Automated Sample Handling Systems

John S. Brussolo and Sheila H. DeWitt*

Parke-Davis Pharmaceutical Research
Division of Warner-Lambert Company
2800 Plymouth Road
Ann Arbor, Michigan 48105 USA


Pharmaceutical research and development has become significantly more complex, time-consuming, and costly. Currently, the discovery and development of a new drug requires an average of twelve years at a cost of $359 million [1]. The exploitation of molecular diversity to expedite and enhance this process relies upon current and emerging methods for:

  1. compound collections;
  2. biological testing;
  3. information management; and
  4. computational evaluation as depicted in Figure 1.

[Figure 1]

Figure 1
Methods for Implementation of Molecular Diversity Strategies
Click on Image for Full Size

However, identification of the rate-limiting steps for this process is critical to address the emerging needs of the pharmaceutical industry. Existing methods for sample handling have recently been identified as rate-limiting in this process.

Historically, compound collections or "libraries" for testing in biological assays were obtained from proprietary databases of compounds accumulated over many years, natural products, fermentation broths, or rational drug design. Recent advances in molecular biology and automation have resulted in the development of rapid, High Throughput Screening (HTS) which have significantly affected the drug discovery process. Consequently, the provision and maintenance of compounds to support HTS has become a critical task. New and innovative methods for the rapid generation of compound libraries for both lead generation and lead optimization have emerged as one method to address this need [2-4].

Compound Conservation

Pharmaceutical companies typically maintain compound collections of 50,000 to 500,000 compounds. These proprietary compound collections or libraries represent an invaluable source of diversity and every effort should be made to build and maintain a comprehensive collection. However, the evaluation of sample submission and usage data reveals some startling trends. Many companies are exhausting available internal sources of chemical diversity without providing for continued use or expansion. The trend by chemists to submit smaller amounts of samples combined with sample retrieval practices that cause unnecessary depletion of compounds severely limits the future utilization of HTS and the ability to conserve and enhance the diversity of compound collections.

A dissolved sample collection has a finite lifetime. Ideally, 25 mg of a sample can be used for 2000 assays (5 ml of a 10 millimolar solution with an average molecular weight of 500 gm/mol @ 2.5 ml per assay). In reality, however, each sample is useful for only about 250 assays (@ 20 ml per assay) using manual methods. This discrepancy is due to errors in sample handling and distribution as well as a tendency for the tester to request more sample than necessary. With an active HTS of 50 assays per year, the lifetime of the dissolved sample collection is only 5 years. Currently at Parke-Davis, 500,000 samples are directed to HTS each month. This translates into 6.2 million samples which are tested each year and a projected lifetime of the dissolved compound collection of less than 10 years. An immediate objective is to encourage conservation of samples in compound collections.

Furthermore, a growing trend is to synthesize and submit smaller quantities of compounds. This reduction in sample size ultimately limits the compounds available for the HTS. The depletion of a sample from the compound collection limits the utility and diversity of the collection. Few mechanisms exist for preventing the depletion of samples in corporate compound collections or the recovery of unused samples from HTS laboratories. Therefore, efforts to encourage the synthesis and submission of larger sample amounts and more efficient data management, storage, and distribution is warranted. Automated sample handling systems have begun to emerge to address the issues of HTS, compound conservation, and more efficient data and sample management.

System Requirements

A. Automation Hardware

There are two primary types of automation equipment, laboratory and industrial. Historically, the implementation of robotic automation has been realized in the industrial setting which requires high performance, low maintenance, high load capacities (e.g. 20-1000 lbs.), and reproducibility. Laboratory robots are limited to a payload of less than 4 pounds and require higher maintenance and calibration than industrial robots. Despite the more robust nature of industrial robots, both types of robots range in price from $25,000 to $150,000. Unfortunately, very few systems integrators have implemented industrial robots in the laboratory environment to date. This, however, is likely to change in the near future as more flexible and innovative solutions are developed for laboratory operations that share similar objectives with industrial processes.

The installation, maintenance, and support of automation equipment is critical for continued and safe use within a laboratory or industrial setting. Automation hardware needs to provide safety features and recovery from errors introduced by internal failure or external inputs such as collisions with other equipment or users. In combination with error recovery in the hardware, the software also needs to respond to the interruption to retry or abort an operation. This feedback loop can, and should, be defined by the user prior to installation.

Safety is a very important requirement when using robotic automation. The system should always provide at least one "panic" button which will immediately halt the robot movements and necessitate operator intervention before proceeding. Most laboratory robots employ a hot key, invoked from the computer keyboard, which serves this purpose. However, an ominous red button provides more visibility and doesn't require prior knowledge of the system. Alternative mechanisms employ force-activated sensing interrupts which are triggered when an operator enters into the work envelope of the robot.

The operating environment in which the automation is expected to perform can also affect the hardware construction. Although most equipment is compatible with ambient temperatures, exposure to temperature variations or humidity will impact the mechanical performance and requirements of the system. These specifications need to be determined before selection and installation of a system. Following installation, a routine service schedule implemented by an in-house support group or an external service contract is important for long term utility of the equipment.

B. User Interface

A user-friendly interface that accommodates the objectives of both conventional and advanced users of an automation system is paramount. This interface may reside on a programmed logic controller (PLC), mainframe, or personal computer (PC). However, for data transfer and manipulation, the PC is preferred to take advantage of spreadsheet, presentation, and statistical analysis software. Furthermore, the PC provides very flexible instrument control. Although it is not critical that the interface platform for instrument control match the implementation platform, it can increase the efficiency and productivity of the system operator. The operating software on the PC should provide the most efficient and state-of-the-art package. Therefore, while both Windows and DOS applications are viable, Windows is highly recommended.

The most efficient operation of an automation system requires that the sample processing be performed in batch. This means that the system processes individual data and samples as a set. However, the software must also be flexible enough to interrupt this batch process and process individual samples before resuming the batch process.

Information management is best achieved by interfacing the automation software with local or central databases. This enables the optimal storage of archival information within a database that is regularly maintained and remote from the automation system. The accessibility of this information is more important than the selection of the database management system. When considering the purchase of an automated sample handling system, a viable information management system is also recommended.

C. Data Handling

The primary objective of data handling in an automated sample handling system is to track the location of samples. Any automated system should allow and direct the user to manually locate and retrieve samples. However, if the association of data between the sample and the location is not accurate, then both the automated and the manual processes will fail.

Retaining an event log of sample transactions is necessary for both transfer to a database and for error recovery. If the system misfiles containers, review of the event log enables the user to identify the first aberrant sample. The system should also be able to recover from minor errors and notify the user when a major error occurs that requires system administrator intervention. A common minor error occurs when a file is incorrectly copied. The error-handling component of the system must confirm the event and attempt to copy the file again. For the storage of any data outside a central database, data recovery is critical. For example, processing a batch of samples necessitates transfer of the information to a database at a later time. If the system fails during the batch process, adequate backup procedures are necessary to capture all data. At least three types of reports should be provided by the software including:

  1. data transfers to and from the database;
  2. actual daily production; and
  3. error recovery and event log.

Sample containers for input into the system should be labeled prior to introduction. However, automated methods for labeling the output sample containers should be provided in the system. These protocols minimize errors in the labeling and tracking of samples for use in HTS.

Current Systems

Very few companies have succeeded in developing and implementing automated sample handling systems. Sagian, Inc. [5] and The Automation Partnership [6] are two companies which have successfully marketed products to meet these objectives. Both companies provide a modular system design with an open architecture which is fully customized to meet the requirements of the customer. A general description of the functionality of these systems is outlined below [7].

A. Sagian, Inc.

Sagian Incorporated is a vendor and integrator of laboratory information management systems and laboratory automation. Among many other applications, Sagian has developed and currently markets an integrated automated sample retrieval system.

1. Equipment & Operation

The Sagian system automates one of the most time consuming and tedious steps in the sample handling process - picking and placement of samples. To pick a sample is to retrieve it from the sample file, to place it is to re-file it back into the sample file. This system works with neat samples at ambient temperature only and is not, in its current design, able to retrieve plates or minitubes [8]. The system tracks samples completely and uses any available space for filing via a random access protocol. The capacity of the system is limited only by the available space. Currently installed systems have capacity for about 500,000 samples.

Two industrial robots are used to move samples to and from the operator area. The first is a mini-trieve robot which moves to the drawer with the target sample. This robot pulls out the drawer which contains, depending on container size, approximately 400 samples. The robot delivers this drawer to another work area where a CRS articulated robot removes the sample(s) requested, verifies that it is the correct container by passing the container in front of a bar-code scanner, and places it in a one of a series of racks which are accessible by the operator. The mini-trieve then returns the drawer to its proper location. Throughput is approximately 4800 samples per day.

*as the variety of containers increases, the complexity of the sensing and number of racks to accommodate the containers also increases.

2. User Interface & Data Handling

The electronic interface and data handling module used by Sagian is Camille. Camille is a personal computer-based "system for data acquisition and control," developed by The Dow Chemical Company and sold through certified systems integrators. Camille easily handles all of the interface, data handling, and error recovery requirements which are detailed above. Camille operates on a PC Windows platform and enables automated batch scheduling or manual interrupt for individual sample processing. The system interfaces with database management systems readily.

3. Benefits

This system effectively eliminates the extremely high labor burden and sample handling errors associated with manual sample handling. While achieving a higher sample throughput, this system also operates in a smaller area than conventional manual systems. This system also facilitates greater flexibility to creatively exploit the value of a sample file. However, the necessary manual intervention to complete the process is less than optimum.

B. The Automation Partnership - "Haystack"

The Automation Partnership (TAP) provides an automated sample handling system called "Haystack".

1. Equipment & Operation

A distinctive feature of "Haystack" is its modularity. There are numerous, discrete components which can be used alone, in combination with each other, or in combination with equipment from other vendors. The functions required by the customer drive which modules are necessary for implementation. The basic modules of "Haystack" are:

  1. neat sample handling;
  2. sample dispensing;
  3. sample dissolution;
  4. dissolved sample handling; and
  5. handling of minitubes.

The neat sample handling module is similar in function to the Sagian system. These samples are stored at ambient temperature and one Fanuc industrial robot is used for both the pick and place operations. The system delivers the proper drawer of containers by rotating into position the vertical lateral file containing the desired sample. The robot pulls the drawer out into the work area and proceeds to retrieve the sample requested. The container is verified by scanning a bar-code. In the absence of any competing tasks, the system can retrieve 6,000 samples per day. However, the system is designed to implement numerous tasks in a day. Although the system is flexible enough to accommodate a variety of containers, a limited selection improves the efficiency and reduces the system complexity. The capacity of the unit is flexible and driven by customer needs. Existing systems can accommodate a collection of 650,000 compounds.

TAP has developed a proprietary, automated sample dispensing module which can satisfactorily weigh 80-90% of a neat sample collection comprised of powders, oils, and tars. This module can be used alone or in combination with the automated dissolution and aliquoting modules. Regardless of the format, this module can be of great benefit to sample handling managers struggling to automate as much of the sample weighing process as possible. The robot delivers a container to this module which then uncaps and dispenses the targeted amount of sample, typically 5-10 mg, to a dissolution vessel. The actual weight is used to calculate and dispense a volume of solvent necessary for the user-defined targeted concentration. The robot then aliquots, in user defined quantities (i.e. 50 microliter), to minitubes until the solution is depleted. The minitubes are placed in microtiter racks and individually capped. This weighing and dissolution system can process approximately 300 samples per day. The aliquoting of 10-15 minitubes per compound corresponds to a sample throughput of 3000 - 4500 minitubes per day.

"Haystack" receives the microtiter plates on a sensor-activated conveyor belt into a temperature controlled environment (i.e. 3 degrees C) for processing and storage. The system is interfaced with a Fanuc industrial robot which accesses automated lateral drawers analogous to the neat sample module. The individual minitubes are removed from the microtiter plate and placed in the closest available position in the lateral drawers by random access processing. The throughput for sample filing is approximately 9,200 minitubes, per day. This filing capacity easily accommodates the 3,000 minitubes generated from the weighing and dissolution module while enabling retrieval of an additional 6,200 filed minitubes from "Haystack" for HTS. The automated retrieval of minitubes provide whole or partial microtiter plates based upon the request. The sample in each minitube is retained by the tester and is not re-filed in the system. This module has a capacity of approximately 10 times the neat compound module (i.e. 5,000,000 samples for 500,000 compounds)

2. Interface & Data Handling

The proprietary system software operates on a PC Windows platform and enables automated batch scheduling or manual interrupt for individual sample processing. The system interfaces with database management systems readily. Furthermore, the system has two servers which run in parallel to ensure data integrity and backup. Each server also provides its own internal backup with two sets of disks. When considering the tracking of five million unlabeled containers, the critical nature of a fail-safe system is obvious. Because the software tracks each sample by location, no manual or automated labeling of minitubes is required.

3. Benefits

Like the Sagian automated sample handling system, the TAP system also effectively eliminates the extremely high labor burden and placement errors associated with manual sample handling. The modules described also maximize available space limitations. The added functionality of dissolved sample retrieval overcomes two other major pitfalls of a manual system; sample conservation and sample throughput. By aliquoting and storing all of the available stock solution prepared for testing, samples are conserved and more is retained for future use. The ability to execute 10-15 assays with 3-5 milligrams of sample is dramatically contrasted to the previous method of dispensing 3-5 milligrams of one compound for one assay, effectively increasing the availability and use of a single compound ten times.

The higher throughput imparts a higher degree of flexibility for the tester. For example, to adequately represent the diversity in the sample file, a number of different clustering techniques may be used. Using "Haystack", these unique cluster sets could be rapidly generated to assess the utility of the clustering technique.

Summary and Conclusions

More efficient and productive methods for research and discovery in a variety of companies, including pharmaceutical research, are necessary to remain competitive. New and emerging technologies to affect these advances rely on automated systems. As the objectives of these systems are met, additional utilities and extended use are being realized. For example, although automated sample handling systems may be purchased to address follow-up screening and compound conservation concerns, they may also provide a mechanism to test and validate diversity assessment tools in the future. Continued developments in automated sample handling systems will provide expanded utilities and new applications for automation within conventional laboratory environments.

Notes and References

1. Pharmaceutical Manufacturers Association, Facts at a Glance (1992).

2. M.A. Gallop, R.W. Barrett, W.J. Dower, S.P.W. Fodor, and E.M. Gordon, Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries, J. Med. Chem., 37: 1233-1251 (1994).

3. E.M. Gordon, R.W. Barrett, W.J. Dower, S.P.W. Fodor, and M.A. Gallop, Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions, J. Med. Chem., 37: 1385-1401 (1994).

4. S. H. DeWitt. Molecular Diversity Strategies, Pharmaceutical News, 1 (4): 11-14 (1994).

5. Sagian Incorporated, 5835 W. 7th St., Indianapolis, IN 46278

6. The Automation Partnership, Melbourn Science Park, Melbourn, Royston, Hertfordshire SG8 6HB, UK

7. It is the authors' hope that the information presented in this article will facilitate an evaluation process for automated sample handling systems. The authors have investigated these two companies and offer only their own interpretation of the general features and functionality. Any misrepresentation due to out-of-date information or opinion is wholly unintentional and apology is made in advance for any misstatement of facts. To obtain a current, detailed description of the systems, please contact the vendors directly.

8. Sagian has developed sample dissolution systems and microtiter plate dispensing systems which are not seamlessly integrated with the system described here.

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