Why Are Real-Time PCR Panels Gaining Popularity for Molecular Testing?

Accurate, versatile, fast, and affordable testing for infectious diseases, oncology, and pharmacogenomics

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Zahraa Chorghay, PhD

Zahraa Chorghay, PhD, is Today's Clinical Lab's clinical writer/editor.

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Published:May 16, 2023
|4 min read

Real-time PCR testing is being broadly adopted for an array of research applications. For infectious diseases and more, the ability to use this technology has introduced a fast and economical yet highly sensitive and accurate way to detect pathogens.

Real-time PCR increasingly adopted for pathogen detection

Illustration of cylindrical blue-grey pathogenic cells interspersed with disk-shaped red blood cells going through an artery to represent pathogens in the bloodstream during sepsis.
Accurate but quick pathogen detection during sepsis or septic shock could lead to life-saving antibiotic administration.
iStock, Artur Plawgo

The traditional way to detect infectious diseases was through culture- or microscopy-based techniques, which can sometimes take days or even weeks to reliably identify a pathogen. Such a long wait time can severely limit the usefulness of these techniques for patients who need immediate care, for example, if they have sepsis or septic shock. Furthermore, not all targets can be cultured, which limits the scope of which pathogens can be identified.

Newer approaches for pathogen detection include probe hybridization, serological tests, or further analysis after culturing the pathogen, but such approaches also have limited sensitivity. Compared to these technologies, “real-time PCR is the best overall,” says Rui Yang, PhD, a staff scientist at Thermo Fisher Scientific.

Beyond just detecting SARS-CoV-2, real-time PCR can be used to detect pathogens underlying gastrointestinal, respiratory, sexually transmitted, urinary, vaginal, and wound infections, as well as antibiotic resistance. With regards to this technology, Yang adds, “it’s reliable and highly sensitive, because PCR allows for amplification of the target, which is then detected by the specific probe. It’s very fast, providing quick turnaround time for labs. It’s relatively affordable. And it’s versatile, ranging from single- or limited-target assays to comprehensive, multiplex assays.”

Limited-target real-time PCR panels for faster pathogen detection

Illustration of different cell types, including pathogens and healthy cells, representing the need for molecular detection of a wide number of disease states.
TrueMarkTM Infectious Disease Research Panels enable molecular detection of a wide range of pathogens.
Thermo Fisher Scientific

Single- and limited-targeted real-time PCR assays can increase efficiency in your clinical research lab, because they are faster and more affordable than comprehensive assays, without compromising accuracy. Examples of such panels include the Applied BiosystemsTM TrueMarkTM ** Infectious Disease Research Panels: they can be used with Thermo Fisher Scientific’s real-time PCR systems, like their QuantStudio™ systems, and enable rapid molecular detection that takes only a few hours from sample collection to final results.

Importantly, even though they are targeted panels, the TrueMark Infectious Disease Panels enable molecular detection of a wide number of disease states from either a predefined panel in a 96-well plate (with eight targets) or a custom 96- or 384-well plate (with up to 24 targets), where you can choose from a list of more than 162 microbial assays and 62 antibiotic resistance assays. These plates include positive internal controls, where every well has an RNase P human internal control or Bacillus atrophaeus bacterial spike-in control, for added confidence in the results.

Larger real-time PCR panels for comprehensive, higher-throughput pathogen detection

While limited panels boost the efficiency for detecting a predefined set of targets, they may not include a wide enough range of targets for some research questions. In this case, clinical research labs have usually turned to next-generation sequencing (NGS) because it provides a comprehensive readout of genetic changes, but NGS is costly, more time-consuming, and can produce excessive data that needs more complex analysis than real-time PCR panels. With the introduction of technologies like Applied BiosystemsTM OpenArray™, you can test for significantly more targets and samples at a time. This can be used for high-throughput gene expression analysis, genotyping, microRNA (miRNA) analysis, and digital PCR applications, with same-day results and better affordability compared to NGS.

The OpenArray technology can help your lab increase testing throughput. The technology uses a microscope slide-sized plate that can hold 3,072 assays of 33 nL volume, i.e., each plate can hold as many samples as eight traditional 384-well PCR plates. Due to hydrophilic and hydrophobic plate coatings, the liquid reagents are retained within the open well by surface tension. Up to four OpenArray® plates can be run simultaneously on the QuantStudio 12K Flex Real-Time PCR instrument, allowing your lab to process up to 1,728 genotyping samples and 2,304 gene expression samples within a typical eight-hour workday.

OpenArray plates are also customizable into 1 of 11 formats that best suit your lab’s testing needs. You can select from 17 million single nucleotide polymorphisms (SNP), 1.6 million copy number, 1.3 million TaqMan® Gene Expression, and 4.5 million predesigned drug-metabolizing enzyme (DME) genotyping assays, or your own custom TaqMan assays. The selected assays for your OpenArray panel are preloaded onto the plate during manufacturing, such that to use the panel, you simply mix the prepared samples with the master mix, pre-amplify samples if needed (for increased sensitivity), and load the samples onto the plate and into the PCR system. Overall, OpenArray helps simplify the workflow for research lab personnel without compromising testing accuracy, thus boosting efficiency.

Real-time PCR for a diverse range of research applications

Illustration of three capsules. The capsules are half-blue, half-red, each holding a strand of double helix DNA. The background is a silver tiled floor, with each hexagonal tile having the letter A, T, C, or G on it. The illustration represents the concept of pharmacogenomics.
The broad range of available real-time PCR panels expand molecular testing capabilities, not only for more pathogen detection, but also for oncology and pharmacogenomics applications.
Thermo Fisher Scientific

The broad range of available real-time PCR panels can provide your lab with the flexibility to expand your molecular research testing capabilities, not only for detecting more pathogens, but also for oncology and pharmacogenomics research applications. For example, TrueMark has a specific microsatellite instability analysis for Lynch syndrome-related cancers and for studying immunotherapy. Alongside panels specifically designed to look at the most common genes for pharmacogenomic research, you have the choice of 2,700 inventoried DME assays to create a custom OpenArray plate.

Compared to traditional infectious disease detection methods and other sequencing technologies like NGS, running real-time PCR panels can be significantly faster, cost-effective, and less labor intensive, yet highly sensitive and accurate.

*For in vitro diagnostic use. Regulatory requirements vary by country. Product may not be available in your geographic region. Regulated by CE-IVD for GI and respiratory panels.

**For research use only. Not for use in diagnostic procedures. 

Photo portrait of Zahraa Chorghay
Zahraa Chorghay, PhD

Zahraa Chorghay, PhD, is Today's Clinical Lab's clinical writer/editor. Zahraa obtained her HBSc from the University of Toronto and her PhD from McGill University, where she explored her passion for neuroscience and for making science accessible and inclusive. Her doctoral dissertation on how experience changes the developing nervous system used a combination of cell biology and advanced microscopy techniques. She is excited to contribute her expertise to her role as editor and writer for Today's Clinical Lab.


Cancer Diagnosticsmolecular diagnosticspathogen detectionPCR / qPCR/ ddPCRPCR / Thermal CyclersPharmacogenetics