk-of-coronary-heart-disease-in-russian-population
#18
Alexey Polonikov, Alexander Kharchenko, Marina Bykanova, Svetlana Sirotina, Irina Ponomarenko, Anna Bocharova, Kseniya Vagaytseva, Vadim Stepanov, Olga Bushueva, Mikhail Churnosov, Maria Solodilova
Epoxyeicosatrienoic acids (EETs) are important vasoactive products of arachidonic acid metabolism with a wide range of biological actions in the cardiovascular system. The present study investigated whether single nucleotide polymorphisms (SNP) of genes coding cytochrome P450 2C subfamily, enzymes involved in biosynthesis of EETs, are associated with the risk of coronary heart disease (CHD). A total of 1255 unrelated Russian subjects comprising 561 patients with angiographically diagnosed CHD and 694 age- and sex-matched healthy subjects were included in the study...
July 4, 2017: Gene
https://www.readbyqxmd.com/read/28686328/genetically-contextual-effects-of-smoking-on-genome-wide-dna-methylation
#19
Meeshanthini V Dogan, Steven R H Beach, Robert A Philibert
Smoking is the leading cause of death in the United States. It exerts its effects by increasing susceptibility to a variety of complex disorders among those who smoke, and if pregnant, to their unborn children. In prior efforts to understand the epigenetic mechanisms through which this increased vulnerability is conveyed, a number of investigators have conducted genome wide methylation analyses. Unfortunately, secondary to methodological limitations, these studies were unable to examine methylation in gene regions with significant amounts of genetic variation...
July 7, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28680433/allelic-interactions-among-pto-mir475b-and-its-four-target-genes-potentially-affect-growth-and-wood-properties-in-populus
#20
Liang Xiao, Mingyang Quan, Qingzhang Du, Jinhui Chen, Jianbo Xie, Deqiang Zhang
MicroRNAs (miRNAs) play crucial roles in plant growth and development, but few studies have illuminated the allelic interactions among miRNAs and their targets in perennial plants. Here, we combined analysis of expression patterns and single-nucleotide polymorphism (SNP)-based association studies to explore the interactions between Pto-MIR475b and its four target genes (Pto-PPR1, Pto-PPR2, Pto-PPR3, and Pto-PPR4) in 435 unrelated individuals of Populus tomentosa. Expression patterns showed a significant negative correlation (r = -0...
2017: Frontiers in Plant Science
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