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Expression quantitative trait loci ( eQTLs )

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https://www.readbyqxmd.com/read/28088792/impact-of-nudt15-polymorphisms-on-thiopurines-induced-myelotoxicity-and-thiopurines-tolerance-dose
#1
Dandan Yin, Xuyang Xia, Junlong Zhang, Shouyue Zhang, Fei Liao, Ge Zhang, Yan Zhang, Qianqian Hou, Xue Yang, Hong Wang, Zhigui Ma, Heyao Wang, Yiping Zhu, Wei Zhang, Yuelan Wang, Bo Liu, Lanlan Wang, Heng Xu, Yang Shu
Thiopurines are widely used as anticancer and immunosuppressive agents. However, life-threatening myelotoxicity has been noticed and largely explained by genetic variations, including NUDT15 polymorphisms (e.g., rs116855232). In this study, we conduct a meta-analysis to investigate the impact of rs116855232 on thiopurines-induced myelotoxicity susceptibility (1752 patients from 7 independent cohorts), as well as on thiopurines intolerance dose (2745 patients from 13 cohorts). Variant allele of rs116855232 contributes 7...
January 11, 2017: Oncotarget
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/28068351/phenotype-and-tissue-expression-as-a-function-of-genetic-risk-in-polycystic-ovary-syndrome
#4
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
#5
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/28035029/geneattribution-trait-agnostic-identification-of-candidate-genes-associated-with-noncoding-variation
#6
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
#7
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
#8
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/28024300/genetic-variants-regulating-expression-levels-and-isoform-diversity-during-embryogenesis
#9
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/28000566/inferring-alcoholism-snps-and-regulatory-chemical-compounds-based-on-ensemble-bayesian-network
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/27980060/quantifying-deleterious-effects-of-regulatory-variants
#14
Shan Li, Roberto Vera Alvarez, Roded Sharan, David Landsman, Ivan Ovcharenko
The majority of genome-wide association study (GWAS) risk variants reside in non-coding DNA sequences. Understanding how these sequence modifications lead to transcriptional alterations and cell-to-cell variability can help unraveling genotype-phenotype relationships. Here, we describe a computational method, dubbed CAPE, which calculates the likelihood of a genetic variant deactivating enhancers by disrupting the binding of transcription factors (TFs) in a given cellular context. CAPE learns sequence signatures associated with putative enhancers originating from large-scale sequencing experiments (such as ChIP-seq or DNase-seq) and models the change in enhancer signature upon a single nucleotide substitution...
December 15, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27976820/integration-of-expression-quantitative-trait-loci-and-pleiotropy-identifies-novel-psoriasis-susceptibility-gene-ptpn1
#15
Xianyong Yin, Yuan Lin, Changbing Shen, Ling Wang, Xianbo Zuo, Xiaodong Zheng, Sen Yang, Jianjun Liu, Kirk C Wilhelmsen, Xuejun Zhang
BACKGROUND: Psoriasis is a common inflammatory skin disease, whereas schizophrenia is a psychiatric disorder with substantial comorbidity. While these two disorders manifest with seemingly unrelated phenotypes, there is some evidence suggesting that they share common genetic factors. METHODS: We implemented a Genetic analysis incorporating Pleiotropy and Annotation (GPA) method in genome-wide association summary statistics data for ~ 120,000 psoriasis and schizophrenia samples, and whole blood expression quantitative trait loci in 5,311 samples...
December 15, 2016: Journal of Gene Medicine
https://www.readbyqxmd.com/read/27974436/genetic-and-targeted-eqtl-mapping-reveals-strong-candidate-genes-modulating-the-stress-response-during-chicken-domestication
#16
Amir Fallahsharoudi, Neil de Kock, Martin Johnsson, Lejla Bektic, S J Kumari A Ubhayasekera, Jonas Bergquist, Dominic Wright, Per Jensen
The stress response has been largely modified in all domesticated animals, offering a strong tool for genetic mapping. In chickens, ancestral Red Junglefowl react stronger both in terms of physiology and behavior to a brief restraint stress than domesticated White Leghorn, demonstrating modified functions of the hypothalamic-pituitary-adrenal (HPA) axis. We mapped quantitative trait loci (QTL) underlying variations in stress induced hormone levels using 232 birds from the 12th generation of an advanced intercross between White Leghorn and Red Junglefowl, genotyped for 739 genetic markers...
December 14, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27964755/xgr-software-for-enhanced-interpretation-of-genomic-summary-data-illustrated-by-application-to-immunological-traits
#17
Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
BACKGROUND: Biological interpretation of genomic summary data such as those resulting from genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) studies is one of the major bottlenecks in medical genomics research, calling for efficient and integrative tools to resolve this problem. RESULTS: We introduce eXploring Genomic Relations (XGR), an open source tool designed for enhanced interpretation of genomic summary data enabling downstream knowledge discovery...
December 13, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27964730/prior-knowledge-guided-eqtl-mapping-for-identifying-candidate-genes
#18
Yunli Wang, Rene Richard, Youlian Pan
BACKGROUND: Expression quantitative trait loci (eQTL) mapping is often used to identify genetic loci and candidate genes correlated with traits. Although usually a group of genes affect complex traits, genes in most eQTL mapping methods are considered as independent. Recently, some eQTL mapping methods have accounted for correlated genes, used biological prior knowledge and applied these in model species such as yeast or mouse. However, biological prior knowledge might be very limited for most species...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27942838/deciphering-the-regulation-of-porcine-genes-influencing-growth-fatness-and-yield-related-traits-through-genetical-genomics
#19
Angel M Martínez-Montes, Anixa Muiños-Bühl, Almudena Fernández, Josep M Folch, Noelia Ibáñez-Escriche, Ana I Fernández
Genetical genomics approaches aim at identifying quantitative trait loci for molecular traits, also known as intermediate phenotypes, such as gene expression, that could link variation in genetic information to physiological traits. In the current study, an expression GWAS has been carried out on an experimental Iberian × Landrace backcross in order to identify the genomic regions regulating the gene expression of those genes whose expression is correlated with growth, fat deposition, and premium cut yield measures in pig...
December 10, 2016: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/27934696/high-throughput-allele-specific-expression-across-250-environmental-conditions
#20
Gregory A Moyerbrailean, Allison L Richards, Daniel Kurtz, Cynthia A Kalita, Gordon O Davis, Chris T Harvey, Adnan Alazizi, Donovan Watza, Yoram Sorokin, Nancy Hauff, Xiang Zhou, Xiaoquan Wen, Roger Pique-Regi, Francesca Luca
Gene-by-environment (GxE) interactions determine common disease risk factors and biomedically relevant complex traits. However, quantifying how the environment modulates genetic effects on human quantitative phenotypes presents unique challenges. Environmental covariates are complex and difficult to measure and control at the organismal level, as found in GWAS and epidemiological studies. An alternative approach focuses on the cellular environment using in vitro treatments as a proxy for the organismal environment...
December 2016: Genome Research
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