Read by QxMD icon Read

rna eqtl

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
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
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)
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
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 effects of SNPs within a ~410-kb region encompassing CD36 and its proximal and distal promoters on chylomicron remnants (CM) and LDL particles at fasting, 3.5 and 6 hours following a high-fat meal (GOLDN study, n=1117). Five promoter variants associated with CM, four with delayed triglyceride clearance and five with LDL particle number...
October 11, 2016: Journal of Lipid Research
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
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
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
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...
2016: BMC Genomics
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
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
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
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
Clarissa C Parker, Shyam Gopalakrishnan, Peter Carbonetto, Natalia M Gonzales, Emily Leung, Yeonhee J Park, Emmanuel Aryee, Joe Davis, David A Blizard, Cheryl L Ackert-Bicknell, Arimantas Lionikas, Jonathan K Pritchard, Abraham A Palmer
Although mice are the most widely used mammalian model organism, genetic studies have suffered from limited mapping resolution due to extensive linkage disequilibrium (LD) that is characteristic of crosses among inbred strains. Carworth Farms White (CFW) mice are a commercially available outbred mouse population that exhibit rapid LD decay in comparison to other available mouse populations. We performed a genome-wide association study (GWAS) of behavioral, physiological and gene expression phenotypes using 1,200 male CFW mice...
August 2016: Nature Genetics
Zhiyuan Chen, Darren E Hagen, Juanbin Wang, Christine G Elsik, Tieming Ji, Luiz G Siqueira, Peter J Hansen, Rocío M Rivera
Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ∼105 Bos taurus indicus × Bos taurus taurus F1 conceptuses using RNA sequencing. To accomplish this, we developed a bioinformatics pipeline to identify parent-specific single nucleotide polymorphism alleles after filtering adenosine to inosine (A-to-I) RNA editing sites...
July 2, 2016: Epigenetics: Official Journal of the DNA Methylation Society
Yanjun Zan, Xia Shen, Simon K G Forsberg, Örjan Carlborg
An increased knowledge of the genetic regulation of expression in Arabidopsis thaliana is likely to provide important insights about the basis of the plant's extensive phenotypic variation. Here, we reanalyzed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of natural A. thaliana accessions. Transcripts from more than half of all genes were detected in the leaves of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions, but no transcripts at all in others, and this pattern was correlated with the genome-wide genotype...
2016: G3: Genes—Genomes—Genetics
Jing Han, Wen Zhou, Meiqun Jia, Juan Wen, Jie Jiang, Jufang Shi, Kai Zhang, Hongxia Ma, Jibin Liu, Jiansong Ren, Min Dai, Zhibin Hu, Dong Hang, Ni Li, Hongbing Shen
Paired box 8 (PAX8) is a crucial nephric-lineage transcription factor, and its aberrant expression has been detected in various types of cancer including Müllerian carcinomas. PAX8 antisense RNA 1 (PAX8-AS1), a potential regulator of PAX8, contains specific single nucleotide polymorphisms (SNPs) that may represent expression quantitative trait loci (eQTLs) for PAX8. In this study, we hypothesized that these eQTLs SNPs in PAX8-AS1 may influence the risk of cervical cancer. A case-control study of 1486 cervical cancer patients and 1536 cancer-free controls was conducted to identify the associations between two eQTLs SNPs (rs4848320 and rs1110839) and cervical cancer...
August 2016: Molecular Genetics and Genomics: MGG
Fuencisla Matesanz, María Fedetz, Cristina Barrionuevo, Mohamad Karaky, Antonio Catalá-Rabasa, Victor Potenciano, Raquel Bello-Morales, Jose-Antonio López-Guerrero, Antonio Alcina
Genome-wide association studies (GWAS) in migraine are providing the molecular basis of this heterogeneous disease, but the understanding of its aetiology is still incomplete. Although some biomarkers have currently been accepted for migraine, large amount of studies for identifying new ones is needed. The migraine-associated variant rs12355831:A>G (P=2 × 10(-6)), described in a GWAS of the International Headache Genetic Consortium, is localized in a non-coding sequence with unknown function. We sought to identify the causal variant and the genetic mechanism involved in the migraine risk...
May 18, 2016: European Journal of Human Genetics: EJHG
Ben M Brumpton, Manuel A R Ferreira
Very few studies have investigated the associations between genetic polymorphisms and gene expression on the X-chromosome. This is a major bottleneck when conducting functional follow-up studies of trait-associated variants, as those identified in genome-wide association studies (GWAS). We used a multivariate approach to test the association between individual single nucleotide polymorphisms (SNPs) and exon expression levels measured in 356 Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs) from the Geuvadis RNA sequencing project to identify SNPs associated with variation in gene expression on the X-chromosome, which we refer to as eSNPs...
July 2016: Human Genetics
Mathew D Littlejohn, Kathryn Tiplady, Tania A Fink, Klaus Lehnert, Thomas Lopdell, Thomas Johnson, Christine Couldrey, Mike Keehan, Richard G Sherlock, Chad Harland, Andrew Scott, Russell G Snell, Stephen R Davis, Richard J Spelman
The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. The fat content of milk varies widely both between and within species, and recent independent genome-wide association studies have highlighted a milk fat percentage quantitative trait locus (QTL) of large effect on bovine chromosome 5. Although both EPS8 and MGST1 have been proposed to underlie these signals, the causative status of these genes has not been functionally confirmed. To investigate this QTL in detail, we report genome sequence-based imputation and association mapping in a population of 64,244 taurine cattle...
2016: Scientific Reports
Lukas M Simon, Edward S Chen, Leonard C Edelstein, Xianguo Kong, Seema Bhatlekar, Isidore Rigoutsos, Paul F Bray, Chad A Shaw
Platelets play a central role in ischemic cardiovascular events. Cardiovascular disease (CVD) is a major cause of death worldwide. Numerous genome-wide association studies (GWASs) have identified loci associated with CVD risk. However, our understanding of how these variants contribute to disease is limited. Using data from the platelet RNA and expression 1 (PRAX1) study, we analyzed cis expression quantitative trait loci (eQTLs) in platelets from 154 normal human subjects. We confirmed these results in silico by performing allele-specific expression (ASE) analysis, which demonstrated that the allelic directionality of eQTLs and ASE patterns correlate significantly...
May 5, 2016: American Journal of Human Genetics
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"