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Snp-snp interaction

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https://www.readbyqxmd.com/read/29331705/catechol-o-methyltransferase-comt-functional-haplotype-is-associated-with-recurrence-of-affective-symptoms-a-prospective-birth-cohort-study
#1
Shinsuke Koike, Darya Gaysina, Peter B Jones, Andrew Wong, Marcus Richards
BACKGROUND: Catechol-O-methyltransferase (COMT) polymorphisms play an essential role in dopamine availability in the brain. However, there has been no study investigating whether a functional four-SNP (rs6269-rs4633-rs4818-rs4680) haplotype is associated with affective symptoms over the life course. METHODS: We tested this using 2093 members of the Medical Research Council National Survey of Health and Development (MRC NSHD), who had been followed up since birth in 1946, and had data for COMT genotypes, adolescent emotional problems (age 13-15) and at least one measure of adult affective symptoms at ages 36, 43, 53, or 60-64 years...
January 6, 2018: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29325965/genome-wide-association-mapping-for-seed-protein-and-oil-contents-using-a-large-panel-of-soybean-accessions
#2
Dongmei Li, Xue Zhao, Yingpeng Han, Wenbin Li, Futi Xie
Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0...
January 8, 2018: Genomics
https://www.readbyqxmd.com/read/29325759/snps-in-the-vicinity-of-p2x7r-rank-rankl-opg-and-wnt-signalling-pathways-and-their-association-with-bone-phenotypes-in-academy-footballers
#3
Ian Varley, David C Hughes, Julie P Greeves, William D Fraser, Craig Sale
CONTEXT: Genotype plays an important role in influencing bone phenotypes, such as bone mineral density, but the role of genotype in determining responses of bone to exercise has yet to be elucidated. OBJECTIVE: To determine whether 10 SNPs associated with genes in the vicinity of P2X7R, RANK/RANKL/OPG and Wnt Signalling Pathways are associated with bone phenotypes in elite academy footballers (Soccer players) and to determine whether these genotypes are associated with training induced changes in bone...
January 8, 2018: Bone
https://www.readbyqxmd.com/read/29323246/modulediscoverer-identification-of-regulatory-modules-in-protein-protein-interaction-networks
#4
Sebastian Vlaic, Theresia Conrad, Christian Tokarski-Schnelle, Mika Gustafsson, Uta Dahmen, Reinhard Guthke, Stefan Schuster
The identification of disease-associated modules based on protein-protein interaction networks (PPINs) and gene expression data has provided new insights into the mechanistic nature of diverse diseases. However, their identification is hampered by the detection of protein communities within large-scale, whole-genome PPINs. A presented successful strategy detects a PPIN's community structure based on the maximal clique enumeration problem (MCE), which is a non-deterministic polynomial time-hard problem. This renders the approach computationally challenging for large PPINs implying the need for new strategies...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320438/modeling-unobserved-heterogeneity-in-susceptibility-to-ambient-benzo-a-pyrene-concentration-among-children-with-allergic-asthma-using-an-unsupervised-learning-algorithm
#5
Daniel Fernández, Radim J Sram, Miroslav Dostal, Anna Pastorkova, Hans Gmuender, Hyunok Choi
Current studies of gene × air pollution interaction typically seek to identify unknown heritability of common complex illnesses arising from variability in the host's susceptibility to environmental pollutants of interest. Accordingly, a single component generalized linear models are often used to model the risk posed by an environmental exposure variable of interest in relation to a priori determined DNA variants. However, reducing the phenotypic heterogeneity may further optimize such approach, primarily represented by the modeled DNA variants...
January 10, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29317594/polymorphism-in-tmem132d-regulates-expression-and-anxiety-related-behavior-through-binding-of-rna-polymerase-ii-complex
#6
Roshan R Naik, Sergey V Sotnikov, Rebekka P Diepold, Stella Iurato, Patrick O Markt, Andrea Bultmann, Nadine Brehm, Tobias Mattheus, Beat Lutz, Angelika Erhardt, Elisabeth B Binder, Ulrike Schmidt, Florian Holsboer, Rainer Landgraf, Ludwig Czibere
TMEM132D is a candidate gene, where risk genotypes have been associated with anxiety severity along with higher mRNA expression in the frontal cortex of panic disorder patients. Concurrently, in a high (HAB) and low (LAB) trait anxiety mouse model, Tmem132d was found to show increased expression in the anterior cingulate cortex (aCC) of HAB as compared to LAB mice. To understand the molecular underpinnings underlying the differential expression, we sequenced the gene and found two single-nucleotide polymorphisms (SNPs) in the promoter differing between both lines which could explain the observed mRNA expression profiles using gene reporter assays...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29315403/joint-associations-of-a-polygenic-risk-score-and-environmental-risk-factors-for-breast-cancer-in-the-breast-cancer-association-consortium
#7
Anja Rudolph, Minsun Song, Mark N Brook, Roger L Milne, Nasim Mavaddat, Kyriaki Michailidou, Manjeet K Bolla, Qin Wang, Joe Dennis, Amber N Wilcox, John L Hopper, Melissa C Southey, Renske Keeman, Peter A Fasching, Matthias W Beckmann, Manuela Gago-Dominguez, Jose E Castelao, Pascal Guénel, Thérèse Truong, Stig E Bojesen, Henrik Flyger, Hermann Brenner, Volker Arndt, Hiltrud Brauch, Thomas Brüning, Arto Mannermaa, Veli-Matti Kosma, Diether Lambrechts, Machteld Keupers, Fergus J Couch, Celine Vachon, Graham G Giles, Robert J MacInnis, Jonine Figueroa, Louise Brinton, Kamila Czene, Judith S Brand, Marike Gabrielson, Keith Humphreys, Angela Cox, Simon S Cross, Alison M Dunning, Nick Orr, Anthony Swerdlow, Per Hall, Paul D P Pharoah, Marjanka K Schmidt, Douglas F Easton, Nilanjan Chatterjee, Jenny Chang-Claude, Montserrat García-Closas
Background: Polygenic risk scores (PRS) for breast cancer can be used to stratify the population into groups at substantially different levels of risk. Combining PRS and environmental risk factors will improve risk prediction; however, integrating PRS into risk prediction models requires evaluation of their joint association with known environmental risk factors. Methods: Analyses were based on data from 20 studies; datasets analysed ranged from 3453 to 23 104 invasive breast cancer cases and similar numbers of controls, depending on the analysed environmental risk factor...
January 5, 2018: International Journal of Epidemiology
https://www.readbyqxmd.com/read/29311295/cfh-and-arms2-genetic-risk-determines-progression-to-neovascular-age-related-macular-degeneration-after-antioxidant-and-zinc-supplementation
#8
Demetrios G Vavvas, Kent W Small, Carl C Awh, Brent W Zanke, Robert J Tibshirani, Rafal Kustra
We evaluated the influence of an antioxidant and zinc nutritional supplement [the Age-Related Eye Disease Study (AREDS) formulation] on delaying or preventing progression to neovascular AMD (NV) in persons with age-related macular degeneration (AMD). AREDS subjects (n = 802) with category 3 or 4 AMD at baseline who had been treated with placebo or the AREDS formulation were evaluated for differences in the risk of progression to NV as a function of complement factor H (CFH) and age-related maculopathy susceptibility 2 (ARMS2) genotype groups...
January 8, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29303685/characterization-of-novel-gene-yr79-and-four-additional-qtl-for-all-stage-and-high-temperature-adult-plant-resistance-to-stripe-rust-in-spring-wheat-pi-182103
#9
Junyan Feng, Meinan Wang, Deven R See, Shiaoman Chao, You-Liang Zheng, Xianming Chen
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important disease of wheat worldwide. Exploring new resistance genes is essential for breeding resistant wheat cultivars. PI 182103, a spring wheat landrace originally from Pakistan, has shown a high level of resistance to stripe rust in fields for many years, but genes for resistance to stripe rust in the variety have not been studied. To map the resistance gene(s) in PI 182103, 185 recombinant inbred lines (RILs) were developed from a cross with Avocet Susceptible (AvS)...
January 5, 2018: Phytopathology
https://www.readbyqxmd.com/read/29287921/the-effect-of-age-and-gender-on-the-genetic-regulation-of-serum-25-hydroxyvitamin-d-the-fin-d2d-population-based-study
#10
Maija E Miettinen, Melissa C Smart, Leena Kinnunen, Sirkka Keinänen-Kiukaanniemi, Leena Moilanen, Hannu Puolijoki, Juha Saltevo, Heikki Oksa, Graham A Hitman, Jaakko Tuomilehto, Markku Peltonen
In addition to sunlight and dietary sources, several genes in the metabolic pathway of vitamin D affect serum 25-hydroxyvitamin D (25OHD) concentration. It is not known whether this genetic regulation is influenced by host characteristics. We investigated the effect of age and gender on the genetic regulation of serum 25OHD concentration. In total, 2868 Finnish men and women aged 45-74 years participated in FIN-D2D population-based health survey in 2007. Of the 2822 participants that had serum 25OHD concentration available, 2757 were successfully genotyped...
December 26, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29285564/the-effects-of-cxcl10-polymorphisms-on-copd-susceptibility
#11
Yan Wang, Qipeng Zhou, Lian Dong, Mingmei Xiong, Hua Jiang, Meihua Guo, Li Zhao, Liang Yuan, Ziying Li, Hanwei Liu, Jian Wang, Nanshan Zhong, Wenju Lu
The polymorphisms of cytokine genes has been reported to modulate the individual's susceptibility to environmental stimuli in COPD development. C-X-C motif chemokine 10 (CXCL10) mediates recruitment inflammatory cells such as monocytes. Therefore, it may play a key role in COPD. Here, a case-control study was conducted to evaluate the association between CXCL10 tag-SNPs and COPD risk. Four tag-SNPs including rs4256246, rs4508917, rs56061981, and rs56316945 were identified based on the linkage disequilibrium (LD) analysis in 30 healthy controls...
December 28, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29281972/mycoplasma-genitalium-whole-genome-sequence-analysis-recombination-and-population-structure
#12
Maria C Fookes, James Hadfield, Simon Harris, Surendra Parmar, Magnus Unemo, Jørgen S Jensen, Nicholas R Thomson
BACKGROUND: Although Mycoplasma genitalium is a common sexually transmitted pathogen causing clinically distinct diseases both in male and females, few genomes have been sequenced up to now, due mainly to its fastidious nature and slow growth. Hence, we lack a robust phylogenetic framework to provide insights into the population structure of the species. Currently our understanding of the nature and diversity of M. genitalium relies on molecular tests targeting specific genes or regions of the genome and knowledge is limited by a general under-testing internationally...
December 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29280414/the-relationship-between-dietary-quality-serum-brain-derived-neurotrophic-factor-bdnf-level-and-the-val66met-polymorphism-in-predicting-depression
#13
Amy Froud, Jenifer Murphy, Lachlan Cribb, Chee H Ng, Jerome Sarris
BACKGROUND: Brain-derived neurotrophic factor (BDNF), a neurotrophic factor implicated in the pathogenesis of depression, may be influenced by dietary quality. Both dietary quality and serum BDNF have been researched independently in regard to their effect on depression; however, there is limited research investigating the relationship between the two factors and how they interact in depression. Additionally, a single-nucleotide polymorphism (SNP) (Val66Met) in the BDNF gene, which has been implicated in BDNF levels and depression, may contribute to the complex relationship between depression, dietary quality, and BDNF level...
December 27, 2017: Nutritional Neuroscience
https://www.readbyqxmd.com/read/29275155/htr1a-1b-dna-methylation-may-predict-escitalopram-treatment-response-in-depressed-chinese-han-patients
#14
Peipei Wang, Qinyu Lv, Yemeng Mao, Cuizhen Zhang, Chenxi Bao, Hong Sun, Hanmei Chen, Zhenghui Yi, Weimin Cai, Yiru Fang
BACKGROUND: The serotonin receptor 1A and 1B (HTR1A/1B) gene have been suggested to be involved in the pathogenesis of major depressive disorder (MDD) and the antidepressant treatment response. Gene expression differences were partly mediated by genetic polymorphism and DNA methylation which might be affected by environmental factors. In the present study, we attempt to identify whether HTR1A/1B DNA methylation and genetic polymorphism could predict antidepressant treatment response. METHODS: 85 Chinese Han MDD patients were clinically assessed 8 weeks after of initiating escitalopram treatment for the first time...
December 7, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29249828/analysis-of-the-joint-effect-of-snps-to-identify-independent-loci-and-allelic-heterogeneity-in-schizophrenia-gwas-data
#15
Tatiana Polushina, Sudheer Giddaluru, Francesco Bettella, Thomas Espeseth, Astri J Lundervold, Srdjan Djurovic, Sven Cichon, Per Hoffmann, Markus M Nöthen, Vidar M Steen, Ole A Andreassen, Stéphanie Le Hellard
We have tested published methods for capturing allelic heterogeneity and identifying loci of joint effects to uncover more of the "hidden heritability" of schizophrenia (SCZ). We used two tools, cojo-GCTA and multi-SNP, to analyze meta-statistics from the latest genome-wide association study (GWAS) on SCZ by the Psychiatric Genomics Consortium (PGC). Stepwise regression on markers with p values <10-7 in cojo-GCTA identified 96 independent signals. Eighty-five passed the genome-wide significance threshold...
December 18, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/29246113/comparison-of-weighting-approaches-for-genetic-risk-scores-in-gene-environment-interaction-studies
#16
Anke Hüls, Ursula Krämer, Christopher Carlsten, Tamara Schikowski, Katja Ickstadt, Holger Schwender
BACKGROUND: Weighted genetic risk scores (GRS), defined as weighted sums of risk alleles of single nucleotide polymorphisms (SNPs), are statistically powerful for detection gene-environment (GxE) interactions. To assign weights, the gold standard is to use external weights from an independent study. However, appropriate external weights are not always available. In such situations and in the presence of predominant marginal genetic effects, we have shown in a previous study that GRS with internal weights from marginal genetic effects ("GRS-marginal-internal") are a powerful and reliable alternative to single SNP approaches or the use of unweighted GRS...
December 16, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29243845/fc%C3%AE%C2%B5r1%C3%AE-gene-polymorphism-shows-association-with-high-ige-and-anti-fc%C3%AE%C2%B5r1%C3%AE-in-chronic-rhinosinusitis-with-nasal-polyposis
#17
Sajad Ahmad Dar, Gargi Rai, Mohammad Ahmed Ansari, Naseem Akhter, Neelima Gupta, Sonal Sharma, Shafiul Haque, Vishnampettai Ganapathysubramanian Ramachandran, Mohd Wahid, M Rudramurthy Shivprakash, Arunaloke Chakrabarti, Shukla Das
Despite large number of investigations, the etiology of chronic rhinosinusitis (CRS) remains unclear. Several factors are likely involved in its onset. The genetic susceptibility of IgE-responsiveness likely caused by polymorphism(s) in high affinity receptor for IgE (FcεR1α) gene can help in understanding the pathophysiology of CRS with nasal polyposis (CRSwNP). A population-based case-control association analysis was conducted to assess the risk of CRSwNP conferred by single nucleotide polymorphisms (SNPs) in FcεR1α gene in a North Indian cohort...
December 15, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29238857/fto-rs9939609-a-allele-influences-anthropometric-outcome-in-response-to-dietary-intervention-but-not-in-response-to-physical-exercise-program
#18
Gabrielle Araujo do Nascimento, Mayza Dalcin Teixeira, Lupe Furtado-Alle, Neiva Leite, Ricardo Lehtonen Rodrigues de Souza, Louise Farah Saliba, Gerusa Eisfeld Milano, Larissa Rosa da Silva, Juliana Pizzi, Wendell Arthur Lopes, Maria de Fátima Aguiar Lopes, Ana Cláudia Kapp Titski, Luciane Viater Tureck
PURPOSE: The fat mass and obesity-associated (FTO) gene is involved in energy homeostasis. The A allele of the rs9939609 (SNP; T>A) is associated with obesity and higher food intake, while its effect in energy expenditure remains unclear. The aim of this study is to examine whether FTO rs9939609 is associated with the anthropometric outcomes of a physical exercise program and a dietary intervention. METHODS: We studied two independent samples. The first was composed by children and adolescents in which overweight and obese individuals were submitted to a physical exercise program (n = 136) and normal weight participants served as a control group (n = 172)...
December 13, 2017: European Journal of Nutrition
https://www.readbyqxmd.com/read/29237140/high-density-snp-mapping-reveals-closely-linked-qtl-for-resistance-to-stagonospora-nodorum-blotch-snb-in-flag-leaf-and-glume-of-hexaploid-wheat
#19
Michael Francki, Esther Walker, Dora Li, Kerrie Forrest
The genetic control of adult plant resistance to Stagonospora nodorum blotch (SNB) is complex consisting of genes with minor effects interacting in an additive manner. Earlier studies detected quantitative trait loci (QTL) for flag leaf resistance in successive years on chromosomes 1B, 2A, 2D, 5B using SSR- and DArT-based genetic maps of progeny from the crosses EGA Blanco/Millewa, 6HRWSN125/WAWHT2074 and P92201D5/P91193D1. Similarly, QTL for glume resistance detected in successive years and multiple environments were identified on chromosomes 2D and 4B from genetic maps of P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively...
December 13, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29233086/functional-polymorphisms-in-asporin-and-cilp-together-with-joint-loading-predispose-to-hand-osteoarthritis
#20
Mari Taipale, Svetlana Solovieva, Päivi Leino-Arjas, Minna Männikkö
BACKGROUND: Osteoarthritis (OA) is the most common degenerative joint disease afflicting people in the Western world and has a strong genetic influence. The aim of this study was to examine the association of two known functional polymorphisms in the TGF-β inhibiting genes, asporin (ASPN) and cartilage intermediate layer protein (CILP), with hand OA and potential gene-occupational hand loading interaction. RESULTS: Statistically significant interaction of the CILP rs2073711 T and ASPN D15 alleles with hand OA was observed (OR = 2...
December 12, 2017: BMC Genetics
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