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: 

Discover tools to support your dPCR analyses

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.

Rare mutation detection (RMD) refers to detecting a sequence variant that is only present at a very low frequency in a pool of wild-type backgrounds (less than 1% or even 0.1%). Thus, for detecting and quantifying rare events, such as point mutations or single nucleotide polymorphisms (SNPs), a sensitive, accurate and precise method is necessary. The challenge is the discrimination between two highly similar sequences, of which one is significantly more abundant than the other.

Benefits of using nanoplate dPCR for detecting rare mutations: 

  • Ability to load a large input reaction volume into 26,000 partitions, which substantially increases the chances of finding a rare target 

  • Multiplexing for mutant and wild-type sequencing to detect low fractions of rare mutant molecules against an abundant wild-type background

Rare mutation
Copy variation

Multiplex digital PCR for mitochondrial and genomic target copy number analysis

Explore a workflow for high-throughput analyses of target copy numbers in cultured cells. The process combines fast and accurate cell sorting from CellenONE to ensure an exact number of cells are used in downstream reactions. The samples are subjected to probe-based detection on the QIAcuity Digital PCR System with multiplexing of up to five targets in a single dPCR reaction with minimal optimization. The workflow achieves accurate absolute DNA quantification by dPCR for analysis of low abundance targets as well as multi-copy targets at single-cell level.

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
Multiplex dPCR for single-cell gene expression analysis
Discover the CellenONE-QIAcuity workflow for absolute quantification of low abundance targets at the single-cell level.
group of dividing cells

Digital PCR enables a range of gene therapy applications, including adeno-associated virus (AAV) vector genome titer and lentiviral vector copy number measurements 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 cell and 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 traditional ddPCR method at increased speed and overall higher throughput and scalability.

Whitepaper: High throughput AAV Viral titering using nanoplate-based digital PCR 
Discover how The Center for Breakthrough Medicines saves resources by using nanoplate dPCR to obtain more consistent titers, five hours faster, from more sample matrices, at more stages of AAV production than droplet digital PCR.

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
3D illustration of a e. Coli bacteria, microbiome, gut bacteria, gastro, microorganism
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.

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Digital PCR Services

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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Let us do all the hard work. Get expert-designed custom single or multiplex dPCR and PCR assays.

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