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https://www.readbyqxmd.com/read/29755505/integrative-analysis-identifies-genetic-variants-associated-with-autoimmune-diseases-affecting-putative-microrna-binding-sites
#1
Rodrigo C de Almeida, Vinícius S Chagas, Mauro A A Castro, Maria L Petzl-Erler
Genome-wide and fine mapping studies have shown that more than 90% of genetic variants associated with autoimmune diseases (AID) are located in non-coding regions of the human genome and especially in regulatory sequences, including microRNAs (miRNA) target sites. MiRNAs are small endogenous noncoding RNAs that modulate gene expression at the post-transcriptional level. Single nucleotide polymorphisms (SNPs) located within the 3' untranslated region of their target mRNAs (miRSNP) can alter miRNA binding sites...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29625054/a-pan-cancer-analysis-of-enhancer-expression-in-nearly-9000-patient-samples
#2
Han Chen, Chunyan Li, Xinxin Peng, Zhicheng Zhou, John N Weinstein, Han Liang
The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on "chromatin-state" to explain their interplay...
April 5, 2018: Cell
https://www.readbyqxmd.com/read/29610479/single-cell-rna-sequencing-identifies-celltype-specific-cis-eqtls-and-co-expression-qtls
#3
Monique G P van der Wijst, Harm Brugge, Dylan H de Vries, Patrick Deelen, Morris A Swertz, Lude Franke
Genome-wide association studies have identified thousands of genetic variants that are associated with disease1 . Most of these variants have small effect sizes, but their downstream expression effects, so-called expression quantitative trait loci (eQTLs), are often large2 and celltype-specific3-5 . To identify these celltype-specific eQTLs using an unbiased approach, we used single-cell RNA sequencing to generate expression profiles of ~25,000 peripheral blood mononuclear cells from 45 donors. We identified previously reported cis-eQTLs, but also identified new celltype-specific cis-eQTLs...
April 2, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29601440/a-celiac-diasease-associated-lncrna-named-hcg14-regulates-nod1-expression-in-intestinal-cells
#4
Izortze Santin, Amaia Jauregi-Miguel, Teresa Velayos, Ainara Castellanos-Rubio, Koldo Garcia-Etxebarria, Irati Romero-Garmendia, Nora Fernandez-Jimenez, Iñaki Irastorza, Luis Castaño, Jose Ramón Bilbao
OBJECTIVE: To identify additional celiac disease associated loci in the Major Histocompatibility Complex independent from classical HLA risk alleles (HLA-DR3-DQ2) and to characterize their potential functional impact in celiac disease pathogenesis at the intestinal level. METHODS: We performed a high resolution SNP genotyping of the MHC region, comparing HLA-DR3 homozygous celiac patients and non-celiac controls carrying a single copy of the B8-DR3-DQ2 conserved extended haplotype...
March 29, 2018: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/29487953/fam13a-and-pom121c-are-candidate-genes-for-fasting-insulin-functional-follow-up-analysis-of-a-genome-wide-association-study
#5
Veroniqa Lundbäck, Agne Kulyte, Rona J Strawbridge, Mikael Ryden, Peter Arner, Claude Marcus, Ingrid Dahlman
AIMS/HYPOTHESIS: By genome-wide association meta-analysis, 17 genetic loci associated with fasting serum insulin (FSI), a marker of systemic insulin resistance, have been identified. To define potential culprit genes in these loci, in a cross-sectional study we analysed white adipose tissue (WAT) expression of 120 genes in these loci in relation to systemic and adipose tissue variables, and functionally evaluated genes demonstrating genotype-specific expression in WAT (eQTLs). METHODS: Abdominal subcutaneous adipose tissue biopsies were obtained from 114 women...
May 2018: Diabetologia
https://www.readbyqxmd.com/read/29476079/co-occurring-expression-and-methylation-qtls-allow-detection-of-common-causal-variants-and-shared-biological-mechanisms
#6
RANDOMIZED CONTROLLED TRIAL
Brandon L Pierce, Lin Tong, Maria Argos, Kathryn Demanelis, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwar, Md Tariqul Islam, Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, Md Yunus, Muhammad G Kibriya, Lin S Chen, Habibul Ahsan
Inherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as a methylation QTL (cis-meQTL), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing evidence of a causal relationship between expression and methylation (i...
February 23, 2018: Nature Communications
https://www.readbyqxmd.com/read/29438444/systems-genomics-study-reveals-expression-quantitative-trait-loci-regulator-genes-and-pathways-associated-with-boar-taint-in-pigs
#7
Markus Drag, Mathias B Hansen, Haja N Kadarmideen
Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg...
2018: PloS One
https://www.readbyqxmd.com/read/29425116/integrated-systems-approach-reveals-sphingolipid-metabolism-pathway-dysregulation-in-association-with-late-onset-alzheimer-s-disease
#8
John Stephen Malamon, Andres Kriete
Late-onset Alzheimer's disease (LOAD) and age are significantly correlated such that one-third of Americans beyond 85 years of age are afflicted. We have designed and implemented a pilot study that combines systems biology approaches with traditional next-generation sequencing (NGS) analysis techniques to identify relevant regulatory pathways, infer functional relationships and confirm the dysregulation of these biological pathways in LOAD. Our study design is a most comprehensive systems approach combining co-expression network modeling derived from RNA-seq data, rigorous quality control (QC) standards, functional ontology, and expression quantitative trait loci (eQTL) derived from whole exome (WES) single nucleotide variant (SNV) genotype data...
February 9, 2018: Biology
https://www.readbyqxmd.com/read/29385635/deciphering-genetic-factors-that-determine-melon-fruit-quality-traits-using-rna-seq-based-high-resolution-qtl-and-eqtl-mapping
#9
Navot Galpaz, Itay Gonda, Doron Shem-Tov, Omer Barad, Galil Tzuri, Shery Lev, Zhangjun Fei, Yimin Xu, Linyong Mao, Chen Jiao, Rotem Harel-Beja, Adi Doron-Faigenboim, Oren Tzfadia, Einat Bar, Ayala Meir, Uzi Sa'ar, Aaron Fait, Eran Halperin, Merav Kenigswald, Elazar Fallik, Nadia Lombardi, Guy Kol, Gil Ronen, Yosef Burger, Amit Gur, Ya'akov Tadmor, Vitaly Portnoy, Arthur A Schaffer, Efraim Lewinsohn, James J Giovannoni, Nurit Katzir
Combined quantitative trait loci (QTL) and expression-QTL (eQTL) mapping analysis was performed to identify genetic factors affecting melon (Cucumis melo) fruit quality, by linking genotypic, metabolic and transcriptomic data from a melon recombinant inbred line (RIL) population. RNA sequencing (RNA-Seq) of fruit from 96 RILs yielded a highly saturated collection of > 58 000 single-nucleotide polymorphisms, identifying 6636 recombination events that separated the genome into 3663 genomic bins. Bin-based QTL analysis of 79 RILs and 129 fruit-quality traits affecting taste, aroma and color resulted in the mapping of 241 QTL...
April 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29374346/accessing-gene-expression-in-treatment-resistant-schizophrenia
#10
Patricia N Moretti, Vanessa K Ota, Eduardo S Gouvea, Mariana Pedrini, Marcos L Santoro, Fernanda Talarico, Leticia M Spindola, Carolina Muniz Carvalho, Cristiano Noto, Gabriela Xavier, Elisa Brietzke, Ary Gadelha, Rodrigo Bressan, Jair Mari, Sintia Belangero
Schizophrenia (SCZ) is a mental disorder arising from a complex interaction of genetic and environmental factors. It has been suggested that treatment-resistant schizophrenia (TRS) is a distinct, more severe, and homogenous subgroup of schizophrenia that could present specific biological markers. Our aim was to characterize expression of target genes in blood of TRS patients compared with non-TRS (NTRS) patients and healthy controls (HC). TRS has been defined using failure to respond to two previous antipsychotic trials...
January 26, 2018: Molecular Neurobiology
https://www.readbyqxmd.com/read/29348297/changes-in-macrophage-transcriptome-associate-with-systemic-sclerosis-and-mediate-gsdma-contribution-to-disease-risk
#11
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...
April 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
#12
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
#13
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). As a large proportion of expression quantitative trait loci (eQTLs) are context-specific, we performed RNA-Seq in peripheral blood mononuclear cells from MS patients (n = 145) to identify eQTLs in regions centered on 109 MS risk single nucleotide polymorphisms and 7 associated human leukocyte antigen variants...
March 1, 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
#14
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
#15
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
#16
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
#17
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 the 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 with 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...
February 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29227470/multiplexed-droplet-single-cell-rna-sequencing-using-natural-genetic-variation
#18
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...
January 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29193869/cd4-and-b-lymphocyte-expression-quantitative-traits-at-rheumatoid-arthritis-risk-loci-in-patients-with-untreated-early-arthritis-implications-for-causal-gene-identification
#19
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. This study sought to gain further insight into the genetic risk mechanisms of RA by conducting an expression quantitative trait locus (eQTL) analysis of confirmed genetic risk loci in CD4+ T cells and B cells from carefully phenotyped patients with early arthritis who were naive to therapeutic immunomodulation. METHODS: RNA and DNA were isolated from purified B and/or CD4+ T cells obtained from the peripheral blood of 344 patients with early arthritis...
March 2018: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29186329/aselux-an-ultra-fast-and-accurate-allelic-reads-counter
#20
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...
April 15, 2018: Bioinformatics
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