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- Study Description
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.
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.
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.
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 900 post-mortem donors with several dozen tissues from each, a resource large enough to study both cis- and trans- gene expression quantitative trait loci (eQTLs). Some tissue will also be banked for additional molecular analyses.
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.
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.
The Genotype-Tissue Expression (GTEx) project is considered a "community resource and as such falls under the "Ft. Lauderdale" meeting principles of rapid, pre-publication data release (see Sharing Data from Large-Scale Biological Research Projects: A System of Tripartite Responsibility, 2003). GTEx data will be released through dbGaP on a periodic basis as it is generated, and there is no formal publication embargo. However, the GTEx Consortium requests that users of GTEx data respect the data producer's interest to publish a full analysis of the data first. Additional information about the GTEx Data Release and Publication policy can be found on the GTEx Data Portal at www.gtexportal.org. Investigators are encouraged to contact NIH program staff at firstname.lastname@example.org to discuss publication plans and whether they would conflict with Consortium publication plans.
- Authorized Access
- Publicly Available Data (Public ftp)
Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.
- Study Inclusion/Exclusion Criteria
Donor Inclusion/Exclusion Criteria are as follows:
- 21 ≤ Age (years) ≤ 70
- 18.5 < Body Mass Index < 35
- Time between death and tissue collection less than 24 hours
- No whole blood transfusion within 48 hours prior to death
- No history of metastatic cancer
- No chemotherapy or radiation therapy within the 2 years prior to death
- Generally unselected for presence or absence of diseases or disorders, except for potentially communicable diseases that disqualify someone to donate organs or tissues would also be disqualifying for GTEx.
- Molecular Data
Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment Whole Genome Genotyping Illumina HumanOmni5-Quad 4301332 N/A Whole Genome Genotyping Illumina HumanOmni2.5 2443179 N/A Exome Genotyping Illumina Infinium HumanExome BeadChip N/A N/A Whole Exome Sequencing Illumina HiSeq 2000 N/A N/A RNA Sequencing Illumina HiSeq 2000 N/A N/A Indexed, 76bp, paired-end run Gene Expression Affymetrix GeneChip Human Gene 1.0 ST Array N/A N/A
- Study History
June 2008 - GTEx Planning Workshop held in Bethesda, MD
July 2010 - Laboratory, Data Analysis, and Coordinating Center awarded
August 2010 - Biospecimen Source Sites awarded
September 2010 - Statistical methods development R01 awards made
December 2010 - First donor enrolled comparing collection methods
May 2011 - First donors enrolled under full protocol
June 2012 - Initial dbGaP release
November 2012 - "Enhancing GTEx" RFA (RM12-009) published
April 2013 - dbGaP release of "Pilot" data from first 175 donors
June 2013 - First GTEx Community Meeting
August 2013 - New R01 Statistical Methods grants awarded
- Selected publications
- Diseases/Traits Related to Study (MESH terms)
- Primary Phenotype: Reference Values
- Authorized Data Access Requests
- Study Attribution