The growth of personalized medicine that is transforming the medical landscape poses a challenge to biorepositories: The old ways just don’t cut it anymore.
“If you’re just looking at histologic changes, the way we’ve been cutting and staining tissues for the last 75 years or so is fine,” says Philip Branton, MD, consulting pathologist to the Biorepositories and Biospecimens Research Branch of the National Cancer Institute. “But if you want to look at molecular changes in tissues, you have to preserve the tissues in slightly different ways. And we’re kind of on the cusp of discovery in learning how best to preserve biopsy specimens for molecular analysis.”
Researchers rely on biorepositories to maintain and supply quality biospecimens, but without a clear set of standards and procedures, biorepository staff may inadvertently change the molecular signature or otherwise damage the specimen, Dr. Branton says. And research, which drives improvements in patient care, is only as good as the quality of the specimen, says Paul Bachner, professor and immediate past chair of the Department of Pathology and Laboratory Medicine at the University of Kentucky Chandler Medical Center. “The ultimate specimen is no better than the methodologies used to get that specimen,” he says, “and that ranges all the way from identifying what the specimen should be, how it’s collected, how it’s preserved, and how it’s identified so that the ultimate user knows what the tissue is and yet patient confidentiality is preserved.”
For biorepository managers striving to understand and attain best practices, the CAP’s new Biorepository Accreditation Program (BAP) provides a clear set of quality measures and a path to achieving them. The CAP recognized that while biorepositories were growing in size and number, Dr. Bachner says, “there was very little opportunity for standardization of practice, very few resources for labs that wanted some external verification of how they were performing and how they were conforming to benchmark standards of quality.”
Like the CAP’s 50-year-old Laboratory Accreditation Program, the BAP uses a peer-inspector model. Inspectors may be pathologists, PhDs, or managers of biorepositories, and they must be involved with an active biorepository. Inspectors are qualified through a CAP training program; most inspections involve one or two inspectors. The inspection encompasses procedures for patient consent and collection of biospecimens, their processing and annotation, and their storage, transport, and distribution. Currently the program accredits only facilities that store biospecimens for research.
Before an inspection, a biorepository can get help in addressing the accreditation requirements via educational modules; applicants can assess their readiness by purchasing checklists of the requirements and performing a self-inspection, at a cost of $799 (labs that purchase the checklists and apply for accreditation within a year won’t be charged another $799 application fee). After the on-site inspection, the biobank receives a detailed, actionable performance report and a certificate of accreditation, after demonstrating that deficiencies discovered during the inspection, if any, were addressed. The program operates on a three-year cycle, with the biorepository performing self-inspections in years two and three.
Introduced last year, the BAP has now accredited seven biorepositories, and another 30 are in the application/pre-inspection process. The initial plan was to limit the early participants so that the checklists and inspection process could be fine-tuned, but the program was expanded as “additional people were banging on the door wanting to be part of the first wave,” says Dr. Branton, who serves on the Biorepository Accreditation Program working group and as a BAP inspector. The program is now open to all interested biorepositories.
Why the rush of enthusiasm? If they’re like the labs that seek accreditation through the Laboratory Accreditation Program, biorepositories “truly want to improve, and they see accreditation as a way to achieve that,” says Dr. Bachner, who also serves on the BAP working group and has 40 years of experience with the Laboratory Accreditation Program. Moreover, they may pursue accreditation to “satisfy some internal pressures; they see an accreditation stamp from the CAP as a competitive advantage; or they feel it’s an opportunity to get education for their staff.” Accreditation confers a measure of credibility, Dr. Branton adds: “If you’re being asked to receive specimens from another biorepository, you want to know you can trust the integrity of the samples you’re receiving into your own institution.”
One of the co-chairs of the BAP working group who is pursuing accreditation for her own institution says that just because she has a thorough knowledge of current best practices “doesn’t mean I don’t have to work hard to get them [biorepositories] ready for inspection.” Nilsa Ramirez, MD, medical director of the Biopathology Center at Nationwide Children’s Hospital in Columbus, says the intense self-examination that precedes an inspection “also allows you to take a good look at what you have—an inventory of services—and prepare for the future, decide where you want to go from here.” Dr. Ramirez’s center houses several biorepositories, most of which are funded by the National Cancer Institute. As an inspector, she expects to use what she learns while visiting other biorepositories to improve her own, and she expects that accredited biorepositories will begin to share information “rather than work separately in little silos.”
If it meets expectations, the program will be “fantastic” for research, Dr. Ramirez says. “It will allow institutions to concentrate on the quality of the specimens, and that will benefit patients dramatically.” Even specimens of less than stellar quality are of value to research if their limitations are understood, says Rajesh C. Dash, MD, director of laboratory informatics strategy, Duke University Health System. “If you have a biospecimen that hasn’t been controlled well for temperature, at least that is recognized to preclude temperature-sensitive downstream testing that would be a waste of money. Depending on specifics, other testing might work fine. Knowing what the pitfalls are in regard to biospecimen quality and downstream testing will be a huge boon to the community.”
One of the key challenges confronting the BAP working group was determining best practices and designing a checklist that would be appropriate for all types of biorepositories, Dr. Branton says. He characterizes the state of biorepositories in the U.S. as “kind of like the Wild West: I could have an old broken-down subzero freezer in the basement with minimal temperature controls and call it my biorepository. My inventory log could be a grubby old green notebook with a pencil hanging off a dirty string. There are probably some so-called biorepositories that aren’t much better than that,” he says. Even sophisticated biorepositories can employ different operating procedures, depending on their purpose, says Dr. Ramirez, who adds: “It’s very difficult to have a cookie-cutter approach to biorepositories because the operation, the size, and the complexity of what they do are all over the place.” For example, a biobank with 3 million-plus specimens taken from a specific, homogeneous group of patients will likely require a less complex set of procedures than a smaller biobank that stores biospecimens taken from children with cancer, because the age and sex of the patients, their geographic locations, and the type of cancer are all key variables that the procedures must address.
Tasked with determining a set of best practices that any biorepository could draw from, the working group started with guidelines published by the National Cancer Institute, which were updated late last year, and the International Society for Biological and Environmental Repositories, or ISBER, which were updated this year. Then the group sought input from biobanking experts nationwide, Dr. Branton says. Their goal was to follow the precedent set by the Laboratory Accreditation Program and “avoid being overly micromanagerial,” he notes. Regarding data collection and annotation of samples, for example, the BAP guidelines don’t spell out the process “because, for one thing, we don’t know yet what data need to be collected. But if you are collecting specimens for a given project, the accreditation requires that you show you’ve given thought to that. You have to show you know what data are important, and that you’re collecting them in a uniform manner.”
The sheer volatility of the science associated with molecular analysis is another factor the CAP must take into account, Dr. Bachner says. “So much is in flux, there’s continual change and improvement, and new methods are developed, which is why the CAP historically has never tried to dictate methodologies.”
That uncertainty takes hold at the very birth of the biospecimen. Researchers are still investigating which parameters are most important to consider when a specimen is obtained from the operating room. “Up until the last couple of years,” Dr. Branton says, “no one worried about cold ischemia time, which is the amount of time that elapses from when the specimen leaves the patient’s body until it gets into its preservative. Nobody really knows at this point what the optimal, minimum cold ischemia time is.” What is known, he says, is that loss of blood supply almost immediately causes changes in the genetic expression of cells that make up tissues. “If you’re removing a lung mass, say, the genes that are turned on and active while in the patient will undergo changes when the surgeon starts removing the tumor. If I evaluate a tumor two hours after removal, histologically it’s going to be the same, but the molecular signature may be very, very different based on what was done to it.”
The methods that biorepositories use to preserve specimens are subject not only to advances in research but also to space and financial considerations. Freezing and storage at temperatures ranging from -70°C to -200°C is still the most common method, as it preserves both DNA and RNA for later analysis, says Dr. Branton. Formalin-fixed, paraffin-embedded tissue is suitable for DNA, not great for RNA, he says. “Formalin will preserve RNA up to a point, but with long-term storage RNA tends to degrade more and it gets chopped up into smaller pieces.” Freezing also has its drawbacks, Dr. Branton points out: It’s expensive, takes up more space than paraffin blocks, and “there’s a big carbon footprint associated with running rooms full of subzero freezers.” Dr. Ramirez confirms that the expense of properly maintaining freezers can be prohibitive for a noncommercial biorepository that lacks outside funding: “We have 24/7 monitoring, and if our freezers deviate from a certain temperature, the system may page a couple of people at 3 AM. Not everyone has the money for that.” Another problem: Thawing a specimen, using only part of it, and refreezing the rest damages both the DNA and RNA. The upshot is that researchers at the NCI are investigating a number of preservatives and fixatives that will do a better job of preserving both DNA and RNA for later analysis, Dr. Branton says.
Promising advances in informatics may eventually reduce the need for freezing biospecimens. Thanks to robust IT support and a better understanding of the human genome, “the methodologies for analyzing biospecimens have improved tremendously over the last couple of years, and there’s much more that can be done with DNA that previously required RNA,” Dr. Dash says. As a result, the “treasure trove of biospecimens” that many community hospitals and cancer centers have stored in formalin-fixed paraffin blocks become more valuable to the researcher, he says.
Community-based and smaller, private hospitals often have the “pristine” tumor specimens every investigator wants, Dr. Ramirez says, because the patient goes there for the first resection and has not undergone multiple rounds of chemotherapy. But without the appropriate IT component, Dr. Dash says, biorepository staff won’t know which samples have received pretreatment and which haven’t. “And that’s where the electronic health record, and the data elements contained in the lab information system, need to tie together with the biospecimen in all the downstream testing data to allow researchers and clinicians to come to reasonable conclusions based on the results they get.”
As molecular testing and analysis become more routine in the community hospital setting, pathologists there have a key role to play in building the quality and sophistication of their biorepositories, Dr. Dash says. In a white paper published in Archives of Pathology & Laboratory Medicine (Dash RC, et al. Biospecimens and biorepositories for the community pathologist. 2012;136:668–678), he argues that pathology’s traditional role in storing biospecimens used in clinical care can naturally extend to establishing quality biorepositories for research and clinical care.
Community hospital pathologists who want to establish a biorepository for research face logistical and resource challenges. In an academic medical center where a biorepository is funded, a pathologist or biorepository staff member can ensure that appropriate clinical data are collected and take care of a specimen from the time it’s removed from the patient “to the time the pathologist involved in the clinical care says you can have a piece of the tissue,” Dr. Ramirez says. In a community hospital, pathologists are not compensated for any of those activities, not to mention the cutting, preservation, storage, and tracking of biospecimens. “Somebody has to pay for that. Where are those resources coming from?”
Dr. Dash agrees that a community pathologist shouldn’t be expected to take on those extra duties without compensation, but he poses an alternative approach: Make the case to hospital governance that in the era of personalized medicine, many of these procedures are required for better care of a patient. “Then I think it’s very reasonable to make the request of the surgeon, the OR nurses, the pathologist, the technician, to do that little extra bit of effort and document in the clinical chart” all the information necessary to establish “a robust chain of custody so you know what happened to that specimen.”
The bottom line for pathologists, Dr. Dash says, is that they’re the physicians in the best position to champion the importance of quality biospecimens and the data associated with their testing. To that end, “the BAP can really serve as a valuable resource to pathologists, regardless of their level of experience,” to assess and document the strengths and shortcomings of their own programs, then take the information to their leadership to remedy issues “that might be very difficult for them to find funding to fix without some external, unbiased review.”
Jan Bowers is a writer in Evanston, Ill.