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Sep 15, 2011 (Vol. 31, No. 16)

Sample Integrity in Biobanking

Tips and Tricks to Optimize Preservation and Monitor Biorepository Specimen Handling

  • Destroy the Matrix

    Click Image To Enlarge +
    Cohorts of extracted DNA samples used for subsequent SNP genotyping at KBioscience

    KBioscience isn’t a biobank in the traditional sense: “We destroy the matrix,” explained sales director Niels Kruize. Rather, blood, tissue, saliva, and other biologicals including agricultural samples such as seeds, are processed into DNA as quickly as possible, and it is this that is banked for the CRO’s customers.

    Sample collections are often larger than the customer can hold and need to be condensed, normalized, and standardized. Sometimes they come in with labels that are wrong or just can’t be read.

    Among the first things KBioscience does is separate these out and apply common barcodes to all the tubes and plates they get in. Samples are then transferred to individual barcoded tubes. “That’s a critical step,” Kruize said. So critical, in fact, that they dedicate two people to the process, “to make sure that you get the right sample into the right tube.”

    Samples are mixed with buffer and silica, and as such can remain stable at room temperature for weeks. There is no need for a precipitation step during purification. Eluted samples are tested—including a 220–350 nm scan to test for purity, PCR-based genotyping, and customer-specific assays for quality control—and aliquotted into three portions.

    Of the eluted DNA, 80% goes into the 2-D barcoded tube, and 10% goes into plates that are shipped back to the customer. The last 10% is frozen down at -20°C and stored at KBioscience for future SNP genotyping.

    The tube with the remaining silica resin, still containing a small percentage of the DNA, is dried and then taped to and stored along with the original sample tube and housed off-site for long-term storage. All fractions remain the property of the customer.

    Every step along the way is controlled and documented in the company’s custom LIMS. But rather than automating the entire process, which Kruize explained would have been too expensive and error prone, “we buy simple plastic trays and we label them per project. Individual plates and tubes go in these labeled barcoded trays and can be retrieved at any given time.”

    Within days of the conference, it was announced that KBioscience had been acquired by LGC and will join with LGC’s genomics division.

  • Extremeophiles Turn Up the Heat

    Shadow storage can guard against a catastrophic failure. But that doesn’t change the fact that “it’s very difficult to handle cold-chain logistics,” pointed out Rolf Muller, Ph.D., CSO of Biomatrica. “This goes for the life of the sample from collection, transport, and analysis, to storage.”

    Freezers are very expensive to operate, equipment-intense, unreliable, and environmentally unfriendly. Dr. Muller thinks it’s time for a paradigm shift—for scientists to get past the “paranoia” of the last 100 years of thinking that the only way to protect our samples is to stick them in the freezer.

    There are extremophiles called anhydrobiotes that can survive in a dry state without refrigeration, preserving their DNA, RNA, proteins, and cell membranes intact. Biomatrica set out to mimic this process in a laboratory setting.

    Beginning with large libraries of potentially stabilizing molecules, the company utilizes “screens to define the best way to stabilize these biological materials at room temperature,” Dr. Muller said. Among the company’s offerings are products that essentially turn the solution into glass and “shrink-wrap every single biomolecule in the sample.”

    More recently, the company has developed room-temperature liquid stabilization tools based on osmolytes found in organisms around thermal vents—“molecules that prevent the degradation of proteins in hot environments.”

    Stabilization in liquid has the advantage that the sample needn’t be dried down or speed-vac’d. The sample is stored or transported just like traditionally frozen samples, only they needn’t be put in the freezer or shipped with dry ice.

    Having samples at room temperature can facilitate a lot of projects that are ongoing in Third-World countries where samples can be collected in fairly crude locations and crudely done, explained Rod Westrop, Ph.D., director of European operations for GeneVault (acquired in February by IntegenX).

    “Biomatica’s products, we believe, will aid that process by stabilizing the point of collection so that you’re getting good quality material coming through.”

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