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https://www.readbyqxmd.com/read/27918533/identification-of-context-dependent-expression-quantitative-trait-loci-in-whole-blood
#1
Daria V Zhernakova, Patrick Deelen, Martijn Vermaat, Maarten van Iterson, Michiel van Galen, Wibowo Arindrarto, Peter van 't Hof, Hailiang Mei, Freerk van Dijk, Harm-Jan Westra, Marc Jan Bonder, Jeroen van Rooij, Marijn Verkerk, P Mila Jhamai, Matthijs Moed, Szymon M Kielbasa, Jan Bot, Irene Nooren, René Pool, Jenny van Dongen, Jouke J Hottenga, Coen D A Stehouwer, Carla J H van der Kallen, Casper G Schalkwijk, Alexandra Zhernakova, Yang Li, Ettje F Tigchelaar, Niek de Klein, Marian Beekman, Joris Deelen, Diana van Heemst, Leonard H van den Berg, Albert Hofman, André G Uitterlinden, Marleen M J van Greevenbroek, Jan H Veldink, Dorret I Boomsma, Cornelia M van Duijn, Cisca Wijmenga, P Eline Slagboom, Morris A Swertz, Aaron Isaacs, Joyce B J van Meurs, Rick Jansen, Bastiaan T Heijmans, Peter A C 't Hoen, Lude Franke
Genetic risk factors often localize to noncoding regions of the genome with unknown effects on disease etiology. Expression quantitative trait loci (eQTLs) help to explain the regulatory mechanisms underlying these genetic associations. Knowledge of the context that determines the nature and strength of eQTLs may help identify cell types relevant to pathophysiology and the regulatory networks underlying disease. Here we generated peripheral blood RNA-seq data from 2,116 unrelated individuals and systematically identified context-dependent eQTLs using a hypothesis-free strategy that does not require previous knowledge of the identity of the modifiers...
December 5, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27906459/integrative-genomic-analysis-identifies-ancestry-related-expression-quantitative-trait-loci-on-dna-polymerase-%C3%AE-and-supports-the-association-of-genetic-ancestry-with-survival-disparities-in-head-and-neck-squamous-cell-carcinoma
#2
Meganathan P Ramakodi, Karthik Devarajan, Elizabeth Blackman, Denise Gibbs, Danièle Luce, Jacqueline Deloumeaux, Suzy Duflo, Jeffrey C Liu, Ranee Mehra, Rob J Kulathinal, Camille C Ragin
BACKGROUND: African Americans with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than whites. This study investigated the functional importance of ancestry-informative single-nucleotide polymorphisms (SNPs) in HNSCC and also examined the effect of functionally important genetic elements on racial disparities in HNSCC survival. METHODS: Ancestry-informative SNPs, RNA sequencing, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes...
December 1, 2016: Cancer
https://www.readbyqxmd.com/read/27902686/genomic-characterization-of-metformin-hepatic-response
#3
Marcelo R Luizon, Walter L Eckalbar, Yao Wang, Stacy L Jones, Robin P Smith, Megan Laurance, Lawrence Lin, Paul J Gallins, Amy S Etheridge, Fred Wright, Yihui Zhou, Cliona Molony, Federico Innocenti, Sook Wah Yee, Kathleen M Giacomini, Nadav Ahituv
Metformin is used as a first-line therapy for type 2 diabetes (T2D) and prescribed for numerous other diseases. However, its mechanism of action in the liver has yet to be characterized in a systematic manner. To comprehensively identify genes and regulatory elements associated with metformin treatment, we carried out RNA-seq and ChIP-seq (H3K27ac, H3K27me3) on primary human hepatocytes from the same donor treated with vehicle control, metformin or metformin and compound C, an AMP-activated protein kinase (AMPK) inhibitor (allowing to identify AMPK-independent pathways)...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27827986/replicated-risk-nicotinic-cholinergic-receptor-genes-for-nicotine-dependence
#4
Lingjun Zuo, Rolando Garcia-Milian, Xiaoyun Guo, Chunlong Zhong, Yunlong Tan, Zhiren Wang, Jijun Wang, Xiaoping Wang, Longli Kang, Lu Lu, Xiangning Chen, Chiang-Shan R Li, Xingguang Luo
It has been hypothesized that the nicotinic acetylcholine receptors (nAChRs) play important roles in nicotine dependence (ND) and influence the number of cigarettes smoked per day (CPD) in smokers. We compiled the associations between nicotinic cholinergic receptor genes (CHRNs) and ND/CPD that were replicated across different studies, reviewed the expression of these risk genes in human/mouse brains, and verified their expression using independent samples of both human and mouse brains. The potential functions of the replicated risk variants were examined using cis-eQTL analysis or predicted using a series of bioinformatics analyses...
November 7, 2016: Genes
https://www.readbyqxmd.com/read/27799337/small-rna-sequencing-in-cells-and-exosomes-identifies-eqtls-and-14q32-as-a-region-of-active-export
#5
Emily K Tsang, Nathan S Abell, Xin Li, Vanessa Anaya, Konrad J Karczewski, David A Knowles, Raymond G Sierra, Kevin S Smith, Stephen B Montgomery
Exosomes are small extracellular vesicles that carry heterogeneous cargo, including RNA, between cells. Increasing evidence suggests that exosomes are important mediators of intercellular communication and biomarkers of disease. Despite this, the variability of exosomal RNA between individuals has not been well quantified. To assess this variability, we sequenced the small RNA of cells and exosomes from a 17-member family. Across individuals, we show that selective export of miRNAs occurs not only at the level of specific transcripts, but that a cluster of 74 mature miRNAs on chromosome 14q32 is massively exported in exosomes while mostly absent from cells...
October 31, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27775175/genetic-risk-mechanisms-of-posttraumatic-stress-disorder-in-the-human-brain
#6
Rahul A Bharadwaj, Andrew E Jaffe, Qiang Chen, Amy Deep-Soboslay, Aaron L Goldman, Michelle I Mighdoll, John A Cotoia, Anna C Brandtjen, JooHeon Shin, Thomas M Hyde, Venkata S Mattay, Daniel R Weinberger, Joel E Kleinman
Posttraumatic stress disorder (PTSD) follows exposure to a traumatic event in susceptible individuals. Recently, genome-wide association studies have identified a number of genetic sequence variants that are associated with the risk of developing PTSD. To follow up on identifying the molecular mechanisms of these risk variants, we performed genotype to RNA sequencing-derived quantitative expression (whole gene, exon, and exon junction levels) analysis in the dorsolateral prefrontal cortex (DLPFC) of normal postmortem human brains...
October 24, 2016: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27768888/genetic-adaptation-and-neandertal-admixture-shaped-the-immune-system-of-human-populations
#7
Hélène Quach, Maxime Rotival, Julien Pothlichet, Yong-Hwee Eddie Loh, Michael Dannemann, Nora Zidane, Guillaume Laval, Etienne Patin, Christine Harmant, Marie Lopez, Matthieu Deschamps, Nadia Naffakh, Darragh Duffy, Anja Coen, Geert Leroux-Roels, Frederic Clément, Anne Boland, Jean-François Deleuze, Janet Kelso, Matthew L Albert, Lluis Quintana-Murci
Humans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli-ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus-and mapped expression quantitative trait loci (eQTLs)...
October 20, 2016: Cell
https://www.readbyqxmd.com/read/27765809/discovering-snps-regulating-human-gene-expression-using-allele-specific-expression-from-rna-seq-data
#8
Eun Yong Kang, Lisa Martin, Serghei Mangul, Warin Isvilanonda, Jennifer Zou, Eyal Ben-David, Buhm Han, Aldons J Lusis, Sagiv Shifman, Eleazar Eskin
The study of the genetics of gene expression is of considerable importance to understanding the nature of common, complex diseases. The most widely applied approach to identifying relationships between genetic variation and gene expression is the expression quantitative trait loci (eQTL) approach. Here we increase the computational power of eQTL with an alternative and complementary approach based on analyzing allele specific expression (ASE). We design a novel analytical method to identify cis-acting regulatory variants based on genome sequencing and measurements of ASE from RNA-seq data...
October 7, 2016: Genetics
https://www.readbyqxmd.com/read/27761138/dissecting-the-effect-of-genetic-variation-on-the-hepatic-expression-of-drug-disposition-genes-across-the-collaborative-cross-mouse-strains
#9
Aharon Nachshon, Hanifa J Abu-Toamih Atamni, Yael Steuerman, Roa'a Sheikh-Hamed, Alexandra Dorman, Richard Mott, Juliane C Dohm, Hans Lehrach, Marc Sultan, Ron Shamir, Sascha Sauer, Heinz Himmelbauer, Fuad A Iraqi, Irit Gat-Viks
A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. Here we systematically measured RNA-sequencing expression profiles from livers of 29 CC lines under baseline conditions...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27760139/local-adaptation-of-sun-exposure-dependent-gene-expression-regulation-in-human-skin
#10
Ryosuke Kita, Hunter B Fraser
Sun-exposure is a key environmental variable in the study of human evolution. Several skin-pigmentation genes serve as classical examples of positive selection, suggesting that sun-exposure has significantly shaped worldwide genomic variation. Here we investigate the interaction between genetic variation and sun-exposure, and how this impacts gene expression regulation. Using RNA-Seq data from 607 human skin samples, we identified thousands of transcripts that are differentially expressed between sun-exposed skin and non-sun-exposed skin...
October 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27759658/genome-wide-identification-of-expression-quantitative-trait-loci-for-human-telomerase
#11
Hanseol Kim, Jihye Ryu, Chaeyoung Lee
A genome-wide association study was conducted to identify expression quantitative trait loci (eQTL) for human telomerase.We tested the genetic associations of nucleotide variants with expression of the genes encoding human telomerase reverse transcriptase (hTERT) and telomerase RNA components (TERC) in lymphoblastoid cell lines derived from 373 Europeans.Our results revealed 6 eQTLs associated with hTERT (P < 5 × 10). One eQTL (rs17755753) was located in the intron 1 of the gene encoding R-spondin-3 (RSPO3), a well-known Wnt signaling regulator...
October 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27729386/higher-chylomicron-remnants-and-ldl-particle-numbers-associate-with-cd36-snps-and-dna-methylation-sites-that-reduce-cd36
#12
Latisha Love-Gregory, Aldi T Kraja, Fiona Allum, Stella Aslibekyan, Åsa K Hedman, Yanan Duan, Ingrid B Borecki, Donna K Arnett, Mark I McCarthy, Panos Deloukas, Jose M Ordovas, Paul N Hopkins, Elin Grundberg, Nada A Abumrad
Cluster of differentiation 36 (CD36) variants influence fasting lipids and risk of metabolic syndrome, but their impact on postprandial lipids, an independent risk factor for cardiovascular disease, is unclear. We determined the effects of SNPs within a ∼410 kb region encompassing CD36 and its proximal and distal promoters on chylomicron (CM) remnants and LDL particles at fasting and at 3.5 and 6 h following a high-fat meal (Genetics of Lipid Lowering Drugs and Diet Network study, n = 1,117). Five promoter variants associated with CMs, four with delayed TG clearance and five with LDL particle number...
December 2016: Journal of Lipid Research
https://www.readbyqxmd.com/read/27722582/spire-a-modular-pipeline-for-eqtl-analysis-of-rna-seq-data-reveals-a-regulatory-hotspot-controlling-mirna-expression-in-c-elegans
#13
Ivan Kel, Zisong Chang, Nadia Galluccio, Margherita Romeo, Stefano Beretta, Luisa Diomede, Alessandra Mezzelani, Luciano Milanesi, Christoph Dieterich, Ivan Merelli
The interpretation of genome-wide association study is difficult, as it is hard to understand how polymorphisms can affect gene regulation, in particular for trans-regulatory elements located far from their controlling gene. Using RNA or protein expression data as phenotypes, it is possible to correlate their variations with specific genotypes. This technique is usually referred to as expression Quantitative Trait Loci (eQTLs) analysis and only few packages exist for the integration of genotype patterns and expression profiles...
September 22, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27623010/hypothalamic-transcriptomes-of-99-mouse-strains-reveal-trans-eqtl-hotspots-splicing-qtls-and-novel-non-coding-genes
#14
Yehudit Hasin-Brumshtein, Arshad H Khan, Farhad Hormozdiari, Calvin Pan, Brian W Parks, Vladislav A Petyuk, Paul D Piehowski, Anneke Brümmer, Matteo Pellegrini, Xinshu Xiao, Eleazar Eskin, Richard D Smith, Aldons J Lusis, Desmond J Smith
Previous studies had shown that the integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs...
September 13, 2016: ELife
https://www.readbyqxmd.com/read/27580880/functional-characterization-of-a-chr13q22-1-pancreatic-cancer-risk-locus-reveals-long-range-interaction-and-allele-specific-effects-on-dis3-expression
#15
Jason W Hoskins, Abdisamad Ibrahim, Mickey A Emmanuel, Sarah M Manmiller, Yinglun Wu, Maura O'Neill, Jinping Jia, Irene Collins, Mingfeng Zhang, Janelle V Thomas, Lauren M Rost, Sudipto Das, Hemang Parikh, Jefferson M Haake, Gail L Matters, Robert C Kurtz, William R Bamlet, Alison Klein, Rachael Stolzenberg-Solomon, Brian M Wolpin, Ronit Yarden, Zhaoming Wang, Jill Smith, Sara H Olson, Thorkell Andresson, Gloria M Petersen, Laufey T Amundadottir
Genome-wide association studies (GWAS) have identified multiple common susceptibility loci for pancreatic cancer. Here we report fine-mapping and functional analysis of one such locus residing in a 610 kb gene desert on chr13q22.1 (marked by rs9543325). The closest candidate genes, KLF5, KLF12, PIBF1, DIS3 and BORA, range in distance from 265-586 kb. Sequencing three sub-regions containing the top ranked SNPs by imputation P-value revealed a 30 bp insertion/deletion (indel) variant that was significantly associated with pancreatic cancer risk (rs386772267, P = 2...
August 30, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/27515598/the-abundance-of-cis-acting-loci-leading-to-differential-allele-expression-in-f1-mice-and-their-relationship-to-loci-harboring-genes-affecting-complex-traits
#16
Seungeun Yeo, Colin A Hodgkinson, Zhifeng Zhou, Jeesun Jung, Ming Leung, Qiaoping Yuan, David Goldman
BACKGROUND: Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL's for complex phenotypes...
August 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27504011/modem-multi-omics-data-envelopment-and-mining-in-maize
#17
Haijun Liu, Fan Wang, Yingjie Xiao, Zonglin Tian, Weiwei Wen, Xuehai Zhang, Xi Chen, Nannan Liu, Wenqiang Li, Lei Liu, Jie Liu, Jianbing Yan, Jianxiao Liu
MODEM is a comprehensive database of maize multidimensional omics data, including genomic, transcriptomic, metabolic and phenotypic information from the cellular to individual plant level. This initial release contains approximately 1.06 M high quality SNPs for 508 diverse inbred lines obtained by combining variations from RNA sequencing on whole kernels (15 days after pollination) of 368 lines and a 50 K array for all 508 individuals. As all of these data were derived from the same diverse panel of lines, the database also allows various types of genetic mapping (including characterization of phenotypic QTLs, pQTLs; expression QTLs, eQTLs and metabolic QTLs, mQTLs)...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27479908/tensor-decomposition-for-multiple-tissue-gene-expression-experiments
#18
Victoria Hore, Ana Viñuela, Alfonso Buil, Julian Knight, Mark I McCarthy, Kerrin Small, Jonathan Marchini
Genome-wide association studies of gene expression traits and other cellular phenotypes have successfully identified links between genetic variation and biological processes. The majority of discoveries have uncovered cis-expression quantitative trait locus (eQTL) effects via mass univariate testing of SNPs against gene expression in single tissues. Here we present a Bayesian method for multiple-tissue experiments focusing on uncovering gene networks linked to genetic variation. Our method decomposes the 3D array (or tensor) of gene expression measurements into a set of latent components...
September 2016: Nature Genetics
https://www.readbyqxmd.com/read/27424220/a-3-utr-polymorphism-marks-differential-klrg1-mrna-levels-through-disruption-of-a-mir-584-5p-binding-site-and-associates-with-pemphigus-foliaceus-susceptibility
#19
Gabriel A Cipolla, Jong Kook Park, Liana A de Oliveira, Sara Cristina Lobo-Alves, Rodrigo C de Almeida, Ticiana D J Farias, Débora de S Lemos, Danielle Malheiros, Robert M Lavker, Maria Luiza Petzl-Erler
Genetic variations mapping to 3' untranslated regions (3'UTRs) may overlap with microRNA (miRNA) binding sites, therefore potentially interfering with translation inhibition or messenger RNA (mRNA) degradation. The aim of this study was to investigate whether single nucleotide polymorphisms (SNPs) located within the 3'UTRs of six candidate genes and predicted to interfere with miRNA ligation could account for disease-relevant differential mRNA levels. Focusing on pemphigus foliaceus (PF) - an autoimmune blistering skin condition with unique endemic patterns - we investigated whether nine 3'UTR SNPs from the CD1D, CTLA4, KLRD1, KLRG1, NKG7, and TNFSF13B genes differentially expressed in PF were disease-associated...
October 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27381443/distant-eqtls-and-non-coding-sequences-play-critical-roles-in-regulating-gene-expression-and-quantitative-trait-variation-in-maize
#20
Haijun Liu, Xin Luo, Luyao Niu, Yingjie Xiao, Lu Chen, Jie Liu, Xiaqing Wang, Minliang Jin, Wenqiang Li, Qinghua Zhang, Jianbing Yan
A detailed understanding of the genetic architecture of mRNA expression by millions of genetic variants is important for studying quantitative trait variation. In this study, we identified 1.25M SNPs with a minor allele frequency (MAF) greater than 0.05 by combining reduced genome sequencing (GBS), high-density array technologies (600K), and previous deep RNA-sequencing data from 368 diverse inbred lines of maize. The balanced alleleic frequencies and distributions in a relatively large and diverse natural panel helped to identify eQTLs associated with more than 18,000 genes (63...
July 2, 2016: Molecular Plant
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