The Common Fund's Genotype-Tissue Expression (GTEx) Program established a data resource and tissue bank to study the relationship between genetic variants (inherited changes in DNA sequence) and gene expression (how genes are turned on and off) in multiple human tissues and across individuals. GTEx also increased our understanding of how gene expression varies between male and female.
The GTEx program has transitioned from Common Fund support. Common Fund programs are strategic investments that achieve a set of high-impact goals within a 5-10 year timeframe. At the conclusion of each program, deliverables will transition to other sources of support or use within the scientific community.
The GTEx program supported by the Common Fund from 2010 to 2019. Currently, GTEx data are widely used as a reference dataset to design new methods and tools, such as a statistical method called PrediXcan. This novel method is used to predict the expression of a gene using DNA sequence data. PrediXcan also predicts visible traits of diseases. GTEx researchers used this method to identify specific genes associated with five diseases: bipolar disorder, coronary artery disease, Crohn's disease, rheumatoid arthritis and type 1 diabetes. The GTEx’s final dataset (V8) contains DNA data from 838 postmortem donors and 17,382 RNA-seq across 54 tissue sites and two cell lines. GTEx data is accessible through the National Center for Biotechnology Information’s database of Genotypes and Phenotypes (dbGaP), the National Human Genome Research Institute's (NHGRI) Genomic Analysis and Visualization and Informatics Labspace (AnVIL) and GTEx Portal. GTEx resources are valuable tools for exploring the impact of genetic variation on complex traits and diseases.
Program Major Accomplishments
Highlights of the Genotype-Tissue Expression (GTEx) Program major accomplishments are:
- Established a comprehensive catalog of genetics variants that effect gene expression across multiple tissue for the research community to evaluate tissue-specific gene expression and regulation in many different tissues. Genetic variants that influence how genes behave are called expression quantitative trait loci (eQTLs). Researchers are using GTEx data to enhance the functional interpretation of genome-wide association study (GWAS) findings from and identification of disease-relevant genes.
- Created an online data resource (GTEx Portal) for storing, cataloging, searching, and sharing aggregated level data. Researchers used data from the GTEx Portal to publish over 7,000 papers.
- GTEx data was integrated into genomics browsers including the UCSC Genome Browser and Ensembl to visualize gene and variant information.
- Developed a biobank of tissue biospecimens (e.g. lung, brain, pancreas, skin, etc) as well as RNA, DNA, blood samples and cell lines from ~960 donors. The GTEx biobank also features an image library of the tissue samples for researchers to browse the complete collection. These biospecimens are stored at the Broad Institute of Harvard and MIT.
Please note that since the GTEx program is no longer supported by the Common Fund, the program website is being maintained as an archive and will not be updated on a regular basis.
Watch a video on the GTEx project for more details.
The GTEx (Genotype-Tissue Expression) Project identified genetic variants that influence how genes are turned on and off in human tissues and organs. Genetic variants that influence how genes behave are called expression quantitative trait loci (eQTLs). These eQTLs regulate the behavior of genes like a light-switch turns on a light in a room. A GTEx pilot study found that the number of eQTLs differ in multiple tissues and individuals.
GTEx collected multiple human tissues (i.e. brain, heart, lung, breast, skin and whole blood etc.) from ~960 donors and over 30,000 samples. These tissues and samples are stored through the National Cancer Institute's Cancer Human Biobank initiative on behalf of GTEx. The GTEx database is available to researchers through the GTEx Portal. GTEx is helping researchers understand the inherited susceptibility to common diseases such as cancer, heart disease, Parkinson’s and diabetes.
GTEx also included a study to understand the ethical, legal and social issues (ELSI) related to donor recruitment and consent to tissue donation for biobanking purposes. In 2017, the GTEx ELSI researchers published a paper in Genetic Testing and Molecular Biomarkers. The findings indicated that a clear discussion about risks and benefits associated with participation in biobanking research is needed during the consent process.
The GTEx Program supported the following initiatives:
- Online data resource (GTEx Portal) for storing, cataloging, searching, and sharing aggregated level data
- Novel Statistical Methods for Human Gene Expression Quantitative Trait Loci (eQTL) Analysis
- Laboratory, Data Analysis, and Coordinating Center (LDACC) for acquiring and analyzing DNA and RNA from multiple human tissues
- Enhanced GTEx projects: including additional dimensions beyond gene expression to the GTEx data
The GTEx version 8 is now available
The GTEx Portal has been updated to data release V8 (dbGaP accession phs000424.v8.p2)! This release includes genotype data from approximately 948 post-mortem donors and approximately 17,382 RNA-seq samples across 54 tissue sites and 2 cell lines, with adequate power to detect Expression Quantitative Trait Loci in 48 tissues. Full gene expression datasets are available for download through the GTEx Portal while genotypes and RNA-seq bam files are available via dbGaP.