Progress updates on pilot milestones were given:
Pilot Milestone 1: Enroll 10 donors per month by the end of the Pilot
- At least 10 donors were enrolled in 7 out of 13 months
Pilot Milestone 2: Obtain high-quality RNA, defined as a RNA Integrity Number (RIN) > 6 for at least 70% of 12 tissues
- Based on analysis of the first 97 eligible donors, for 14 tissues, more than 70% have RIN > 6
- Many additional tissues are very near this cut-off (the median RIN is > 6 for 37 tissues)
Pilot Milestone 3: Identify cis-eQTLs for 4-10%, at a FDR <0.05, of all transcripts
- RNA-Seq Quality Control metrics are excellent, and preliminary eQTL results look very robust
- When all pilot samples are through RNA-Seq in late 2012, we expect to be able to make reliable estimates
The GTEx Scale Up was also discussed. Goals and deliverables after scale up include:
- 900 post-mortem donors, completely genotyped
- Over 25,000 peripheral tissues
- Gene expression levels measured by RNA-Seq for >20,000
- Methylation, somatic DNA mosaicism, etc.
- Associated clinical and histopathological information
- Access system for data and samples (user-friendly data access)
- ELSI study of donor families
- Human Gene Expression Atlas
- Comprehensive cis- and trans-eQTL results for each tissue
- Contrast with surgery data to find out if eQTLs are replicated in post-mortem tissues, and if overall post-mortem gene expression measurements are reflective of “normal/baseline” gene expression
Anticipated initial publications by GTEx consortium investigators were discussed, including the design-marker paper, the caHUB descriptive paper, and the Genome-wide gene expression and eQTL analyses paper.
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The GTEx Investigator poster session displayed 17 posters containing work ranging from donor recruitment to sample preparation, molecular analysis, and statistical analysis.
The next GTEx Investigators Meeting is scheduled for December 13-14, 2012 in Rockville, MD.