April 15, 2005 (Vol. 25, No. 8)

Maintaining and Tracking Samples Safely and Efficiently with Integrated Components

Many pharmaceutical companies and research institutions are looking for more efficient ways of managing their high throughput drug discovery processes. HTS typically requires the assembly of focused sublibraries for primary HTS screens, cherry picking of groups of hits for appropriate reformatting for secondary screening, and performance of the required assay screens.

Compound libraries have become larger and more diverse. Regulatory requirements have increased the demands on sample management and storage systems for drug discovery applications. Valuable samples have to be stored over long periods of time for clinical trials. Business factors such as globalization, mergers, and acquisitions have made management issues difficult.

Sample tracking, which is critical, is challenging when attempted in multiple sites, instruments, and formats. Integration of all components of sample management and storage systems to suit a particular requirement is key, according to most manufacturers.

“Careful thought has to be given to sample handling, especially in the area of 384-tube storage and picking techniques,” says Kelly Warrington, Ph.D., life science marketing director of RTS Life Science International (www.rts-group.com). “A reliable automated solution minimizes the risk of handling hazardous substances, while reducing the likelihood of sample confusion and loss.”

“Some compound management systems are local to a company, some are global, and others are centralized,” according to Peter Woods of The Automation Partnership (TAP; www.automationpartnership.com). “Coordination of systems across multiple sites is critical for an effective drug discovery organization.”

“We see a shift of focus from the quantitative aspects of sample management toward quality of sample storage and processing,” says Donat Elsener, sales and marketing director for Europe, Remp (www.remp.com). “A similar trend is the move toward screens with focused or targeted libraries, again, more quality than quantity.”

Dr. Jas Sanghera, commercial director, TTP LabTech (www.ttplabtech.com), stresses the need for flexibility in compound management systems. “With today’s changes in business markets, business unit reorganizations, and company mergers, physical relocation of staff and facilities is a major challenge for hard-pressed management.

“Sometimes, existing libraries have to be consolidated, while on other occasions, libraries will be split up to provide distributed satellite storage.”

When TTP LabTech added wheels to its compound tube cherry-picking sample store, the company anticipated that the stores would be moved only a few meters for service and support. Now the system’s modularity is proving to be valuable to customers who need to resituate their labs for business or process reasons.

Typically, downtime is only a few days, building work is kept to a minimum, and no expensive dismantling of the system is required. “ComPound’s flexibility helps with a variety of scenarios because it fits into a standard laboratory, and its built-in refrigeration eliminates the need for special building or services,” Dr. Sanghera adds.

Remp has provided huge sample storage and retrieval systems to large pharmaceutical companies, as well as attempting to increase the quality of sample storage in parallel in combination with the development of optimized consumables, according to Elsener.

Fulfilling Demands

The objective is to fulfill the demands created by the current trends, such as high sample integrity and fast and easy library reformatting.

“The introduction of individually sealed tubes, and the concept of storing small aliquots ready for single use, eliminated unnecessary freeze/thaw cycles, reduced carry-over and dilution effects, and greatly reduced water uptake and exposure to air,” Elsener says.

“The exposure is intrinsic to traditional sample preparation and liquid/solid transfer steps. Our tube-punching mechanism has also led to a decrease in the error rates for tube picking as compared to traditional pick and place methods.”

Tubes are manipulated in a punching fashion using an automated device, the Remp Tube Punching Module (TPM), according to Elsener. All tube transfers are logged in a database so that tube locations are always known. An optional 2-D DataMatrix code can be applied on each tube for redundant identification and verification.

A controlled dry environment makes it possible to store dissolved compounds in DMSO for several years with minimal deterioration in sample quality. Other tube formats can be closed either by individual seals or with individual caps. Devices and consumables enable sealing, piercing, capping, and decapping the tubes in both automated and manual formats.

The Remp Tube Technology enables focused screening and library management, according to Elsener.

Targeted libraries can be assembled in a controlled storage environment using the company’s modular software package to cover all aspects of sample preparation and management or only powder dosage, compound dissolution, sample storage, and retrieval in automated, semi-automated, or manual sample stores, as well as plate production.

The software can be instituted globally to support research activities within multiple sample storage facilities around the world.

Remp’s Automated Plate Replicator (APR), a system for high-quantity plate storage and screening, minimizes water absorption and exposure to air. The latest addition to this product line is the nanoAPR, which enables the mass production of low-volume, high-density plates in a dry environment, according to the company.

Increasing Efficiency

TAP’s Solar automated -20C DNA archiving system is designed to increase the efficiency of genetic analyses. The system includes in-store arraying (cherry picking) of individually 2-D-coded samples and controlled thawing, mixing, and pipetting.

Solar, a liquid inventory management system for life science applications, integrates TAP’s storage and liquid-handling technologies, according to Ian Ransome, director of sample management and screening at TAP.

Keeping all the samples in one place and plating DNA samples at normalized concentration within a range of different volumes enables researchers to set up a Phase III genetics study in one day, instead of up to six weeks, Ransome says.

Because there is no manual handling, Solar minimizes errors. Because individual samples can be cherry picked without removing the entire tray, it is easier to maintain long-term sample integrity, according to TAP.

RTS has developed four high-density sample storage systems, as well as software and tracking systems. They include compact, high-density storage trays, as well as three-way robotic grippers, 384-tube handling, flexibility for multiple storage formats, and temperatures ranging from ambient to -80C, Dr. Warrington says.

The company also has developed a new picking head that pushes tubes from the top of the source 384-tube plate through to a receiver plate positioned below. The receiver plate is shifted to an open position as more tubes are picked until it is full.

In addition, RTS software performs initial collection of screening sets, processes results data, and automatically coordinates compound retrieval and reformatting of hits for subsequent assaying. Integrated compound storage and reformatting capabilities are designed to turn primary and secondary screening campaigns around from locally held compound storage.

Robotic Approach

Bioanalytical Systems (www.bioanalytical.com) offers the Sample Sentinel Programmable Autosampler, which provides a robotic approach to liquid chromatography autosampling for microbore, standard bore, or preparative applications. By moving the sample vial to the sampling, diluting, or mixing stations, the autosampler eliminates the need for complex mechanical drivers, according to the company.

A sample cooling option is available for applications involving labile samples requiring storage at reduced temperatures, and a sample preparation capability option enables the unit to provide multiple derivatization and dilution functions, as well as vortex mixing with selectable heating of the vortex chamber.

WellMate from Matrix Technologies (www.matrixtechcorp.com) offers disposable, presterilized tubing cartridges and dispensing in a wide volume range (12,000 L). It accommodates microplates from 6 to 384 wells or any height 96-position tube rack.

For automatic filling of multiple microplates, Matrix offers the WellMate stacker, an automatic plate storage and handling module. The stacker unit shuttles microplates between the stacker unit and the WellMate dispensing head for unattended microplate filling for up to 25 or 50 microplates.

By raising or lowering the dispensing head to the required height, WellMate can handle anything from deep and shallow well plates to storage tubes as tall as 89 mm. Disposable, presterilized tubing cartridges have standard or small-bore needle options.

GenPlates are the core of GenVault’s (www.genvault.com) integrated biosample management system, according to David Wellis, vp, business development. This building block eliminates the need for freezers and liquid nitrogen tanks while maintaining biosamples in a stable format suitable for long term archiving, automated retrieval, and simplified distribution, he says.

The 384-well GenPlate contains 6-mm disc-shaped elements of Whatman (www.whatman.com) FTA paper in each well and allows biosamples to be stored at room temperature.

Each element within the GenPlate is an experiment-sized aliquot that can be removed without risk of cross-contamination or sample degradation from multiple freeze-thaw cycles. Additionally, the GenPlate is approximately half the height of a standard multiwell plate for maximum storage efficiency.

The basic GenPlate, which is configured to hold a single patient sample across 384 aliquots, requires about 4 mL of biological fluid to fill the entire plate. The sample is applied directly to each element within the GenPlate and allowed to dry.

Cells within the sample lyse upon contact with the FTA material and the extruded DNA binds to the cellulose matrix. Then the GenPlate is sealed and ready for short- or long-term archiving.

FTA inactivates bacteria and viruses upon contact, allowing sample shipping without any biohazard labeling. DNA stored on FTA paper as long as 14 years ago has been recovered in sufficient quantity and quality for current genotyping techniques, Wellis adds.

Once a sample is applied to a GenPlate, chain of custody is established. Each GenPlate is labeled with a unique physical barcode, and each element within the GenPlate is labeled with GenCode, GenVault’s biological barcode, which permanently identifies the actual sample regardless of its physical state.

GenVault and Whatman are collaborating on the EasyClone 384 plate, which is designed to deliver shipping, storage, and backup of sample or samples to the clone market by formatting Whatman technology into a 384-well storage and extraction plate designed by GenVault. The plates will be based on the FTA technology.

Downstream Analysis

Qiagen (www.qiagen.com) provides products for preparing nucleic acids and proteins for downstream analysis. QIAamp and QIAamp DSP Kits purify genomic DNA or viral DNA and RNA from clinical samples in spin-column, 96-well plate and automated formats. DNeasy Kits purify DNA from animal and plant tissues. The PAXgene Blood DNA system standardizes blood collection and stabilization and DNA purification.

Qiagen offers kits for small-scale purification of plasmid DNA at molecular biology, sequencing, or transfection grade, as well as kits for large-scale purification of plasmid DNA at transfection or advanced transfection grade. Kits in spin-column or 96-well format are available for PCR cleanup, gel extraction, enzyme reaction cleanup, nucleotide removal, and dye-terminator removal.

RNeasy Kits purify RNA from a wide range of sample types and sizes in spin-column, 96-well plate, and automated formats. The PAXgene Blood RNA system, RNeasy Protect Kits, and RNeasy Bacteria Kits combine stabilization of blood, tissue, or bacteria with RNA purification. The RNeasy MinElute Cleanup Kit enables cleanup of RNA samples with elution in small volumes.

There are Qiagen kits for micro- to large-scale purification of 6xHis-tagged or Strep-tagged proteins, as well as kits for removal of His tags from recombinant proteins. Automated formats are also available for a variety of throughputs. The new range of Qproteome Kits provide a method for reducing sample complexity in proteomics samples, facilitating analysis of low-abundance species, according to Qiagen.

Qiagen’s BioRobot EZ1, M48, and MDx automate the purification of nucleic acids up to 96 clinical samples. For high throughput research applications, BioRobot systems are available for purification of DNA, RNA, or 6xHis-tagged protein.

BioSprint 15 and 96, which process 15 or 96 samples per run, provide economical sample preparation for smaller research labs. The TissueLyser simultaneously disrupts up to 192 biological samples, including cells, tissues, plants, and bacteria.

The Next Logical Step

What does the future bring? According to Dr. Warrington, “The next logical step is linking screening and storage together in an integrated system. RTS has begun a collaboration with Novartis (www.novartis.com) to create a combined store and ultrahigh throughput screening system (RTS Symphony) that generates one million data points per day and maintains 48 hours of unattended operation.”

Woods concludes, “New demands on sample management and storage are being introduced because of the attrition rate of new drugs from clinical trials. Picking for in silico screening, support of chemical profiling, and the evolution of compound libraries also will put pressure on the compound management systems.”

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