January 15, 2008 (Vol. 28, No. 2)
Personalized Medicine Brings Unique Requirements for Managing Specimens
The importance of standardizing conventions for storing biological samples is becoming increasingly obvious, and the growing need for standardization was the focus of Informa Life Sciences’ “Biobanking and Biorepositories” conference held in Munich in November.
Attendees from national biobanks, pharmaceutical companies, and key industry and government bodies came to learn about the latest developments and regulations in this fast-growing industry. Case studies presented at the meeting revealed ongoing conundrums and some of the resultant solutions.
One thing everyone agreed on is that standards and normalization across the field are imperative. Scott D. Jewell, Ph.D., associate professor of pathology at Ohio State University, presented a case study on how his lab has dealt with potential adverse events in downstream storage.
“In cancer research, there is an increased focus on documenting and improving the quality of biospecimens prior to downstream analysis. It is important to know how the samples were collected, processed, and stored. It is also important to document that biospecimens are managed in the same way,” said Dr. Jewell. “The larger the pool of samples, the more important it is that those samples are managed in standardized procedures and as equal as possible to one another.”
Dr. Jewell also discussed the importance of preanalytical and postanalytical storage of biospecimens. “These parameters may affect the quality of biospecimens. Determining the best practices with data-driven standards and putting them in place is of utmost importance.”
“In our related research, we’re trying to define the utilization and utility of specimens based on quality control measures,” explained Dr. Jewell. “And the question we’re asking is, can we develop the ability to measure molecular markers within the tissue to predetermine the quality of the tissue prior to use in research. Right now, it’s a paper in progress.”
Specimen collection and storage conditions performed by different laboratories create variations in specimen quality. According to Dr. Jewell, although differences in specimen quality can be detected, little is known about the effects on test results when the samples are used. “Research into this critical aspect of biobanking has not received the attention it deserves, consequently, standards to ensure sample quality have not been ideal.”
To that end, Dr. Jewell’s group froze tissues samples from the gastrointestinal tract under different conditions and measured induced affects by comparing the quantity of mRNA for molecular markers used for routine diagnostics. The samples were analyzed at various intervals to document the change over time for storage conditions of packaging and temperature.
“We wanted to document if deterioration could be measured and to what degree samples deteriorated based on various conditions,” said Dr. Jewell. “We wanted to see what happens to the sample and, ultimately, how useful that sample is. We found that the quantity of the marker can be lost quickly, suggesting that the usability of frozen tissues for some downstream analysis may degrade as well.
“We hope to show that quality specimens make a difference and that standardizing practices for tissue preparation storage would make things simpler, not harder, for scientists,” Dr. Jewell noted. “One possible measure would be to ask journals to place a higher importance on more thorough materials and methods for biospecimen collection and storage. It would help science move forward by enabling researchers to better understand data more quickly.”
Large-scale biobanking poses two new challenges to the automation community, observed David Harding, technical director of RTS (www.rts-group.com). The first challenge is to ship and prepare samples in controlled environments within short time periods. The next challenge is the storage of biological samples where low-temperature requirements coupled with concerns such as avoiding unnecessary thawing/temperature increases are generally seen as key.
Not surprisingly, the challenge arose from UK Biobank, which has defined a protocol for the fractionation of whole blood. UK Biobank is in the process of collecting five blood samples each from 500,000 people to provide a resource for researchers to study correlations between disease, genes, and the environment.
Manually fractioning blood, Harding noted, is time consuming. “A single lab technician can fraction around 50 samples a day, which includes other operations like tube labeling and recapping. It’s easy to see that processing 3,500 samples per day would require a fairly large workforce. Automation was the obvious solution.”
The UK Biobank issued a request for proposals (RFP) knowing that there were no standard machines to fractionate blood according to its protocol available on the market. “Our team reviewed the RFP and not only was it clear that high throughputs were required at a level where our industrial approach would be a benefit,” Harding noted, “but it also seemed possible that our computer vision technology and expertise could be put to good use as well.”
Harding’s team took images of spun blood at a local university and processed them with the RTS Vision System. While it was clear that the RTS system could identify the two interfaces between the three layers of blood, there were many practical challenges to overcome to turn this concept into reliable automation. “These included the variability of blood samples and performing the whole protocol at a reduced temperature,” Harding explained. “So, we embarked on a collaboration with UK Biobank to solve the problem of identifying and separating all three layers in the blood in a reliable automated fashion.”
The combination of the Vision System with the company’s high-throughput automation went live in April 2007 and is now processing samples from over 300 participants a day, six days a week. From each participant, six tubes (five blood, one urine) are obtained, and four are processed on a fractionation system. “The Biobank processes 1,800 samples a day, operating with four technicians,” Harding noted.
Finally, Harding addressed the problems associated with automated sample storage. “Currently, -20ºC is the standard,” said Harding, “but we are in the process of researching and developing a -80ºC storage unit. Our solution solves key hurdles of temperature stability of the sample, frosting, and the price.”
Conventionally, storage of biological samples has been dominated by freezing and fixation techniques. “These techniques have major limitations such as lengthy preparation of samples with associated risks of sample deterioration, cost of maintenance at low temperature, and creation of artifacts due to invasive procedures,” noted David Wellis, Ph.D., president and CEO of GenVault (www.genvault.com).
Novel Storage Technologies
“GenVault is developing environmentally friendly methods of storage to reduce the need for sample manipulation; facilitate storage, transport, and retrieval; and, ultimately, improve the quality and efficiency of research.” This makes it possible to store these samples at room temperature.
“We are wondering if cryogenics will be the way forward,” Dr. Wellis said. “Typically, samples are stored in a freezer, which is not efficient. We started in this field concentrating mostly on collecting and preserving DNA samples; now, we are developing new matrices and protocols for transporting, storing, and recovering RNA and proteins at room temperature.”
The foundation of GenVault’s technology is the FTA card, which is filter paper impregnated with a proprietary mix of chemicals to lyse cells, to prevent bacterial growth, and to protect DNA. Such cards have long been standard in forensics and animal health.
“What we’re doing is not all that new, but we’ve enabled novel applications by improving the workflow around the card. And, in leveraging a proven, viable technology that already exists, we find that we are gaining attention and penetration in the worldwide market.” GenVault has also extended room temperature biosample management beyond DNA to RNA and proteins with two new storage matrices: one, nanoparticle based and the other, elastomeric based.
Standardization of sample handling is another concern. GenVault has a number of national biobanks using its technology, and it is finding that customers are eager for standardization.
Probably the biggest argument for this technology, Dr. Wellis noted, is how green it is. “If you move your samples out of a single freezer into one of our space-saving archive systems, how much money do you save?” said Dr. Wellis. “It’s like taking four cars off the road and saving acres of forest. As interest grows in sustainability and reducing energy costs, storing samples at room temperature becomes increasingly attractive.”
Extraction of New Data from Older Samples
Biological samples have been collected for many decades, and many sit untouched in large repositories. “One of the first questions anyone asks after looking at samples that have been stored for over 25 years is can I still use them,” said Randi Gislefoss of the Norwegian Cancer Registry (www.kreftregisteret.no). “Researchers have long realized the huge potential of these poorly explored resources and are developing new methods to extract further information from older samples.”
The Janus serum bank was initiated by the Norwegian Cancer Society in 1973 and has been storing samples since its inception. Janus now stores serum for about 330,000 people. “Nowadays, we only collect samples from Janus donors who have developed cancer,” said Gislefoss. “And when you are dealing with cancer, you need extensive follow-up time to generate the required number of cases for a research project.”
As of October 2007, 38,000 cancer cases have been registered in Janus, and the biobank material has so far been used in more than 50 epidemiological studies and has generated 60 scientific publications. This collection has also allowed Gislefoss’s group to study the effects of time on samples.
“Of course, there will be preanalytical influences that will affect the long-term quality of the sample like exposure to light, but we looked specifically at what happens during storage,” said Gislefoss. “And not surprisingly, the biggest problems were evaporation, degradation, and changes in protein conformation.”
Much More than Store and Retrieve
Biotechnology and pharmaceutical companies face a number of key issues, noted Graham Wilson, EU business development manager at LabVantage (www.labvantage.com).
First, managing the increasing number of biospecimens generated during clinical discovery, clinical trials, and when establishing patient registries is becoming more and more complex. Second, the costs to collect and maintain these biospecimens are continually growing. “To collect a single vial of blood can run into hundreds of dollars, with pharmacogenomic samples collected in rare studies costing over $10,000 per biospecimen,” said Wilson.
In addition, companies are under unprecedented pressure to meet heightened regulatory and privacy compliance, necessitated by different regulations. With personalized medicine starting to take a firm hold, integrating discovery and development is imperative and requires a link between every sample, treatment, case history, and outcome.
An efficient and effective biobanking solution covers many facets of specimen handling, location management, data collection, chain of custody, aliquot generation and management, and more, while also adhering to strict and verifiable governing policies. “The solution has to deliver a mix of both functional and operational features while also providing tangible benefits and return on investment,” said Wilson.
The take-away messages from the meeting were both industry and solutions oriented. The trend toward personalized medicine is taking shape at a rapid pace and will require more sophisticated methods and solutions for banking and managing biospecimens. This combined with the overarching requirements to curb discovery and development costs while also driving products to market at a faster pace and assuring the product’s safety demands that a biobanking solution meet complete and exacting standards.