How to cite the GTEx project

The GTEx consortium has just published a collection of papers in a special issue of Nature that together provide an unprecedented view of the human transcriptome across dozens of tissues. The work is based on a large-scale RNA-Seq experiment of postmortem tissue from hundreds of human donors, illustrated in Figure 1 of the overview by Ward and Gilad 2017:

The data provide a powerful new opportunity for several analyses, highlighted (at least for me) by the discovery of 673 trans-eQTLs at 10% genome-wide FDR. Undoubtedly more discoveries will be published when the sequencing data, available via dbGAP, is analyzed in future studies. As a result, the GTEx project is likely to garner many citations, both for specific results, but also drive-by-citations that highlight the scope and innovation of the project. Hopefully, these citations will include the key GTEx paper:

Carithers, Latarsha J, Ardlie, Kristin, Barcus, Mary, Branton, Philip A, Britton, Angela, Buia, Stephen A, Compton, Carolyn C, DeLuca, David S, Peter-Demchok, Joanne, Gelfand, Ellen T, Guan, Ping, Korzeniewski, Greg E, Lockhart, Nicole C, Rabiner, Chana A, Rao, Abhi K, Robinson, Karna L, Roche, Nancy V, Sawyer, Sherilyn J, Segrè, Ayellet V, Shive, Charles E, Smith, Anna M, Sobin, Leslie H, Undale, Anita H, Valentino, Kimberly M, Vaught, Jim, Young, Taylor R, Moore, Helen M, on behalf of the GTEx consortium, A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project, Biopreservation and Biobanking 13(5), 2015, p 311–319.

The paper by Latarsha Carithers et al. provides an overview of the consent and laboratory procedures that GTEx developed and applied to obtain tissues from hundreds of deceased donors. The monumental effort is, to my knowledge, unprecedented in scale and scope, and it relied on the kindness and generosity of hundreds of family members and next-of-kin of donors, who consented to donate their loved ones to science.

To develop effective and appropriate consent procedures, the GTEx project organized a sub-study to determine how best to approach, interact and explain the project to family members. Ultimately consent was obtained either in person or over the phone, and one can only imagine the courage of families to agree to donate, especially during times of grief and for a project whose goals could only be explained in terms of the long-term benefits of basic science.

The consent procedures for GTEx were complicated by a need to rapidly place tissue in preservative postmortem. RNA degrades rapidly after the time of death, and there is a window of only a few hours before expression can no longer be effectively measured. The RNA Integrity Number (RIN) measures the extent of degradation of RNA. It used to be measured with gel electrophoresis by examining the ratio of 28S:18S rRNA; more recently RIN is computed using more sophisticated analyses with, e.g. the Agilent bioanalyzer (see Schroeder et al. 2006 for details). GTEx conducted extensive studies to determine the correspondence between postmortem interval (time taken to preserve tissue) and RIN, and also examined the RIN necessary for effective RNA-Seq library construction.

The effect of ischemic time time on RIN values (Fig 6 from Carithers et al. 2015).

These studies were used to deploy standard operating procedures across multiple source sites (an obvious necessity given the number of donors needed). All of this research was not only crucial for GTEx, but will be extremely valuable for studies relying on postmortem RNA-Seq in the future.

The collection of specimens from each source site required training of individuals at that site, and one of GTEx’s achievements is the gathering of knowledge of how to orchestrate such a complex distributed sample collection and preparation enterprise. The workflow shown below (Figure 2 from Carithers et al. 2015) hints at the complexities involved (e.g. the need for separate treatment of brain due to the requirement of proper sectioning).

A meeting discussing the findings of Carithers et al. was held on May 20-21 2015 and I encourage all users of GTEx data/results to view the recording of it (Day 1, Day 2).

It is truly moving and humbling to consider the generosity of the hundreds of families, in many cases of donors in their twenties or thirties, who enabled GTEx. The scale of their contribution, and the suffering that preceded collection of the data cannot be captured in cartoons that describe the experiment. The families can also never be fully acknowledged, not matter how many times they are thanked in acknowledgment sections. But at a minimum, I think that reading Carithers et al. 2015 is the least one can do to honor them, and those who turned their good-will into science.

Acknowledgment: the idea for this blog post originated during a conversation with Roderic Guigó.