Creating solutions driven by focused systems biology questions demands new technological approaches. Automation of detection systems has allowed biologists to move beyond the limits of manually driven tools. One technology that has not traditionally been easy to automate is flow cytometry. New developments have led to the emergence of flow cytometry as a remarkable tool in automated high-content screening. The process requires the optimization and standardization of many procedures and, importantly, solutions for rapid and robust analysis that match the time savings generated by automation.
Perhaps the most difficulty is encountered in the need to quickly reduce very large datasets into something meaningful. Most current procedures operate in a purely vertical fashion that does not translate well into large volume processing. Furthermore, flow cytometry is a field in which the typical software package is a complex tool designed for universal use, not to handle assays based on high well number plates, particularly those with 384 or more wells. Even with 96-well plates, most flow-cytometry analysis approaches are inefficient and cumbersome.
The approach we propose requires the creation of robust, module-specific tools focused on solving specific analytical problems. For example, if the need is for IC50 values, then tools can be designed for high-speed flow-cytometry analysis with direct output of IC50 values from raw list-mode data. Such a tool may be highly efficient for this application, but not effective for a different assay.
The fundamental approach can be modified from one application to another, but this does require alteration of the software. For HT flow to be efficient and adopted, software specific for a given application may be required. As an example, for drug screening, we have designed a robust process that uses a combination of plate-design profiles, plate-analysis profiles, and predesignated outputs. A second approach has been designed for immunophenotyping applications.
The drug-screening example is shown in Figure 1. Here the assay design is optimized for a 384-well plate and for 10-point drug dilutions. The most efficient way is to use two blocks of 16 drugs, leaving four columns available for negative and positive controls. This efficient design allows 32 drugs to be tested on a 384-well plate.
To ensure high-quality control, together with necessary speed, all processes are performed on automated systems (Biomek®, Beckman Coulter). Thus cells, reagents, dyes, and chemicals are robotically added to plates, and of course, plates are run on the flow cytometer (CyAn®, Beckman Coulter) supplied by an automated robotic delivery system (HyperCyt®, IntelliCyt). Automation at the preparative level brings good quality control, reproducible results, and economy of scale.
The results are then analyzed by our software, which was created to provide entire plate-based results in what is essentially a single step directly from the flow-cytometry list-mode files. The creation of assay-specific, robust analytical tools to automate analysis is an innovation that transforms what would otherwise be a slow and cumbersome process of data reduction. Using such tools, we are able to reduce 384-well plate data to final results in about one minute—something traditional flow-cytometry software approaches cannot do.
To design an HT flow-cytometry system, one should have a well-defined result in mind, such as IC50 values when doing drug screens. Once this is established, it is possible to use a plug-and-play type interface to create the analysis protocol (Figure 2). Usually, the leading component is a gating region defining a specific subset of cells.