Pilot milestones were discussed including the ability to:
To enroll at least 10 donors per month by the end of the pilot period.
- Active accrual began in May 2011, and at least 10 donors were collected in 4 of the first 9 months of collection, with an average of ~11 donors per month. This represents a phenomenal effort by NCI-caHUB, SAIC-F, NIH program staff, and the dedicated collection and processing subcontract personnel. A total quality management system has been an integral part of the launch of GTEx.
To obtain high-quality RNA, defined as a RNA Integrity Number (RIN) of > 6 for at least 70% of 12 tissues.
- RNA quality in GTEx tissues has been very good. Based on analysis of over 1,200 samples from the first 36 donors, the target RIN values have been met for 10 of the 20 tissues deemed highest-priority for immediate gene expression analysis. While not formally reaching our target in this interim analysis, we are very pleased with RNA quality and as processes improve, expect to meet the target by the next data freeze.
To identify cis-eQTLs for 4% - 10% of all transcripts.
- Based on extremely preliminary analysis (of only 10 donors), numerous cis-eQTLs were identified. The quality metrics for expression arrays and RNA-Seq experiments from GTEx tissues have, with rare exceptions, been indistinguishable from quality metrics for reference samples from cell lines. Owing to the seeming high quality of gene expression metrics thus far, we are confident that we will identify eQTLS at expected rates. Analysis of a March 2012, data freeze, based on the first 48 donors, is expected by April 2012 when progress toward this milestone will be re-evaluated.
In summary, the GTEx milestones are very close to be met especially the two that relate most directly to the predominant concerns going into the project, namely the ability to establish a low post-mortem interval collection system to identify donors in whom we can obtain multiple, high-quality tissues, and we expect to have preliminary data on the eQTL milestone by the spring of 2012.
Members from the External Scientific Panel (ESP) attended in-person and provided recommendations for moving forward.
Next meeting is scheduled for June 13-14, 2012 in the Washington area.
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