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Expression quantitative trait loci

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https://www.readbyqxmd.com/read/28442482/a-bag3-coding-variant-in-mice-determines-susceptibility-to-ischemic-limb-muscle-myopathy-by-directing-autophagy
#1
Joseph M McClung, Timothy J McCord, Terence E Ryan, Cameron A Schmidt, Thomas D Green, Kevin W Southerland, Jessica L Reinardy, Sarah B Mueller, Talaignair N Venkatraman, Christopher D Lascola, Sehoon Keum, Douglas A Marchuk, Espen E Spangenburg, Ayotunde O Dokun, Brian H Annex, Christopher D Kontos
Background -Critical limb ischemia (CLI) is a manifestation of peripheral artery disease (PAD) that carries significant mortality and morbidity risk in humans, although its genetic determinants remain largely unknown. We previously discovered two overlapping quantitative trait loci (QTL) in mice, Lsq-1 and Civq-1, that affected limb muscle survival and stroke volume following femoral artery or middle cerebral artery ligation, respectively. Here we report that a Bag3 variant (Ile81Met) segregates with tissue protection from hindlimb ischemia (HLI)...
April 25, 2017: Circulation
https://www.readbyqxmd.com/read/28442423/slc6a1-gene-involvement-in-susceptibility-to-attention-deficit-hyperactivity-disorder-a-case-control-study-and-gene-environment-interaction
#2
Fang-Fen Yuan, Xue Gu, Xin Huang, Yan Zhong, Jing Wu
Attention-deficit/hyperactivity disorder (ADHD) is an early onset childhood neurodevelopmental disorder with an estimated heritability of approximately 76%. We conducted a case-control study to explore the role of the SLC6A1 gene in ADHD. The genotypes of eight variants were determined using Sequenom MassARRAY technology. The participants in the study were 302 children with ADHD and 411 controls. ADHD symptoms were assessed using the Conners Parent Symptom Questionnaire. In our study, rs2944366 was consistently shown to be associated with the ADHD risk in the dominant model (odds ratio [OR]=0...
April 22, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28441029/variable-susceptibility-to-cigarette-smoke-induced-emphysema-in-34-inbred-strains-of-mice-implicates-abi3bp-in-emphysema-susceptibility
#3
Josiah E Radder, Alyssa D Gregory, Adriana S Leme, Michael H Cho, Yanxia Chu, Neil J Kelly, Per Bakke, Amund Gulsvik, Augusto A Litonjua, David Sparrow, Terri H Beaty, James D Crapo, Edwin K Silverman, Yingze Zhang, Annerose Berndt, Steven D Shapiro
RATIONALE: Chronic obstructive pulmonary disease (COPD) is caused by a complex interaction of environmental exposures, most commonly cigarette smoke, and genetic factors. Chronic cigarette smoke exposure in the mouse is a commonly used animal model of COPD. We aimed to expand our knowledge of the variable susceptibility of inbred strains to this model and test for genetic variants associated with this trait. OBJECTIVE: To measure differential susceptibility to cigarette smoke-induced emphysema in the mouse, identify genetic loci associated with this quantitative trait, and find homologous human genes associated with COPD...
April 25, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28429576/suppression-of-osmads7-in-rice-endosperm-stabilizes-amylose-content-under-high-temperature-stress
#4
Hua Zhang, Heng Xu, Mengjie Feng, Ying Zhu
High temperature significantly alters the amylose content of rice, resulting in mature grains with poor eating quality. However, only few genes and/or quantitative trait loci (QTLs) involved in this process have been isolated and the molecular mechanisms of this effect remain unclear. Here, we describe a floral organ identity gene, OsMADS7, involved in stabilizing rice amylose content at high temperature. OsMADS7 is greatly induced by high temperature at the early filling stage. Constitutive suppression of OsMADS7 stabilizes amylose content under high temperature stress but results in low spikelet fertility...
April 20, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28429084/rs4878104-contributes-to-alzheimer-s-disease-risk-and-regulates-dapk1-gene-expression
#5
Yang Hu, Liang Cheng, Ying Zhang, Weiyang Bai, Wenyang Zhou, Tao Wang, Zhifa Han, Jian Zong, Shuilin Jin, Jun Zhang, Qinghua Jiang, Guiyou Liu
In 2006, a candidate gene study reported death-associated protein kinase 1 (DAPK1) rs4878104 variant to be significantly associated with Alzheimer's disease (AD) risk. However, the following studies showed inconsistent association results. Here, we conducted an updated analysis to investigate the potential association between rs4878104 and AD using a total of 60,751 samples (20,161 AD cases and 40,590 controls). In the pooled population, the results based on the allele and genotype genetic models show that rs4878104 variant is not significantly associated with AD risk...
April 20, 2017: Neurological Sciences
https://www.readbyqxmd.com/read/28424372/effects-of-drought-stress-on-global-gene-expression-profile-in-leaf-and-root-samples-of-dongxiang-wild-rice-oryza-rufipogon
#6
Fantao Zhang, Yi Zhou, Meng Zhang, Xiangdong Luo, Jiankun Xie
Drought is a serious constraint to rice production throughout the world, and although Dongxiang wild rice ( Oryza rufipogon , DXWR) possesses a high degree of drought resistance, the underlying mechanisms of this trait remains unclear. In the present study, cDNA libraries were constructed from the leaf and root tissues of drought-stressed and untreated DXWR seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in drought stress response. The results indicated that 11,231 transcripts were differentially expressed in the leaves (4,040 up-regulated and 7,191 down-regulated) and 7,025 transcripts were differentially expressed in the roots (3,097 up-regulated and 3,928 down-regulated)...
April 19, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28422318/computational-analysis-of-breast-cancer-gwas-loci-identifies-the-putative-deleterious-effect-of-stxbp4-and-znf404-gene-variants
#7
Tariq Ahmad Masoodi, Babajan Banaganapalli, Venkatesh Vaidyanathan, Venkateswar Rao Talluri, Noor Ahmad Shaik
The genome-wide association studies (GWAS) have enabled us in identifying different breast cancer susceptibility loci. However, majority of these are non-coding variants with no annotated biological function. We investigated such 78 noncoding genome wide associated SNPs of breast cancer and further expanded the list to 2162 variants with strong linkage-disequilibrium (LD, r2 ≥0.8). Using multiple publically available algorithms such as CADD, GWAVA and FATHAMM, we classified all these variants in to deleterious, damaging or benign categories...
April 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28422143/dissecting-the-genetic-architecture-of-fusarium-verticillioides-seed-rot-resistance-in-maize-by-combining-qtl-mapping-and-genome-wide-association-analysis
#8
Ming Ju, Zijian Zhou, Cong Mu, Xuecai Zhang, Jingyang Gao, Yakun Liang, Jiafa Chen, Yabin Wu, Xiaopeng Li, Shiwei Wang, Jingjing Wen, Luming Yang, Jianyu Wu
Fusarium verticillioides can be transmitted via seeds and cause systemic infection in maize (Zea mays L.); its mycotoxin has harmful effects on animal and human health. We combined QTL mapping in recombinant inbred line (RIL) populations with a genome-wide association study (GWAS) of 217 diverse maize lines using 224,152 single nucleotide polymorphisms (SNPs) under controlled conditions to determine the genetic architecture of F. verticillioides seed rot (FSR) resistance. Our study identified 8 quantitative trait loci (QTLs) and 43 genes associated with 57 SNPs that were correlated with FSR resistance through linkage mapping and GWAS, respectively...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28421666/genetic-interplay-between-human-longevity-and-metabolic-pathways-a-large-scale-eqtl-study
#9
Robert Häsler, Geetha Venkatesh, Qihua Tan, Friederike Flachsbart, Anupam Sinha, Philip Rosenstiel, Wolfgang Lieb, Stefan Schreiber, Kaare Christensen, Lene Christiansen, Almut Nebel
Human longevity is a complex phenotype influenced by genetic and environmental components. Unraveling the contribution of genetic vs. nongenetic factors to longevity is a challenging task. Here, we conducted a large-scale RNA-sequencing-based expression quantitative trait loci study (eQTL) with subsequent heritability analysis. The investigation was performed on blood samples from 244 individuals from Germany and Denmark, representing various age groups including long-lived subjects up to the age of 104 years...
April 19, 2017: Aging Cell
https://www.readbyqxmd.com/read/28416812/a-new-locus-regulating-micall2-expression-was-identified-for-association-with-executive-inhibition-in-children-with-attention-deficit-hyperactivity-disorder
#10
L Yang, S Chang, Q Lu, Y Zhang, Z Wu, X Sun, Q Cao, Y Qian, T Jia, B Xu, Q Duan, Y Li, K Zhang, G Schumann, D Liu, J Wang, Y Wang, L Lu
Impaired executive inhibition is a core deficit of attention deficit hyperactivity disorder (ADHD), which is a common childhood-onset psychiatric disorder with high heritability. In this study, we performed a two-stage genome-wide association study of executive inhibition in ADHD in Han Chinese. We used the Stroop color-word interference test to evaluate executive inhibition. After quality control, 780 samples with phenotype and covariate data were included in the discovery stage, whereas 922 samples were included in the replication stage...
April 18, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28409418/polymorphisms-in-cars-are-associated-with-gastric-cancer-risk-a-two-stage-case-control-study-in-the-chinese-population
#11
Tian Tian, Ling Xiao, Jiangbo Du, Xun Zhu, Yayun Gu, Na Qin, Caiwang Yan, Li Liu, Hongxia Ma, Yue Jiang, Jiaping Chen, Hao Yu, Juncheng Dai
BACKGROUND: The cysteinyl transfer RNA synthetase gene (CARS) is located on chromosome band 11p15.5, which is an important tumor-suppressor gene region. Mutations in CARS have been identified in many kinds of cancers; however, evidence for a relationship between genetic variants in CARS and gastric cancer at the population level is still lacking. Thus, we explored the association of variants in CARS with gastric cancer using a two-stage case-control strategy in Chinese. METHODS: We undertook a two-stage case-control study to investigate the association between polymorphisms in CARS and risk of gastric cancer with use of an Illumina Infinium(®) BeadChip and an ABI 7900 system...
April 13, 2017: Gastric Cancer
https://www.readbyqxmd.com/read/28407015/parkinson-s-disease-associated-genetic-variation-is-linked-to-quantitative-expression-of-inflammatory-genes
#12
Steven Pierce, Gerhard A Coetzee
Genome-wide association studies (GWAS) have linked dozens of single nucleotide polymorphisms (SNPs) with Parkinson's disease (PD) risk. Ascertaining the functional and eventual causal mechanisms underlying these relationships has proven difficult. The majority of risk SNPs, and nearby SNPs in linkage disequilibrium (LD), are found in intergenic or intronic regions and confer risk through allele-dependent expression of multiple unknown target genes. Combining GWAS results with publicly available GTEx data, generated through eQTL (expression quantitative trait loci) identification studies, enables a direct association of SNPs to gene expression levels and aids in narrowing the large population of potential genetic targets for hypothesis-driven experimental cell biology...
2017: PloS One
https://www.readbyqxmd.com/read/28406955/predictive-long-range-allele-specific-mapping-of-regulatory-variants-and-target-transcripts
#13
Kibaick Lee, Seulkee Lee, Hyoeun Bang, Jung Kyoon Choi
Genome-wide association studies (GWASs) have identified a large number of noncoding associations, calling for systematic mapping to causal regulatory variants and their distal target genes. A widely used method, quantitative trait loci (QTL) mapping for chromatin or expression traits, suffers from sample-to-sample experimental variation and trans-acting or environmental effects. Instead, alleles at heterozygous loci can be compared within a sample, thereby controlling for those confounding factors. Here we introduce a method for chromatin structure-based allele-specific pairing of regulatory variants and target transcripts...
2017: PloS One
https://www.readbyqxmd.com/read/28400196/association-of-rnaset2-gene-polymorphisms-with-decreased-expression-and-clinical-characteristics-of-severity-in-crohn-s-disease
#14
Rivkah Gonsky, Phillip Fleshner, Richard L Deem, Eva Biener-Ramanujan, Dalin Li, Alka A Potdar, Janine Bilsborough, Shaohong Yang, Dermot P B McGovern, Stephan R Targan
BACKGROUND & AIMS: Variants in the tumor necrosis factor superfamily member 15 gene (TNFSF15, also called TL1A) have been associated with risk for inflammatory bowel diseases (IBD). TL1A affects expression of multiple cytokines to promote mucosal inflammation. Little is known about the TL1A-response pathways that regulate cytokine expression. We investigated T-cell gene expression patterns to determine the mechanisms by which TL1A regulates cytokine production, and whether these associate with outcomes of patients with Crohn's disease (CD)...
April 8, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28396530/downregulation-of-plzf-gene-ameliorates-metabolic-and-cardiac-traits-in-the-spontaneously-hypertensive-rat
#15
František Liška, Vladimír Landa, Václav Zídek, Petr Mlejnek, Jan Šilhavý, Miroslava Šimáková, Hynek Strnad, Jaroslava Trnovská, Vojtěch Škop, Ludmila Kazdová, Colby G Starker, Daniel F Voytas, Zsuzsanna Izsvák, Massimiliano Mancini, Ondřej Šeda, Vladimír Křen, Michal Pravenec
The spontaneously hypertensive rat (SHR), one of the most widely used model of essential hypertension, is predisposed to left ventricular hypertrophy, myocardial fibrosis, and metabolic disturbances. Recently, quantitative trait loci influencing blood pressure, left ventricular mass, and heart interstitial fibrosis were genetically isolated within a minimal congenic subline that contains only 7 genes, including mutant Plzf (promyelocytic leukemia zinc finger) candidate gene. To identify Plzf as a quantitative trait gene, we targeted Plzf in the SHR using the transcription activator-like effector nuclease technique and obtained SHR line harboring targeted Plzf gene with a premature stop codon...
April 10, 2017: Hypertension
https://www.readbyqxmd.com/read/28394350/population-and-individual-specific-regulatory-variation-in-sardinia
#16
Mauro Pala, Zachary Zappala, Mara Marongiu, Xin Li, Joe R Davis, Roberto Cusano, Francesca Crobu, Kimberly R Kukurba, Michael J Gloudemans, Frederic Reinier, Riccardo Berutti, Maria G Piras, Antonella Mulas, Magdalena Zoledziewska, Michele Marongiu, Elena P Sorokin, Gaelen T Hess, Kevin S Smith, Fabio Busonero, Andrea Maschio, Maristella Steri, Carlo Sidore, Serena Sanna, Edoardo Fiorillo, Michael C Bassik, Stephen J Sawcer, Alexis Battle, John Novembre, Chris Jones, Andrea Angius, Gonçalo R Abecasis, David Schlessinger, Francesco Cucca, Stephen B Montgomery
Genetic studies of complex traits have mainly identified associations with noncoding variants. To further determine the contribution of regulatory variation, we combined whole-genome and transcriptome data for 624 individuals from Sardinia to identify common and rare variants that influence gene expression and splicing. We identified 21,183 expression quantitative trait loci (eQTLs) and 6,768 splicing quantitative trait loci (sQTLs), including 619 new QTLs. We identified high-frequency QTLs and found evidence of selection near genes involved in malarial resistance and increased multiple sclerosis risk, reflecting the epidemiological history of Sardinia...
May 2017: Nature Genetics
https://www.readbyqxmd.com/read/28393889/genetic-architecture-of-gene-expression-underlying-variation-in-host-response-to-porcine-reproductive-and-respiratory-syndrome-virus-infection
#17
Arun Kommadath, Hua Bao, Igseo Choi, James M Reecy, James E Koltes, Elyn Fritz-Waters, Chris J Eisley, Jason R Grant, Robert R R Rowland, Christopher K Tuggle, Jack C M Dekkers, Joan K Lunney, Le Luo Guan, Paul Stothard, Graham S Plastow
It has been shown that inter-individual variation in host response to porcine reproductive and respiratory syndrome (PRRS) has a heritable component, yet little is known about the underlying genetic architecture of gene expression in response to PRRS virus (PRRSV) infection. Here, we integrated genome-wide genotype, gene expression, viremia level, and weight gain data to identify genetic polymorphisms that are associated with variation in inter-individual gene expression and response to PRRSV infection in pigs...
April 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28388432/large-diverse-population-cohorts-of-hipscs-and-derived-hepatocyte-like-cells-reveal-functional-genetic-variation-at-blood-lipid-associated-loci
#18
Evanthia E Pashos, YoSon Park, Xiao Wang, Avanthi Raghavan, Wenli Yang, Deepti Abbey, Derek T Peters, Juan Arbelaez, Mayda Hernandez, Nicolas Kuperwasser, Wenjun Li, Zhaorui Lian, Ying Liu, Wenjian Lv, Stacey L Lytle-Gabbin, Dawn H Marchadier, Peter Rogov, Jianting Shi, Katherine J Slovik, Ioannis M Stylianou, Li Wang, Ruilan Yan, Xiaolan Zhang, Sekar Kathiresan, Stephen A Duncan, Tarjei S Mikkelsen, Edward E Morrisey, Daniel J Rader, Christopher D Brown, Kiran Musunuru
Genome-wide association studies have struggled to identify functional genes and variants underlying complex phenotypes. We recruited a multi-ethnic cohort of healthy volunteers (n = 91) and used their tissue to generate induced pluripotent stem cells (iPSCs) and hepatocyte-like cells (HLCs) for genome-wide mapping of expression quantitative trait loci (eQTLs) and allele-specific expression (ASE). We identified many eQTL genes (eGenes) not observed in the comparably sized Genotype-Tissue Expression project's human liver cohort (n = 96)...
April 6, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28388430/large-scale-profiling-reveals-the-influence-of-genetic-variation-on-gene-expression-in-human-induced-pluripotent-stem-cells
#19
Christopher DeBoever, He Li, David Jakubosky, Paola Benaglio, Joaquin Reyna, Katrina M Olson, Hui Huang, William Biggs, Efren Sandoval, Matteo D'Antonio, Kristen Jepsen, Hiroko Matsui, Angelo Arias, Bing Ren, Naoki Nariai, Erin N Smith, Agnieszka D'Antonio-Chronowska, Emma K Farley, Kelly A Frazer
In this study, we used whole-genome sequencing and gene expression profiling of 215 human induced pluripotent stem cell (iPSC) lines from different donors to identify genetic variants associated with RNA expression for 5,746 genes. We were able to predict causal variants for these expression quantitative trait loci (eQTLs) that disrupt transcription factor binding and validated a subset of them experimentally. We also identified copy-number variant (CNV) eQTLs, including some that appear to affect gene expression by altering the copy number of intergenic regulatory regions...
April 6, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28384292/molecular-mapping-of-the-grain-iron-and-zinc-concentration-protein-content-and-thousand-kernel-weight-in-wheat-triticum-aestivum-l
#20
Gopalareddy Krishnappa, Anju Mahendru Singh, Swati Chaudhary, Arvind Kumar Ahlawat, Santosh Kumar Singh, Ram Bihari Shukla, Jai Prakash Jaiswal, Gyanendra Pratap Singh, Ishwar Singh Solanki
Genomic regions responsible for accumulation of grain iron concentration (Fe), grain zinc concentration (Zn), grain protein content (PC) and thousand kernel weight (TKW) were investigated in 286 recombinant inbred lines (RILs) derived from a cross between an old Indian wheat variety WH542 and a synthetic derivative (Triticum dicoccon PI94624/Aegilops squarrosa [409]//BCN). RILs were grown in six environments and evaluated for Fe, Zn, PC, and TKW. The population showed the continuous distribution for all the four traits, that for pooled Fe and PC was near normal, whereas, for pooled Zn, RILs exhibited positively skewed distribution...
2017: PloS One
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