keyword
MENU ▼
Read by QxMD icon Read
search

rna eqtl

keyword
https://www.readbyqxmd.com/read/28903782/natural-genetic-variation-of-the-cardiac-transcriptome-in-non-diseased-donors-and-patients-with-dilated-cardiomyopathy
#1
Matthias Heinig, Michiel E Adriaens, Sebastian Schafer, Hanneke W M van Deutekom, Elisabeth M Lodder, James S Ware, Valentin Schneider, Leanne E Felkin, Esther E Creemers, Benjamin Meder, Hugo A Katus, Frank Rühle, Monika Stoll, François Cambien, Eric Villard, Philippe Charron, Andras Varro, Nanette H Bishopric, Alfred L George, Cristobal Dos Remedios, Aida Moreno-Moral, Francesco Pesce, Anja Bauerfeind, Franz Rüschendorf, Carola Rintisch, Enrico Petretto, Paul J Barton, Stuart A Cook, Yigal M Pinto, Connie R Bezzina, Norbert Hubner
BACKGROUND: Genetic variation is an important determinant of RNA transcription and splicing, which in turn contributes to variation in human traits, including cardiovascular diseases. RESULTS: Here we report the first in-depth survey of heart transcriptome variation using RNA-sequencing in 97 patients with dilated cardiomyopathy and 108 non-diseased controls. We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls, affecting known as well as novel dilated cardiomyopathy genes...
September 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28879530/correlation-analyses-revealed-global-microrna-mrna-expression-associations-in-human-peripheral-blood-mononuclear-cells
#2
Lan Wang, Jiang Zhu, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Xiao-Wei Zhu, Wei Xia, Fang-Fei Xie, Pei He, Peng-Fei Bing, Ying-Hua Qiu, Xiang Lin, Xin Lu, Lei Zhang, Neng-Jun Yi, Yong-Hong Zhang, Shu-Feng Lei
MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study...
September 6, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28877428/what-has-gwas-done-for-hla-and-disease-associations
#3
REVIEW
A E Kennedy, U Ozbek, M T Dorak
The major histocompatibility complex (MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen (HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans-eQTLs/meQTLs in the genome and is known as a hot spot for disease associations...
October 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/28869584/an-xqtl-map-integrates-the-genetic-architecture-of-the-human-brain-s-transcriptome-and-epigenome
#4
Bernard Ng, Charles C White, Hans-Ulrich Klein, Solveig K Sieberts, Cristin McCabe, Ellis Patrick, Jishu Xu, Lei Yu, Chris Gaiteri, David A Bennett, Sara Mostafavi, Philip L De Jager
We report a multi-omic resource generated by applying quantitative trait locus (xQTL) analyses to RNA sequence, DNA methylation and histone acetylation data from the dorsolateral prefrontal cortex of 411 older adults who have all three data types. We identify SNPs significantly associated with gene expression, DNA methylation and histone modification levels. Many of these SNPs influence multiple molecular features, and we demonstrate that SNP effects on RNA expression are fully mediated by epigenetic features in 9% of these loci...
September 4, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28854703/expression-quantitative-trait-loci-eqtls-in-human-placentas-suggest-developmental-origins-of-complex-diseases
#5
Shouneng Peng, Maya A Deyssenroth, Antonio F Di Narzo, Luca Lambertini, Carmen J Marsit, Jia Chen, Ke Hao
Epidemiologic studies support that at least part of the risk of chronic diseases in childhood and even adulthood may have an in utero origin, and the placenta is a key organ that plays a pivotal role in fetal growth and development. The transcriptomes of 159 human placenta tissues were profiled by genome-wide RNA sequencing (Illumina High-Seq 2500), and linked to fetal genotypes assessed by a high density single nucleotide polymorphism (SNP) genotyping array (Illumina MegaEx). Expression quantitative trait loci (eQTLs) across all annotated transcripts were mapped and examined for enrichment for disease susceptibility loci annotated in the genome-wide association studies (GWAS) catalog...
September 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28805827/transcriptional-risk-scores-link-gwas-to-eqtls-and-predict-complications-in-crohn-s-disease
#6
Urko M Marigorta, Lee A Denson, Jeffrey S Hyams, Kajari Mondal, Jarod Prince, Thomas D Walters, Anne Griffiths, Joshua D Noe, Wallace V Crandall, Joel R Rosh, David R Mack, Richard Kellermayer, Melvin B Heyman, Susan S Baker, Michael C Stephens, Robert N Baldassano, James F Markowitz, Mi-Ok Kim, Marla C Dubinsky, Judy Cho, Bruce J Aronow, Subra Kugathasan, Greg Gibson
Gene expression profiling can be used to uncover the mechanisms by which loci identified through genome-wide association studies (GWAS) contribute to pathology. Given that most GWAS hits are in putative regulatory regions and transcript abundance is physiologically closer to the phenotype of interest, we hypothesized that summation of risk-allele-associated gene expression, namely a transcriptional risk score (TRS), should provide accurate estimates of disease risk. We integrate summary-level GWAS and expression quantitative trait locus (eQTL) data with RNA-seq data from the RISK study, an inception cohort of pediatric Crohn's disease...
August 14, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28792098/identification-of-expression-quantitative-trait-loci-eqtls-in-human-peripheral-blood-mononuclear-cells-pbmcs-and-shared-with-liver-and-brain
#7
Pei He, Wei Xia, Lan Wang, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Peng-Fei Bing, Fang-Fei Xie, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei, Fei-Yan Deng
PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified...
August 9, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28634199/characterising-cis-regulatory-variation-in-the-transcriptome-of-histologically-normal-and-tumour-derived-pancreatic-tissues
#8
Mingfeng Zhang, Soren Lykke-Andersen, Bin Zhu, Wenming Xiao, Jason W Hoskins, Xijun Zhang, Lauren M Rost, Irene Collins, Martijn van de Bunt, Jinping Jia, Hemang Parikh, Tongwu Zhang, Lei Song, Ashley Jermusyk, Charles C Chung, Bin Zhu, Weiyin Zhou, Gail L Matters, Robert C Kurtz, Meredith Yeager, Torben Heick Jensen, Kevin M Brown, Halit Ongen, William R Bamlet, Bradley A Murray, Mark I McCarthy, Stephen J Chanock, Nilanjan Chatterjee, Brian M Wolpin, Jill P Smith, Sara H Olson, Gloria M Petersen, Jianxin Shi, Laufey Amundadottir
OBJECTIVE: To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN: We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS: We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0...
June 20, 2017: Gut
https://www.readbyqxmd.com/read/28627442/the-association-of-rs710886-in-lncrna-pcat1-with-bladder-cancer-risk-in-a-chinese-population
#9
Yadi Lin, Yuqiu Ge, Yunyan Wang, Gaoxiang Ma, Xiaowei Wang, Hanting Liu, Meilin Wang, Zhengdong Zhang, Haiyan Chu
OBJECTIVE: The long noncoding RNA PCAT1 is an important gene involved in urinary tumors. In this study, we aimed to explore the association between polymorphisms in PCAT1 and bladder cancer susceptibility. METHODS: A two-stage case-control study was conducted to assess the association between four tagging SNPs (i.e., rs4871771, rs1902432, rs16901904 and rs710886) and bladder cancer risk. Odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated with unconditional univariate and multivariate logistic regression...
September 5, 2017: Gene
https://www.readbyqxmd.com/read/28575649/genetic-variation-driven-gene-expression-changes-highlight-genes-with-important-functions-for-kidney-disease
#10
Yi-An Ko, Huiguang Yi, Chengxiang Qiu, Shizheng Huang, Jihwan Park, Nora Ledo, Anna Köttgen, Hongzhe Li, Daniel J Rader, Michael A Pack, Christopher D Brown, Katalin Susztak
Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of the US population. Genome-wide association studies (GWASs) have identified sequence variants, localized to non-coding genomic regions, associated with kidney function. Despite these robust observations, the mechanism by which variants lead to CKD remains a critical unanswered question. Expression quantitative trait loci (eQTL) analysis is a method to identify genetic variation associated with gene expression changes in specific tissue types...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575251/hierarchical-probabilistic-models-for-multiple-gene-variant-associations-based-on-next-generation-sequencing-data
#11
Dimitrios V Vavoulis, Jenny C Taylor, Anna Schuh
Motivation: The identification of genetic variants influencing gene expression (known as expression quantitative trait loci or eQTLs ) is important in unravelling the genetic basis of complex traits. Detecting multiple eQTLs simultaneously in a population based on paired DNA-seq and RNA-seq assays employs two competing types of models: models which rely on appropriate transformations of RNA-seq data (and are powered by a mature mathematical theory), or count-based models , which represent digital gene expression explicitly, thus rendering such transformations unnecessary...
May 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28521784/functional-regression-method-for-whole-genome-eqtl-epistasis-analysis-with-sequencing-data
#12
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/28472449/exploring-genetic-associations-with-cerna-regulation-in-the-human-genome
#13
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...
June 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28470677/genetic-polymorphisms-associated-with-pancreatic-cancer-survival-a-genome-wide-association-study
#14
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...
August 15, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28464817/post-operative-atrial-fibrillation-examined-using-whole-genome-rna-sequencing-in-human-left-atrial-tissue
#15
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/28421666/genetic-interplay-between-human-longevity-and-metabolic-pathways-a-large-scale-eqtl-study
#16
Robert Häsler, Geetha Venkatesh, Qihua Tan, Friederike Flachsbart, Anupam Sinha, Philip Rosenstiel, Wolfgang Lieb, Stefan Schreiber, Kaare Christensen, Lene Christiansen, Almut Nebel
Human longevity is a complex phenotype influenced by genetic and environmental components. Unraveling the contribution of genetic vs. nongenetic factors to longevity is a challenging task. Here, we conducted a large-scale RNA-sequencing-based expression quantitative trait loci study (eQTL) with subsequent heritability analysis. The investigation was performed on blood samples from 244 individuals from Germany and Denmark, representing various age groups including long-lived subjects up to the age of 104 years...
August 2017: Aging Cell
https://www.readbyqxmd.com/read/28406900/gene-co-expression-network-connectivity-is-an-important-determinant-of-selective-constraint
#17
Niklas Mähler, Jing Wang, Barbara K Terebieniec, Pär K Ingvarsson, Nathaniel R Street, Torgeir R Hvidsten
While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28393889/genetic-architecture-of-gene-expression-underlying-variation-in-host-response-to-porcine-reproductive-and-respiratory-syndrome-virus-infection
#18
Arun Kommadath, Hua Bao, Igseo Choi, James M Reecy, James E Koltes, Elyn Fritz-Waters, Chris J Eisley, Jason R Grant, Robert R R Rowland, Christopher K Tuggle, Jack C M Dekkers, Joan K Lunney, Le Luo Guan, Paul Stothard, Graham S Plastow
It has been shown that inter-individual variation in host response to porcine reproductive and respiratory syndrome (PRRS) has a heritable component, yet little is known about the underlying genetic architecture of gene expression in response to PRRS virus (PRRSV) infection. Here, we integrated genome-wide genotype, gene expression, viremia level, and weight gain data to identify genetic polymorphisms that are associated with variation in inter-individual gene expression and response to PRRSV infection in pigs...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28391543/increased-brain-expression-of-gpnmb-is-associated-with-genome-wide-significant-risk-for-parkinson-s-disease-on-chromosome-7p15-3
#19
Megha N Murthy, Cornelis Blauwendraat, Sebastian Guelfi, John Hardy, Patrick A Lewis, Daniah Trabzuni
Genome wide association studies (GWAS) for Parkinson's disease (PD) have previously revealed a significant association with a locus on chromosome 7p15.3, initially designated as the glycoprotein non-metastatic melanoma protein B (GPNMB) locus. In this study, the functional consequences of this association on expression were explored in depth by integrating different expression quantitative trait locus (eQTL) datasets (Braineac, CAGEseq, GTEx, and Phenotype-Genotype Integrator (PheGenI)). Top risk SNP rs199347 eQTLs demonstrated increased expressions of GPNMB, KLHL7, and NUPL2 with the major allele (AA) in brain, with most significant eQTLs in cortical regions, followed by putamen...
July 2017: Neurogenetics
https://www.readbyqxmd.com/read/28388430/large-scale-profiling-reveals-the-influence-of-genetic-variation-on-gene-expression-in-human-induced-pluripotent-stem-cells
#20
Christopher DeBoever, He Li, David Jakubosky, Paola Benaglio, Joaquin Reyna, Katrina M Olson, Hui Huang, William Biggs, Efren Sandoval, Matteo D'Antonio, Kristen Jepsen, Hiroko Matsui, Angelo Arias, Bing Ren, Naoki Nariai, Erin N Smith, Agnieszka D'Antonio-Chronowska, Emma K Farley, Kelly A Frazer
In this study, we used whole-genome sequencing and gene expression profiling of 215 human induced pluripotent stem cell (iPSC) lines from different donors to identify genetic variants associated with RNA expression for 5,746 genes. We were able to predict causal variants for these expression quantitative trait loci (eQTLs) that disrupt transcription factor binding and validated a subset of them experimentally. We also identified copy-number variant (CNV) eQTLs, including some that appear to affect gene expression by altering the copy number of intergenic regulatory regions...
April 6, 2017: Cell Stem Cell
keyword
keyword
50660
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"