Projects and improvements under way in the Biospecimens Accessioning and Processing Core include:
- Automated freezer storage. Additional minus 80 degrees Celsius freezer systems, similar to the Nexus freezer systems, will be installed in 2013. These freezers will store 1.5 million biological specimens in 1.4-milliliter cryovials and have the ability to robotically retrieve them from storage.
Tissue accessioning in the Research Laboratory Information Management System (RLIMS). The Biospecimens Accessioning and Processing Core has partnered with the RLIMS team to define the business needs and work flows to track tissue processing. Tissue specimens arriving in the core will be accessioned into RLIMS and tracked in the freezer systems.
Study groups will have the opportunity to add quality assessment data to those tissues to track information such as diagnosis, percent tumor and size. The data tracked can be customized for each study and entered by their collaborating pathologists.
The quality assurance review can be completed several times with each freshly cut hematoxylin-eosin (H&E) stain, allowing for up-to-date information on the tissue block as the tissue is consumed. The core is also exploring robotic retrieval systems for storing tissue in a similar fashion as the blood products in the Nexus BioStore.
Prospective DNA fingerprinting. In September 2012, the Biospecimens Accessioning and Processing Core and Gene Analysis Shared Resource started fingerprinting newly purified DNA as part of a project called Sample ID Validation. A small amount of DNA is analyzed on the Sequenom using 24 single-nucleotide polymorphisms (SNPs) for fingerprinting.
The resulting data will be assessed to determine if:
- The reported gender of the individual matches the DNA fingerprint
- Matching DNA fingerprints list the same Mayo Clinic ID
- Matching Mayo Clinic IDs have the same DNA fingerprint
- The initial DNA fingerprint matches DNA sequences reported in other downstream analysis
Fingerprinting is performed on all DNA purified from blood or saliva. Nonblood and nonsaliva DNA fingerprinting is planned for late 2012. Fingerprinting RNA and externally submitted samples will be explored at a future date.
DNA migration into RLIMS and Nexus. The core implemented a Nexus BioStore freezer system in 2011, allowing for the robotic retrieval and organization of samples. The robotic sample pickers can run several retrieval requests throughout the day and night and will organize these optimally for downstream processing. More than 90 percent of the samples retrieved from core storage include DNA, though legacy samples were in a tube format not compatible with the robotic system.
In June 2012, the core began transferring the legacy DNA into robot-compatible tubes and storing samples in the Nexus BioStore. In the first quarter of 2013, more than 250,000 legacy samples will have been transferred, allowing for faster specimen retrieval and pre-analytical preparation.
Added instrumentation for DNA purification, quantification and storage. In September 2012, the core implemented several new instruments to facilitate prospective DNA storage in tubes compatible with the Nexus BioStore, double-stranded DNA (dsDNA) quantification and DNA volume inventory. A PerkinElmer Janus liquid-handling robot was integrated with RLIMS to robotically prepare blood and saliva products for automated extraction. The purified DNA is transferred into robotic freezer-compatible tubes using the Janus robot while updating sample identifiers and locations in RLIMS.
DNA samples are quantified using the Trinean LabChip DS, and the resulting dsDNA and total DNA concentrations are automatically recorded in RLIMS. Previously, the dsDNA and total DNA concentrations were assessed using two or more platforms. The addition of the Trinean LabChip DS cuts the cost in half to determine both concentration values. It also consumes less DNA volume in order to perform the analysis.
DNA sample volumes are determined using the VolumeCheck and recorded in RLIMS. This instrument uses sonar to detect the meniscus of the specimen and calculates the volume for each tube type. The VolumeCheck is run after each manipulation of the DNA sample, providing researchers with an accurate inventory of their samples.
- TempTrak freezer monitoring system. The core is installing TempTrak monitoring systems on minus 80 degrees Celsius upright freezers. This system will have added temperature monitoring as well as enhanced and more accessible temperature reports.