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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/28077804/the-complex-genetics-of-gait-speed-genome-wide-meta-analysis-approach
#2
Dan Ben-Avraham, David Karasik, Joe Verghese, Kathryn L Lunetta, Jennifer A Smith, John D Eicher, Rotem Vered, Joris Deelen, Alice M Arnold, Aron S Buchman, Toshiko Tanaka, Jessica D Faul, Maria Nethander, Myriam Fornage, Hieab H Adams, Amy M Matteini, Michele L Callisaya, Albert V Smith, Lei Yu, Philip L De Jager, Denis A Evans, Vilmundur Gudnason, Albert Hofman, Alison Pattie, Janie Corley, Lenore J Launer, Davis S Knopman, Neeta Parimi, Stephen T Turner, Stefania Bandinelli, Marian Beekman, Danielle Gutman, Lital Sharvit, Simon P Mooijaart, David C Liewald, Jeanine J Houwing-Duistermaat, Claes Ohlsson, Matthijs Moed, Vincent J Verlinden, Dan Mellström, Jos N van der Geest, Magnus Karlsson, Dena Hernandez, Rebekah McWhirter, Yongmei Liu, Russell Thomson, Gregory J Tranah, Andre G Uitterlinden, David R Weir, Wei Zhao, John M Starr, Andrew D Johnson, M Arfan Ikram, David A Bennett, Steven R Cummings, Ian J Deary, Tamara B Harris, Sharon L R Kardia, Thomas H Mosley, Velandai K Srikanth, Beverly G Windham, Ann B Newman, Jeremy D Walston, Gail Davies, Daniel S Evans, Eline P Slagboom, Luigi Ferrucci, Douglas P Kiel, Joanne M Murabito, Gil Atzmon
Emerging evidence suggests that the basis for variation in late-life mobility is attributable, in part, to genetic factors, which may become increasingly important with age. Our objective was to systematically assess the contribution of genetic variation to gait speed in older individuals. We conducted a meta-analysis of gait speed GWASs in 31,478 older adults from 17 cohorts of the CHARGE consortium, and validated our results in 2,588 older adults from 4 independent studies. We followed our initial discoveries with network and eQTL analysis of candidate signals in tissues...
January 10, 2017: Aging
https://www.readbyqxmd.com/read/28075479/different-contributions-of-local-and-distant-regulatory-changes-to-transcriptome-divergence-between-stickleback-ecotypes
#3
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
#4
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/28069798/integrative-comparison-of-mrna-expression-patterns-in-breast-cancers-from-caucasian-and-asian-americans-with-implications-for-precision-medicine
#5
Yanxia Shi, Albert Steppi, Ye Cao, Jianan Wang, Max M He, Liren Li, Jinfeng Zhang
Asian Americans (AS) have significantly lower incidence and mortality rates of breast cancer than Caucasian Americans (CA). Although this racial disparity has been documented, the underlying pathogenetic factors explaining it are obscure. We addressed this issue by an integrative genomics approach to compare mRNA expression between AS and CA cases of breast cancer. RNA-seq data from the Cancer Genome Atlas showed that mRNA expression revealed significant differences at gene and pathway levels. Increased susceptibility and severity in CA patients were likely the result of synergistic environmental and genetic risk factors, with arachidonic acid metabolism and PPAR signaling pathways implicated in linking environmental and genetic factors...
January 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28068351/phenotype-and-tissue-expression-as-a-function-of-genetic-risk-in-polycystic-ovary-syndrome
#6
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
#7
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/28062664/mapping-eqtls-with-rna-seq-reveals-novel-susceptibility-genes-non-coding-rnas-and-alternative-splicing-events-in-systemic-lupus-erythematosus
#8
Christopher A Odhams, Andrea Cortini, Lingyan Chen, Amy L Roberts, Ana Viñuela, Alfonso Buil, Kerrin S Small, Emmanouil T Dermitzakis, David L Morris, Timothy J Vyse, Deborah S Cunninghame Graham
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines...
January 5, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28059456/comprehensive-computational-analysis-of-gwas-loci-identifies-ccr2-as-a-candidate-gene-for-celiac-disease-pathogenesis
#9
Babajan Banaganapalli, Omran Rashidi, Omar Saadah, Jun Wang, Imran Ali Khan Muhammed, Jumana Y Al-Aama, Noor Ahmad Shaik, Ramu Elango
Celiac disease (CD) is a gluten intolerance disorder with known genetic contribution. The recent fine mapping andgenome-wide association studies (GWAS) have identified up to 57 non-HLA CD susceptibility SNPs, majority of which are non-coding variants lacking any functional annotation. Therefore, we adopted multidimensional computational approach for uncovering the plausible mechanisms through which these GWAS SNPs are connected to CD pathogenesis. At initial phase, we identified that 25 (43.85%) out of 57 CD-SNPs lies in evolutionarily constrained genetic element regions...
January 6, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28054563/joint-qtl-mapping-and-gene-expression-analysis-identify-positional-candidate-genes-influencing-pork-quality-traits
#10
Rayner González-Prendes, Raquel Quintanilla, Angela Cánovas, Arianna Manunza, Tainã Figueiredo Cardoso, Jordi Jordana, José Luis Noguera, Ramona N Pena, Marcel Amills
Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level...
January 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28040410/a-genome-wide-association-study-of-fast-beta-eeg-in-families-of-european-ancestry
#11
Jacquelyn L Meyers, Jian Zhang, Niklas Manz, Madhavi Rangaswamy, Chella Kamarajan, Leah Wetherill, David B Chorlian, Sun J Kang, Lance Bauer, Victor Hesselbrock, John Kramer, Samuel Kuperman, John I Nurnberger, Jay Tischfield, Jen Chyong Wang, Howard J Edenberg, Alison Goate, Tatiana Foroud, Bernice Porjesz
BACKGROUND: Differences in fast beta (20-28 Hz) electroencephalogram (EEG) oscillatory activity distinguish some individuals with psychiatric and substance use disorders, suggesting that it may be a useful endophenotype for studying the genetics of disorders characterized by neural hyper-excitability. Despite the high heritability estimates provided by twin and family studies, there have been relatively few genetic studies of beta EEG, and to date only one genetic association finding has replicated (i...
December 28, 2016: International Journal of Psychophysiology
https://www.readbyqxmd.com/read/28039263/variants-in-wfs1-and-other-mendelian-deafness-genes-are-associated-with-cisplatin-associated-ototoxicity
#12
Heather E Wheeler, Eric R Gamazon, Robert Frisina, Carlos Perez-Cervantes, Omar El Charif, Brandon Mapes, Sophie D Fossa, Darren Feldman, Robert Hamilton, David J Vaughn, Clair Beard, Chunkit Fung, Christian Kollmannsberger, Jeri Kim, Taisei Mushiroda, Michiaki Kubo, Shirin Ardeshir-Rouhani-Fard, Lawrence H Einhorn, Nancy Cox, M Eileen Dolan, Lois Travis
PURPOSE: Cisplatin is one of the most commonly used chemotherapy drugs worldwide and one of the most ototoxic. We sought to identify genetic variants that modulate cisplatin-associated ototoxicity (CAO). EXPERIMENTAL DESIGN: We performed a genome-wide association study (GWAS) of CAO using quantitative audiometry (4-12 kHz) in 511 testicular cancer survivors of European genetic ancestry. We performed polygenic modeling and functional analyses using a variety of publicly available databases...
December 30, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28035029/geneattribution-trait-agnostic-identification-of-candidate-genes-associated-with-noncoding-variation
#13
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
#14
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
#15
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
#16
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...
January 19, 2017: Nature
https://www.readbyqxmd.com/read/28008225/identifying-cell-type-specific-transcription-factors-by-integrating-chip-seq-and-eqtl-data-application-to-monocyte-gene-regulation
#17
Mudra Choudhury, Stephen A Ramsey
We describe a novel computational approach to identify transcription factors (TFs) that are candidate regulators in a human cell type of interest. Our approach involves integrating cell type-specific expression quantitative trait locus (eQTL) data and TF data from chromatin immunoprecipitation-to-tag-sequencing (ChIP-seq) experiments in cell lines. To test the method, we used eQTL data from human monocytes in order to screen for TFs. Using a list of known monocyte-regulating TFs, we tested the hypothesis that the binding sites of cell type-specific TF regulators would be concentrated in the vicinity of monocyte eQTLs...
2016: Gene Regulation and Systems Biology
https://www.readbyqxmd.com/read/28000754/genetically-regulated-hepatic-transcripts-and-pathways-orchestrate-haematological-biochemical-and-body-composition-traits
#18
Siriluck Ponsuksili, Nares Trakooljul, Frieder Hadlich, Fiete Haack, Eduard Murani, Klaus Wimmers
The liver is the central metabolic organ and exhibits fundamental functions in haematological traits. Hepatic expression, haematological, plasma biochemical, and body composition traits were assessed in a porcine model (n = 297) to establish tissue-specific genetic variations that influence the function of immune-metabolism-correlated expression networks. At FDR (false discovery rate) <1%, more than 3,600 transcripts were jointly correlated (r = |0.22-0.48|) with the traits. Functional enrichment analysis demonstrated common links of metabolic and immune traits...
December 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28000566/inferring-alcoholism-snps-and-regulatory-chemical-compounds-based-on-ensemble-bayesian-network
#19
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
#20
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
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