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Expression quantitative trait loci

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https://www.readbyqxmd.com/read/28079285/a-pathway-based-association-study-reveals-variants-from-wnt-signaling-genes-contributing-to-asthma-susceptibility
#1
A Barreto-Luis, A Corrales, M Acosta-Herrera, C Gonzalez-Colino, J Cumplido, J Martinez-Tadeo, A Carracedo, J Villar, T Carrillo, M Pino-Yanes, C Flores
BACKGROUND: Genetic susceptibility to asthma is currently linked to a handful of genes which have a limited ability to predict the overall disease risk, suggesting the existence of many other genes involved in disease development. Accumulated evidence from association studies in genes related by biological pathways could reveal novel asthma genes. OBJECTIVE: To reveal novel asthma susceptibility genes by means of a pathway-based association study. METHODS: Based on summary data from a previous a genome-wide association study (GWAS) of asthma, we first identified significant biological pathways using a gene-set enrichment analysis...
January 12, 2017: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28075479/different-contributions-of-local-and-distant-regulatory-changes-to-transcriptome-divergence-between-stickleback-ecotypes
#2
Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano
Differential gene expression can play an important role in phenotypic evolution and divergent adaptation. Although differential gene expression can be caused by both local- and distant-regulatory changes, we know little about their relative contribution to transcriptome evolution in natural populations. Here, we conducted expression quantitative trait loci (eQTL) analysis to investigate the genetic architecture underlying transcriptome divergence between marine and stream ecotypes of threespine sticklebacks (Gasterosteus aculeatus)...
January 11, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28072738/expression-quantitative-trait-loci-for-pi3k-akt-pathway
#3
Dongchan Ryu, Chaeyoung Lee
A genome-wide association study (GWAS) was conducted to identify expression quantitative trait loci (eQTLs) for the genes involved in phosphatidylinositol-3-kinase/v-akt murine thymoma viral oncogene homolog (PI3K/AKT) pathway.Data on mRNA expression of 341 genes in lymphoblastoid cell lines of 373 Europeans recruited by the 1000 Genomes Project using Illumina HiSeq2000 were utilized. We used their genotypes at 5,941,815 nucleotide variants obtained by Genome Analyzer II and SOLiD.The association analysis revealed 4166 nucleotide variants associated with expression of 85 genes (P < 5 × 10)...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28068921/co-localization-of-major-quantitative-trait-loci-for-pod-size-and-weight-to-a-3-7%C3%A2-cm-interval-on-chromosome-a05-in-cultivated-peanut-arachis-hypogaea-l
#4
Huaiyong Luo, Xiaoping Ren, Zhendong Li, Zhijun Xu, Xinping Li, Li Huang, Xiaojing Zhou, Yuning Chen, Weigang Chen, Yong Lei, Boshou Liao, Manish K Pandey, Rajeev K Varshney, Baozhu Guo, Xiangguo Jiang, Fei Liu, Huifang Jiang
BACKGROUND: Cultivated peanut (Arachis hypogaea L.), an important source of edible oil and protein, is widely grown in tropical and subtropical areas of the world. Genetic improvement of yield-related traits is essential for improving yield potential of new peanut varieties. Genomics-assisted breeding (GAB) can accelerate the process of genetic improvement but requires linked markers for the traits of interest. In this context, we developed a recombinant inbred line (RIL) mapping population (Yuanza 9102 × Xuzhou 68-4) with 195 individuals and used to map quantitative trait loci (QTLs) associated with three important pod features, namely pod length, pod width and hundred-pod weight...
January 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068351/phenotype-and-tissue-expression-as-a-function-of-genetic-risk-in-polycystic-ovary-syndrome
#5
Cindy T Pau, Tim Mosbruger, Richa Saxena, Corrine K Welt
Genome-wide association studies and replication analyses have identified (n = 5) or replicated (n = 10) DNA variants associated with risk for polycystic ovary syndrome (PCOS) in European women. However, the causal gene and underlying mechanism for PCOS risk at these loci have not been determined. We hypothesized that analysis of phenotype, gene expression and metformin response as a function of genotype would identify candidate genes and pathways that could provide insight into the underlying mechanism for risk at these loci...
2017: PloS One
https://www.readbyqxmd.com/read/28065468/the-genetic-architecture-of-gene-expression-in-peripheral-blood
#6
Luke R Lloyd-Jones, Alexander Holloway, Allan McRae, Jian Yang, Kerrin Small, Biao Zeng, Andrew Bakshi, Andres Metspalu, Manolis Dermitzakis, Greg Gibson, Tim Spector, Grant Montgomery, Tonu Esko, Peter M Visscher, Joseph E Powell
We analyzed the mRNA levels for 36,778 transcript expression traits (probes) from 2,765 individuals to comprehensively investigate the genetic architecture and degree of missing heritability for gene expression in peripheral blood. We identified 11,204 cis and 3,791 trans independent expression quantitative trait loci (eQTL) by using linear mixed models to perform genome-wide association analyses. Furthermore, using information on both closely and distantly related individuals, heritability was estimated for all expression traits...
December 24, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28055133/drought-coping-strategies-in-cotton-increased-crop-per-drop
#7
REVIEW
Abid Ullah, Heng Sun, Xiyan Yang, Xianlong Zhang
The growth and yield of many crops, including cotton, are affected by water deficit. Cotton has evolved drought-specific as well as general morpho-physiological, biochemical and molecular responses to drought stress, which are discussed in this review. The key physiological responses against drought stress in cotton, including stomata closing, root development, cellular adaptations, photosynthesis, abscisic acid (ABA) and jasmonic acid (JA) production, and reactive oxygen species (ROS) scavenging, have been identified by researchers...
January 5, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28052024/single-nucleotide-polymorphisms-in-znrd1-as1-increase-cancer-risk-in-an-asian-population
#8
Ping-Yu Wang, Jing-Hua Li, Yue-Mei Liu, Qing Lv, Ning Xie, Han-Han Zhang, Shu-Yang Xie
Single nucleotide polymorphisms (SNPs) in human zinc ribbon domain containing 1 antisense RNA 1 (ZNRD1-AS1) have been associated with cancer development. In this meta-analysis, we more precisely estimated the associations between three expression quantitative trait loci SNPs in ZNRD1-AS1 (rs3757328, rs6940552, and rs9261204) and cancer susceptibility. The data for three SNPs were extracted from eligible studies, which included 5,293 patients and 5,440 controls. Overall, no significant associations between SNPs in ZNRD1-AS1 (rs3757328, rs6940552, and rs9261204) and cancer risk were observed...
December 28, 2016: Oncotarget
https://www.readbyqxmd.com/read/28039429/limited-potential-of-genetic-predisposition-scores-to-predict-muscle-mass-and-strength-performance-in-flemish-caucasians-between-19-73-years-of-age
#9
Ruben Charlier, Maarten Caspers, Sara Knaeps, Evelien Mertens, Diether Lambrechts, Johan Lefevre, Martine Thomis
Since both muscle mass and strength performance are polygenic in nature, the current study compared four Genetic Predisposition Scores (GPS) in their ability to predict these phenotypes. Data were gathered within the framework of the first generation Flemish Policy Research Centre 'Sport, Physical Activity and Health' (2002-2004). Results are based on muscle characteristics data of 565 Flemish Caucasians (19-73 yr, 365 men). Skeletal muscle mass (SMM) was determined using bioelectrical impedance. The Biodex dynamometer was used to measure isometric (PTstatic120°) and isokinetic strength (PTdynamic60° and PTdynamic240°), ballistic movement speed (S20%) and muscular endurance (Work) of the knee extensors...
December 30, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/28035029/geneattribution-trait-agnostic-identification-of-candidate-genes-associated-with-noncoding-variation
#10
Arthur Wuster, Diana Chang, Timothy W Behrens, Tushar R Bhangale
MOTIVATION: We have developed geneAttribution, an R package that assigns candidate causal gene(s) to a risk variant identified by a genetic association study such as a GWAS. The method combines user-supplied functional annotation such as expression quantitative trait loci (eQTL) or Hi-C genome conformation data and reports the most likely candidate genes. In the absence of annotation data, geneAttribution relies on the distances between the genes and the input variant. AVAILABILITY AND IMPLEMENTATION: The package is freely available from http://www...
December 28, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28035019/integration-of-population-level-genotype-data-with-functional-annotation-reveals-over-representation-of-long-noncoding-rnas-at-ovarian-cancer-susceptibility-loci
#11
Brett M Reid, Jennifer B Permuth, Y Ann Chen, Jamie K Teer, Alvaro N A Monteiro, Zhihua Chen, Jonathan Tyrer, Andrew Berchuck, Georgia Chenevix-Trench, Jennifer A Doherty, Ellen L Goode, Edwin S Iverson, Kate Lawrenson, Celeste L Pearce, Paul D Pharoah, Catherine M Phelan, Susan J Ramus, Mary Anne Rossing, Joellen M Schildkraut, Jin Q Cheng, Simon A Gayther, Thomas A Sellers
BACKGROUND: Genome-wide association studies (GWAS) have identified multiple loci associated with epithelial ovarian cancer (EOC) susceptibility, but further progress requires integration of epidemiology and biology to illuminate true risk loci below genome-wide significance levels (P < 5 × 10(-8)). Most risk SNPs lie within non-protein-encoding regions, and we hypothesize that long noncoding RNA (lncRNA) genes are enriched at EOC risk regions and represent biologically relevant functional targets...
December 29, 2016: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28033303/strong-cis-acting-expression-quantitative-trait-loci-for-the-genes-encoding-snhg5-and-pex6
#12
Jihyeon Lee, Jihye Ryu, Chaeyoung Lee
Expression of quantitative trait loci (eQTLs) for the genes located in human chromosome 6 were examined. Data on RNA expression in lymphoblastoid cells of 373 unrelated Europeans were used to identify eQTLs.Genome-wide analysis resulted in 24,447 nucleotide variants associated with gene expression (P < 2.16 × 10). We found 36variants with P < 10, which were all associated with expression levels of the genes encoding small nucleolar RNA host gene 5 (SNHG5) and peroxisomal biogenesis factor 6 (PEX6)...
December 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28031287/genome-wide-quantitative-trait-loci-mapping-of-the-human-cerebrospinal-fluid-proteome
#13
Daimei Sasayama, Kotaro Hattori, Shintaro Ogawa, Yuuki Yokota, Ryo Matsumura, Toshiya Teraishi, Hiroaki Hori, Miho Ota, Sumiko Yoshida, Hiroshi Kunugi
Cerebrospinal fluid (CSF) is virtually the only one accessible source of proteins derived from the central nervous system (CNS) of living humans and possibly reflects the pathophysiology of a variety of neuropsychiatric diseases. However, little is known regarding the genetic basis of variation in protein levels of human CSF. We examined CSF levels of 1,126 proteins in 133 subjects and performed a genome-wide association analysis of 514,227 single nucleotide polymorphisms (SNPs) to detect protein quantitative trait loci (pQTLs)...
December 27, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/28025877/new-insights-into-the-understanding-of-mhc-associations-with-immune-mediated-disorders
#14
REVIEW
S Caillat-Zucman
Recent advances in technologies such as high density array-based genotyping, DNA and RNA deep sequencing, expression quantitative-trait loci mapping, epigenome analyses, and new computational strategies, have introduced drastic shifts into our understanding of major histocompatibility complex (MHC) association with immune-mediated diseases. Here, we review the most exciting findings in this field. We show how the fine characterization of structural features and expression levels of MHC alleles, posttranslational or environmental modifications of HLA-bound peptides, and epistatic interactions with non-HLA genes, has made it possible not only to provide mechanistic explanations for MHC associations with immune-mediated diseases but also to help choose relevant therapeutic targets...
January 2017: HLA
https://www.readbyqxmd.com/read/28024300/genetic-variants-regulating-expression-levels-and-isoform-diversity-during-embryogenesis
#15
Enrico Cannavò, Nils Koelling, Dermot Harnett, David Garfield, Francesco P Casale, Lucia Ciglar, Hilary E Gustafson, Rebecca R Viales, Raquel Marco-Ferreres, Jacob F Degner, Bingqing Zhao, Oliver Stegle, Ewan Birney, Eileen E M Furlong
Embryonic development is driven by tightly regulated patterns of gene expression, despite extensive genetic variation among individuals. Studies of expression quantitative trait loci (eQTL) indicate that genetic variation frequently alters gene expression in cell-culture models and differentiated tissues. However, the extent and types of genetic variation impacting embryonic gene expression, and their interactions with developmental programs, remain largely unknown. Here we assessed the effect of genetic variation on transcriptional (expression levels) and post-transcriptional (3' RNA processing) regulation across multiple stages of metazoan development, using 80 inbred Drosophila wild isolates, identifying thousands of developmental-stage-specific and shared QTL...
December 26, 2016: Nature
https://www.readbyqxmd.com/read/28017796/analysis-of-transcriptional-variability-in-a-large-human-ipsc-library-reveals-genetic-and-non-genetic-determinants-of-heterogeneity
#16
Ivan Carcamo-Orive, Gabriel E Hoffman, Paige Cundiff, Noam D Beckmann, Sunita L D'Souza, Joshua W Knowles, Achchhe Patel, Dimitri Papatsenko, Fahim Abbasi, Gerald M Reaven, Sean Whalen, Philip Lee, Mohammad Shahbazi, Marc Y R Henrion, Kuixi Zhu, Sven Wang, Panos Roussos, Eric E Schadt, Gaurav Pandey, Rui Chang, Thomas Quertermous, Ihor Lemischka
Variability in induced pluripotent stem cell (iPSC) lines remains a concern for disease modeling and regenerative medicine. We have used RNA-sequencing analysis and linear mixed models to examine the sources of gene expression variability in 317 human iPSC lines from 101 individuals. We found that ∼50% of genome-wide expression variability is explained by variation across individuals and identified a set of expression quantitative trait loci that contribute to this variation. These analyses coupled with allele-specific expression show that iPSCs retain a donor-specific gene expression pattern...
December 2, 2016: Cell Stem Cell
https://www.readbyqxmd.com/read/28000566/inferring-alcoholism-snps-and-regulatory-chemical-compounds-based-on-ensemble-bayesian-network
#17
Huan Chen, Jiatong Sun, Hong Jiang, Xianyue Wang, Lingxiang Wu, Wei Wu, Qh Wang
The disturbance of consciousness is one of the most common symptoms of those have alcoholism and may cause disability and mortality. Previous studies indicated that several single nucleotide polymorphisms (SNP) increase the susceptibility of alcoholism. In this study, we utilized the Ensemble Bayesian Network (EBN) method to identify causal SNPs of alcoholism based on the verified GAW14 data. Thirteen out of eighteen SNPs directly connected with alcoholism were found concordance with potential risk regions of alcoholism in OMIM database...
December 20, 2016: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/27998931/human-population-specific-gene-expression-and-transcriptional-network-modification-with-polymorphic-transposable-elements
#18
Lu Wang, Lavanya Rishishwar, Leonardo Mariño-Ramírez, I King Jordan
Transposable element (TE) derived sequences are known to contribute to the regulation of the human genome. The majority of known TE-derived regulatory sequences correspond to relatively ancient insertions, which are fixed across human populations. The extent to which human genetic variation caused by recent TE activity leads to regulatory polymorphisms among populations has yet to be thoroughly explored. In this study, we searched for associations between polymorphic TE (polyTE) loci and human gene expression levels using an expression quantitative trait loci (eQTL) approach...
December 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27995664/araqtl-workbench-and-archive-for-systems-genetics-in-arabidopsis-thaliana
#19
Harm Nijveen, Wilco Ligterink, Joost J B Keurentjes, Olivier Loudet, Jiao Long, Mark G Sterken, Pjotr Prins, Henk W Hilhorst, Dick de Ridder, Jan E Kammenga, Basten L Snoek
Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations enabled the investigation of the genetic architecture of gene expression variation. This has the potential to enrich the understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data...
December 20, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27992444/evidence-of-recent-intricate-adaptation-in-human-populations
#20
Leeyoung Park
Recent human adaptations have shaped population differentiation in genomic regions containing putative functional variants, mostly located in predicted regulatory elements. However, their actual functionalities and the underlying mechanism of recent adaptation remain poorly understood. In the current study, regions of genes and repeats were investigated for functionality depending on the degree of population differentiation, FST or ΔDAF (a difference in derived allele frequency). The high FST in the 5´ or 3´ untranslated regions (UTRs), in particular, confirmed that population differences arose mainly from differences in regulation...
2016: PloS One
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