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Digital PCR

Nanoplate dPCR applications

Top applications of nanoplate digital PCR

Thanks to the high sensitivity, superior precision and absolute quantification, digital PCR can detect low abundance targets, targets in complex mixtures, allelic variants and monitor small fold-change differences in target levels across a wide range of samples and applications, including but not limited to:

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Find and configure the latest assays on our GeneGlobe Design & Analysis Hub for quantification of DNA, RNA and lncRNA targets by digital PCR.

Due to the highly heterogeneous wastewater composition, a method capable of identifying very small amounts of viral RNA from a mixture of non-target nucleic acid molecules is warranted. Digital PCR can measure low concentrations of SARS-CoV-2 RNA present in wastewater with good precision and shows a good correlation with qPCR results. Moreover, digital PCR can accurately distinguish and quantify the variants resulting from the mutating virus in a sample and also provide an accurate measure of the copy number of both wild-type and variant genomes.

How dPCR can detect target sequences in challenging samples

From environmental sampling to liquid biopsies, qPCR can help quantify small amounts of genetic targets. But for complex samples with a low concentration of target molecules, dPCR may be a better option, especially with new nanoplate-based systems.

Digital PCR allows for increased sensitivity in the detection and absolute quantification of rare events/sequence variants because target quantification is independent of the number of amplification cycles. Besides, partitioning increases the signal-to-noise ratio and decreases false-positive rates when detecting low-frequency targets (allelic variants, SNPs) in a pool of wild-type background.

Emerging uses of digital PCR for rare mutation detection include:

  • Identifying residual cancer below current detection levels
  • Detecting new mutations and duplications in cancer
  • Monitoring rare drug-resistance mutations

Digital PCR can easily detect small fold-change differences such as less than a 1.2-fold change in CNV from four to five copies, without requiring a standard curve. The precision and sensitivity of the technology allows the system to distinguish subtle changes in copy number, and the accuracy is less sensitive to changes in amplification efficiency and presence of inhibitors. Emerging uses of digital PCR for copy number variation lie in the field of cancer research (screening and monitoring of cancer biomarkers), research into neurological conditions, and population studies.

The increased precision of digital PCR can provide higher resolution in many aspects of gene expression analysis. It enables monitoring finer changes in expression levels, even less than two-fold. Digital PCR also provides a greater sensitivity when quantifying rare targets, or RNA from very limited starting material.

Emerging uses of digital PCR for gene expression analysis include:

  • Studying methylation events
  • Quantifying transcription levels
  • Measuring changes in miRNA levels
gene expression analysis
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Digital PCR enables a range of cell and gene therapy applications, including viral titer and vector copy number measurements, gene and CAR T-cell therapy development and manufacturing. It also helps validate the quality of your therapeutic product with confidence. This is critical when developing effective and reproducible gene therapies while ensuring patient safety.

Discover how QIAcuity dPCR can generate the same level of accuracy and precision in viral titer quantification as the current gold standard ddPCR system but with an increased speed and overall higher throughput and scalability.

Microbial pathogens are ubiquitous and touch all aspects of our lives, from health to food production. However, their presence at low levels in metagenomic samples, isolated colonies or other challenging sample types have impeded the specific detection and monitoring of these pathogens. That's where digital PCR comes in handy with its high precision and sensitivity in the identification of a wide range of microbial targets, including bacterial, fungal, parasitic, viral, antibiotic resistance and virulence factor genes from diverse samples.

With the new dPCR Microbial DNA Detection Assay portfolio:

  • Identify >680 targets
  • Combine microbial DNA and viral RNA detection in one reaction
  • Detect up to five targets per reaction
  • Follow a simple and fast dPCR workflow in about two hours
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Pathogen detection by digital PCR
Learn about the new dPCR assays that identify microbial species, antibiotic resistance genes and virulence genes rapidly from diverse samples.

Testimonials
what our customers say

“When you have a gene that's really highly variable with a large number of copies, the resolution is just not good enough with quantitative PCR,” said Dr. Johanna Andersson-Assarsson, Researcher and Coordinator for the Swedish Obese Subjects (SOS) study, Department of Molecular and Clinical Medicine, University of Gothenburg. Andersson-Assarsson states that digital PCR has been somewhat of a revolution in the field of copy number analysis because of the resolution. There are different solutions for digital PCR that give good results; what I like about the QIAcuity system is the simple and fast workflow and that you use less plastic tips and plates in the process which is good for the environment.”

"We use environmental DNA (eDNA) to investigate species distributions in marine coastal ecosystems. Digital PCR has higher detection rates at low DNA concentrations and can handle high concentrations of PCR inhibitors present in such ecosystems. We recently ordered a QIAGEN dPCR platform, the QIAcuity, because we found it especially straightforward and fast. It can quantify eDNA from invasive species with more accuracy and sensitivity, independent of the amplification efficiency," said Per Sundberg, CEO, SeAnalytics AB, Gothenburg, Sweden.
"In a trial run with the new, high-throughput QIAcuity Eight, we were able to detect new variants of SARS-CoV-2 in wastewater samples successfully," said Dr. Franz Durandet, President of I.A.G.E. in Montpellier, France. "Our tests have proven that this fast and scalable technology from QIAGEN can provide a valuable addition to our environmental, biological testing services, which we will offer to our clients in the near future."
dPCR, Nicole Masters, John Spear, QIAcuity, customer testimonial, Colorado School of Mines
“When working with low microbial biomass concentrations, qPCR is a good tool for quantification, but dPCR is the best approach. The QIAcuity dPCR instrument allows us to consistently detect and quantify microorganisms in soil, rock and water,” said Prof. John R. Spear, Department of Civil and Environmental Engineering, Colorado School of Mines, Colorado, USA.
In the picture: Nicole Masters, Graduate Student
“Our lab loves using the QIAcuity digital PCR system for absolute quantification of targets from a wide range of samples. The workflow is straightforward, easy to learn, and generates incredibly consistent and sensitive results,” said Drew Capone (in the middle) and colleagues at the University of North Carolina at Chapel Hill, NC (UNC).
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Sometimes it is convenient and faster to extend your in-house resources with expertise and perfectly tailored services that ensure high-quality data. Explore what our Digital PCR Services have to offer for sensitive and reproducible nucleic acid quantification in rare mutation detection and copy number variation applications.

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