Digital PCR
Application notes
Quantifying EGFR Mutations
with Multiplex Crystal dPCR
with Multiplex Crystal dPCR
Detecting activating and resistance EGFR mutations in a single assay
In non-small cell lung cancer (nsclc), the epidermal growth factor receptor (EGFR) is an important therapeutic target. EGFR activating mutations, such as L858R and L861Q are predictive of disease respondiveness to targeted therapy using tyrosine kinase inhibitors (TKIs). On the contrary, the presence of EGFR T790M mutation is associated with tumor resistance to TKIs.
To monitor patient response to TKIs treatment with a simple assay, a multiplex digital PCR assay targeting EGFR L858R, L861Q and T790M, as well as wild-type EGFR was developed. These mutations were successfully and reliably detected in a background of wild-type DNA at concentrations down to 0.25 copies per microliter (final concentration), representing a mutant allele frequency of 0.05%.
Detection of HER2 Copy Number Variation
Detecting Triplex Crystal Digital PCR assay to detect HER2 Copy Number Variation
Investigating HER2 amplification status is crucial in breast cancer to determine the indication of anti-HER2 targeted therapy. Assessing HER2 copy number variation is challenging especially when tumor DNA is diluted in DNA from healthy cells. Here, we illustrate how Crystal Digital PCR is capable of reliably identifying HER2 amplification in samples with low tumoral fraction.
An assay previously described for the detection of HER2 (ERBB2) and MRM1 on chromosome 17, and TSN (reference gene) on chromosome 2, was optimized for Crystal Digital PCR. This assay enables the quantification of HER2 copy number and the distinction between HER2 amplification and chromosome 17 polysomy, a condition that could lead to HER2 status misinterpretation.
Droplet recovery
With Crystal Digital PCR
With Crystal Digital PCR
Recovering Droplets from Sapphire Chips
The Naica System allows the recovery of droplets from the Sapphire chips with a simple procedure that can be performed before or after PCR. DNA contained in the recovered emulsion is extracted using a standard chloroform protocol and is suitable for downstream analysis using NGS, digital or real-time PCR, or gel electrophoresis. The recovery and extraction procedure takes approximately 1h for up to 24 samples.
The recovery rate for this protocol was assessed by generating a droplet crystal containing known amounts of human genomic DNA, counting droplets in the Sapphire Chips before and after recovery, extracting DNA from droplets using the protocol described above, and quantifying the amount of DNA recovered by Crystal Digital PCR. We found that:
- at least 98% of the droplets are recovered from the Sapphire Chips
- on average, 70% of the total DNA present in the initial droplet crystal is recovered.
Effect of Inhibitors
Crystal dPCR vs qPCR
Crystal dPCR vs qPCR
Quantification using real-time PCR (qPCR) vs Crystal Digital PCR
Real-time PCR quantification is based on comparing Cq values between unknown samples and standards containing known amounts of DNA. For adequate quantification, this technique therefore relies on similar PCR efficiencies between the analyzed samples and the standards. However, in presence of an inhibitory concentration of a given substance in the sample, PCR efficiency may differ between standard and sample, thus biasing quantification (Figure 1A). In Crystal Digital PCR, the droplets are characterized as either positive or negative, whereas the amplitude of fluorescence separating the two populations indicates PCR efficiency. Even in case of decreased PCR efficiency due to inhibitors, accurate quantification can still be achieved.
Crystal Digital PCR
Using EvaGreen®
Using EvaGreen®
Setting-up EvaGreen™-based quantification in Crystal Digital PCR
EvaGreen is a non-mutagenic and non-cytotoxic DNA-binding dye compatible with Crystal Digital PCR. EvaGreen, which is non-fluorescent when free in solution, becomes strongly fluorescent upon binding in a sequence-independent manner to double-stranded DNA.
When used with Crystal Digital PCR, EvaGreen enables absolute quantification of a target by using a simple primer pair. Similarly to probe-based Crystal Digital PCR, experiments using EvaGreen will enable reliable quantification down to 0.2 copies per microliter.