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https://www.readbyqxmd.com/read/28547032/car8-dorsal-root-ganglion-expression-and-genetic-regulation-of-analgesic-responses-are-associated-with-a-cis-eqtl-in-mice
#1
Roy C Levitt, Gerald Y Zhuang, Yuan Kang, Diana M Erasso, Udita Upadhyay, Mehtap Ozdemir, Eugene S Fu, Konstantinos D Sarantopoulos, Shad B Smith, William Maixner, Luda Diatchenko, Eden R Martin, Tim Wiltshire
Carbonic anhydrase-8 (Car8 mouse gene symbol) is devoid of enzymatic activity, but instead functions as an allosteric inhibitor of inositol trisphosphate receptor-1 (ITPR1) to regulate this intracellular calcium release channel important in synaptic functions and neuronal excitability. Causative mutations in ITPR1 and carbonic anhydrase-8 in mice and humans are associated with certain subtypes of spinal cerebellar ataxia (SCA). SCA mice are genetically deficient in dorsal root ganglia (DRG) Car8 expression and display mechanical and thermal hypersensitivity and susceptibility to subacute and chronic inflammatory pain behaviors...
May 25, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28542600/snp-in-human-arhgef3-promoter-is-associated-with-dnase-hypersensitivity-transcript-level-and-platelet-function-and-arhgef3-ko-mice-have-increased-mean-platelet-volume
#2
Siying Zou, Alexandra M Teixeira, Myrto Kostadima, William J Astle, Aparna Radhakrishnan, Lukas Mikolaj Simon, Lucy Truman, Jennifer S Fang, John Hwa, Ping-Xia Zhang, Pim van der Harst, Paul F Bray, Willem H Ouwehand, Mattia Frontini, Diane S Krause
Genome-wide association studies have identified a genetic variant at 3p14.3 (SNP rs1354034) that strongly associates with platelet number and mean platelet volume in humans. While originally proposed to be intronic, analysis of mRNA expression in primary human hematopoietic subpopulations reveals that this SNP is located directly upstream of the predominantly expressed ARHGEF3 isoform in megakaryocytes (MK). We found that ARHGEF3, which encodes a Rho guanine exchange factor, is dramatically upregulated during both human and murine MK maturation...
2017: PloS One
https://www.readbyqxmd.com/read/28528868/pleiotropic-effects-of-trait-associated-genetic-variation-on-dna-methylation-utility-for-refining-gwas-loci
#3
Eilis Hannon, Mike Weedon, Nicholas Bray, Michael O'Donovan, Jonathan Mill
Most genetic variants identified in genome-wide association studies (GWASs) of complex traits are thought to act by affecting gene regulation rather than directly altering the protein product. As a consequence, the actual genes involved in disease are not necessarily the most proximal to the associated variants. By integrating data from GWAS analyses with those from genetic studies of regulatory variation, it is possible to identify variants pleiotropically associated with both a complex trait and measures of gene regulation...
May 13, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28527213/sorl1-variants-show-different-association-with-early-onset-and-late-onset-alzheimer-s-disease-risk
#4
Guiyou Liu, Jing-Yi Sun, Meiling Xu, Xiao-Yi Yang, Bao-Liang Sun
A recent study sequenced the full coding region of SORL1 in 1,255 early-onset Alzheimer's disease (EOAD) cases and 1,938 control individuals, and investigated the contribution of genetic variability in SORL1 to EOAD risk in a European cohort. This study identified six common variants and five low frequency variants in the SORL1 coding sequence. However, none of these 11 variants was significantly associated with EOAD risk after adjusting for multiple testing. We consider whether these 11 SORL1 variants identified in European EOAD contribute to late-onset Alzheimer's disease (LOAD) risk in individuals of European ancestry...
May 17, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28521784/functional-regression-method-for-whole-genome-eqtl-epistasis-analysis-with-sequencing-data
#5
Kelin Xu, Li Jin, Momiao Xiong
BACKGROUND: Epistasis plays an essential rule in understanding the regulation mechanisms and is an essential component of the genetic architecture of the gene expressions. However, interaction analysis of gene expressions remains fundamentally unexplored due to great computational challenges and data availability. Due to variation in splicing, transcription start sites, polyadenylation sites, post-transcriptional RNA editing across the entire gene, and transcription rates of the cells, RNA-seq measurements generate large expression variability and collectively create the observed position level read count curves...
May 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28515850/dissection-of-z-disc-myopalladin-gene-network-involved-in-the-development-of-restrictive-cardiomyopathy-using-system-genetics-approach
#6
Qingqing Gu, Uzmee Mendsaikhan, Zaza Khuchua, Byron C Jones, Lu Lu, Jeffrey A Towbin, Biao Xu, Enkhsaikhan Purevjav
AIM: To investigate the regulation of Myopalladin (Mypn) and identify its gene network involved in restrictive cardiomyopathy (RCM). METHODS: Gene expression values were measured in the heart of a large family of BXD recombinant inbred (RI) mice derived from C57BL/6J and DBA/2J. The proteomics data were collected from Mypn knock-in and knock-out mice. Expression quantitative trait locus (eQTL) mapping methods and gene enrichment analysis were used to identify Mypn regulation, gene pathway and co-expression networks...
April 26, 2017: World Journal of Cardiology
https://www.readbyqxmd.com/read/28510302/association-study-of-genetic-variation-in-dna-repair-pathway-genes-and-risk-of-basal-cell-carcinoma
#7
Yuan Lin, Harvind S Chahal, Wenting Wu, Hyunje G Cho, Katherine J Ransohoff, Fengju Song, Jean Y Tang, Kavita Y Sarin, Jiali Han
DNA repair plays a critical role in protecting the genome from ultraviolet radiation and maintaining the genomic integrity of cells. Genetic variants in DNA repair-related genes can influence an individual's DNA repair capacity, which may be related to the risk of developing basal cell carcinoma (BCC). We comprehensively assessed the associations of 2,965 independent single-nucleotide polymorphisms (SNPs) across 165 DNA repair pathway genes with BCC risk in a genome-wide association meta-analysis totaling 17,187 BCC cases and 287,054 controls from two data sets...
May 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28506205/in-silico-pathway-analysis-and-tissue-specific-cis-eqtl-for-colorectal-cancer-gwas-risk-variants
#8
Lenora W M Loo, Mathieu Lemire, Loïc Le Marchand
BACKGROUND: Genome-wide association studies have identified 55 genetic variants associated with colorectal cancer risk to date. However, potential causal genes and pathways regulated by these risk variants remain to be characterized. Therefore, we performed gene ontology enrichment and pathway analyses to determine if there was an enrichment of genes in proximity to the colorectal cancer risk variants that could further elucidate the probable causal genes and pathways involved in colorectal cancer biology...
May 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28505156/an-independent-component-analysis-confounding-factor-correction-framework-for-identifying-broad-impact-expression-quantitative-trait-loci
#9
Jin Hyun Ju, Sushila A Shenoy, Ronald G Crystal, Jason G Mezey
Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis. CONFETI is designed to address two conflicting issues when searching for broad impact eQTL: the need to account for non-genetic confounding factors that can lower the power of the analysis or produce broad impact eQTL false positives, and the tendency of methods that account for confounding factors to model broad impact eQTL as non-genetic variation...
May 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28482007/molecular-biomarkers-for-weight-control-in-obese-individuals-subjected-to-a-multi-phase-dietary-intervention
#10
Jennifer Bolton, Emilie Montastier, Jérôme Carayol, Sophie Bonnel, Lucile Mir, Marie-Adeline Marques, Arne Astrup, Wim Saris, Jason Iacovoni, Nathalie Villa-Vialaneix, Armand Valsesia, Dominique Langin, Nathalie Viguerie
Context: While calorie restriction has proven beneficial for weight loss, long-term weight control is variable between individuals. Objective: To identify biomarkers of successful weight control during a dietary intervention (DI). Design, Setting, and Participants: Adipose tissue (AT) transcriptomes were compared between 21 obese individuals that either maintained weight loss or regained weight during the DI. Results were validated on 310 individuals from the same study using RT-qPCR, and protein levels of potential circulating biomarkers measured by ELISA...
May 5, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28475861/widespread-allelic-heterogeneity-in-complex-traits
#11
Farhad Hormozdiari, Anthony Zhu, Gleb Kichaev, Chelsea J-T Ju, Ayellet V Segrè, Jong Wha J Joo, Hyejung Won, Sriram Sankararaman, Bogdan Pasaniuc, Sagiv Shifman, Eleazar Eskin
Recent successes in genome-wide association studies (GWASs) make it possible to address important questions about the genetic architecture of complex traits, such as allele frequency and effect size. One lesser-known aspect of complex traits is the extent of allelic heterogeneity (AH) arising from multiple causal variants at a locus. We developed a computational method to infer the probability of AH and applied it to three GWASs and four expression quantitative trait loci (eQTL) datasets. We identified a total of 4,152 loci with strong evidence of AH...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28472449/exploring-genetic-associations-with-cerna-regulation-in-the-human-genome
#12
Mulin Jun Li, Jian Zhang, Qian Liang, Chenghao Xuan, Jiexing Wu, Peng Jiang, Wei Li, Yun Zhu, Panwen Wang, Daniel Fernandez, Yujun Shen, Yiwen Chen, Jean-Pierre A Kocher, Ying Yu, Pak Chung Sham, Junwen Wang, Jun S Liu, X Shirley Liu
Competing endogenous RNAs (ceRNAs) are RNA molecules that sequester shared microRNAs (miRNAs) thereby affecting the expression of other targets of the miRNAs. Whether genetic variants in ceRNA can affect its biological function and disease development is still an open question. Here we identified a large number of genetic variants that are associated with ceRNA's function using Geuvaids RNA-seq data for 462 individuals from the 1000 Genomes Project. We call these loci competing endogenous RNA expression quantitative trait loci or 'cerQTL', and found that a large number of them were unexplored in conventional eQTL mapping...
May 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28470677/genetic-polymorphisms-associated-with-pancreatic-cancer-survival-a-genome-wide-association-study
#13
Hongwei Tang, Peng Wei, Ping Chang, Yanan Li, Dong Yan, Chang Liu, Manal Hassan, Donghui Li
Previous findings on the association of genetic factors and pancreatic cancer survival are limited and inconsistent. In a two-stage study, we analyzed the existing genome-wide association study dataset of 868 pancreatic cancer patients from MD Anderson Cancer Center in relation to overall survival using Cox regression. Top hits were selected for replication in another 820 patients from the same institution using the Taqman genotyping method. Functional annotation, pathway analysis, and gene expression analysis were conducted using existing software and databases...
May 3, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28469621/snp-variants-in-major-histocompatibility-complex-are-associated-with-sarcoidosis-susceptibility-a-joint-analysis-in-four-european-populations
#14
Annika Wolin, Elisa Laura Lahtela, Verneri Anttila, Martin Petrek, Johan Grunewald, Coline H M van Moorsel, Anders Eklund, Jan C Grutters, Vitezslav Kolek, Frantisek Mrazek, Amit Kishore, Leonid Padyukov, Anne Pietinalho, Marcus Ronninger, Mikko Seppänen, Olof Selroos, Marja-Liisa Lokki
Sarcoidosis is a multiorgan inflammatory disorder with heritability estimates up to 66%. Previous studies have shown the major histocompatibility complex (MHC) region to be associated with sarcoidosis, suggesting a functional role for antigen-presenting molecules and immune mediators in the disease pathogenesis. To detect variants predisposing to sarcoidosis and to identify genetic differences between patient subgroups, we studied four genes in the MHC Class III region (LTA, TNF, AGER, BTNL2) and HLA-DRA with tag-SNPs and their relation to HLA-DRB1 alleles...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28467369/developmental-control-of-nramp1-slc11a1-expression-in-professional-phagocytes
#15
Mathieu F M Cellier
NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs)...
May 3, 2017: Biology
https://www.readbyqxmd.com/read/28464818/sulfatase-modifying-factor-1-sumf1-is-associated-with-chronic-obstructive-pulmonary-disease
#16
Julie Weidner, Linnea Jarenbäck, Kim de Jong, Judith M Vonk, Maarten van den Berge, Corry-Anke Brandsma, H Marike Boezen, Don Sin, Yohan Bossé, David Nickle, Jaro Ankerst, Leif Bjermer, Dirkje S Postma, Alen Faiz, Ellen Tufvesson
BACKGROUND: It has been observed that mice lacking the sulfatase modifying factor (Sumf1) developed an emphysema-like phenotype. However, it is unknown if SUMF1 may play a role in Chronic Obstructive Pulmonary Disease (COPD) in humans. The aim was to investigate if the expression and genetic regulation of SUMF1 differs between smokers with and without COPD. METHODS: SUMF1 mRNA was investigated in sputum cells and whole blood from controls and COPD patients (all current or former smokers)...
May 2, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28464817/post-operative-atrial-fibrillation-examined-using-whole-genome-rna-sequencing-in-human-left-atrial-tissue
#17
Martin I Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S Couper, Stanton K Shernan, Jochen D Muehlschlegel, Simon C Body
BACKGROUND: Both ambulatory atrial fibrillation (AF) and post-operative AF (poAF) are associated with substantial morbidity and mortality. Analyzing the tissue-specific gene expression in the left atrium (LA) can identify novel genes associated with AF and further the understanding of the mechanism by which previously identified genetic variants associated with AF mediate their effects. METHODS: LA free wall samples were obtained intraoperatively immediately prior to mitral valve surgery in 62 Caucasian individuals...
May 2, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28461224/responsiveness-to-ipratropium-bromide-in-male-and-female-patients-with-mild-to-moderate-chronic-obstructive-pulmonary-disease
#18
Xuan Li, Ma'en Obeidat, Guohai Zhou, Janice M Leung, Donald Tashkin, Robert Wise, John Connett, Philippe Joubert, Yohan Bossé, Maarten van den Berge, Corry-Anke Brandsma, David C Nickle, Ke Hao, Peter D Paré, Don D Sin
INTRODUCTION: Although the prevalence of chronic obstructive pulmonary disease (COPD) is similar between men and women, current evidence used to support bronchodilator therapy has been generated in therapeutic trials that have predominately enrolled male patients. Here, we determined whether there is any significant sex-related differences in FEV1 responses to ipratropium bromide. METHODS: Data from the Lung Health Study (n=5887; 37% females) were used to determine changes in FEV1 with ipratropium or placebo in male and female subjects with mild to moderate COPD over 5years...
April 12, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28456096/identifying-low-density-lipoprotein-cholesterol-associated-variants-in-the-annexin-a2-anxa2-gene
#19
Roaa Hani Fairoozy, Jackie Cooper, Jon White, Claudia Giambartolomei, Lasse Folkersen, S Goya Wannamethee, Barbara J Jefferis, Peter Whincup, Yoav Ben-Shlomo, Meena Kumari, Mika Kivimaki, Andrew Wong, Rebecca Hardy, Diana Kuh, Tom R Gaunt, J P Casas, Stela McLachlan, Jackie F Price, Aroon Hingorani, Anders Franco-Cereceda, Thomas Grewal, Anastasia Z Kalea, Steve E Humphries
BACKGROUND AND AIMS: Annexin-A2 (AnxA2) is an endogenous inhibitor of proprotein convertase subtilisin/kexin type-9 (PCSK9). The repeat-one (R1) domain of AnxA2 binds to PCSK9, blocking its ability to promote degradation of low-density lipoprotein cholesterol-receptors (LDL-R) and thereby regulate low-density lipoprotein cholesterol (LDL-C) levels. Here we identify variants in ANXA2 influencing LDL-C levels and we determine the molecular mechanisms of their effects. RESULTS: The ANXA2 single nucleotide polymorphism (SNP) genotype-phenotype association was examined using the Second-Northwick-Park Heart Study (NPHSII) (n∼2700) and the UCL-LSHTM-Edinburgh-Bristol (UCLEB) consortium (n∼14,600)...
April 13, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28453699/microrna-related-genetic-variants-in-iron-regulatory-genes-dietary-iron-intake-micrornas-and-lung-cancer-risk
#20
L Zhang, Y Ye, H Tu, M A Hildebrandt, L Zhao, J V Heymach, J A Roth, X Wu
Background: Genetic variations in MicroRNA (miRNA) binding sites may alter structural accessibility of miRNA binding sites to modulate risk of cancer. This large-scale integrative multistage study was aimed to evaluate the interplay of genetic variations in miRNA binding sites of iron regulatory pathway, dietary iron intake and lung cancer (LC) risk. Patients and methods: The interplay of genetic variant, dietary iron intake and LC risk was assessed in large-scale case-control study...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
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