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https://www.readbyqxmd.com/read/28421666/genetic-interplay-between-human-longevity-and-metabolic-pathways-a-large-scale-eqtl-study
#1
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/28406900/gene-co-expression-network-connectivity-is-an-important-determinant-of-selective-constraint
#2
Niklas Mähler, Jing Wang, Barbara K Terebieniec, Pär K Ingvarsson, Nathaniel R Street, Torgeir R Hvidsten
While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure...
April 2017: PLoS 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
#3
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/28391543/increased-brain-expression-of-gpnmb-is-associated-with-genome-wide-significant-risk-for-parkinson-s-disease-on-chromosome-7p15-3
#4
Megha N Murthy, Cornelis Blauwendraat, Sebastian Guelfi, John Hardy, Patrick A Lewis, Daniah Trabzuni
Genome wide association studies (GWAS) for Parkinson's disease (PD) have previously revealed a significant association with a locus on chromosome 7p15.3, initially designated as the glycoprotein non-metastatic melanoma protein B (GPNMB) locus. In this study, the functional consequences of this association on expression were explored in depth by integrating different expression quantitative trait locus (eQTL) datasets (Braineac, CAGEseq, GTEx, and Phenotype-Genotype Integrator (PheGenI)). Top risk SNP rs199347 eQTLs demonstrated increased expressions of GPNMB, KLHL7, and NUPL2 with the major allele (AA) in brain, with most significant eQTLs in cortical regions, followed by putamen...
April 8, 2017: Neurogenetics
https://www.readbyqxmd.com/read/28388430/large-scale-profiling-reveals-the-influence-of-genetic-variation-on-gene-expression-in-human-induced-pluripotent-stem-cells
#5
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/28339471/expression-quantitative-trait-loci-for-pax8-contributes-to-the-prognosis-of-hepatocellular-carcinoma
#6
Shijie Ma, Jianshui Yang, Ci Song, Zijun Ge, Jing Zhou, Guoxin Zhang, Zhibin Hu
Paired-box family member PAX8 encodes a transcription factor that has a role in cell differentiation and cell growth and may participate in the prognosis of hepatocellular carcinoma (HCC). By bioinformatics analysis, we identified several single nucleotide polymorphisms (SNPs) within a newly identified long non-coding RNA (lncRNA) AC016683.6 as expression quantitative trait loci (eQTLs) for PAX8. Hence, we hypothesized that PAX8eQTLs in lncRNA AC016683.6 may influence the HCC prognosis. We then performed a case-only study to assess the association between the two SNPs as well as the prognosis of HCC in 331 HBV-positive HCC patients without surgical treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28301596/screening-for-interaction-effects-in-gene-expression-data
#7
Peter J Castaldi, Michael H Cho, Liming Liang, Edwin K Silverman, Craig P Hersh, Kenneth Rice, Hugues Aschard
Expression quantitative trait (eQTL) studies are a powerful tool for identifying genetic variants that affect levels of messenger RNA. Since gene expression is controlled by a complex network of gene-regulating factors, one way to identify these factors is to search for interaction effects between genetic variants and mRNA levels of transcription factors (TFs) and their respective target genes. However, identification of interaction effects in gene expression data pose a variety of methodological challenges, and it has become clear that such analyses should be conducted and interpreted with caution...
2017: PloS One
https://www.readbyqxmd.com/read/28243742/integrative-multi-omics-analysis-revealed-snp-lncrna-mrna-slm-networks-in-human-peripheral-blood-mononuclear-cells
#8
Wei Xia, Xiao-Wei Zhu, Xin-Bo Mo, Long-Fei Wu, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Xiang Lin, Ying-Hua Qiu, Lan Wang, Pei He, Fang-Fei Xie, Peng-Fei Bing, Xin Lu, Yao-Zhong Liu, Neng-Jun Yi, Fei-Yan Deng, Shu-Feng Lei
Long non-coding RNAs (lncRNAs) serve as important controller of cellular functions via regulating RNA transcription, degradation and translation. However, what are the regulation patterns of lncRNAs on downstream mRNA and how the upstream genetic variants regulate lncRNAs are largely unknown. We first performed a comprehensive expression quantitative trait locus (eQTL) analysis (MatrixeQTL package, R) using genome-wide lncRNA expression and SNP genotype data from human peripheral blood mononuclear cells (PBMCs) of 43 unrelated individuals...
April 2017: Human Genetics
https://www.readbyqxmd.com/read/28139761/genome-wide-association-study-of-polymorphisms-predisposing-to-bronchiolitis
#9
Anu Pasanen, Minna K Karjalainen, Louis Bont, Eija Piippo-Savolainen, Marja Ruotsalainen, Emma Goksör, Kuldeep Kumawat, Hennie Hodemaekers, Kirsi Nuolivirta, Tuomas Jartti, Göran Wennergren, Mikko Hallman, Mika Rämet, Matti Korppi
Bronchiolitis is a major cause of hospitalization among infants. Severe bronchiolitis is associated with later asthma, suggesting a common genetic predisposition. Genetic background of bronchiolitis is not well characterized. To identify polymorphisms associated with bronchiolitis, we conducted a genome-wide association study (GWAS) in which 5,300,000 single nucleotide polymorphisms (SNPs) were tested for association in a Finnish-Swedish population of 217 children hospitalized for bronchiolitis and 778 controls...
January 31, 2017: Scientific Reports
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
#10
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
#11
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/28062664/mapping-eqtls-with-rna-seq-reveals-novel-susceptibility-genes-non-coding-rnas-and-alternative-splicing-events-in-systemic-lupus-erythematosus
#12
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 the integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines...
March 1, 2017: Human Molecular Genetics
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
#13
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...
January 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/28033303/strong-cis-acting-expression-quantitative-trait-loci-for-the-genes-encoding-snhg5-and-pex6
#14
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
#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...
January 19, 2017: Nature
https://www.readbyqxmd.com/read/27942838/deciphering-the-regulation-of-porcine-genes-influencing-growth-fatness-and-yield-related-traits-through-genetical-genomics
#16
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/27933526/epigenetics-and-control-of-rnas
#17
Henrike Maatz, Sebastiaan van Heesch, Franziska Kreuchwig, Allison Faber, Eleonora Adami, Norbert Hubner, Matthias Heinig
Histone modifications are epigenetic marks that fundamentally impact the regulation of gene expression. Integrating histone modification information in the analysis of gene expression traits (eQTL mapping) has been shown to significantly enhance the prediction of eQTLs. In this chapter, we describe (1) how to perform quantitative trait locus (QTL) analysis using histone modification levels as traits and (2) how to integrate these data with information on RNA expression for the elucidation of the epigenetic control of transcript levels...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27918533/identification-of-context-dependent-expression-quantitative-trait-loci-in-whole-blood
#18
Daria V Zhernakova, Patrick Deelen, Martijn Vermaat, Maarten van Iterson, Michiel van Galen, Wibowo Arindrarto, Peter van 't Hof, Hailiang Mei, Freerk van Dijk, Harm-Jan Westra, Marc Jan Bonder, Jeroen van Rooij, Marijn Verkerk, P Mila Jhamai, Matthijs Moed, Szymon M Kielbasa, Jan Bot, Irene Nooren, René Pool, Jenny van Dongen, Jouke J Hottenga, Coen D A Stehouwer, Carla J H van der Kallen, Casper G Schalkwijk, Alexandra Zhernakova, Yang Li, Ettje F Tigchelaar, Niek de Klein, Marian Beekman, Joris Deelen, Diana van Heemst, Leonard H van den Berg, Albert Hofman, André G Uitterlinden, Marleen M J van Greevenbroek, Jan H Veldink, Dorret I Boomsma, Cornelia M van Duijn, Cisca Wijmenga, P Eline Slagboom, Morris A Swertz, Aaron Isaacs, Joyce B J van Meurs, Rick Jansen, Bastiaan T Heijmans, Peter A C 't Hoen, Lude Franke
Genetic risk factors often localize to noncoding regions of the genome with unknown effects on disease etiology. Expression quantitative trait loci (eQTLs) help to explain the regulatory mechanisms underlying these genetic associations. Knowledge of the context that determines the nature and strength of eQTLs may help identify cell types relevant to pathophysiology and the regulatory networks underlying disease. Here we generated peripheral blood RNA-seq data from 2,116 unrelated individuals and systematically identified context-dependent eQTLs using a hypothesis-free strategy that does not require previous knowledge of the identity of the modifiers...
January 2017: Nature Genetics
https://www.readbyqxmd.com/read/27906459/integrative-genomic-analysis-identifies-ancestry-related-expression-quantitative-trait-loci-on-dna-polymerase-%C3%AE-and-supports-the-association-of-genetic-ancestry-with-survival-disparities-in-head-and-neck-squamous-cell-carcinoma
#19
Meganathan P Ramakodi, Karthik Devarajan, Elizabeth Blackman, Denise Gibbs, Danièle Luce, Jacqueline Deloumeaux, Suzy Duflo, Jeffrey C Liu, Ranee Mehra, Rob J Kulathinal, Camille C Ragin
BACKGROUND: African Americans with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than whites. This study investigated the functional importance of ancestry-informative single-nucleotide polymorphisms (SNPs) in HNSCC and also examined the effect of functionally important genetic elements on racial disparities in HNSCC survival. METHODS: Ancestry-informative SNPs, RNA sequencing, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes...
March 1, 2017: Cancer
https://www.readbyqxmd.com/read/27902686/genomic-characterization-of-metformin-hepatic-response
#20
Marcelo R Luizon, Walter L Eckalbar, Yao Wang, Stacy L Jones, Robin P Smith, Megan Laurance, Lawrence Lin, Paul J Gallins, Amy S Etheridge, Fred Wright, Yihui Zhou, Cliona Molony, Federico Innocenti, Sook Wah Yee, Kathleen M Giacomini, Nadav Ahituv
Metformin is used as a first-line therapy for type 2 diabetes (T2D) and prescribed for numerous other diseases. However, its mechanism of action in the liver has yet to be characterized in a systematic manner. To comprehensively identify genes and regulatory elements associated with metformin treatment, we carried out RNA-seq and ChIP-seq (H3K27ac, H3K27me3) on primary human hepatocytes from the same donor treated with vehicle control, metformin or metformin and compound C, an AMP-activated protein kinase (AMPK) inhibitor (allowing to identify AMPK-independent pathways)...
November 2016: PLoS Genetics
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