Enhancing Research Through the Use of the Genotype-Tissue Expression (GTEx) Database.
Ontology highlight
ABSTRACT:
SUBMITTER: Stanfill AG
PROVIDER: S-EPMC8191158 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
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Project description:Genotype-Tissue Expression Project (GTEx)
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Project description:Genetic variants have been associated with myriad molecular phenotypes that provide new insight into the range of mechanisms underlying genetic traits and diseases. Identifying any particular genetic variant's cascade of effects, from molecule to individual, requires assaying multiple layers of molecular complexity. We introduce the Enhancing GTEx (eGTEx) project that extends the GTEx project to combine gene expression with additional intermediate molecular measurements on the same tissues to provide a resource for studying how genetic differences cascade through molecular phenotypes to impact human health.
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Project description:Understanding the functional consequences of genetic variation, and how it affects complex human disease and quantitative traits, remains a critical challenge for biomedicine. We present an analysis of RNA sequencing data from 1641 samples across 43 tissues from 175 individuals, generated as part of the pilot phase of the Genotype-Tissue Expression (GTEx) project. We describe the landscape of gene expression across tissues, catalog thousands of tissue-specific and shared regulatory expression quantitative trait loci (eQTL) variants, describe complex network relationships, and identify signals from genome-wide association studies explained by eQTLs. These findings provide a systematic understanding of the cellular and biological consequences of human genetic variation and of the heterogeneity of such effects among a diverse set of human tissues.
| S-EPMC4547484 | biostudies-literature
Project description:Aging is a complex biological process that is far from being completely understood. Analyzing transcriptional differences across age might help uncover genetic bases of aging. In this study, 1573 differentially expressed genes, related to chronological age, from the Genotype-Tissue Expression (GTEx) project, were categorized as upregulated age-associated genes (UAGs) and downregulated age-associated genes (DAGs). Characteristics in evolution, expression, function and molecular networks were comprehensively described and compared for UAGs, DAGs and other genes. Analyses revealed that UAGs are more clustered, more quickly evolving, more tissue specific and have accumulated more single-nucleotide polymorphisms (SNPs) and disease genes than DAGs. DAGs were found with a lower evolutionary rate, higher expression level, greater homologous gene number, smaller phyletic age and earlier expression in body development. UAGs are more likely to be located in the extracellular region and to occur in both immune-relevant processes and cancer-related pathways. By contrast, DAGs are more likely to be located intracellularly and to be enriched in catabolic and metabolic processes. Moreover, DAGs are also critical in a protein-protein interaction (PPI) network, whereas UAGs have more influence on a signaling network. This study highlights characteristics of the aging transcriptional landscape in a healthy population, which may benefit future studies on the aging process and provide a broader horizon for age-dependent precision medicine.
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Project description:<p><b>Lay Description</b></p> <p>The aim of the Genotype-Tissue Expression (GTEx) Project is to increase our understanding of how changes in our genes affect human health and disease with the ultimate goal of improving health care for future generations. GTEx will create a database that researchers can use to study how inherited changes in genes lead to common diseases.</p> <p>GTEx researchers are studying genes in different tissues obtained from many different people. The GTEx project also includes a study of the GTEx donor consent process - this study will help ensure that the consent process and other aspects of the project effectively address the concerns and expectations of participants in the study. GTEx is a pioneering project that uses state-of-the-art protocols for obtaining and storing a large range of organs and tissues, and for testing them in the lab. Until now, no project has analyzed genetic variation and expression in as many tissues from the same person in such a large population as planned for GTEx.</p> <p><b>Scientific Description</b></p> <p>Understanding the role of variation in the human genome is crucial to elucidating genetic contributions to human health and disease. Despite the results of genome-wide association studies (GWAS) documenting strong statistical associations between genetic variation and human traits, the functional role for most of these variants is largely unexplained. Nearly 90% of these GWAS-implicated sites lie outside of protein-coding sequences, suggesting that these variants might regulate gene expression.</p> <p>The goal of the Genotype-Tissue Expression (GTEx) project is to establish a resource database and tissue biobank in which to study the relationship between genetic variation and gene expression and other molecular phenotypes in reference/non-diseased tissues. The ultimate resource will include approximately 960 post-mortem donors with several dozen tissues from each, a resource large enough to study both <i>cis</i>- and <i>trans</i>- gene expression quantitative trait loci (eQTLs). Some tissue will also be banked for additional molecular analyses. To request biosamples, please see the <a href="http://www.gtexportal.org/home/samplesPage" target="_blank">Biobank page</a> for more information.</p> <p>GTEx was initially funded as a 2-year pilot project by the NIH Common Fund (CF) in 2010, and has been scaled up after demonstration of feasibility. The project will collect and analyze RNA levels in many different human tissues and each donor will be characterized for germline genetic variation through dense genotyping arrays and sequencing of either whole exomes or whole genomes.</p> <p>By treating RNA expression levels as quantitative traits, eQTLs will be identified as sites containing genetic variation that correlate with changes in RNA expression. Such eQTLs have been associated with 4%-12% of expressed human genes, and with common complex human diseases, including obesity, atherosclerosis, type 2 diabetes, Crohn's disease, and asthma. Additionally, few studies have examined the tissue specificity of eQTLs. A subset of banked tissue samples will also be analyzed for other molecular phenotypes, such as DNA methylation, DNaseI hypersensitivity sites, and proteomics. The GTEx project will thus serve as a resource database and tissue bank for many future studies, especially for understanding the functional basis of inherited susceptibility to disease.</p> <p>All GTEx releases since Version 5 follow the NIH Genomic Data Sharing (GDS) Policy whereby there are no restrictions on use or publication after release. Additional information about the GTEx Data Release and Publication policy can be found on the GTEx Data Portal at <a href="http://www.gtexportal.org" target="_blank">www.gtexportal.org</a>.</p>
| phs000424 | dbGaP
Project description:Genotype-Tissue Expression (GTEx) Common Fund Project
| PRJNA75897 | ENA
Project description:<p><b>Lay Description</b></p> <p>The aim of the Genotype-Tissue Expression (GTEx) Project is to increase our understanding of how changes in our genes affect human health and disease with the ultimate goal of improving health care for future generations. It was launched in 2010 as a two-year pilot project supported by the Office of the Director, National Institutes of Health (NIH). GTEx will create a database that researchers can use to study how inherited changes in genes lead to common diseases.</p> <p>GTEx researchers are studying genes in different tissues obtained from many different people. The GTEx project also includes a study to explore the effectiveness of the GTEx donor consent process - this study will help ensure that the consent process and other aspects of the project effectively address the concerns and expectations of participants in the study. GTEx is a pioneering project that uses state-of-the-art protocols for obtaining and storing a large range of organs and tissues and for testing them in the lab. Until now, no project has analyzed genetic variation and expression in as many tissues in such a large population as planned for GTEx.</p> <p><b>Scientific Description</b></p> <p>Understanding the role of variation in the human genome is crucial to elucidating genetic contributions to human health and disease. Despite the results of genome-wide association studies (GWAS) documenting strong statistical associations between genetic variation and human traits, the functional role for most of these variants is largely unexplained. Nearly 90% of these GWAS-implicated sites lie outside of protein-coding sequences, suggesting that these variants might regulate gene expression.</p> <p>The goal of the Genotype-Tissue Expression (GTEx) project is to establish a resource database in which to study the relationship between genetic variation and gene expression in reference/non-diseased tissues. The ultimate resource would include up to 1,000 post-mortem donors with several dozen tissues from each, a resource large enough to study both <i>cis</i>- and <i>trans</i>- gene expression quantitative trait loci (eQTLs). Some tissue will also be banked for additional molecular analyses.</p> <p>GTEx was funded as a 2-year pilot project by the NIH Common Fund (CF), and will assess the feasibility of collecting high-quality RNA from multiple tissues from healthy donors. The project will collect and analyze RNA levels in 30 or more different human tissues from 160 postmortem donors and 5 tissues from a similar number of surgical controls. Each donor will be characterized for germline genetic variation through dense genotyping arrays.</p> <p>By treating RNA expression levels as quantitative traits, eQTLs will be identified as sites containing genetic variation that correlate with changes in RNA expression. Such eQTLs have been associated with 4%-12% of expressed human genes, and with common complex human diseases, including obesity, atherosclerosis, type 2 diabetes, Crohn's disease, and asthma. Additionally, few studies have examined the tissue specificity of eQTLs. The GTEx project will thus serve as a resource database and tissue bank for many future studies, especially for understanding the functional basis of inherited susceptibility to disease.</p> <p>It is anticipated that GTEx data will be made available through dbGaP on a periodic basis as it is generated.</p>
| phs000424.v1.p1 | EGA
Project description:RNA-seq from human tissue samples from the Genotype-Tissue Expression (GTEx) Project (http://www.gtexportal.org/home/). This dataset is part of the TransQST collection.
2015-05-29 | E-MTAB-2919 | biostudies-arrayexpress
Project description:The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes. By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs. The present dataset contains RNA-seq from human reference/non-diseased tissues (thus, we have excluded K-562 cell line that is a chronic myelogenous leukemia cell line) from the Genotype-Tissue Expression (GTEx) Project (http://www.gtexportal.org/home/).
2016-12-07 | E-MTAB-5214 | biostudies-arrayexpress