keyword
MENU ▼
Read by QxMD icon Read
search

Expression quantitative trait loci ( eQTLs )

keyword
https://www.readbyqxmd.com/read/29325110/impact-of-genetic-risk-loci-for-multiple-sclerosis-on-expression-of-proximal-genes-in-patients
#1
Tojo James, Magdalena Lindén, Hiromasa Morikawa, Sunjay Jude Fernandes, Sabrina Ruhrmann, Mikael Huss, Maya Brandi, Fredrik Piehl, Maja Jagodic, Jesper Tegnér, Mohsen Khademi, Tomas Olsson, David Gomez-Cabrero, Ingrid Kockum
Despite advancements in genetic studies, it is difficult to understand and characterize the functional relevance of disease-associated genetic variants, especially in the context of a complex multifactorial disease such as Multiple Sclerosis (MS). Since a large proportion of expression quantitative trait loci (eQTLs) are context-specific, we performed RNA-Seq in peripheral blood mononuclear cells (PBMCs) from MS patients (n = 145) to identify eQTLs in regions centered on 109 MS risk SNPs and seven associated HLA variants...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29317604/beta-defensin-1-aryl-hydrocarbon-receptor-and-plasma-kynurenine-in-major-depressive-disorder-metabolomics-informed-genomics
#2
Duan Liu, Balmiki Ray, Drew R Neavin, Jiabin Zhang, Arjun P Athreya, Joanna M Biernacka, William V Bobo, Daniel K Hall-Flavin, Michelle K Skime, Hongjie Zhu, Gregory D Jenkins, Anthony Batzler, Krishna R Kalari, Felix Boakye-Agyeman, Wayne R Matson, Swati S Bhasin, Taisei Mushiroda, Yusuke Nakamura, Michiaki Kubo, Ravishankar K Iyer, Liewei Wang, Mark A Frye, Rima Kaddurah-Daouk, Richard M Weinshilboum
Major depressive disorder (MDD) is a heterogeneous disease. Efforts to identify biomarkers for sub-classifying MDD and antidepressant therapy by genome-wide association studies (GWAS) alone have generally yielded disappointing results. We applied a metabolomics-informed genomic research strategy to study the contribution of genetic variation to MDD pathophysiology by assaying 31 metabolites, including compounds from the tryptophan, tyrosine, and purine pathways, in plasma samples from 290 MDD patients. Associations of metabolite concentrations with depressive symptoms were determined, followed by GWAS for selected metabolites and functional validation studies of the genes identified...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29298996/the-phosphatidylinositide-3-kinase-pi3k-signaling-pathway-is-a-determinant-of-zileuton-response-in-adults-with-asthma
#3
Amber Dahlin, Weiliang Qiu, Augusto A Litonjua, John J Lima, Mayumi Tamari, Michiaki Kubo, Charles G Irvin, Stephen P Peters, Ann C Wu, Scott T Weiss, Kelan G Tantisira
Variable responsiveness to zileuton, a leukotriene antagonist used to treat asthma, may be due in part to genetic variation. While individual SNPs were previously associated with zileuton-related lung function changes, specific quantitative trait loci (QTLs) and biological pathways that may contribute have not been identified. In this study, we investigated the hypothesis that genetic variation within biological pathways is associated with zileuton response. We performed an integrative QTL mapping and pathway enrichment study to investigate data from a GWAS of zileuton response, in addition to mRNA expression profiles and leukotriene production data from lymphoblastoid cell lines (LCLs) (derived from asthmatics) that were treated with zileuton or ethanol (control)...
January 3, 2018: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29282317/distinctive-roles-of-age-sex-and-genetics-in-shaping-transcriptional-variation-of-human-immune-responses-to-microbial-challenges
#4
Barbara Piasecka, Darragh Duffy, Alejandra Urrutia, Hélène Quach, Etienne Patin, Céline Posseme, Jacob Bergstedt, Bruno Charbit, Vincent Rouilly, Cameron R MacPherson, Milena Hasan, Benoit Albaud, David Gentien, Jacques Fellay, Matthew L Albert, Lluis Quintana-Murci
The contribution of host genetic and nongenetic factors to immunological differences in humans remains largely undefined. Here, we generated bacterial-, fungal-, and viral-induced immune transcriptional profiles in an age- and sex-balanced cohort of 1,000 healthy individuals and searched for the determinants of immune response variation. We found that age and sex affected the transcriptional response of most immune-related genes, with age effects being more stimulus-specific relative to sex effects, which were largely shared across conditions...
December 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29275164/genome-wide-analysis-of-transcriptional-variability-in-a-large-maize-teosinte-population
#5
Xufeng Wang, Qiuyue Chen, Yaoyao Wu, Zachary H Lemmon, Guanghui Xu, Cheng Huang, Yameng Liang, Dingyi Xu, Dan Li, John F Doebley, Feng Tian
The regulation of gene expression plays an important role in controlling plant phenotypes and adaptation. Here, we report a comprehensive assessment of gene expression variation by sequencing the transcriptome of a large maize-teosinte experimental population. Genome-wide mapping identified 25,660 expression quantitative trait loci (eQTL) for 17,311 genes, capturing an unprecedented range of expression variation. We found that local-eQTL more frequently mapped to adjacent genes, displaying a mode of expression piggybacking, which consequently created co-regulated gene clusters...
December 21, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29273740/rna-sequencing-provides-insights-into-the-evolution-of-lettuce-and-the-regulation-of-flavonoid-biosynthesis
#6
Lei Zhang, Wenqing Su, Rong Tao, Weiyi Zhang, Jiongjiong Chen, Peiyao Wu, Chenghuan Yan, Yue Jia, Robert M Larkin, Dean Lavelle, Maria-Jose Truco, Sebastian Reyes Chin-Wo, Richard W Michelmore, Hanhui Kuang
Different horticultural types of lettuce exhibit tremendous morphological variation. However, the molecular basis for domestication and divergence among the different horticultural types of lettuce remains unknown. Here, we report the RNA sequencing of 240 lettuce accessions sampled from the major horticultural types and wild relatives, generating 1.1 million single-nucleotide polymorphisms (SNPs). Demographic modeling indicates that there was a single domestication event for lettuce. We identify a list of regions as putative selective sweeps that occurred during domestication and divergence, respectively...
December 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/29259604/novel-non-histocompatibility-antigen-mismatched-variants-improve-the-ability-to-predict-antibody-mediated-rejection-risk-in-kidney-transplant
#7
Silvia Pineda, Tara K Sigdel, Jieming Chen, Annette M Jackson, Marina Sirota, Minnie M Sarwal
Transplant rejection is the critical clinical end-point limiting indefinite survival after histocompatibility antigen (HLA) mismatched organ transplantation. The predominant cause of late graft loss is antibody-mediated rejection (AMR), a process whereby injury to the organ is caused by donor-specific antibodies, which bind to HLA and non-HLA (nHLA) antigens. AMR is incompletely diagnosed as donor/recipient (D/R) matching is only limited to the HLA locus and critical nHLA immunogenic antigens remain to be identified...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29248712/genetic-variant-repressing-adh1a-expression-confers-susceptibility-to-esophageal-squamous-cell-carcinoma
#8
Qionghua Cui, Linna Peng, Lixuan Wei, Jiang Chang, Wenle Tan, Yingying Luo, Xudong Huang, Yanjie Zhao, Jun Li, Jiahui Chu, Mingming Shao, Chao Zhang, Cheng Li, Wen Tan, Dongxin Lin, Chen Wu
Genome-wide association studies (GWAS) have discovered numerous genetic susceptibility loci including a cluster of alcohol dehydrogenase (ADH) gene family for esophageal squamous-cell carcinoma (ESCC). However, the underlying mechanism has not fully been elucidated. In this study, we integrated the GWAS data, gene-drinking interaction, expression quantitative trait locus (eQTL) analysis and biochemical experiments to clarify the specific mechanism of the polymorphisms in ADH loci. By imputation and eQTL analysis, we identified rs1154402C>G in intron 1 of ADH5 substantially associated with the expression levels of ADH1A...
December 14, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29237423/deciphering-the-genetic-regulation-of-peripheral-blood-transcriptome-in-pigs-through-expression-genome-wide-association-study-and-allele-specific-expression-analysis
#9
T Maroilley, G Lemonnier, J Lecardonnel, D Esquerré, Y Ramayo-Caldas, M J Mercat, C Rogel-Gaillard, J Estellé
BACKGROUND: Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity...
December 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29218904/evaluation-of-predixcan-for-prioritizing-gwas-associations-and-predicting-gene-expression
#10
Binglan Li, Shefali S Verma, Yogasudha C Veturi, Anurag Verma, Yuki Bradford, David W Haas, Marylyn D Ritchie
Genome-wide association studies (GWAS) have been successful in facilitating the understanding of genetic architecture behind human diseases, but this approach faces many challenges. To identify disease-related loci with modest to weak effect size, GWAS requires very large sample sizes, which can be computational burdensome. In addition, the interpretation of discovered associations remains difficult. PrediXcan was developed to help address these issues. With built in SNP-expression models, PrediXcan is able to predict the expression of genes that are regulated by putative expression quantitative trait loci (eQTLs), and these predicted expression levels can then be used to perform gene-based association studies...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218884/how-powerful-are-summary-based-methods-for-identifying-expression-trait-associations-under-different-genetic-architectures
#11
Yogasudha Veturi, Marylyn D Ritchie
Transcriptome-wide association studies (TWAS) have recently been employed as an approach that can draw upon the advantages of genome-wide association studies (GWAS) and gene expression studies to identify genes associated with complex traits. Unlike standard GWAS, summary level data suffices for TWAS and offers improved statistical power. Two popular TWAS methods include either (a) imputing the cis genetic component of gene expression from smaller sized studies (using multi-SNP prediction or MP) into much larger effective sample sizes afforded by GWAS - TWAS-MP or (b) using summary-based Mendelian randomization - TWAS-SMR...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29194587/genetic-association-of-molecular-traits-a-help-to-identify-causative-variants-in-complex-diseases
#12
REVIEW
C Vandiedonck
In the past 15 years, major progresses have been made in the understanding of the genetic basis of regulation of gene expression. These new insights have revolutionized our approach to resolve the genetic variation underlying complex diseases. Gene transcript levels were the first expression phenotypes that were studied. They are heritable and therefore amenable to genome-wide association studies (GWAS). The genetic variants that modulate them are called expression quantitative trait loci (eQTL). Their study has been extended to other molecular quantitative trait loci (molQTL) that regulate gene expression at the various levels, from chromatin state to cellular responses...
December 1, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29193869/cd4-and-b-lymphocyte-expression-quantitative-traits-at-rheumatoid-arthritis-risk-loci-in-untreated-early-arthritis-implications-for-causal-gene-identification
#13
Nishanthi Thalayasingam, Nisha Nair, Andrew J Skelton, Jonathan Massey, Amy E Anderson, Alexander D Clark, Julie Diboll, Dennis W Lendrem, Louise N Reynard, Heather J Cordell, Stephen Eyre, John D Isaacs, Anne Barton, Arthur G Pratt
OBJECTIVE: Rheumatoid arthritis (RA) is a genetically complex disease of immune dysregulation. Seeking insight into genetic risk mechanisms, we conducted an expression quantitative trait locus (eQTL) analysis of confirmed genetic risk loci in CD4+ T cells and B cells from carefully phenotyped early arthritis patients naïve to therapeutic immunomodulation. METHODS: 344 patients donated RNA and DNA from purified B and/or CD4+ T-cells. Genotyping and global gene expression measurement were carried out using Illumina BeadChip microarrays...
November 28, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29184056/functional-mapping-and-annotation-of-genetic-associations-with-fuma
#14
Kyoko Watanabe, Erdogan Taskesen, Arjen van Bochoven, Danielle Posthuma
A main challenge in genome-wide association studies (GWAS) is to pinpoint possible causal variants. Results from GWAS typically do not directly translate into causal variants because the majority of hits are in non-coding or intergenic regions, and the presence of linkage disequilibrium leads to effects being statistically spread out across multiple variants. Post-GWAS annotation facilitates the selection of most likely causal variant(s). Multiple resources are available for post-GWAS annotation, yet these can be time consuming and do not provide integrated visual aids for data interpretation...
November 28, 2017: Nature Communications
https://www.readbyqxmd.com/read/29183975/high-resolution-mapping-of-cis-regulatory-variation-in-budding-yeast
#15
Ryosuke Kita, Sandeep Venkataram, Yiqi Zhou, Hunter B Fraser
Genetic variants affecting gene-expression levels are a major source of phenotypic variation. The approximate locations of these variants can be mapped as expression quantitative trait loci (eQTLs); however, a major limitation of eQTLs is their low resolution, which precludes investigation of the causal variants and their molecular mechanisms. Here we report RNA-seq and full genome sequences for 85 diverse isolates of the yeast Saccharomyces cerevisiae-including wild, domesticated, and human clinical strains-which allowed us to perform eQTL mapping with 50-fold higher resolution than previously possible...
November 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29170203/identification-of-a-novel-locus-on-chromosome-2q13-which-predisposes-to-clinical-vertebral-fractures-independently-of-bone-density
#16
Nerea Alonso, Karol Estrada, Omar M E Albagha, Lizbeth Herrera, Sjur Reppe, Ole K Olstad, Kaare M Gautvik, Niamh M Ryan, Kathryn L Evans, Carrie M Nielson, Yi-Hsiang Hsu, Douglas P Kiel, George Markozannes, Evangelia E Ntzani, Evangelos Evangelou, Bjarke Feenstra, Xueping Liu, Mads Melbye, Laura Masi, Maria Luisa Brandi, Philip Riches, Anna Daroszewska, José Manuel Olmos, Carmen Valero, Jesús Castillo, José A Riancho, Lise B Husted, Bente L Langdahl, Matthew A Brown, Emma L Duncan, Stephen Kaptoge, Kay-Tee Khaw, Ricardo Usategui-Martín, Javier Del Pino-Montes, Rogelio González-Sarmiento, Joshua R Lewis, Richard L Prince, Patrizia D'Amelio, Natalia García-Giralt, Xavier Nogués, Simona Mencej-Bedrac, Janja Marc, Orit Wolstein, John A Eisman, Ling Oei, Carolina Medina-Gómez, Katharina E Schraut, Pau Navarro, James F Wilson, Gail Davies, John Starr, Ian Deary, Toshiko Tanaka, Luigi Ferrucci, Fernando Gianfrancesco, Luigi Gennari, Gavin Lucas, Roberto Elosua, André G Uitterlinden, Fernando Rivadeneira, Stuart H Ralston
OBJECTIVES: To identify genetic determinants of susceptibility to clinical vertebral fractures, which is an important complication of osteoporosis. METHODS: Here we conduct a genome-wide association study in 1553 postmenopausal women with clinical vertebral fractures and 4340 controls, with a two-stage replication involving 1028 cases and 3762 controls. Potentially causal variants were identified using expression quantitative trait loci (eQTL) data from transiliac bone biopsies and bioinformatic studies...
November 23, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/29168174/genetic-variants-in-the-platelet-derived-growth-factor-subunit-b-gene-associated-with-pancreatic-cancer-risk
#17
Bensong Duan, Jiangfeng Hu, Hongliang Liu, Yanru Wang, Hongyu Li, Shun Liu, Jichun Xie, Kouros Owzar, James Abbruzzese, Herbert Hurwitz, Hengjun Gao, Qingyi Wei
The platelet-derived growth factor (PDGF) signaling pathway plays important roles in development and progression of human cancers. In our study, we aimed to identify genetic variants of the PDGF pathway genes associated with pancreatic cancer (PC) risk in European populations using three published genome-wide association study datasets, which consisted of 9,381 cases and 7,719 controls. The expression quantitative trait loci (eQTL) analysis was also performed using data from the 1000 Genomes, TCGA and GTEx projects...
November 23, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29156765/network-directed-cis-mediator-analysis-of-normal-prostate-tissue-expression-profiles-reveals-downstream-regulatory-associations-of-prostate-cancer-susceptibility-loci
#18
Nicholas B Larson, Shannon K McDonnell, Zach Fogarty, Melissa C Larson, John Cheville, Shaun Riska, Saurabh Baheti, Alexandra M Weber, Asha A Nair, Liang Wang, Daniel O'Brien, Jaime Davila, Daniel J Schaid, Stephen N Thibodeau
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis-acting associations due to study limitations. While trans-eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans-eQTL associations are mediated by cis-regulated genes, such as transcription factors...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29149290/discovering-the-3-utr-mediated-regulation-of-alpha-synuclein
#19
Domenica Marchese, Teresa Botta-Orfila, Davide Cirillo, Juan Antonio Rodriguez, Carmen Maria Livi, Rubén Fernández-Santiago, Mario Ezquerra, Maria J Martí, Elias Bechara, Gian Gaetano Tartaglia
Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro/in silico screening we identified RNA-binding proteins (RBPs) that interact with SNCA 3' UTRs. We identified two RBPs, ELAVL1 and TIAR, that bind with high affinity to the most abundant and translationally active 3' UTR isoform (575 nt)...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#20
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
keyword
keyword
65283
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"