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Workshop Report
This Workshop was held to gather information to inform the proposed NIH Roadmap Initiative “GTEx.” The Workshop was planned by the GTEx Working Group and was attended by approximately 90 scientists, half of whom were from outside the NIH.
The first portion of the Workshop included six presentations followed by four Breakout Sessions. The Breakout session topics included Statistical\epidemiologic Issues, Building a Public Database, Tissue Procurement, and Laboratory Analyses. All except for the Building a Public Database Breakout group were repeated for a second 90-minute session, with participants switching from their original group to increase the diversity of input on the issues.
Summary Discussion
adapted from slides presented by Francis Collins (last updated 11/19/08)
Immediate Next Steps
- Database can be designed and implemented now
- Pilot project can be designed and implemented now
Database
- Need to establish immediately to capture all existing high quality datasets and prepare for much more data to come
- GTEx lives at the interface of dbGaP and GEO, take advantage of that
- Aim for public access to eQTL analysis results (computed by NCBI) and array-based expression data
- Expect controlled access to genotypes and sequence-based expression data (unless they can be made anonymous)
Pilot Project (Issues to be considered)
- Number of donors needed
- Age 18 – 50? (as narrow as feasible), both genders
- Exclude extreme cases (cachexia, disseminated infection)
- Aim for ~160 donors in total and assume that there will be ~80-100 of at least one geographic population
- Source of tissues
- Organ donors may provide valuable sources, but have limitations; tissue donors have other pros and cons; rapid autopsy & medical examiner cases also have pros and cons
- Tissues to collect
- Collect as many tissues as possible from each donor
- Collect blood and CSF for drugs, toxins; measure brain lactate and pH levels
- Ideally establish lymphoblastoid cell lines (LCLs) and skin fibroblast cultures
- Clinical information to collect
- As much as practical (especially about mode of death), including family history?
- Prospective pathological exam of each tissue, with images deposited in GTEx database
- Collection and storage of tissue using a standard operating procedure (SOP) to maximize utility for:
- Histopathology
- DNA, RNA
- Frozen aliquots of homogenized tissue (possibly pulverized for homogeneity)
- Frozen tissue that has not been homogenized for possible laser capture microdissection, other future uses
- Lab issues
- Compare array-based RNA analysis with sequencing approach
- QC standards must be established for each assay
- Capture miRNAs if possible
- Prepare for future analyses such as histone modifications and DNA methylation
- Consider use of molecular barcodes to track samples
Other Parallel Pilots to Consider
- Carry out similar DNA and RNA analyses on surgical specimens for comparison
- Test archived paraffin blocks to see whether it is practical to get digital transcriptome data
- Systematically test effects of postmortem handling on RNA results, possibly using animal tissues
- Explore retroactive genotyping of human tissue samples with data already in GEO
ELSI considerations
- Survey all existing relevant data on public attitudes for this kind of project and decide if further input is needed
- Write a summary/white paper on existing standards for obtaining consent/authorization/permission in different tissue donation settings;
- Develop standard GTEx permission request language – to supplement or add to existing donor consents
General Issues
- As discussed at this meeting, the pilot will potentially require at least two years
- Need to work closely with NCI (tissue acquisition and standardization efforts) to avoid duplication and take advantage of shared goals
- If Pilot is successful, is it feasible to do the larger study of 1000 (or maybe 840) donors over three more years (total of five years)?
- These samples and the attached database will have many uses beyond the original GTEx design
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