Scientists Use GTEx Data to Help Predict Genes Associated with Disease
Researchers at the University of Chicago and their collaborators have developed PrediXcan, a computational method that links genetic variation and gene activity to disease traits. The method uses gene activity datasets like the Genotype-Tissue Expression (GTEx) data to train the computer to associate certain genetic profiles with certain diseases. The technique has important implications for linking genetics to disease susceptibility.
A Gene-Based Association Method for Mapping Traits Using Reference Transcriptome Data. Eric R Gamazon, Heather E Wheeler, Kaanan P Shah, Sahar V Mozaffari, Keston Aquino-Michaels, Robert J Carroll, Anne E Eyler, Joshua C Denny, GTEx Consortium, Dan L Nicolae, Nancy J Cox & Hae Kyung Im. Nature Genetics. August, 2015. doi:10.1038/ng.3367. Read the article abstract.
GTEx Symposium: All Things Considered - Biospecimens, 'Omics Data, and Ethical Issues
This 2 day symposium took place on the NIH Campus May 20-21, 2015. It covered a broad range of topics that focused on the collection of normal biospecimens for GTEx and the scientific discoveries made possible by the biospecimens. The symposium was open to the public.
We have known for many years that differences in the DNA that codes for our genes affect everything from our eye color to our susceptibility for certain diseases. Now we are finding that differences in genes are only part of the story. Differences in DNA that control when and how much genes are turned on and off can have a profound impact on health and disease. Researchers funded by the Genotype-Tissue Expression (GTEx) program have created a new data resource to help find out how differences in an individual’s genetic make-up can affect gene activity and contribute to disease.
Scientists can use the new resource to examine genes and gene regulation in many different types of human tissues at the same time. Investigators are collecting more than 30 tissue types from autopsy or organ donations and tissue transplant programs, and analyzing both DNA and RNA from samples. The project will eventually include tissue samples from about 900 deceased donors.
The resource is already beginning to bear fruit. One study looked at mutations called protein-truncating variants which shorten the protein-coding sequence of genes. Rare protein-truncating variants can lead to diseases like Duchenne muscular dystrophy. Most protein-truncating variants are harmless, and researchers found that each person’s genome carries about 100 of them. Another study looked at gene activity in a variety of tissues from multiple donors. Researchers found slightly fewer than 2,000 genes that vary with age, including genes related to Alzheimer’s disease. They also found more than 750 genes with differences in activity between men and women, with most in breast tissue.
The Genotype-Tissue Expression (GTEx) Pilot Analysis: Mutitissue Gene Regulation in Humans. The GTEx Consortium. Science, May 2015, Vol. 348 no. 6235 pp. 648-660. Read the article abstract.
Read the NIH Press Release.
Read more about the Genotype-Tissue Expression (GTEx) program here.
A list of companion papers to the GTEx Pilot Analysis is available via the GTEx Portal website.
Eight Genotype-Tissue Expression grants will contribute to a resource database and tissue bank researchers can use them to study how inherited genomic variants — inherited spelling changes in the DNA code — may influence gene activity and lead to disease. Read the Press Release from the NIH National Human Genome Research Institute.
In October of 2013, a mechanism was put in place to allow researchers access to banked GTEx biospecimens. The goal of this policy is to facilitate the efficient use of this valuable resource. Requests to access the biospecimens can be made either through a "Short" or "Full" Sample Availability/Access Request, depending on the size and scope of the project and whether grant funding for the work is already in place, among other factors. More information on the GTEx Biospecimens Access Policy and related forms can be found on the GTEx Portal Sample Request Forms page. The Access Policy can also be viewed directly here.
GTEx pilot project described as one of the most ambitious tissue-collection studies - Nature’s Technology Feature “Building Better Biobanks
The June 2012 issue of Nature, highlights efforts being made to store high-quality, data-rich biological samples that are essential for research. In the article, GTEx Coordinator Dr. Jeff Struewing, M.D., M.S. (NHGRI) and other members of the GTEx Working Group discuss the various steps throughout the collection process where attention to detail results in high-quality specimens.
Reference: Nature 2012 June; Volume 486 “
The June 2013 issue of Nature Genetics highlights the GTEx project published by the GTEx Consortium.