Time plays a key role in sequencing. In brief, sequencing scientists want results as soon as possible, as long as the results remain accurate. With next-generation sequencing (NGS), microplate technology—from the plates themselves to plate handlers and other accessories—impacts many steps in the process. Let’s see why these tools still need improvements, as well as the places where microplate technology already enhances the NGS workflow.
“Microplate technology and accompanying instrumentation have greatly increased sample throughput and reduced the time taken to produce experimental results in NGS, but there are still challenges,” says Henry Shu, product manager, automation solutions, Agilent Technologies. Nonetheless, he points out the need for improvements in many features, including uniformity of temperatures and reaction times within each well, volumes dispensed and aspirated, dead volumes required, and, potentially, cross contamination. Uniformity across these features, he says, “affects the individual reactions, which are reflected in the results.”
Technologies related to the microplates can also slow down NGS. As an example, Shu says, “Upstream issues include the relatively slow process of transferring samples into the microplate format.” Not all NGS challenges can be solved with better microplates, but let’s look at which ones can, keeping in mind that a specific lab’s needs play a big part in the microplate features that really matter.
Improving the parts
The miniaturization of reactions in microplates drives the need for automation for accuracy and throughput. That means that “microplates specifically designed and optimized for automation are required,” Shu says.
Making such microplates requires application-specific decisions from the start, all beginning with developing a mold for manufacturing the plasticware, which might be designed to work with a specific handler. In addition, a manufacturer considers the type of plastic used and treatments to the surface. In a microplate designed for NGS applications, a vendor should possess data that validates the expected results.
Quantitation also plays a key role in NGS. “When sequencing samples using a microwell plate, you want a robust, sensitive, and reproducible quantitation method,” says Michael Bjerke, senior product manager, cell health at Promega. The reagents play an important role in quantitation, and so does the microplate reader. So, Bjerke encourages scientists to “select a microplate reader and reagents with proven success for NGS applications, with robust and sensitive detection limits, and that are easy to use.”
In selecting a microplate reader, various features should be considered, including recent improvements. Some of the most exciting advances in microplate reader technology for NGS applications improve the user experience and workflow. “Instruments that combine data collection with data analysis make the user experience and workflow seamless,” says Bjerke. As an example, NGS templates can be quantitated and then automatically analyzed for the user, which eliminates the need for user input during data analysis.
As customers, scientists can seek a complete solution in microplates for NGS—that is, plates made for a specific platform that can automate many NGS steps. That won’t necessarily be the least expensive solution, but it could be the best one for a lab that depends on running NGS at the highest possible throughput.