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https://www.readbyqxmd.com/read/28737243/investigating-the-genetic-regulation-of-the-expression-of-63-lipid-metabolism-genes-in-the-pig-skeletal-muscle
#1
R González-Prendes, R Quintanilla, M Amills
A comprehensive and systematic view of the genetic regulation of lipid metabolism genes is still lacking in pigs. Herewith, we have investigated the genetic regulation of 63 porcine genes with crucial roles in the uptake, transport, synthesis and catabolism of lipids. With this aim, we have performed an expression QTL (eQTL) scan in 104 pigs with available genotypes for the Illumina Porcine SNP60 chip and microarray measurements of gene expression in the gluteus medius muscle. Analysis of the data with gemma software revealed 13 cis- and 18 trans-eQTL modulating the expression of 19 loci...
July 24, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28735351/multiple-correlation-analyses-revealed-complex-relationship-between-dna-methylation-and-mrna-expression-in-human-peripheral-blood-mononuclear-cells
#2
Fang-Fei Xie, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Hong Zhu, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Xiao-Wei Zhu, Wei Xia, Lan Wang, Pei He, Peng-Fei Bing, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei
DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28715484/multiple-renal-cancer-susceptibility-polymorphisms-modulate-the-hif-pathway
#3
Steffen Grampp, Virginia Schmid, Rafik Salama, Victoria Lauer, Franziska Kranz, James L Platt, James Smythies, Hani Choudhry, Margarete Goppelt-Struebe, Peter J Ratcliffe, David R Mole, Johannes Schödel
Un-physiological activation of hypoxia inducible factor (HIF) is an early event in most renal cell cancers (RCC) following inactivation of the von Hippel-Lindau tumor suppressor. Despite intense study, how this impinges on cancer development is incompletely understood. To test for the impact of genetic signals on this pathway, we aligned human RCC-susceptibility polymorphisms with genome-wide assays of HIF-binding and observed highly significant overlap. Allele-specific assays of HIF binding, chromatin conformation and gene expression together with eQTL analyses in human tumors were applied to mechanistic analysis of one such overlapping site at chromosome 12p12...
July 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28714988/snp-mediated-disruption-of-ctcf-binding-at-the-ifitm3-promoter-is-associated-with-risk-of-severe-influenza-in-humans
#4
E Kaitlynn Allen, Adrienne G Randolph, Tushar Bhangale, Pranay Dogra, Maikke Ohlson, Christine M Oshansky, Anthony E Zamora, John P Shannon, David Finkelstein, Amy Dressen, John DeVincenzo, Miguela Caniza, Ben Youngblood, Carrie M Rosenberger, Paul G Thomas
Previous studies have reported associations of IFITM3 SNP rs12252 with severe influenza, but evidence of association and the mechanism by which risk is conferred remain controversial. We prioritized SNPs in IFITM3 on the basis of putative biological function and identified rs34481144 in the 5' UTR. We found evidence of a new association of rs34481144 with severe influenza in three influenza-infected cohorts characterized by different levels of influenza illness severity. We determined a role for rs34481144 as an expression quantitative trait locus (eQTL) for IFITM3, with the risk allele associated with lower mRNA expression...
July 17, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28714864/an-erythroid-specific-atp2b4-enhancer-mediates-red-blood-cell-hydration-and-malaria-susceptibility
#5
Samuel Lessard, Emily Stern Gatof, Mélissa Beaudoin, Patrick G Schupp, Falak Sher, Adnan Ali, Sukhpal Prehar, Ryo Kurita, Yukio Nakamura, Esther Baena, Jonathan Ledoux, Delvac Oceandy, Daniel E Bauer, Guillaume Lettre
The lack of mechanistic explanations for many genotype-phenotype associations identified by GWAS precludes thorough assessment of their impact on human health. Here, we conducted an expression quantitative trait locus (eQTL) mapping analysis in erythroblasts and found erythroid-specific eQTLs for ATP2B4, the main calcium ATPase of red blood cells (rbc). The same SNPs were previously associated with mean corpuscular hemoglobin concentration (MCHC) and susceptibility to severe malaria infection. We showed that Atp2b4-/- mice demonstrate increased MCHC, confirming ATP2B4 as the causal gene at this GWAS locus...
July 17, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28703219/genome-wide-association-and-expression-quantitative-trait-loci-studies-identify-multiple-susceptibility-loci-for-thyroid-cancer
#6
Ho-Young Son, Yul Hwangbo, Seong-Keun Yoo, Sun-Wha Im, San Duk Yang, Soo-Jung Kwak, Min Seon Park, Soo Heon Kwak, Sun Wook Cho, Jun Sun Ryu, Jeongseon Kim, Yuh-Seog Jung, Tae Hyun Kim, Su-Jin Kim, Kyu Eun Lee, Do Joon Park, Nam Han Cho, Joohon Sung, Jeong-Sun Seo, Eun Kyung Lee, Young Joo Park, Jong-Il Kim
Thyroid cancer is the most common cancer in Korea. Several susceptibility loci of differentiated thyroid cancer (DTC) were identified by previous genome-wide association studies (GWASs) in Europeans only. Here we conducted a GWAS and a replication study in Koreans using a total of 1,085 DTC cases and 8,884 controls, and validated these results using expression quantitative trait loci (eQTL) analysis and clinical phenotypes. The most robust associations were observed in the NRG1 gene (rs6996585, P=1.08 × 10(-10)) and this SNP was also associated with NRG1 expression in thyroid tissues...
July 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28684774/tumoral-expression-of-drug-and-xenobiotic-metabolizing-enzymes-in-breast-cancer-patients-of-different-ethnicities-with-implications-to-personalized-medicine
#7
Yan Li, Albert Steppi, Yidong Zhou, Feng Mao, Philip Craig Miller, Max M He, Tingting Zhao, Qiang Sun, Jinfeng Zhang
Drug and xenobiotic metabolizing enzymes (DXME) play important roles in drug responses and carcinogenesis. Recent studies have found that expression of DXME in cancer cells significantly affects drug clearance and the onset of drug resistance. In this study we compared the expression of DXME in breast tumor tissue samples from patients representing three ethnic groups: Caucasian Americans (CA), African Americans (AA), and Asian Americans (AS). We further combined DXME gene expression data with eQTL data from the GTEx project and with allele frequency data from the 1000 Genomes project to identify SNPs that may be associated with differential expression of DXME genes...
July 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28668716/replication-of-rs300774-a-genetic-biomarker-near-acp1-associated-with-suicide-attempts-in-patients-with-schizophrenia-relation-to-brain-cholesterol-biosynthesis
#8
Jiang Li, Akane Yoshikawa, Herbert Y Meltzer
The aim of this study was to determine if three biomarkers for suicide attempts previously identified and replicated in a genome-wide association (GWAS) study of bipolar disorder (BD) suicide attempters also predicted suicide attempts in patients prospectively diagnosed with schizophrenia (SCZ) or schizoaffective disorder (SAD). 162 genetically-verified Caucasian patients with SCZ or SAD were phenotyped for presence (45.7%) or absence of a lifetime suicide attempt. Three single nucleotide polymorphisms (SNPs) were genotyped or partially imputed from a GWAS dataset...
June 16, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28664150/coexpression-and-expression-quantitative-trait-loci-analyses-of-the-angiogenesis-gene-gene-interaction-network-in-prostate-cancer
#9
Hui-Yi Lin, Chia-Ho Cheng, Dung-Tsa Chen, Y Ann Chen, Jong Y Park
BACKGROUND: Prostate cancer (PCa) shows a substantial clinical heterogeneity. The existing risk classification for PCa prognosis based on clinical factors is not sufficient. Although some biomarkers for PCa aggressiveness have been identified, their underlying functional mechanisms are still unclear. We previously reported a gene-gene interaction network associated with PCa aggressiveness based on single nucleotide polymorphism (SNP)-SNP interactions in the angiogenesis pathway. The goal of this study is to investigate potential functional evidence of the involvement of the genes in this gene-gene interaction network...
October 2016: Translational Cancer Research
https://www.readbyqxmd.com/read/28662696/contribution-of-trans-regulatory-eqtl-to-cryptic-genetic-variation-in-c-elegans
#10
Basten L Snoek, Mark G Sterken, Roel P J Bevers, Rita J M Volkers, Arjen Van't Hof, Rachel Brenchley, Joost A G Riksen, Andrew Cossins, Jan E Kammenga
BACKGROUND: Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans...
June 29, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28656603/a-genetic-variant-near-gata3-implicated-in-inherited-susceptibility-and-etiology-of-benign-prostatic-hyperplasia-bph-and-lower-urinary-tract-symptoms-luts
#11
Rong Na, Brian T Helfand, Haitao Chen, Carly A Conran, Susan E Crawford, Simon W Hayward, Teuvo L J Tammela, Judy Hoffman-Bolton, Siqun L Zheng, Patrick C Walsh, Johanna Schleutker, Elizabeth A Platz, William B Isaacs, Jianfeng Xu
BACKGROUND: Benign prostatic hyperplasia (BPH) and associated lower urinary tract symptoms (LUTS) are common conditions. Little is known about their etiologies except that studies have suggested a substantial heritable component. Our objective is to provide a comprehensive, genome-wide evaluation of inherited risks and possible mechanisms of etiology in BPH. METHODS: We performed a three-stage, genome-wide association study (GWAS) of men from three independent populations, the REduction by DUtasteride of prostate Cancer Events (REDUCE) trial, the CLUE II cohort, and a Finnish hospital-based population...
June 28, 2017: Prostate
https://www.readbyqxmd.com/read/28653172/a-cis-eqtl-genetic-variant-of-the-cancer-testis-gene-ccdc116-is-associated-with-risk-of-multiple-cancers
#12
Na Qin, Cheng Wang, Qun Lu, Tongtong Huang, Meng Zhu, Lihua Wang, Fei Yu, Mingtao Huang, Yue Jiang, Juncheng Dai, Hongxia Ma, Guangfu Jin, Chen Wu, Dongxin Lin, Hongbing Shen, Zhibin Hu
Recent studies have found that cancer-testis (CT) genes, which are expressed predominantly in germ and cancer cells, may be candidate cancer drivers. Because of their crucial roles, genetic variants in these genes may contribute to the development of cancer. Here, we systematically evaluated associations of common variants in CT genes and their promoters for the risk of lung cancer in our initial GWAS (2331 cases and 3077 controls), followed by in silico replication using additional 10,512 lung cancer cases and 9562 controls...
August 2017: Human Genetics
https://www.readbyqxmd.com/read/28650933/cyp2e1-gene-polymorphisms-related-to-the-formation-of-coronary-artery-lesions-in-kawasaki-disease
#13
Ling-Sai Chang, Yu-Wen Hsu, Chien-Chang Lu, Mao-Hung Lo, Kai-Sheng Hsieh, Sung-Chou Li, Wei-Chiao Chang, Ho-Chang Kuo
BACKGROUND: Kawasaki disease (KD) is an acute febrile systemic vasculitis that disturbs coronary arteries. Patients' risks of adverse cardiovascular events and subclinical atherosclerosis have been found to significantly increase with polymorphisms of the human cytochrome P450. This current study aims to research the possible relationship between Cytochrome P450, Family 2, Subfamily E, and Polypeptide 1 (CYP2E1) polymorphisms with KD. METHODS: We selected six tag single-nucleotide polymorphisms (tSNPs) of the CYP2E1 gene for TaqMan allelic discrimination assay in 340 KD patients and performed analysis on the clinical phenotypes and coronary artery lesions (CAL)...
June 23, 2017: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/28647896/omics-based-hybrid-prediction-in-maize
#14
Matthias Westhues, Tobias A Schrag, Claas Heuer, Georg Thaller, H Friedrich Utz, Wolfgang Schipprack, Alexander Thiemann, Felix Seifert, Anita Ehret, Armin Schlereth, Mark Stitt, Zoran Nikoloski, Lothar Willmitzer, Chris C Schön, Stefan Scholten, Albrecht E Melchinger
Complementing genomic data with other "omics" predictors can increase the probability of success for predicting the best hybrid combinations using complex agronomic traits. Accurate prediction of traits with complex genetic architecture is crucial for selecting superior candidates in animal and plant breeding and for guiding decisions in personalized medicine. Whole-genome prediction has revolutionized these areas but has inherent limitations in incorporating intricate epistatic interactions. Downstream "omics" data are expected to integrate interactions within and between different biological strata and provide the opportunity to improve trait prediction...
June 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28643332/integrative-eqtl-analysis-of-tumor-and-host-omics-data-in-individuals-with-bladder-cancer
#15
Silvia Pineda, Kristel Van Steen, Núria Malats
Integrative analyses of several omics data are emerging. The data are usually generated from the same source material (i.e., tumor sample) representing one level of regulation. However, integrating different regulatory levels (i.e., blood) with those from tumor may also reveal important knowledge about the human genetic architecture. To model this multilevel structure, an integrative-expression quantitative trait loci (eQTL) analysis applying two-stage regression (2SR) was proposed. This approach first regressed tumor gene expression levels with tumor markers and the adjusted residuals from the previous model were then regressed with the germline genotypes measured in blood...
June 23, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28642272/networks-underpinning-symbiosis-revealed-through-cross-species-eqtl-mapping
#16
Yuelong Guo, Sylwia Fudali, Jacinta Gimeno, Peter DiGennaro, Stella Chang, Valerie M Williamson, David McK Bird, Dahlia M Nielsen
Organisms engage in extensive cross-species molecular dialogue, yet the underlying molecular actors are known for only a few interactions. Many techniques have been designed to uncover genes involved in signaling between organisms. Typically, these focus on only one of the partners. We developed an expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction. We demonstrated the approach by assaying expression of ninety-eight isogenic plants (Medicago truncatula), each inoculated with a genetically distinct line of the diploid parasitic nematode Meloidogyne hapla With this design, systematic differences in gene expression across host plants could be mapped to genetic polymorphisms of their infecting parasites...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28640813/identification-of-a-sj%C3%A3-gren-s-syndrome-susceptibility-locus-at-oas1-that-influences-isoform-switching-protein-expression-and-responsiveness-to-type-i-interferons
#17
He Li, Tove Ragna Reksten, John A Ice, Jennifer A Kelly, Indra Adrianto, Astrid Rasmussen, Shaofeng Wang, Bo He, Kiely M Grundahl, Stuart B Glenn, Corinne Miceli-Richard, Simon Bowman, Sue Lester, Per Eriksson, Maija-Leena Eloranta, Johan G Brun, Lasse G Gøransson, Erna Harboe, Joel M Guthridge, Kenneth M Kaufman, Marika Kvarnström, Deborah S Cunninghame Graham, Ketan Patel, Adam J Adler, A Darise Farris, Michael T Brennan, James Chodosh, Rajaram Gopalakrishnan, Michael H Weisman, Swamy Venuturupalli, Daniel J Wallace, Kimberly S Hefner, Glen D Houston, Andrew J W Huang, Pamela J Hughes, David M Lewis, Lida Radfar, Evan S Vista, Contessa E Edgar, Michael D Rohrer, Donald U Stone, Timothy J Vyse, John B Harley, Patrick M Gaffney, Judith A James, Sean Turner, Ilias Alevizos, Juan-Manuel Anaya, Nelson L Rhodus, Barbara M Segal, Courtney G Montgomery, R Hal Scofield, Susan Kovats, Xavier Mariette, Lars Rönnblom, Torsten Witte, Maureen Rischmueller, Marie Wahren-Herlenius, Roald Omdal, Roland Jonsson, Wan-Fai Ng, Gunnel Nordmark, Christopher J Lessard, Kathy L Sivils
Sjögren's syndrome (SS) is a common, autoimmune exocrinopathy distinguished by keratoconjunctivitis sicca and xerostomia. Patients frequently develop serious complications including lymphoma, pulmonary dysfunction, neuropathy, vasculitis, and debilitating fatigue. Dysregulation of type I interferon (IFN) pathway is a prominent feature of SS and is correlated with increased autoantibody titers and disease severity. To identify genetic determinants of IFN pathway dysregulation in SS, we performed cis-expression quantitative trait locus (eQTL) analyses focusing on differentially expressed type I IFN-inducible transcripts identified through a transcriptome profiling study...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28639078/a-genome-wide-expression-association-analysis-identifies-genes-and-pathways-associated-with-amyotrophic-lateral-sclerosis
#18
Yanan Du, Yan Wen, Xiong Guo, Jingcan Hao, Wenyu Wang, Awen He, Qianrui Fan, Ping Li, Li Liu, Xiao Liang, Feng Zhang
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with strong genetic components. To identity novel risk variants for ALS, utilizing the latest genome-wide association studies (GWAS) and eQTL study data, we conducted a genome-wide expression association analysis by summary data-based Mendelian randomization (SMR) method. Summary data were derived from a large-scale GWAS of ALS, involving 12577 cases and 23475 controls. The eQTL annotation dataset included 923,021 cis-eQTL for 14,329 genes and 4732 trans-eQTL for 2612 genes...
June 21, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/28637782/the-brugada-syndrome-susceptibility-gene-hey2-modulates-cardiac-transmural-ion-channel-patterning-and-electrical-heterogeneity
#19
Christiaan C Veerman, Svitlana Podliesna, Rafik Tadros, Elisabeth M Lodder, Isabella Mengarelli, Berend de Jonge, Leander Beekman, Julien Barc, Ronald Wilders, Arthur A Wilde, Bastiaan J Boukens, Ruben Coronel, Arie Verkerk, Carol Ann Remme, Connie R Bezzina
Rationale: Genome-wide association studies previously identified an association of rs9388451 at chromosome 6q22.3 (near HEY2) with Brugada syndrome (BrS). The causal gene and underlying mechanism remain unresolved. Objective: We used an integrative approach entailing transcriptomic studies in human hearts and electrophysiological studies in Hey2 heterozygous knockout mice (Hey2(+/-) ) to dissect the underpinnings of the 6q22.31 association with BrS. Methods and Results: We queried expression quantitative trait locus (eQTL) data acquired in 190 human left ventricular (LV) samples from the Genotype-Tissue Expression (GTEx) consortium for cis-eQTL effects of rs9388451 which revealed an association between BrS risk allele dosage and HEY2 expression (β=+0...
June 21, 2017: Circulation Research
https://www.readbyqxmd.com/read/28635624/effects-of-type-1-diabetes-risk-alleles-on-immune-cell-gene-expression
#20
REVIEW
Ramesh Ram, Grant Morahan
Genetic studies have identified 61 variants associated with the risk of developing Type 1 Diabetes (T1D). The functions of most of the non-HLA (Human Leukocyte Antigen) genetic variants remain unknown. We found that only 16 of these risk variants could potentially be linked to a protein-coding change. Therefore, we investigated whether these variants affected susceptibility by regulating changes in gene expression. To do so, we examined whole transcriptome profiles of 600 samples from the Type 1 Diabetes Genetics Consortium (T1DGC)...
June 21, 2017: Genes
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