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https://www.readbyqxmd.com/read/29348297/changes-in-macrophage-transcriptome-associate-with-systemic-sclerosis-and-mediate-gsdma-contribution-to-disease-risk
#1
Aida Moreno-Moral, Marta Bagnati, Surya Koturan, Jeong-Hun Ko, Carmen Fonseca, Nathan Harmston, Laurence Game, Javier Martin, Voon Ong, David J Abraham, Christopher P Denton, Jacques Behmoaras, Enrico Petretto
OBJECTIVES: Several common and rare risk variants have been reported for systemic sclerosis (SSc), but the effector cell(s) mediating the function of these genetic variants remains to be elucidated. While innate immune cells have been proposed as the critical targets to interfere with the disease process underlying SSc, no studies have comprehensively established their effector role. Here we investigated the contribution of monocyte-derived macrophages (MDMs) in mediating genetic susceptibility to SSc...
January 17, 2018: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29335020/ensemble-genomic-analysis-in-human-lung-tissue-identifies-novel-genes-for-chronic-obstructive-pulmonary-disease
#2
Jarrett D Morrow, Michael H Cho, John Platig, Xiaobo Zhou, Dawn L DeMeo, Weiliang Qiu, Bartholome Celli, Nathaniel Marchetti, Gerard J Criner, Raphael Bueno, George R Washko, Kimberly Glass, John Quackenbush, Edwin K Silverman, Craig P Hersh
BACKGROUND: Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context...
January 15, 2018: Human Genomics
https://www.readbyqxmd.com/read/29325110/impact-of-genetic-risk-loci-for-multiple-sclerosis-on-expression-of-proximal-genes-in-patients
#3
Tojo James, Magdalena Lindén, Hiromasa Morikawa, Sunjay Jude Fernandes, Sabrina Ruhrmann, Mikael Huss, Maya Brandi, Fredrik Piehl, Maja Jagodic, Jesper Tegnér, Mohsen Khademi, Tomas Olsson, David Gomez-Cabrero, Ingrid Kockum
Despite advancements in genetic studies, it is difficult to understand and characterize the functional relevance of disease-associated genetic variants, especially in the context of a complex multifactorial disease such as Multiple Sclerosis (MS). Since a large proportion of expression quantitative trait loci (eQTLs) are context-specific, we performed RNA-Seq in peripheral blood mononuclear cells (PBMCs) from MS patients (n = 145) to identify eQTLs in regions centered on 109 MS risk SNPs and seven associated HLA variants...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29273740/rna-sequencing-provides-insights-into-the-evolution-of-lettuce-and-the-regulation-of-flavonoid-biosynthesis
#4
Lei Zhang, Wenqing Su, Rong Tao, Weiyi Zhang, Jiongjiong Chen, Peiyao Wu, Chenghuan Yan, Yue Jia, Robert M Larkin, Dean Lavelle, Maria-Jose Truco, Sebastian Reyes Chin-Wo, Richard W Michelmore, Hanhui Kuang
Different horticultural types of lettuce exhibit tremendous morphological variation. However, the molecular basis for domestication and divergence among the different horticultural types of lettuce remains unknown. Here, we report the RNA sequencing of 240 lettuce accessions sampled from the major horticultural types and wild relatives, generating 1.1 million single-nucleotide polymorphisms (SNPs). Demographic modeling indicates that there was a single domestication event for lettuce. We identify a list of regions as putative selective sweeps that occurred during domestication and divergence, respectively...
December 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/29246110/dna-and-rna-sequence-based-gwas-highlights-membrane-transport-genes-as-key-modulators-of-milk-lactose-content
#5
Thomas J Lopdell, Kathryn Tiplady, Maksim Struchalin, Thomas J J Johnson, Michael Keehan, Ric Sherlock, Christine Couldrey, Stephen R Davis, Russell G Snell, Richard J Spelman, Mathew D Littlejohn
BACKGROUND: Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we present the first GWAS focussed on analysis of milk lactose traits. RESULTS: Using a discovery population of 12,000 taurine dairy cattle, we detail 27 QTL for lactose concentration and yield, and subsequently validate the effects of 26 of these loci in a distinct population of 18,000 cows...
December 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29237423/deciphering-the-genetic-regulation-of-peripheral-blood-transcriptome-in-pigs-through-expression-genome-wide-association-study-and-allele-specific-expression-analysis
#6
T Maroilley, G Lemonnier, J Lecardonnel, D Esquerré, Y Ramayo-Caldas, M J Mercat, C Rogel-Gaillard, J Estellé
BACKGROUND: Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity...
December 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29228364/age-dependent-changes-in-mean-and-variance-of-gene-expression-across-tissues-in-a-twin-cohort
#7
Ana Viñuela, Andrew A Brown, Alfonso Buil, Pei-Chien Tsai, Matthew N Davies, Jordana T Bell, Emmanouil T Dermitzakis, Timothy D Spector, Kerrin S Small
Changes in mean and variance of gene expression with age have consequences for healthy aging and disease development. Age-dependent changes in phenotypic variance have been associated to a decline in regulatory functions leading to increase in disease risk. Here we investigate age-related mean and variance changes in gene expression measured by RNA-seq of fat, skin, whole blood and derived lymphoblastoid cell lines (LCLs) expression from 855 adult female twins. We see evidence of up to 60% of age effects on transcription levels shared across tissues, and 47% of those on splicing...
December 8, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29227470/multiplexed-droplet-single-cell-rna-sequencing-using-natural-genetic-variation
#8
Hyun Min Kang, Meena Subramaniam, Sasha Targ, Michelle Nguyen, Lenka Maliskova, Elizabeth McCarthy, Eunice Wan, Simon Wong, Lauren Byrnes, Cristina M Lanata, Rachel E Gate, Sara Mostafavi, Alexander Marson, Noah Zaitlen, Lindsey A Criswell, Chun Jimmie Ye
Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29193869/cd4-and-b-lymphocyte-expression-quantitative-traits-at-rheumatoid-arthritis-risk-loci-in-untreated-early-arthritis-implications-for-causal-gene-identification
#9
Nishanthi Thalayasingam, Nisha Nair, Andrew J Skelton, Jonathan Massey, Amy E Anderson, Alexander D Clark, Julie Diboll, Dennis W Lendrem, Louise N Reynard, Heather J Cordell, Stephen Eyre, John D Isaacs, Anne Barton, Arthur G Pratt
OBJECTIVE: Rheumatoid arthritis (RA) is a genetically complex disease of immune dysregulation. Seeking insight into genetic risk mechanisms, we conducted an expression quantitative trait locus (eQTL) analysis of confirmed genetic risk loci in CD4+ T cells and B cells from carefully phenotyped early arthritis patients naïve to therapeutic immunomodulation. METHODS: 344 patients donated RNA and DNA from purified B and/or CD4+ T-cells. Genotyping and global gene expression measurement were carried out using Illumina BeadChip microarrays...
November 28, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29186329/aselux-an-ultra-fast-and-accurate-allelic-reads-counter
#10
Zong Miao, Marcus Alvarez, Päivi Pajukanta, Arthur Ko
Motivation: Mapping bias causes preferential alignment to the reference allele, forming a major obstacle in allele-specific expression (ASE) analysis. The existing methods, such as simulation and SNP-aware alignment, are either inaccurate or relatively slow. To fast and accurately count allelic reads for ASE analysis, we developed a novel approach, ASElux, which utilizes the personal SNP information and counts allelic reads directly from unmapped RNA-sequence (RNA-seq) data. ASElux significantly reduces runtime by disregarding reads outside single nucleotide polymorphisms (SNPs) during the alignment...
November 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29183975/high-resolution-mapping-of-cis-regulatory-variation-in-budding-yeast
#11
Ryosuke Kita, Sandeep Venkataram, Yiqi Zhou, Hunter B Fraser
Genetic variants affecting gene-expression levels are a major source of phenotypic variation. The approximate locations of these variants can be mapped as expression quantitative trait loci (eQTLs); however, a major limitation of eQTLs is their low resolution, which precludes investigation of the causal variants and their molecular mechanisms. Here we report RNA-seq and full genome sequences for 85 diverse isolates of the yeast Saccharomyces cerevisiae-including wild, domesticated, and human clinical strains-which allowed us to perform eQTL mapping with 50-fold higher resolution than previously possible...
November 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29156765/network-directed-cis-mediator-analysis-of-normal-prostate-tissue-expression-profiles-reveals-downstream-regulatory-associations-of-prostate-cancer-susceptibility-loci
#12
Nicholas B Larson, Shannon K McDonnell, Zach Fogarty, Melissa C Larson, John Cheville, Shaun Riska, Saurabh Baheti, Alexandra M Weber, Asha A Nair, Liang Wang, Daniel O'Brien, Jaime Davila, Daniel J Schaid, Stephen N Thibodeau
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis-acting associations due to study limitations. While trans-eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans-eQTL associations are mediated by cis-regulated genes, such as transcription factors...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29149290/discovering-the-3-utr-mediated-regulation-of-alpha-synuclein
#13
Domenica Marchese, Teresa Botta-Orfila, Davide Cirillo, Juan Antonio Rodriguez, Carmen Maria Livi, Rubén Fernández-Santiago, Mario Ezquerra, Maria J Martí, Elias Bechara, Gian Gaetano Tartaglia
Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro/in silico screening we identified RNA-binding proteins (RBPs) that interact with SNCA 3' UTRs. We identified two RBPs, ELAVL1 and TIAR, that bind with high affinity to the most abundant and translationally active 3' UTR isoform (575 nt)...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#14
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29138229/genomic-structural-variations-lead-to-dysregulation-of-important-coding-and-non-coding-rna-species-in-dilated-cardiomyopathy
#15
Jan Haas, Stefan Mester, Alan Lai, Karen S Frese, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Tobias Rausch, Rouven Nietsch, Jes-Niels Boeckel, Avisha Carstensen, Mirko Völkers, Carsten Dietrich, Dietmar Pils, Ali Amr, Daniel B Holzer, Diana Martins Bordalo, Daniel Oehler, Tanja Weis, Derliz Mereles, Sebastian Buss, Eva Riechert, Emil Wirsz, Maximilian Wuerstle, Jan O Korbel, Andreas Keller, Hugo A Katus, Andreas E Posch, Benjamin Meder
The transcriptome needs to be tightly regulated by mechanisms that include transcription factors, enhancers, and repressors as well as non-coding RNAs. Besides this dynamic regulation, a large part of phenotypic variability of eukaryotes is expressed through changes in gene transcription caused by genetic variation. In this study, we evaluate genome-wide structural genomic variants (SVs) and their association with gene expression in the human heart. We detected 3,898 individual SVs affecting all classes of gene transcripts (e...
November 14, 2017: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/29114259/identification-of-splicing-quantitative-trait-loci-sqtl-in-drosophila-melanogaster-with-developmental-lead-pb-2-exposure
#16
Wen Qu, Katherine Gurdziel, Roger Pique-Regi, Douglas M Ruden
Lead (Pb) poisoning has been a major public health issue globally and the recent Flint water crisis has drawn nation-wide attention to its effects. To better understand how lead plays a role as a neurotoxin, we utilized the Drosophila melanogaster model to study the genetic effects of lead exposure during development and identified lead-responsive genes. In our previous studies, we have successfully identified hundreds of lead-responsive expression QTLs (eQTLs) by using RNA-seq analysis on heads collected from the Drosophila Synthetic Population Resource...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29074555/efficient-prioritization-of-multiple-causal-eqtl-variants-via-sparse-polygenic-modeling
#17
Naoki Nariai, William W Greenwald, Christopher DeBoever, He Li, Kelly A Frazer
Expression quantitative trait loci (eQTL) studies have typically used single-variant association analysis to identify genetic variants correlated with gene expression. However, this approach has several drawbacks: causal variants cannot be distinguished from non-functional variants in strong linkage disequilibrium, combined effects from multiple causal variants cannot be captured, and low-frequency (<5% MAF) eQTL variants are difficult to identify. While these issues possibly could be overcome by using sparse polygenic models which associate multiple genetic variants with gene expression simultaneously, the predictive performance of these models for eQTL studies has not been evaluated...
October 26, 2017: Genetics
https://www.readbyqxmd.com/read/29059182/profiling-rna-seq-at-multiple-resolutions-markedly-increases-the-number-of-causal-eqtls-in-autoimmune-disease
#18
Christopher A Odhams, Deborah S Cunninghame Graham, Timothy J Vyse
Genome-wide association studies have identified hundreds of risk loci for autoimmune disease, yet only a minority (~25%) share genetic effects with changes to gene expression (eQTLs) in immune cells. RNA-Seq based quantification at whole-gene resolution, where abundance is estimated by culminating expression of all transcripts or exons of the same gene, is likely to account for this observed lack of colocalisation as subtle isoform switches and expression variation in independent exons can be concealed. We performed integrative cis-eQTL analysis using association statistics from twenty autoimmune diseases (560 independent loci) and RNA-Seq data from 373 individuals of the Geuvadis cohort profiled at gene-, isoform-, exon-, junction-, and intron-level resolution in lymphoblastoid cell lines...
October 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29058714/predicting-causal-variants-affecting-expression-by-using-whole-genome-sequencing-and-rna-seq-from-multiple-human-tissues
#19
Andrew Anand Brown, Ana Viñuela, Olivier Delaneau, Tim D Spector, Kerrin S Small, Emmanouil T Dermitzakis
Genetic association mapping produces statistical links between phenotypes and genomic regions, but identifying causal variants remains difficult. Whole-genome sequencing (WGS) can help by providing complete knowledge of all genetic variants, but it is financially prohibitive for well-powered GWAS studies. We performed mapping of expression quantitative trait loci (eQTLs) with WGS and RNA-seq, and found that lead eQTL variants called with WGS were more likely to be causal. Through simulations, we derived properties of causal variants and used them to develop a method for identifying likely causal SNPs...
December 2017: Nature Genetics
https://www.readbyqxmd.com/read/29053642/allelic-expression-imbalance-in-the-human-retinal-transcriptome-and-potential-impact-on-inherited-retinal-diseases
#20
Pablo Llavona, Michele Pinelli, Margherita Mutarelli, Veer Singh Marwah, Simone Schimpf-Linzenbold, Sebastian Thaler, Efdal Yoeruek, Jan Vetter, Susanne Kohl, Bernd Wissinger
Inherited retinal diseases (IRDs) are often associated with variable clinical expressivity (VE) and incomplete penetrance (IP). Underlying mechanisms may include environmental, epigenetic, and genetic factors. Cis-acting expression quantitative trait loci (cis-eQTLs) can be implicated in the regulation of genes by favoring or hampering the expression of one allele over the other. Thus, the presence of such loci elicits allelic expression imbalance (AEI) that can be traced by massive parallel sequencing techniques...
October 20, 2017: Genes
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