With a goal of collecting multiple biosamples, researchers in the GTEx (Genotype-Tissue Expression) project faced a problem: where to get samples for a reference library cataloging non-diseased tissue gene expression. Carithers et al. (2015) provide an overview of the resourceful solution to this potentially limiting factor in study design.1
The GTEx project aims to examine the correlation between human genetic variation and tissue-specific gene expression in non-diseased individuals, with a view to investigating how variations correlate with development of disease. In order to accomplish this goal, biobankers with the project needed to acquire multiple and varied non-diseased tissue samples to establish baselines for further studies.
The initial goal was to collect 40 tissue types from females and 34 from males. Currently, in modern medical and research ethics practices, this is not a practical undertaking, since collection of multiple tissue types from healthy donors is rarely sanctioned, ethically or practically. Although taking healthy adjacent tissue for comparison during certain curative or investigational surgical procedures is normal, it would be unusual for this to encompass harvesting from the entire body. However, procuring multiple samples from a cadaver is permissible, and this is where the GTEx biobankers turned their attention.
GTEx team members, including the National Cancer Institute’s Biorepositories and Biospecimen Research Branch, the National Human Genome Research Institute and the National Institute for Mental Health, among others, collaborated to develop ethical and logistical plans for tissue collection post-mortem. The biobankers partnered with existing organ donor teams to ensure rapid access and harvesting. They also established screening criteria for inclusion into the study, which included obtaining consent from next of kin.
For success, the samples collected need to be of sufficiently high standard to allow onward genomic investigation; for this reason, biobankers used RNA integrity numbers (RINs) to set a quality benchmark for tissue preservation. Previous studies identified that a RIN higher than 6 denoted high-quality tissue preservation sufficient for satisfactory DNA and RNA recovery. They also found that RINs varied according to time of harvesting after death, noting that sample collection within eight hours gave best results. For this reason, the team developed a protocol using a novel tissue harvesting and storage procedure that gave good results for both histopathology and genomic preservation.
In addition to the screening criteria for inclusion, the biobankers also established centralized quality control with standard operating procedures for handling, transportation, storage and data entry, managed via a custom web portal. They also implemented a pathology review process to ensure sample quality for onward research use. This review process included checks on sample integrity in addition to absence of disease in the tissues collected. In this way, the biobank could assure GTEx researchers of biosample quality for the study.
The pilot stage of the GTEx project has collected 10,152 preserved tissue samples from 190 donors within its first two and a half years, with initial RNA sequencing data released in May 2015. On collection and verification, biobank staff subdivided these tissue samples into multiple aliquots to make them available for research requests. Furthermore, in response to user feedback, the biobank is including frozen samples alongside the preserved biospecimens in its collection protocols. Biosample collection continues, with the aim to increase the collection to specimens from 900 donors by the end of 2015.
1. Carithers, L.J., et al. (2015) “A novel approach to high-quality postmortem tissue procurement: The GTEx project,” Biopreservation and Biobanking, 13. doi: 10.1089/bio.2015.0032