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Snp interaction

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https://www.readbyqxmd.com/read/28930911/an-enrichment-strategy-yields-seven-novel-single-nucleotide-polymorphisms-associated-with-mortality-and-altered-th17-responses-following-blunt-trauma
#1
Lukas Schimunek, Rami A Namas, Jinling Yin, Dongmei Liu, Derek Barclay, Fayten El-Dehaibi, Andrew Abboud, Haley Lindberg, Ruben Zamora, R Billiar Timothy, Yoram Vodovotz
Trauma is the leading cause of death worldwide for individuals under the age of 55. Interpatient genomic differences, in the form of candidate single nucleotide polymorphisms (SNPs), have been associated previously with adverse outcomes after trauma. However, the utility of these SNPs to predict outcomes based on a meaningful endpoint such as survival is as yet undefined. We hypothesized that specific SNP haplotypes could segregate trauma survivors from non-survivors. Genomic DNA samples were obtained from 453 blunt trauma patients, for whom complete daily clinical and biomarker data were available for 397...
September 19, 2017: Shock
https://www.readbyqxmd.com/read/28928764/exploring-and-harnessing-haplotype-diversity-to-improve-yield-stability-in-crops
#2
REVIEW
Lunwen Qian, Lee T Hickey, Andreas Stahl, Christian R Werner, Ben Hayes, Rod J Snowdon, Kai P Voss-Fels
In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28927989/identification-of-susceptible-genes-for-complex-chronic-diseases-based-on-disease-risk-functional-snps-and-interaction-networks
#3
Wan Li, Lina Zhu, Hao Huang, Yuehan He, Junjie Lv, Weimin Li, Lina Chen, Weiming He
Complex chronic diseases are caused by the effects of genetic and environmental factors. Single nucleotide polymorphisms (SNPs), one common type of genetic variations, played vital roles in diseases. We hypothesized that disease risk functional SNPs in coding regions and protein interaction network modules were more likely to contribute to the identification of disease susceptible genes for complex chronic diseases. This could help to further reveal the pathogenesis of complex chronic diseases. Disease risk SNPs were first recognized from public SNP data for coronary heart disease (CHD), hypertension (HT) and type 2 diabetes (T2D)...
September 16, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28927820/a-novel-role-for-cilia-function-in-atopy-adgrv1-and-dnah5-interactions
#4
Pierre-Emmanuel Sugier, Myriam Brossard, Chloé Sarnowski, Amaury Vaysse, Andréanne Morin, Lucile Pain, Patricia Margaritte-Jeannin, Marie-Hélène Dizier, William O C M Cookson, Mark Lathrop, Miriam F Moffatt, Catherine Laprise, Florence Demenais, Emmanuelle Bouzigon
BACKGROUND: Atopy, an endotype underlying allergic diseases, has a substantial genetic component. OBJECTIVE: Our goal was to identify novel genes associated with atopy in asthma-ascertained families. METHODS: We implemented a three-step analysis strategy in three datasets: The Epidemiological study on the Genetics and Environment of Asthma (EGEA) dataset: 1,660 subjects; The Saguenay-Lac-Saint-Jean (SLSJ) dataset: 1,138 subjects; and The Medical Research Council (MRC) dataset: 446 subjects)...
September 16, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28924022/pan-genomic-analyses-identify-key-helicobacter-pylori-pathogenic-loci-modified-by-carcinogenic-host-microenvironments
#5
Jennifer M Noto, Abha Chopra, John T Loh, Judith Romero-Gallo, M Blanca Piazuelo, Mark Watson, Shay Leary, Amber C Beckett, Keith T Wilson, Timothy L Cover, Simon Mallal, Dawn A Israel, Richard M Peek
OBJECTIVE: Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease...
September 18, 2017: Gut
https://www.readbyqxmd.com/read/28923017/within-breed-and-multi-breed-gwas-on-imputed-whole-genome-sequence-variants-reveal-candidate-mutations-affecting-milk-protein-composition-in-dairy-cattle
#6
Marie-Pierre Sanchez, Armelle Govignon-Gion, Pascal Croiseau, Sébastien Fritz, Chris Hozé, Guy Miranda, Patrice Martin, Anne Barbat-Leterrier, Rabia Letaïef, Dominique Rocha, Mickaël Brochard, Mekki Boussaha, Didier Boichard
BACKGROUND: Genome-wide association studies (GWAS) were performed at the sequence level to identify candidate mutations that affect the expression of six major milk proteins in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) dairy cattle. Whey protein (α-lactalbumin and β-lactoglobulin) and casein (αs1, αs2, β, and κ) contents were estimated by mid-infrared (MIR) spectrometry, with medium to high accuracy (0.59 ≤ R(2) ≤ 0.92), for 848,068 test-day milk samples from 156,660 cows in the first three lactations...
September 18, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28919064/genetics-of-obesity-what-genetic-association-studies-have-taught-us-about-the-biology-of-obesity-and-its-complications
#7
REVIEW
Mark O Goodarzi
Genome-wide association studies (GWAS) for BMI, waist-to-hip ratio, and other adiposity traits have identified more than 300 single-nucleotide polymorphisms (SNPs). Although there is reason to hope that these discoveries will eventually lead to new preventive and therapeutic agents for obesity, this will take time because such developments require detailed mechanistic understanding of how an SNP influences phenotype (and this information is largely unavailable). Fortunately, absence of functional information has not prevented GWAS findings from providing insights into the biology of obesity...
September 14, 2017: Lancet Diabetes & Endocrinology
https://www.readbyqxmd.com/read/28918577/microarray-based-snp-genotyping-to-identify-genetic-risk-factors-of-triple-negative-breast-cancer-tnbc-in-south-indian-population
#8
M Aravind Kumar, Vineeta Singh, Shaik Mohammad Naushad, Uday Shanker, M Lakshmi Narasu
In the view of aggressive nature of Triple-Negative Breast cancer (TNBC) due to the lack of receptors (ER, PR, HER2) and high incidence of drug resistance associated with it, a case-control association study was conducted to identify the contributing genetic risk factors for Triple-negative breast cancer (TNBC). A total of 30 TNBC patients and 50 age and gender-matched controls of Indian origin were screened for 9,00,000 SNP markers using microarray-based SNP genotyping approach. The initial PLINK association analysis (p < 0...
September 16, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28912560/the-srgap2-snps-their-haplotypes-and-g%C3%A2-%C3%A3-%C3%A2-e-interactions-on-serum-lipid-traits
#9
Liu Miao, Rui-Xing Yin, Jin-Zhen Wu, Shuo Yang, Wei-Xiong Lin, Shang-Ling Pan
Maonan nationality is a relatively conservative and isolated minority in China. Little is known about the association of the Slit-Robo Rho GTPase activating protein 2 gene (SRGAP2) single nucleotide polymorphisms (SNPs) and serum lipid levels in the Chinese populations. This study was performed to clarify the association of the SRGAP2 rs2483058 and rs2580520 SNPs and their haplotypes with serum lipid traits in the Maonan and Han populations. Genotyping of the 2 SNPs was performed in 2444 unrelated subjects (Han, 1210 and Maonan, 1234) by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28904253/genetic-variants-of-ramp2-and-clr-are-associated-with-stroke
#10
Teruhide Koyama, Nagato Kuriyama, Etsuko Ozaki, Daisuke Matsui, Isao Watanabe, Wakiko Takeshita, Komei Iwai, Yoshiyuki Watanabe, Masahiro Nakatochi, Chisato Shimanoe, Keitaro Tanaka, Isao Oze, Hidemi Ito, Hirokazu Uemura, Sakurako Katsuura-Kamano, Rie Ibusuki, Ippei Shimoshikiryo, Naoyuki Takashima, Aya Kadota, Sayo Kawai, Tae Sasakabe, Rieko Okada, Asahi Hishida, Mariko Naito, Kiyonori Kuriki, Kaori Endoh, Norihiro Furusyo, Hiroaki Ikezaki, Sadao Suzuki, Akihiro Hosono, Haruo Mikami, Yohko Nakamura, Michiaki Kubo, Kenji Wakai
AIM: Stroke is associated closely with vascular homeostasis, and several complex processes and interacting pathways, which involve various genetic and environmental factors, contribute to the risk of stroke. Although adrenomedullin (ADM) has a number of physiological and vasoprotective functions, there are few studies of the ADM receptor system in humans. The ADM receptor comprises a calcitonin-receptor-like receptor (CLR) and receptor activity-modifying proteins (RAMPs). We analyzed single nucleotide polymorphisms (SNPs) in the RAMP2 and CLR genes to determine their association with stroke in the light of gene-environment interactions...
September 14, 2017: Journal of Atherosclerosis and Thrombosis
https://www.readbyqxmd.com/read/28902459/exome-sequences-of-multiplex-multigenerational-families-reveal-schizophrenia-risk-loci-with-potential-implications-for-neurocognitive-performance
#11
Mark Z Kos, Melanie A Carless, Juan Peralta, Joanne E Curran, Ellen E Quillen, Marcio Almeida, August Blackburn, Lucy Blondell, David R Roalf, Michael F Pogue-Geile, Ruben C Gur, Harald H H Göring, Vishwajit L Nimgaonkar, Raquel E Gur, Laura Almasy
Schizophrenia is a serious mental illness, involving disruptions in thought and behavior, with a worldwide prevalence of about one percent. Although highly heritable, much of the genetic liability of schizophrenia is yet to be explained. We searched for susceptibility loci in multiplex, multigenerational families affected by schizophrenia, targeting protein-altering variation with in silico predicted functional effects. Exome sequencing was performed on 136 samples from eight European-American families, including 23 individuals diagnosed with schizophrenia or schizoaffective disorder...
September 13, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28899360/biological-networks-in-parkinson-s-disease-an-insight-into-the-epigenetic-mechanisms-associated-with-this-disease
#12
Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya, Sanghamitra Bandyopadhyay
BACKGROUND: Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. RESULT: We have studied gene co-expression network obtained from a PD-specific microarray data. The co-expression network identified 11 hub genes, of which eight genes are not previously known to be associated with PD...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28892640/beneficial-effects-of-rosiglitazone-and-losartan-combination-in-diabetic-rats
#13
Hayam Ateyya, Manar Nader, Nagla Ahmad El-Sherbeeny
Diabetes with vascular complication needs strict interventions to retard possible serious complications. This research estimated the possible interaction of rosiglitazone (RGN) with losartan (Los) in diabetic rats. Male Spraque Dawly rats were randomly divided into: non-diabetic rats, diabetic rats, and diabetic rats received RGN, Los or combination of RGN and Los. Measurement of serum glucose, vascular adhesion molecule-1 (VCAM-1), interleukin (IL)-6, tumor necrosis factor and (TNF)-α levels, and aortic lipid peroxide (MDA), glutathione (GSH), superoxide dismutase (SOD) and total nitrate/nitrite (NOx) levels were done...
September 11, 2017: Canadian Journal of Physiology and Pharmacology
https://www.readbyqxmd.com/read/28891930/vitamin-d-receptor-gene-polymorphisms-associated-with-childhood-autism
#14
Anna Cieślińska, Elżbieta Kostyra, Barbara Chwała, Małgorzata Moszyńska-Dumara, Ewa Fiedorowicz, Małgorzata Teodorowicz, Huub F J Savelkoul
BACKGROUND: Autism spectrum disorder (ASD) is a group of heterogeneous, behaviorally defined disorders whereby currently no biological markers are common to all affected individuals. A deregulated immune response may be contributing to the etiology of ASD. The active metabolite of vitamin D₃ has an immunoregulatory role mediated by binding to the vitamin D receptor (VDR) in monocyte, macrophages, and lymphocytes. The effects of vitamin D and interaction with the VDR may be influenced by polymorphism in the VDR gene...
September 9, 2017: Brain Sciences
https://www.readbyqxmd.com/read/28889074/interaction-between-fkbp5-gene-and-childhood-trauma-on-psychosis-depression-and-anxiety-symptoms-in-a-non-clinical-sample
#15
Marta de Castro-Catala, Elionora Peña, Thomas R Kwapil, Sergi Papiol, Tamara Sheinbaum, Paula Cristóbal-Narváez, Sergi Ballespí, Neus Barrantes-Vidal, Araceli Rosa
BACKGROUND: Childhood trauma has been associated with a heightened risk for presenting clinical and non-clinical psychopathology in adulthood. Genes related with the stress response, such as the FK506 binding protein 51 (FKBP5), are plausible candidates moderating the effects of childhood trauma on the emergence of such symptoms later on. The present study aimed to explore the moderating role of FKBP5 genetic variability on the association of different types of childhood trauma with subclinical psychosis, depression and anxiety in a non-clinical sample...
August 26, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28878339/pathogen-lineage-based-genome-wide-association-study-identified-cd53-as-susceptible-locus-in-tuberculosis
#16
Yosuke Omae, Licht Toyo-Oka, Hideki Yanai, Supalert Nedsuwan, Sukanya Wattanapokayakit, Nusara Satproedprai, Nat Smittipat, Prasit Palittapongarnpim, Pathom Sawanpanyalert, Wimala Inunchot, Ekawat Pasomsub, Nuanjun Wichukchinda, Taisei Mushiroda, Michiaki Kubo, Katsushi Tokunaga, Surakameth Mahasirimongkol
Tuberculosis (TB) is known to be affected by host genetic factors. We reported a specific genetic risk factor through a genome-wide association study (GWAS) that focused on young age onset TB. In this study, we further focused on the heterogeneity of Mycobacterium tuberculosis (M. tb) lineages and assessed its possible interaction with age at onset on host genetic factors. We identified the pathogen lineage in 686 Thai TB cases and GWAS stratified by both infected pathogen lineage information and age at onset revealed a genome-wide significant association of one single-nucleotide polymorphism (SNP) on chromosome 1p13, which was specifically associated with non-Beijing lineage-infected old age onset cases (P=2...
September 7, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28877608/genome-wide-integrative-analysis-identified-snp-mirna-mrna-interaction-networks-in-peripheral-blood-mononuclear-cells
#17
Xiang Lin, Wei Xia, Wei Ji, Fang-Fei Xie, Pei He, Xiao-Wei Zhu, Yong-Hong Zhang, Fei-Yan Deng, Shu-Feng Lei
AIM: To detect SNP-miRNA-mRNA interaction networks and to elucidate miRNA-mediated regulation effects on mRNA expression. MATERIALS & METHODS: In human peripheral blood mononuclear cells of 43 females, SNP-miRNA-mRNA interaction networks were established through an integrative analysis. Then causal inference test was followed to detect miRNA-mediated effects on mRNA expressions. RESULTS: About 167 trios corresponding to 56 SNPs, 20 miRNAs and 47 target-mRNAs have the SNP-miRNA-mRNA interactions, but only 22 trios have miRNA-mediated effects between SNP and mRNA...
September 7, 2017: Epigenomics
https://www.readbyqxmd.com/read/28876207/inheritance-of-virulence-construction-of-a-linkage-map-and-mapping-dominant-virulence-genes-in-puccinia-striiformis-f-sp-tritici-through-characterization-of-a-sexual-population-with-genotyping-by-sequencing
#18
Congying Yuan, Meinan Wang, Daniel Z Skinner, Deven R See, Chongjing Xia, Xinhong Guo, Xianming Chen
Puccinia striiformis f. sp. tritici (Pst), the wheat stripe rust pathogen, is a dikaryotic, biotrophic, and macrocyclic fungus. Genetic study of Pst virulence was not possible until the recent discovery of Berberis spp. and Mahonia spp. as alternate hosts. To determine inheritance of virulence and map virulence genes, a segregating population of 119 isolates was developed by self-fertilizing Pst isolate 08-220 (race PSTv-11) on barberry leaves under controlled greenhouse conditions. The progeny isolates were phenotyped on a set of 29 wheat lines with single genes for race-specific resistance and genotyped with simple sequence repeat (SSR) markers, simple sequence repeat derived from secreted protein genes (SP-SNP), and SNP markers from genotyping- by-sequencing (GBS)...
September 6, 2017: Phytopathology
https://www.readbyqxmd.com/read/28876085/joint-analysis-of-snp-snp-environment-interactions-for-chronic-dialysis-by-an-improved-branch-and-bound-algorithm
#19
Cheng-Hong Yang, Yu-Da Lin, Li-Yeh Chuang, Jin-Bor Chen, Hsueh-Wei Chang
In previous studies, both single-nucleotide polymorphism (SNP)-SNP or gene-gene (G × G) interactions and SNP-environmental factor (G × E) interactions were reported to partially account for "missing" heritability. However, (G × G) × E interactions were less commonly addressed. The purpose of this study was to develop a novel strategy to evaluate possible (G × G) × E interactions in D-loop-based chronic dialysis association. Using values from our previously published data set (704 controls and 193 cases) of 77 D-loop SNPs and 7 environmental factors (coronary heart disease, hypertension, diabetes mellitus, triglyceride, cholesterol, blood thiol, and TBARS levels), we compared the performances of G, G × G, G × E, and (G × G) × E...
September 6, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28874875/the-role-of-histone-modification-and-a-regulatory-single-nucleotide-polymorphism-rs2071166-in-the-cx43-promoter-in-patients-with-tof
#20
Ruoyi Gu, Jun Xu, Yixiang Lin, Wei Sheng, Duan Ma, Xiaojing Ma, Guoying Huang
Abnormal level of Cx43 expression could result in CHD. Epigenetic modification and disease-associated, non-coding SNPs might influence gene transcription and expression. Our study aimed to determine the role of histone modification and an rSNP (rs2071166) in the Cx43 promoter in patients with TOF. Our results indicate that H3K18ac bind to Cx43 promoter and that their levels are reduced in TOF patients relative to controls. The relationship between the non-coding SNP in the Cx43 gene and TOF patients was evaluated in 158 patients and 300 controls...
September 5, 2017: Scientific Reports
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