We develop and optimize client-specific qPCR assays for challenging matrices in regulated and research environments, from cell & gene therapy to microbial and industrial applications.
We design, develop and optimize quantitative PCR (qPCR) assays for detection and absolute quantification of DNA targets in biological matrices.
Our work covers the full technical development chain: from target region selection and assay design to experimental optimization of sample pre-treatment, extraction strategies and PCR conditions. Each assay is developed as a fit-for-purpose analytical method and can be tailored to the specific biological and chemical context of the client sample.
This service is used by clients working in regulated and high-complexity environments such as cell & gene therapy, microbial production, fermentation processes, and industrial biotechnology. Typical challenges include detecting low-level DNA targets, distinguishing closely related microbial strains, or quantifying residual nucleic acids in therapeutic products.
Typical use cases include:
Assay development is performed through a combination of in silico target evaluation and experimental optimisation. Primer and probe candidates are identified based on sequence specificity and evaluated under controlled conditions before being tested in relevant sample contexts.
Where applicable, workflows are integrated into a controlled digital environment using an Electronic Lab Notebook (ELN) within LabWare. The ELN functions as a centralized system for recording experimental setups, sample metadata, assay conditions, and results, ensuring traceability and reproducibility of all assay development steps.
Clients receive a tailored qPCR assay workflow designed for their specific target and matrix. This includes optimized extraction and amplification conditions, assay design, and experimentally determined performance within the relevant matrix context.
Where required, we can support method validation in line with the intended application, including performance confirmation under defined experimental conditions. All development work is documented in a structured format, with optional integration into an Electronic Lab Notebook (ELN) for full traceability and reproducibility.
We define the biological context, matrix composition and target characteristics together with the client to understand analytical constraints.
Candidate target regions are identified and evaluated for specificity and suitability in the given matrix context.
Assay performance is tested experimentally using control templates to assess specificity, amplification efficiency, and detection capability.
Validated assays are applied for absolute quantification of target DNA in client samples using appropriate standards and calibration strategies.
Functional testing integrated with genomic analysis for comprehensive risk interpretation
Designed to meet EFSA and international regulatory requirements
Tailored assay design based on strain, product, and regulatory requirements
Indicator strains selected to maximise relevance and detection sensitivity
Antimicrobial activity testing is required to identify whether a production strain produces compounds that inhibit other microorganisms. Such activity may affect microbiota or indicate the presence of bioactive metabolites that need to be evaluated for safety.
Sample selection for antimicrobial activity testing follows EFSA guidance and depends on the intended use of the microorganism. For active agents, the culture supernatant of the strain should be tested. For production strains or biomass-producing organisms, both the culture supernatant and/or the fermentation product should be evaluated. Samples should preferentially be obtained from the industrial-scale process, with the exact manufacturing stage specified. Where industrial material is unavailable, pilot-scale samples may be used, provided it is demonstrated that the process is representative of industrial production.
Indicator strains are selected to represent a range of Gram-positive and Gram-negative bacteria with known susceptibility to different antimicrobial classes. According to EFSA recommendations, a panel of at least six reference strains should be included, such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Enterococcus faecalis, Bacillus spp., and Streptococcus pyogenes. Results are reported individually for each indicator strain to support regulatory evaluation.
Detection of antimicrobial activity requires further investigation but does not automatically indicate a safety concern. EFSA guidance states that the nature of the activity must be characterised to exclude the production of therapeutic antimicrobials. When relevant biosynthetic genes are identified, quantitative analysis of culture supernatants or final products is required, including assessment of sub-inhibitory concentrations. If no genes and no activity are detected, the strain is considered not to produce relevant antimicrobials. In all other cases, a case-by-case assessment is required.
Antimicrobial activity testing may require follow-up studies depending on the observed results. If significant activity is detected, additional investigations such as compound identification, quantification, or toxicological testing may be needed to assess relevance for safety under intended use conditions.
MIC testing alone is not sufficient to fully assess antimicrobial resistance risk. A comprehensive evaluation requires integration of phenotypic MIC results with genomic analysis, including identification of resistance genes and assessment of their relevance.
Genomic analysis of microbial strains for safety assessment
In vitro assessment of potential toxic effects of microbial metabolites
Contact our experts to design a compliant and reliable testing strategy. Your first consultation is free and without obligation
