July 1, 2014 (Vol. 34, No. 13)
Biobanking, already a critical resource for bioresearch and medicine, is becoming even more important. According to a forecast prepared by BCC Research, biobanking will represent a $183 billion worldwide market by 2015.
Besides rising in value, biobanking is growing more complicated. Questions of science, ethics, administration, and business viability are all part of biobanking’s dynamic landscape. Multiple stakeholders including government, academia, industry, and patients are shaping the field’s policy and practices.
All this ferment suggests that it is an opportune time to review the state of biobanking and identify emerging trends. Accordingly, many biobanking experts are planning to gather at the sixth annual Leaders in Biobanking Congress. This CHI event is scheduled to take place September 15–17 in Seattle.
The event will cover both the business and the science of biobanking, prompting discussion of myriad topics including the following developments:
- Physician-researchers have begun banking viable tumor cells that can be revived later to inform cancer therapy and research.
- Researchers are struggling to reconcile legacy consent conditions and emerging (and largely unanticipated) research options.
- Informatics has the potential to streamline biosample procurement.
- Affordable and effective room-temperature tissue preservation techniques may expand procurement options and even extend them to remote settings.
A full exploration of the many issues in biobanking is beyond the scope of this article, but a sampling of notable items on the meeting agenda may provide directional insight and suggest resources for additional study.
Next-Gen Brain Freeze
Use of frozen tissue remains the method of choice for characterizing the genome, transcriptome, and proteome. This method, however, is costly and displays temperature-related degradation differences among nucleic acids that must be taken into account. It’s also far from foolproof, as researchers from the University of California, Los Angeles (UCLA) have emphasized.
In the May 2014 issue of Clinical Biochemistry, these researchers revisited the case of a freezer failure, apparently undetected by redundant alarm systems, that damaged one-third of the specimens in a national autism brain bank and numerous other brain specimens.
“Storing samples in liquid nitrogen (LN2) poses rare but serious risks including LN2 burns, LN2 supply tank explosions, and suffocation from LN2 leaks in an enclosed space,” the authors wrote. “Finding adequate contiguous and practical space for banks of freezers or liquid nitrogen vats is extremely challenging at major medical and research institutions.”
William H. Yong, M.D., Brain Tumor Translational Resource at the David Geffen School of Medicine, UCLA, one of the authors of the UCLA study, is scheduled to deliver a presentation at the Biobanking Congress.
“Frozen biospecimens, while superb for next-generation testing, are costly. In the current environment, increasing the collection and storage of such specimens is not sustainable,” says Dr. Yong. “While next-generation technologies are being developed to work within the limitations of FFPE, the limitations cannot be entirely overcome.”
Nonetheless, Dr. Yong remains optimistic: “I believe that investment by national funding bodies and pharmaceutical institutions in developing broadly usable room-temperature biospecimen alternatives that permit high-quality whole-genome, transcriptome, proteome, and metabolome analyses will be rewarded by larger, more affordable pools of patient biospecimens for clinical trials of targeted therapy.”
Dr. Yong’s talk will focus on brain tissue, but it is likely that much of his talk’s content will be derived from the UCLA overview he helped prepare. This overview, entitled “The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings,” addressed the following questions:
- How quickly must we freeze a biospecimen?
- Is the ubiquitous –80°C freezer really adequate to stabilize biospecimens, or is –150 °C storage superior?
- How much does freeze-thawing, as occurs with removing specimens from freezers repeatedly, affect biospecimen degradation?
- What is the basis for the quality assurance methodologies currently in use?
The overview not only reflected an attempt to organize the fragmented and incomplete data on procurement and preservation of frozen biospecimens, it also summarized “infrastructure considerations for frozen biospecimen banking.”
Banking Viable Live Cells
Banking viable live tumor cells that can be revived later is a simple but powerful idea being enlisted in cancer research and treatment. Deep sequencing plus analysis of molecular defects may be carried out using frozen and fixed tissues, and this approach may yield finely detailed profiles. However, these profiles do not necessarily represent how a cell will respond to treatment.
“We are preserving cells so that in the future they can be brought back and used in assays that require interaction with the cell,” says Wendell G. Yarbrough, M.D., Smilow Cancer Hospital, Yale University.
“It’s not widely done now, but I think there is growing interest,” asserts Dr. Yarbrough. So far, Dr. Yarbrough has used the approach on two patients. One of them, a high-risk patient whose tumor was resected in the fall, chose not to undergo adjunct therapy. Six months after initial sequencing of the patient’s tumor, the cancer recurred.
“A few mutations were initially found for which there are drugs [available to target] those pathways. We brought those cells back from their frozen state and began testing those cells with the different drugs,” explains Dr. Yarbrough.
Banking viable cells is usually straightforward. A cellular suspension is made and cultured short-term—“zero to just a few passages, basically when there are adequate numbers.” Individual tumor types may have different culture requirements (such as special media). The cells are then frozen in liquid nitrogen. Among potential applications are personalized medicine, hypothesis generation, and pre-testing in clinical trials to prioritize which of a group of agents, singly or in combination, should be used.
Leveraging EHRs to Improve Workflow
Obtaining proper consent from patients to bank and subsequently make use of samples taken from them is an ongoing challenge. Informatics—electronic health records (EHRs) in particular—can help mitigate issues around consent acquisition and sample use management according to Stephanie Elaine Soares, Center for Healthcare Policy and Research, Univerity of California, Davis.
The sheer volume of sampling is daunting. In 2010, the number of banked biospecimens was estimated at 600 million, a tripling from a decade earlier. “So many samples go through pathology. Just in our institution we have roughly 15,000 samples and, I think, 2.4 million lab tests each year,” notes Soares. “The majority of those are blood and urine, and we have yet to figure out a way to capture all those. The big hurdle is we have to consent patients. We just don’t have the capacity.”
Biobanks located within large academic medical centers that have access to EHRs, lab information systems, and biobank information systems do not take full advantage of the capabilities provided by the EHRs. Biobanking workflows can be improved with the use of electronic data capture and exchange between these key applications. With the use of an integrated-access informatics model that incorporates EHRs directly into workflow, biobanks located within larger institutions can increase their biospecimen procurement.
The global diversity of privacy attitudes and regulations inevitably complicates efforts to effectively develop and operate biobanks. Yet biosamples and information about samples must be shared across borders to maximize their use and impact on research and the clinic. One effort to foster discussion and produce a framework for policy and decision-making is the DISCUSS Project (Deriving Induced Stem Cells Using Stored Specimens).
One project leader, Geoffrey P. Lomax, Ph.D., California Institute for Regenerative Medicine, explained that DISCUSS grew from conversations with researchers who reported difficulty depositing stem cells into banks. “We’re a funding agency, and efforts we’ve funded were encountering difficulty getting their cells into biobanks,” says Dr. Lomax.
The NIH was having similar issues, according to Dr. Lomax, prompting discussion over possible solutions. DISCUSS was the result. “We considered tackling biobanking more broadly but decided to narrow the focus to induced pluripotent stem cells (iPSCs), where there is an immediate need. The hope is that DISCUSS will contribute to the goal of developing more broadly applicable standards for establishing consent and sample use.”
Dr. Lomax is expected to provide an update on DISCUSS, which produced a 2013 paper with specific “draft considerations.” Since then, the original considerations were refined in several subsequent workshops. Although the modified guidelines reflect modest changes, says Dr. Lomax, he will discuss them at the upcoming congress.
Quality Improvement versus Research
Distinguishing quality improvement (QI) efforts from research has important ramifications for biobanking. Not only is the type of consent required different, but so is the oversight. Research, for example, requires an institutional review board (IRB); QI does not. However, the line between the QI and research is often murky, and with respect to biobanks, it can shift over time depending upon how the biobank is used.
“Let’s say a biobank is established for quality improvement. What if somebody is to use it later for research? How is that biobank to know? Must it have some sort of gate-keeping mechanism to distinguish what’s research and what’s further QI? It’s not always easily answered in black and white. It’s a continuum,” states Shannon Sewards, human subjects division, University of Washington.
Broadly, QI projects are intended to solve a particular problem and should pose no risk to patients. Almost by definition they tend to involve everyone participating in the activity in an attempt to wring out inefficiency.
Research, however, must conform to rigorous federal regulation (and the Belmont principles)—the two salient defining points being whether it is a systematic investigation and if the result will be generalizable knowledge. Also, there is typically a level of risk, of which the subjects are aware and to which they have consented.
“[Let’s say] the original intent was for QI. Then, down the line, some researcher says, ‘Hey, you’ve got some really good data, some really specimens that I could use for this research project,’” Sewards continues “The biobank must recognize that the [proposal] is not a QI project and that the investigator [needs] to get IRB oversight.”
“With genetics, we have a technology where [intent may be hard to identify]. Who knows what may happen in five or ten years? What if we were to deal with an individual who had no idea whatsoever that their data and residual sample could be used for some sort of research purpose?” It is conceivable, contends Sewards, that the individual might approve of uses for some purposes but not others.
Keys to Safeguarding Cryopreserved Cells
To attain reproducible results throughout the cryopreservation workflow, scientists are faced with ensuring that cryopreserved cells are able to reculture with high-cell viability upon thawing. To accomplish this, the right temperatures must be achieved to slow or halt cellular activity, which might cause damage to cryopreserved cells.
The temperature range of -150°C through -196°C is typical for long-term cell storage. Understanding the importance of cooling rates is critical. Rapid cooling minimizes the solute concentration effects as ice forms uniformly, but leads to formation of intracellular ice, while slow cooling results in a greater loss of water and less internal ice. A cooling rate close to 1°C per minute is preferred for cryopreservation so it is advisable to use freezing containers that meet this specification.
Researchers must understand risks and not use plastic cryogenic tubes for freezing in the liquid phase of liquid nitrogen, unless the tubes are properly protected within special tubing designed to prevent leakage of liquid nitrogen during storage. By employing a dense storage mentality, researchers can maximize space by doubling the number of tubes per freezer by using a standard box with a 13 x 13 divider, which fits 169 1.0 mL Nunc Cryobank tubes.
The last key is sample organization and tracking. Barcoded tubes are the safest way to monitor samples, as 2D codes ensure legibility throughout the life of the sample. Thermo Fisher Scientific has developed the VisionTracker™ to provide an intuitive and secure database that stores sample data and corresponding locations, whether storage is done in linear barcoded cryotubes or 2D barcoded tubes.
—Jason Xu, Ph.D., senior product maager, cryostorage, Thermo Fisher Scientific