Technologies → dPCR

GLP/GCLP digital PCR services

Digital PCR (dPCR) assay design, validation, and analysis for advanced therapy bioanalysis, meeting FDA and EMA expectations.

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Custom dPCR assay design and validation

Digital PCR for advanced therapy bioanalysis

Unlike qPCR, digital PCR does not require a standard curve, saving time, reagents, and reference samples while minimizing matrix effects. More importantly, it eliminates variability introduced by interpolation in standard curve-based methods, enhancing accuracy and reproducibility.

The lower variability and absolute quantification capability of dPCR makes it ideal for high-precision applications such as copy number variation (CNV) and vector copy number (VCN) analysis for biodistribution, shedding, pharmacokinetics, and transgene expression in advanced therapies.

Digital PCR is less sensitive to inhibition, offers higher precision for quantifying rare targets, and can detect changes as small as 10%, making it optimal for low-copy number detection.

Method development and assay design for digital PCR

Method development for digital PCR (dPCR) is similar to that of qPCR in many aspects. The optimization of nucleic acid extraction, the reverse transcription (RT) step for RNA-to-cDNA conversion, and primer and probe design follow the same principles.

However, an assay validated on qPCR cannot be directly transferred to dPCR without a new validation, as the two platforms have different quantification ranges and behave differently.

We perform digital PCR on short RNA and DNA targets

Digital PCR assay design and validation services

Feasibility testing

Confirm amplification, specificity, and efficiency

Feasibility testing serves as a proof-of-concept to evaluate whether the dPCR assay can effectively detect and quantify the target nucleic acid under real conditions.

Primary output: Go/no-go decision for further development

Method development

Optimize reaction conditions and assay performance

Method development aims to fine-tune assay performance for optimal sensitivity, specificity, and robustness. The development includes optimizing dPCR reaction component concentrations, refining thermal cycling conditions to improve efficiency, and minimizing variability between runs.

Primary output: Optimized protocol ready for qualification

Method qualification and validation

Assay performance assessment and full regulatory-grade validation

Method qualification confirms that a dPCR method meets key criteria before full validation, including specificity, precision, LOD, LOQ, and robustness. Once qualified, regulatory-grade validation ensures compliance by assessing accuracy, linearity, dynamic range, and sample stability.

Primary output: A validated, regulatory-compliant assay for regulated applications.

Category	Feasibility	Method Development	Method Qualification	Method Validation
Validation or sample analysis study plan		Optional	Required	Required
Assay Design	3 Designs per target	3 Designs per target	3 Designs per target	3 Designs per target
Assay Efficiency and Amplicon Confirmation	√	√	√	√
Establish calibration curve parameters	√	√	√	√
Linear Range of Assay		√	√	√
Accuracy and Precision in surrogate matrix (buffer)		2 runs, 5 levels, 3 sets
Extraction Efficiency		3 kits, 1 level of spike, QC of nucleic acids Quality and Integrity, 1 repeat	1 kit, 3 levels of spike, QC of nucleic acids Quality and Integrity, 2 repeats	1 kit, 3 levels of spike, QC of nucleic acids Quality and Integrity, 2 repeats
Minimum Required Dilution (MRD)		√	√	√
Accuracy and Precision in authentic matrix		2 runs, 5 levels, 3 sets	3 runs, 5 levels, 3 repeats	6 runs, 5 levels, 3 repeats
Selectivity and Specificity in authentic matrix		Optional	√	√
Dilution linearity		Optional	√	√
Stability		Optional	Optional	√
Data QC		20%	50% or 100%	100%
QA involvement			Optional	√
Report		√	√	√
Acceptance criteria		Depending on Context of Use	Depending on Context of Use	Depending on Context of Use
QC levels		LLOQ, LQC, MQC, HQC, ULOQ	LLOQ, LQC, MQC, HQC, ULOQ	LLOQ, LQC, MQC, HQC, ULOQ

GLP for qPCR and dPCR

We are accredited for Good Laboratory Practice (GLP) by the Swedish Board for Accreditation and Conformity Assessment (SWEDAC) for qPCR, dPCR, and molecular biology.

dPCR services at TATAA

Samples

Tissues
Blood
Liquid biopsies
Fresh frozen
FFPE
EDTA
PAX

Test items

Vector copy number (VCN)
Host cell DNA residuals
Copy number variations (CNVs)
Cell-free DNA (cfDNA)
Minimal residual disease (MRD)
Total RNA
Messenger RNA (mRNA)
Micro RNA (miRNA)
Small interfering RNA (siRNA)
Antisense oligonucelotides (ASOs)
DNA
Single nucleotide polymorphism (SNPs)

What is digital PCR?

In digital PCR (dPCR, ddPCR, droplet PCR), the sample is partitioned into thousands of individual reactions, with a PCR reaction occurring in each partition. Each partition yields a positive or negative signal; therefore, it is called digital.

MIQE guidelines and regulatory requirements for digital pcr

The MIQE (Minimum Information for Publication of Quantitative Digital PCR Experiments) guidelines for dPCR extend the original MIQE guidelines developed for qPCR. They provide a framework to ensure transparency, reproducibility, and accuracy in digital PCR experiments.

TATAA Biocenter co-authored the MIQE and dMIQE guidelines, integrating these principles into our workflows to uphold rigorous assay validation, standardized methodologies, and stringent quality controls.

While regulatory guidance from the FDA and EMA on digital PCR assay validation remains incomplete and evolving, TATAA Biocenter has actively shaped industry standards. In 2024, alongside 37 industry experts from 24 organizations, we published the AAPS paper “Recommendations for Method Development and Validation of qPCR and dPCR Assays in Support of Cell and Gene Therapy Drug Development,” establishing industry-aligned best practices for regulated applications.