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Genotype Tissue Expression ( GTEx ) Project

Genotype Tissue Expression ( GTEx ) Project. Broad Institute of Harvard and MIT Laboratory, Data Analysis, and Coordinating Center (LDACC ) June 26, 2013. GTEx goals Generate public resource with tissue-specific eQTLs and gene and isoform expression data across multiple human tissues.

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Genotype Tissue Expression ( GTEx ) Project

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  1. Genotype Tissue Expression (GTEx) Project Broad Institute of Harvard and MIT Laboratory, Data Analysis, and Coordinating Center (LDACC) June 26, 2013

  2. GTEx goals Generate public resource with tissue-specific eQTLs and gene and isoform expression data across multiple human tissues. Contribute to understanding of effects of genetic variation on gene expression and regulation Assist in interpretation of disease/trait GWAS signals Collect on average 30 tissues per postmortem donor. Pilot experiment: 190 donors Goal: 900 donors within the next 2 years Dense genotyping (Illumina 5M, Exome array and imputation) and RNA-Seq across all tissue samples NIH funded project

  3. Expression Quantitative Trait Loci • Ideally test in a disease-specific cell context • Most human tissue types human samples are very difficult to obtain • Large sample sizes are required for statistical power Slide courtesy of David Deluca

  4. There are 9 Tissues that have sufficient sample numbers (> 80): Adipose Subcutaneous Artery Tibial Heart Left Ventricle Lung Muscle Skeletal Nerve Tibial Skin Sun Exposed Lower leg Thyroid Whole Blood From GTEx portal documentation

  5. Summary of data generated in GTEx Pilot experiment: RNA-Seq data on 1,816 tissue samples (.bams and RPKM expression) Illumina 5M, Exome, and imputed genotypes available on 190 donors Robust medical history data on all 190 donors Access to GTEx Pilot data: GTExPilot data (genotypes and RNA-seq) available through the database of Genotypes and Phenotypes (dbGaP, study accessionphs000424.v3.p1) Limited access, de-identified datasets are available from GTExPortal (http://www.broadinstitute.org/gtex/) under ‘Datasets’ tab. Can search for expression Quantitative Trait Loci (eQTL) related to your favorite genes and SNPs and cross-tissue gene expression on the GTEx Portal on the 'Search' tab.

  6. http://www.broadinstitute.org/gtex/

  7. Potential Applications of GTEx in Complex Disease Genetics Studies Are top GWAS SNP associations enriched for eQTLs for a given tissue of interest? Are GWAS signals including more modest ones enriched for eQTLs in a relevant tissue? Tissue-specific eQTLs can be used to propose causal gene and tissue Tissue-specific isoforms can be used to determine which variants are expressed in relevant tissues – useful for rare variant analysis of complex traits.

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