Biobanking: Improving Process to Solve Problems

Process automation can help make biobanking more efficient, but each biobank is unique, and each automation solution will need to be unique and flexible too.

The term “biobanking” is hot right now, but it may have many biologists scratching their heads and wondering: biobanks? What is a biobank?

The latest Promega Webinar covered tools to increase productivity of biobanks and some of the challenges facing modern biobanks. Here I expand some of the discussion of this webinar, specifically talking about the wide range of biobanks that exist today, and the challenges facing biobanks to ensure the best care and use of what are, in many cases, “nonrenewable” resources for researchers.

Biobanks have been around for a long time, and most of us have used them at one point or other in our careers. Have you ever ordered cell lines from ATCC (American Type Culture Collection) or any of the Health Protection Agency Culture Collections? If you have, then you have benefited from the services of a biobank. C. elegans researchers have the Caenorhabditis Genetics Center (CGC) from which they can order a host of genetically defined strains of the nematode C. elegans, and CGC has been around since 1978.

Originally established in 1862, by Brigadier General William Hammond, as the Army Medical Museum to collect specimens from the American Civil War, the Armed Forces Institute of Pathology (which was shut down in 2011 to have some functions become part of the new Joint Pathology Center), was an amazing biobank, with samples of historical importance, including samples from the autopsy performed after the assassination of U.S. President Abraham Lincoln in 1865. Samples from this tissue collection also have been used by modern researchers to study the 1918 flu pandemic.

Blood donation centers maintain critical biobanks.

Biobanks can take many forms beyond collections of tissues or cells. The agricultural industry may preserve genetically modified crop plants as large fields of corn or soybeans. Biobanks of preserved insects or collected and pressed plant materials also exist, and some of these collections may include samples from species that are now extinct or extremely rare. Many hospitals maintain collections of anonymous residual samples that can be used for clinical research studies. Blood and plasma donation centers must maintain biobanks, as must commercial entities that maintain collections of umbilical cord blood, sperm and other human tissues.

One challenge for biobanks is maximizing the use of what can be a “nonrenewable” resource for researchers. For instance historical tissue samples such as the fixed tissue samples from soldiers who died from the 1918 flu pandemic, are extremely limited. So when DNA is extracted from such samples, it’s important for the extracted DNA to be high-quality, of known concentration and usable in downstream assays. Many biobanks are turning to automation to look for ways to increase throughput and efficiency.

According to Tim Sheehy, director of global genomics at Promega and the webinar speaker, a good system will result in higher throughput at a lower cost, with greater reproducibility and give the staff at the biobank the ability to continuously improve their processes as new technology is developed.

Some principles that seem to be emerging about biobanking are:

• All DNA, protein and RNA extraction from the sample should be tracked in one single sample tracking database. Let the robots do the tracking and provide the manifests to eliminate the Excel spreadsheets that provide too many opportunities for copy/paste errors.
• Move prequalification steps upstream in the process: For instance, when extracting DNA from a sample, include quantitation upstream and normalize the samples all to a standard concentration that will work with the anticipated downstream assays. Perform an assay that includes an amplification step upfront, to make sure the DNA is suitable for the kinds of assays biobank users will be most likely to perform.
• Automate the things that can be automate to free staff to do the more important things, like monitor quality and learn new techniques and new technologies so that the biobank can be continually improved.

One problem that was highlighted in the webinar by Sheehy and seemed to generate interest among the participants was the problem of DNA quantitation. DNA quantitation is notorious for variation among labs, but for biobanks to be able to efficiently pool their resources, a international quantitation standard would need to be established. The first step toward this was taken with a study to see just how bad the problem is. In a paper by Brown et al., DNA aliquots varying in concentrations between 10 and 300 ng/µl were dispensed into 96-well plates by a coordinating study center and then shipped to a variety other centers for quantiation by fluorescence emission and absorption spectroscopy measurements. As expected there was huge variation in the result returned by the study centers. This paper clearly documented the variation that exists and the need for a standard protocol for DNA quantitation.

This becomes important when combining resources from multiple biobanks for a study, which will certainly become more of an issue as clinical research studies seek to include more diverse sample types. The standard procedure is also important given the trend of researchers to request more DNA than they need because they often use some of the DNA to perform their on quantitation before they begin their downstream assays. In order to preserve what can be extremely precious samples, the quantitation by the biobanks needs to be completely reliable for the researcher.

Biobanks have become much more than cell and tissue repositories that serve the laboratory researcher, they are historical repositories of flora and fauna on earth, genetic change, and a source for amazing new large scale genomic and proteomic studies to better understand biological systems. They provide the correct blood or stem cell tissue to the correct patient, and they are bringing the power of scale to biological research in unprecedented ways.

http://www.promega.com/webinars provides a schedule of upcoming webinars. In addition there are links to previous webinars that allow you to either view the recording or download a pdf of the presentation. There is also a pdf of additional material available for each past webinar.

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