There are plenty of valuable applications for one-off quantitative PCR (qPCR) studies. But part of the magic of this tool for quantifying nucleic acids is its scalability. Some of the most important qPCR benefits stem from the collection and analysis of massive data sets.

Researchers, diagnostics developers, and clinical scientists have each benefited from the ability to perform these large-scale analyses, particularly when it comes to genomics and transcriptomics for biomarker discovery, the microbiome, agriculture, ecology, oncology, and infectious disease. The COVID-19 pandemic has also shown the public the importance of extensive real-time qPCR (RT-qPCR) data collection, while highlighting critical efforts to maximize throughput.

Various groups will continue to invest in the development and use of qPCR automation, tapping into the current demand for high-throughput qPCR and the potential for future growth and expansion into other fields and industries. While robotic handling and automated qPCR instrumentation are the main focuses of this work, plastic consumables also play a critical role in the rapid collection of massive qPCR data sets using these automated tools.

Most readers probably know that for most low volume qPCR utilization, PCR tubes are the way to go. Whereas, well plates are better for larger volume experiments – but not just any well plate will work when it comes to automated systems that maximize throughput.

If you are considering adopting or using an automated system, check out the following important qPCR compatibility details to ensure success in your high-throughput workflow.

First and foremost, the use of robotic handing in high-throughput PCR necessitates the use of skirted well plates. This outer plastic shell provides stability when robotic “paddles” grip the plate, preventing damage and distortion as the plates are transferred to the next step in the workflow.

In many cases, full-skirted plates are desirable because they provide the greatest structural stability, but semi-skirted plates, whether traditional, fast, or low profile, are often suitable as well. However, semi-skirted plates typically require a support rack on each key location of the robot deck. Since some qPCR instruments need semi-skirted plates, it’s best to check with your automation supplier to ensure you receive a suitable support deck.

A key difference between traditional PCR well plates and those optimized for automated qPCR is the plastic composition and design elements.

Many traditional PCR plates are made entirely from polypropylene. This plastic offers superior heat transfer properties, facilitating accurate temperature manipulation in PCR reactions. However, polypropylene is a fairly pliable plastic; robotic arms can bend or distort it during the handling process. Furthermore, thermocycler blocks can occasionally partially melt or distort polypropylene plates due to excess heat, even sometimes adhering the plate to the block itself. If a plate ends up warped or adhered regardless of cause, this can have downstream consequences in automated qPCR.

To overcome this limitation, the best high-throughput qPCR plates use polycarbonate frames. This plastic offers greater structural strength and a higher melting point. Importantly, these qPCR plates still use polypropylene wells to maintain optimum heat transfer, collectively providing the best of both worlds.

To see these plates in action, watch this How to Select the Best Consumables for High Throughput PCR and qPCR Reactions video.

Separate from the material itself, many high-throughput workflows benefit from having plates with different color frames (often semi-skirted). Colorful plate frames can help with organization and visual tracking of plates throughout a workflow.

It’s also strongly recommended that high-throughput qPCR plates have raised rim wells. Raised rim wells are designed to improve the tightness of plate sealing. With large numbers of plates to process and the resulting potential for wait times during workflows, ensuring maximum seal and limiting evaporation is even more important for high-throughput experimental success.

Lastly, while ANSI:SBS footprint plates are built to be compatible with all robotic systems, you still must check that your plate is compatible with your specific thermocycler block. Naturally, instrument manufacturers provide information on ideal plate specifications, but you can also use our handy selection tool for the rapid identification of plates that will fit your block.

With high-throughput qPCR of massive sample numbers and experiments, you should also carefully track your plates throughout their testing life cycle. Often, labs utilize barcoding to manage this information and track plate-specific data. For best use, we recommend using barcode labels that are scratch and chemical resistant, and able to withstand both high temperatures on the thermocycler block and low temperatures for storage (e.g., –196°C to 120°C).

Remember, the position of a barcode reader in automated systems does vary, so labels should be applied in the correct position for your system.

To discover more on how plastic consumables can optimize your high-throughput experiment needs and performances, check out our PCR Tubes, Plates & Accessories.