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Snp interaction

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https://www.readbyqxmd.com/read/29159863/genome-wide-gene-environment-interaction-in-depression-a-systematic-evaluation-of-candidate-genes-the-childhood-trauma-working-group-of-pgc-mdd
#1
Sandra Van der Auwera, Wouter J Peyrot, Yuri Milaneschi, Johannes Hertel, Bernhard Baune, Gerome Breen, Enda Byrne, Erin C Dunn, Helen Fisher, Georg Homuth, Douglas Levinson, Cathryn Lewis, Natalie Mills, Niamh Mullins, Matthias Nauck, Giorgio Pistis, Martin Preisig, Marcella Rietschel, Stephan Ripke, Patrick Sullivan, Alexander Teumer, Henry Völzke, Dorret I Boomsma, Naomi R Wray, Brenda Penninx, Hans Grabe
Gene by environment (GxE) interaction studies have investigated the influence of a number of candidate genes and variants for major depressive disorder (MDD) on the association between childhood trauma and MDD. Most of these studies are hypothesis driven and investigate only a limited number of SNPs in relevant pathways using differing methodological approaches. Here (1) we identified 27 genes and 268 SNPs previously associated with MDD or with GxE interaction in MDD and (2) analyzed their impact on GxE in MDD using a common approach in 3944 subjects of European ancestry from the Psychiatric Genomics Consortium who had completed the Childhood Trauma Questionnaire...
November 21, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/29156789/xrcc1-mediated-the-development-of-cervival-cancer-through-a-novel-sp1-krox-20-swich
#2
Qingtao Meng, Shizhi Wang, Weiyan Tang, Shenshen Wu, Na Gao, Chengcheng Zhang, Xiaoli Cao, Xiaobo Li, Zhengdong Zhang, Michael Aschner, Hua Jin, Yue Huang, Rui Chen
Cervical cancer is the second leading cause of mortality among women. Impairment of the base excision repair (BER) pathway is one of the major causes of the initiation and progression of cervical cancer. However, whether the polymorphisms of the BER pathway components (i.e., HOGG1, XRCC1, ADPRT, and APE1) can affect the risk of cervical cancer remains unknown. Herein, we applied a hospital-based case-control study covering two independent cohorts and a subsequent functional assay to determine the roles of the single nucleotide polymorphisms (SNPs) of the BER pathway genes in cervical cancer...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29150514/sinorhizobium-meliloti-glutathione-reductase-is-required-for-both-redox-homeostasis-and-symbiosis
#3
Guirong Tang, Ningning Li, Yumin Liu, Liangliang Yu, Junhui Yan, Li Luo
Glutathione (L-γ-glutamyl-L-cysteinylglycine; GSH), one of the key antioxidants in Sinorhizobium meliloti, is required for the development of alfalfa (Medicago sativa) nitrogen-fixing nodules. Glutathione exists either in a reduced form (GSH) or an oxidized form (GSSG), and its content is regulated by two pathways in S. meliloti The first pathway is the de novo synthesis of glutathione from its constituent amino acids, namely, Glu, Cys, and Gly, catalyzed by γ-glutamyl cysteine synthetase (GshA) and glutathione synthetase (GshB)...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29148804/a-nanobionic-light-emitting-plant
#4
Seon-Yeong Kwak, Juan Pablo Giraldo, Min Hao Wong, Volodymyr Koman, Tedrick Lew, Jon Ell, Mark Weidman, Rosalie Sinclair, Markita P Landry, William A Tisdale, Michael S Strano
The engineering of living plants for visible light emission and sustainable illumination is compelling because plants possess independent energy generation and storage mechanisms and autonomous self-repair. Herein, we demonstrate a plant nanobionic approach that enables exceptional luminosity and lifetime utilizing four chemically-interacting nanoparticles, including firefly luciferase conjugated silica (SNP-Luc), D-luciferin releasing poly(lactic-co-glycolic acid) (PLGA-LH2), coenzyme A functionalized chitosan (CS-CoA) and semiconductor nanocrystal phosphors for longer wavelength modulation...
November 17, 2017: Nano Letters
https://www.readbyqxmd.com/read/29142473/genetic-associations-with-adverse-events-from-anti-tumor-necrosis-factor-therapy-in-inflammatory-bowel-disease-patients
#5
Daniel Lew, Soon Man Yoon, Xiaofei Yan, Lori Robbins, Talin Haritunians, Zhenqiu Liu, Dalin Li, Dermot Pb McGovern
AIM: To study the type and frequency of adverse events associated with anti-tumor necrosis factor (TNF) therapy and evaluate for any serologic and genetic associations. METHODS: This study was a retrospective review of patients attending the inflammatory bowel disease (IBD) centers at Cedars-Sinai IBD Center from 2005-2016. Adverse events were identified via chart review. IBD serologies were measured by ELISA. DNA samples were genotyped at Cedars-Sinai using Illumina Infinium Immunochipv1 array per manufacturer's protocol...
October 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29142225/comparative-genomic-analysis-of-esophageal-squamous-cell-carcinoma-between-asian-and-caucasian-patient-populations
#6
Jiaying Deng, Hu Chen, Daizhan Zhou, Junhua Zhang, Yun Chen, Qi Liu, Dashan Ai, Hanting Zhu, Li Chu, Wenjia Ren, Xiaofei Zhang, Yi Xia, Menghong Sun, Huiwen Zhang, Jun Li, Xinxin Peng, Liang Li, Leng Han, Hui Lin, Xiujun Cai, Jiaqing Xiang, Shufeng Chen, Yihua Sun, Yawei Zhang, Jie Zhang, Haiquan Chen, Shijian Zhang, Yi Zhao, Yun Liu, Han Liang, Kuaile Zhao
Esophageal squamous cell carcinoma is a major histological type of esophageal cancer, with distinct incidence and survival patterns among races. Although previous studies have characterized somatic mutations in this disease, a rigorous comparison between different patient populations has not been conducted. Here we sequence the samples of 316 Chinese patients, combine them with those from The Cancer Genome Atlas, and perform a comparative analysis between Asian and Caucasian patients. We find that mutated CSMD3 is associated with better prognosis in Asian patients...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142105/the-nde1-genomic-locus-can-affect-treatment-of-psychiatric-illness-through-gene-expression-changes-related-to-microrna-484
#7
Nicholas J Bradshaw, Liisa Ukkola-Vuoti, Maiju Pankakoski, Amanda B Zheutlin, Alfredo Ortega-Alonso, Minna Torniainen-Holm, Vishal Sinha, Sebastian Therman, Tiina Paunio, Jaana Suvisaari, Jouko Lönnqvist, Tyrone D Cannon, Jari Haukka, William Hennah
Genetic studies of familial schizophrenia in Finland have observed significant associations with a group of biologically related genes, DISC1, NDE1, NDEL1, PDE4B and PDE4D, the 'DISC1 network'. Here, we use gene expression and psychoactive medication use data to study their biological consequences and potential treatment implications. Gene expression levels were determined in 64 individuals from 18 families, while prescription medication information has been collected over a 10-year period for 931 affected individuals...
November 2017: Open Biology
https://www.readbyqxmd.com/read/29140525/rsnpbase-3-0-an-updated-database-of-snp-related-regulatory-elements-element-gene-pairs-and-snp-based-gene-regulatory-networks
#8
Liyuan Guo, Jing Wang
Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29140435/hmdb-4-0-the-human-metabolome-database-for-2018
#9
David S Wishart, Yannick Djoumbou Feunang, Ana Marcu, An Chi Guo, Kevin Liang, Rosa Vázquez-Fresno, Tanvir Sajed, Daniel Johnson, Carin Li, Naama Karu, Zinat Sayeeda, Elvis Lo, Nazanin Assempour, Mark Berjanskii, Sandeep Singhal, David Arndt, Yonjie Liang, Hasan Badran, Jason Grant, Arnau Serra-Cayuela, Yifeng Liu, Rupa Mandal, Vanessa Neveu, Allison Pon, Craig Knox, Michael Wilson, Claudine Manach, Augustin Scalbert
The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29134650/thyroid-associated-genetic-polymorphisms-in-relation-to-breast-cancer-risk-in-the-malm%C3%A3-diet-and-cancer-study
#10
Jasmine Brandt, Signe Borgquist, Peter Almgren, Asta Försti, Linnea Huss, Olle Melander, Jonas Manjer
Previous studies have suggested that thyroid function is associated with breast cancer risk, which could have an important clinical impact, as one in eight women will develop a thyroid disorder during her lifetime. However, the underlying pathomechanism behind the association is still unknown. We used the Malmö Diet and Cancer Study (a population-based prospective study consisting of 17,035 women) to examine 17 single nucleotide polymorphisms (SNPs) previously related to levels of free thyroxine (free T4) and thyroid peroxidase antibodies (TPO-Ab) as potential genetic risk factors for breast cancer...
November 14, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29129846/the-il18-promoter-polymorphism-rs1946518-is-associated-with-the-risk-of-periodontitis-in-japanese-women-the-kyushu-okinawa-maternal-and-child-health-study
#11
Keiko Tanaka, Yoshihiro Miyake, Takashi Hanioka, Shinya Furukawa, Nobuyuki Miyatake, Masashi Arakawa
Interleukin-18 (IL-18) is a proinflammatory cytokine that plays an important role in periodontitis and its polymorphisms might modulate the individual susceptibility to periodontitis. Only a limited number of studies on the association between IL18 single-nucleotide polymorphisms (SNPs) and the risk of periodontitis have been realized, however. The aim of this case-control study among young post-partum Japanese women (18 to 45 years) was to determine the impact of SNPs, rs1946518 (-607 C/A) and rs187238 (-137G/C), on periodontitis...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29126136/drugbank-5-0-a-major-update-to-the-drugbank-database-for-2018
#12
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda, Nazanin Assempour, Ithayavani Iynkkaran, Yifeng Liu, Adam Maciejewski, Nicola Gale, Alex Wilson, Lucy Chin, Ryan Cummings, Diana Le, Allison Pon, Craig Knox, Michael Wilson
DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. First described in 2006, DrugBank has continued to evolve over the past 12 years in response to marked improvements to web standards and changing needs for drug research and development. This year's update, DrugBank 5.0, represents the most significant upgrade to the database in more than 10 years. In many cases, existing data content has grown by 100% or more over the last update...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29121402/incorporating-functional-genomic-information-to-enhance-polygenic-signal-and-identify-variants-involved-in-gene-by-environment-interaction-for-young-adult-alcohol-problems
#13
Jessica E Salvatore, Jeanne E Savage, Peter Barr, Aaron R Wolen, Fazil Aliev, Eero Vuoksimaa, Antti Latvala, Lea Pulkkinen, Richard J Rose, Jaakko Kaprio, Danielle M Dick
BACKGROUND: Characterizing aggregate genetic risk for alcohol misuse and identifying variants involved in gene-by-environment interaction (G×E) effects has so far been a major challenge. We hypothesized that functional genomic information could be used to enhance detection of polygenic signal underlying alcohol misuse, and to prioritize identification of single nucleotide polymorphisms (SNPs) most likely to exhibit G×E effects. METHODS: We examined these questions in the young adult FinnTwin12 sample (n=1170)...
November 9, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29121253/the-role-of-nrg1-in-the-predisposition-to-papillary-thyroid-carcinoma
#14
Huiling He, Wei Li, Sandya Liyanarachchi, Yanqiang Wang, Lianbo Yu, Luke K Genutis, Sophia Maharry, John E Phay, Rulong Shen, Pamela Brock, Albert de la Chapelle
Context: Previous genome-wide association studies (GWAS) have shown that SNP rs2439302 in chromosome 8p12 is significantly associated with papillary thyroid carcinoma (PTC) risk and dysregulated NRG1 expression. The underlying mechanisms remain to be discovered. Objective: To evaluate the expression of NRG1 isoforms, candidate functional variants, and potential genes downstream of NRG1 in thyroid tissue. Methods: Quantitative RT-PCR was applied for gene expression analysis...
November 7, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29118424/methods-for-scarless-selection-free-generation-of-human-cells-and-allele-specific-functional-analysis-of-disease-associated-snps-and-variants-of-uncertain-significance
#15
Nicole B Coggins, Jacob Stultz, Henriette O'Geen, Luis G Carvajal-Carmona, David J Segal
With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Here we combine CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the PALB2 gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29118371/genetic-association-analysis-of-microrna137-and-its-target-complex-1-with-schizophrenia-in-han-chinese
#16
Weihong Lu, Yi Zhang, Xinyu Fang, Weixing Fan, Wei Tang, Jun Cai, Lisheng Song, Chen Zhang
Recent genome-wide association studies (GWAS) have identified a strong association signal of microRNA137 host gene (MIR137) with schizophrenia. MIR137 dysfunction results in downregulation of presynaptic target gene complexin 1 (CPLX1) and impairs synaptic plasticity in the hippocampus. In this study, we aimed to investigate whether the variants of MIR137 and CPLX1 confer susceptibility to schizophrenia in Han Chinese. This study employed 736 patients with schizophrenia patients and 751 well-matched healthy subjects for genetic analysis, and genotyped 12 SNPs within MIR137 and CPLX1...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29108386/single-nucleotide-polymorphisms-in-mlh1-predict-poor-prognosis-of-hepatocellular-carcinoma-in-a-chinese-population
#17
Xiaonian Zhu, Wei Liu, Xiaoqiang Qiu, Zhigang Wang, Chao Tan, Chunhua Bei, Linyuan Qin, Yuan Ren, Shengkui Tan
Hepatocellular carcinoma (HCC) is a malignant cancer causing deleterious health effect worldwide, especially in China. So far clinical cure rate and long-term survival rate of HCC remains low. Most HCC patients after cancer resection have recurrence or metastasis within 5 years. This study aims to explore the genetic association of mutL homolog 1 (MLH1) polymorphisms with HCC risk and prognosis. Four candidate MLH1 polymorphisms, rs1800734, rs10849, rs3774343 and rs1540354 were studied from a hospital-based case-control study including 1,036 cases (HCC patients) and 1,036 controls (non-HCC patients) in Guangxi, China...
October 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29105878/introgression-between-divergent-corn-borer-species-in-a-region-of-sympatry-implications-on-the-evolution-and-adaptation-of-pest-arthropods
#18
Yangzhou Wang, Kyung Seok Kim, Wenchao Guo, Qiyun Li, Yunyue Zhang, Zhenying Wang, Brad S Coates
The Asian corn borer, Ostrinia furnacalis, and European corn borer, O. nubilalis (Lepidoptera: Crambidae), cause damage to cultivated maize in spatially distinct geographies, and have evolved divergent hydrocarbons as the basis of sexual communication. The Yili area of Xinjiang Uyghur Autonomous Region in China represents the only known region where O. furnacalis has invaded a native O. nubilalis range, and these two corn borer species have made secondary contact. Genetic differentiation was estimated between Ostrinia larvae collected from maize plants at 11 locations in Xinjiang Province, and genotyped using high throughput SNP and microsatellite markers...
November 6, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29101603/hypothalamic-pituitary-adrenal-axis-variants-and-childhood-trauma-influence-anxiety-sensitivity-in-south-african-adolescents
#19
Jacqueline S Womersley, Lindi I Martin, Lize van der Merwe, Soraya Seedat, Sian M J Hemmings
Anxiety sensitivity (AS) is characterised by the fear of anxiety-related symptoms and is a risk factor for the development of anxiety-related disorders. We examined whether genetic variation in three stress response genes, CRHR1, NR3C1, and FKBP5, interact with childhood trauma (CT) to predict AS in South African adolescents. Xhosa (n = 634) and Coloured (n = 317) students completed self-report measures of AS and CT, and a total of eighteen polymorphisms within CRHR1, NR3C1, and FKBP5 were genotyped. Differences in AS based on genetic variation and CT were analysed within population and gender groups using multiple linear regression...
November 4, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/29100531/genetic-dissection-of-sharka-disease-tolerance-in-peach-p-persica-l-batsch
#20
Marco Cirilli, Laura Rossini, Filippo Geuna, Francesco Palmisano, Angelantonio Minafra, Tiziana Castrignanò, Stefano Gattolin, Angelo Ciacciulli, Anna Rosa Babini, Alessandro Liverani, Daniele Bassi
BACKGROUND: Plum pox virus (PPV), agent of Sharka disease, is the most important quarantine pathogen of peach (P. persica L. Batsch). Extensive evaluation of peach germplasm has highlighted the lack of resistant sources, while suggesting the presence of a quantitative disease resistance, expressed as reduction in the intensity of symptoms. Unravelling the genetic architecture of peach response to PPV infection is essential for pyramiding resistant genes and for developing more tolerant varieties...
November 3, 2017: BMC Plant Biology
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