Liquid-handling robotic workstations for functional genomics

1. Justification for automation 

Robots have several advantages over manual sample processing in the laboratory1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14.: Robotic workstations perform consistently and learning curve-free from run to run, 24 hours a day/7 days a week. Robots increase throughput, report each step to a log file, reduce labor costs and ensure a safe lab operation. Robotic workstations also allow principle investigators in the beginning of their careers and established investigators, if qualified personal is difficult to maintain or to attract, to maintain a fully operational laboratory. But despite the huge benefits of establishing an automated laboratory, the required budget and space, the limited training options for new workstation users and the challenges to organize the material and data flow should also be considered.

2. The right automation strategy: Flexibility versus throughput 

The optimal degree of laboratory automation depends on the laboratory setting. Flexibility is in general the priority in academia and throughput in industry. But there is a trade off between flexibility and throughput. If high flexibility is required, then throughput is generally low. In academia, a bench approach is mostly sufficient, since it allows higher flexibility. In genomics facilities or industry-like laboratories, a workstation approach with medium flexibility and medium throughput is mostly appropriate. This semi-automated approach with lab technicians moving the plates from station to station combines the benefits for higher throughput and human-error free runs with a reasonable investment fitting to the laboratory's budget. If throughput requirements and laboratory budgets increase, robotic workstations can be upgraded and used to design fully automated robotic laboratories. Full lab automation ensures high throughput at lower flexibility, and is often desired in an industrial setting.

3. Considerations for choosing automations 

Robotic workstations could be classified into liquid-handling “only,” general molecular biological and process specific workstations. Liquid-handling “only” workstations move liquid from one deck location to another, from a reservoir to a plate, from one plate to another, column-by-column, row-by-row or entire plates. General molecular biological liquid-handling workstations (some vendors refer to as sample processors or assay processors) are able to do more than just liquid-handling tasks. They are able to clean up, filter, shake, incubate and move plates from one workstation to another. Some vendors also offer process-specific robots (e.g. plasmid purification robots), which are high throughput, but have limited flexibility. In general, liquid-handling “only” workstations are faster, but less flexible than general molecular biological workstations. But at the end, the availability of accessories decides, whether a liquid-handling workstation is liquid handling “only,” or whether it can be extended to a general molecular biological workstation.

Workstations execute robotic tasks and robotic tasks can be more general or more genomics specific in nature. General robotic tasks include entering, identifying, de-capping or de-lidding, aliquotting, reformatting, replicating, normalizing, serial diluting and exiting of tubes, plates, or samples. These tasks are well accomplished by liquid handling ‘only’ workstations with certain features and accessories as outlined in Table 1. Genomics specific robotic tasks include nucleic acid extraction by solid phase, magnetic separation or precipitation, PCR and sequencing reactions setup and clean-up, gel loading, hit picking, RNA amplification or other enzymatic reactions. These tasks are well performed by molecular biological workstations, which are capable to accommodate special equipment such as vacuum manifolds, magnetic separators, shakers, incubators or indexed centrifuges on, beneath or under the work deck. Examples for genomics specific tasks reported in the literature include identification and picking of colonies,15 purification of DNA from large samples,16 automated sample-preparation technologies in genome sequencing projects,17 high throughput probe production for DNA microarrays,18 plasmid purification,19 high throughput DNA extraction methods for PCR,20 automated cycle sequencing,21 purification of BigDye Terminator fluorescent DNA sequencing reaction,22 purification of PCR products,23 automated agarose gel electrophoresis,24 high throughput RNA purification,25., 26. and printing of microarrays using liquid-handling robots.27 However, some tasks are difficult to automate at all, such as initial sample (e.g. blood, serum) collection and initial bar coding of samples, tubes or plates.

Table 1. Examples of robotics tasks and its recommended accessories

	Category	Robotic tasks	Recommended accessories
	General	Entering and exiting of tubes, plates or samples	Robotic arms, conveyer belts or rail drive systems
		Identifying of tubes, plates or samples	1D or 2D barcode reader
		De-capping or de-lidding	Decapper, gripper
		Aliquotting, replicating, reformatting	Liquid-handling “only” workstation
		Normalizing	Single or oligo-probe capability with liquid level detection and individual probe control
		Serial diluting	Oligo-probe capability
		High throughput liquid handling	96 or 384 probe head
	Genomics Specific	Nucleic acid extraction by solid phase, magnetic separation or precipitation	Vacuum filtration manifold, magnetic separator, indexing centrifuge or process specific workstation
		PCR and sequencing reaction setup	Liquid-handling “only” workstation
		PCR and sequencing reaction clean-up	Vacuum filtration manifold, magnetic separator or indexing centrifuge
		Gel loading	Oligo-probe capability, gel holder
		Hit picking	Single probe or oligo-probe capability with independent probe spanning
		RNA amplification or other enzymatic reactions	Sealer, Piercer, temperature controlled water system or Peltier element

There are literally dozens of companies out there (e.g. Apogent Discoveries, Autogen, Beckman Coulter, Colibri Robotics, Genemachines, Genovision AS, Gentra Systems, Gilson, Genetix, Hamilton, Korvis Automation, MacConnell Research, Matrix, MWG Biotech, Perkin Elmer, Qiagen, Roche Applied Science, Robbins Scientific, Sias, Tecan, Tepnel Life Science, Titertek Instruments, Tomtec, Zinsser Analytic, Zymark Corporation, …), which are specialized in automation devices and are able to fulfill the requirements for genomics laboratories. Some vendors offer process specific robots others liquid handling “only” robots, others molecular biological liquid-handling workstations. In order to be able to narrow down the choices, one should look at the budget, the space available for the workstation, the desired flexibility, the throughput needs, the accepted frequency of user interactions and robotic break-downs, and the possible integration with other systems at both the software and hardware level before doing a purchase decision. Thus, typical questions are: How many tubes or plates do I process per day? How much space do I have available? How many different assays can I run within the same labware footprint or format? Do I process a large set of samples, that all have the basic same requirements? Do I need disposable or filtered tips to prevent cross-contamination or are washable probes sufficient? Does the robot uses universal or proprietary tips? What is the desired pipetting range of the probe or tip? What are my accepted accuracy and precision requirements for robotic pipetting? How much individual control over the probes do I need? What are my accuracy requirements for positioning? Which accessories of which capacity do I need (Table 1)? How much x-, y-, z-axes and rotation freedom should the gripper have? An additional plus is, if the vendor is willing to provide training, technical support, qualified service and maintenance, and is willing to design custom tools and adapters for 3rd party devices. In our experience, cost, space, throughput and flexibility are the most important parameters for the decision-making process. In general, good sources of information are personal sources (colleges), commercial sources (advertisement, sales people), public sources (scientific journals) and experiential sources (handling, examining, using the robot). Thus, good sources of robotics information are the material posted on the company's web site, flyers and sales representatives or product managers. In addition, trade shows offer a good opportunity to see robotic workstations in action and users or web-based discussion groups can be a good source for alternative information of robotic workstations.

4. Contamination 

For genomics applications, special considerations should also be given to prevent cross-contaminations. The methods favored to prevent carry-overs depend strongly on the individual investigator. But most researchers would agree, that fixed probes are sufficient for protocols using the same reagent, do not have downstream amplification steps (e.g. PCR, bacteria inoculation, …) or do not contaminate the probe itself in such a way that it is difficult to clean it later on. All protocols with a potential of contamination are best performed by using disposable or disposable, filtered tips. But disposable tips add an additional expense to the protocol. In our experience, the use of disposable tips, selection of microtiter plates with sufficient well-to-well spacing and the prevention of involuntarily z-axes movements of the robotic gripper during plate transfer or manifold disassembly are the most important factors to prevent carry-overs. The success in fighting carry-overs can be observed by running the robot on microplates having ink/water (for simple liquid handling carry-over testing) or blank/sample (for complex biological sample carry-over testing, e.g., PCR) alternate filled wells.

5. Adding capability 

The right choice of accessories for your robotic workstation can significantly increase the throughput or flexibility of your system, the walk away time or the life span of your reagents. Stackers, carousels and feeders are ideal for storing shallow plates, deep well plates and tip racks. In order to be able to allow enzymatic reactions or to increase the life span of your reagents, reagent reservoirs, deck positions and stackers can be temperature-controlled by water systems or peltier elements. For molecular biological applications such as nucleic acid preparations, vacuum and magnetic separation manifolds or indexing centrifuges could be necessary. Although internal grippers can move plates to all positions on the deck, robotic arms, conveyer belts or rail drive systems can move the plates from one robot to another or to peripheral devices. Grippers can be attached to a probe head or to a separate arm. If the gripper is attached to the probe head, the freedom of the gripper may be limited, but it saves the installation of a separate robotic arm. In general, whenever you increase the complexity of the system with accessories, you also increase the chances for breakdowns.

6. Software 

Most robotic software has a consistent and intuitive graphical user interface to control all movement and pipetting procedures of your workstation. The software should be easy to use and should not require extensive programming skills. Also, start-up screens or wizards to guide lab technicians through their daily routines are helpful. The software should allow the scheduling of the workflow and allow full integration with other software. The software should allow features such as tip touch, multi-target dispensing, timing procedures and complete control over accessories. Some software packages support FDA regulation requirements for multilevel user management, full audit trail, electronic records and electronic signatures. In addition, some vendors offer labware files and methods on their web sites.

7. Summary 

Liquid-handling robotic workstations are valuable tools for genomics laboratories. Robots not only perform consistently and learning curve-free, they also increase throughput and cut labor costs. Liquid-handling robots differ in number and configuration of robotics arms, pipetting heads, functionality of the probes and the availability of accessories. Cost, space, throughput and flexibility are the most important parameters for the decision making process in purchasing a robotic workstation. You should contact multiple vendors and explore the available options to assemble your custom liquid-handling robot by keeping your desired automation needs in mind.