Customer-requested, custom assay development and validation with a systematic, science- and risk-based approach to developing analytical methods that are fit for purpose and robust across the product lifecycle (Analytical Quality by Design; AQbD) in a GMP-environment
Our GMP-compliant assay development and validation service provides end-to-end support for the design, qualification, validation, and routine application of robust analytical methods across the full product lifecycle. We support method development, method qualification, and full GMP-compliant method validation, followed by seamless implementation into routine testing workflows, with lifecycle management to ensure continued method performance over time.
BaseClear develops and validates analytical assays across a broad range of advanced molecular and bioanalytical platforms, including qPCR, dPCR, next-generation sequencing (NGS), ELISA-based assays, and associated bioinformatics workflows. These methods are applied to complex and highly regulated modalities such as ATMPs, vaccines, biologics, and viral products, where analytical robustness, sensitivity, and regulatory compliance are critical.
Each project is designed to ensure that analytical methods are scientifically sound, fit for purpose, and scalable from development into regulated GMP environments, supporting both clinical development and commercial manufacturing stages.
This service is designed for clients operating in highly regulated and innovation-driven sectors, including cell and gene therapy, ATMP development, vaccines, biologics, viral vector platforms, as well as biotech, biopharma, and academic research organizations transitioning from discovery into clinical development. These clients typically require advanced analytical strategies that can support complex modalities and meet stringent regulatory expectations.
The service is particularly valuable for organizations facing challenges in establishing robust, reproducible, and regulatory-compliant analytical methods for novel or complex products. This includes overcoming limitations in early-stage assay performance, ensuring method suitability for GMP environments, and managing the transition from research-grade assays to validated, routine quality control testing.
By addressing these challenges, the service supports teams that need confidence in data integrity, regulatory readiness, and long-term method stability across development and manufacturing stages.
Our approach is grounded in Analytical Quality by Design (AQbD), ensuring that assay development is systematic, risk-based, and scientifically justified from the outset. We define analytical target profiles and critical quality attributes early in the development process, followed by structured method design and optimization using statistically driven approaches such as Design of Experiments (DoE). This enables robust understanding of method performance and the establishment of a defined method operable design region (MODR), where applicable.
All assays are developed and validated in alignment with international regulatory guidelines, including ICH Q14 for analytical procedure development and ICH Q2 for validation of analytical procedures. Where relevant, additional pharmacopeial and regulatory expectations (e.g., USP and Ph. Eur.) are integrated to ensure global compliance. Advanced molecular and bioanalytical technologies such as qPCR, dPCR, NGS, ELISA, and bioinformatics pipelines are applied within controlled, GMP-compliant environments to ensure data integrity and reproducibility.
This integrated framework ensures that each method is not only fit for its intended purpose at the point of validation, but also resilient throughout its lifecycle in regulated manufacturing and quality control settings.
Clients receive a comprehensive package of documentation and outputs that support both regulatory submission and routine testing. This typically includes detailed method development and validation plans, complete validation reports, and associated raw data. For ongoing quality control, validated methods can be implemented with Certificates of Analysis (CoA) for routine testing, ensuring consistent and reliable measurement of product attributes.
All reports are prepared in a clear, GMP-compliant format, suitable for submission to regulatory authorities or inclusion in internal quality systems. Where required, lifecycle management support is available to maintain method performance over time. This structured, fully documented approach provides clients with confidence in data integrity, regulatory readiness, and reproducibility across the product’s lifecycle.
Reach out to discuss your assay needs and project goals. We’ll quickly determine how our expertise aligns with your product and regulatory requirements.
Participate in a personalized call to define assay objectives, platform choice, and regulatory expectations. This ensures the project is tailored to your product and timeline.
Send your samples or relevant materials to our facility. We guide you on handling, shipping, and documentation to maintain sample integrity.
Watch your assay progress from design through validation. We keep you informed with updates on method performance, optimization, and qualification results.
Receive a complete package including development and validation reports, raw data, and Certificates of Analysis (CoA) for routine testing. All outputs are formatted for regulatory readiness and reproducibility.
Maintain long-term confidence in your assays with ongoing monitoring and method support as products evolve and regulatory expectations change.
A biotechnology company developing a recombinant protein production platform needed to qualify a genetically modified mammalian cell line for further process development and manufacturing. The team required confirmation of transgene integration, copy number, and genetic stability to support internal quality requirements and reduce development risks before establishing a Master Cell Bank.
BaseClear performed whole genome characterization using Oxford Nanopore long-read sequencing combined with advanced bioinformatics analysis. The study mapped transgene integration sites, assessed integration structure and copy number, and screened for structural genomic changes that could affect cell line performance or stability.
The analysis confirmed the intended genetic modification, identified the precise integration locations, and demonstrated genomic stability of the production clone. Armed with comprehensive genomic characterization data, the client was able to confidently progress to cell bank establishment and downstream manufacturing activities with a well-documented understanding of their production cell line.
Genomics and sequencing projects completed
Years of sequencing and genomics expertise
Validated molecular analysis workflows
Cell culture samples analysed
We develop and validate a wide range of molecular and bioanalytical assays, including qPCR, dPCR, NGS, ELISA, and bioinformatics workflows. These are applied to small molecules, biologics, vaccines, viral vectors, and ATMPs.
Timelines vary depending on assay complexity, platform, and sample type. After initial consultation, we provide a tailored project plan with estimated milestones.
Yes. All Qualified methods and, validation, and routine testing are conducted under GMP-compliant conditions and aligned with ICH Q2 and Q14 standards.
We follow an Analytical Quality by Design (AQbD) approach, using risk-based assessments and statistical design of experiments to ensure methods are robust, reproducible, and scalable.
While we don’t submit directly on your behalf, all documentation is prepared in a regulatory-ready format to support submissions to authorities such as FDA, EMA, and other global agencies.
We offer flexible timelines for urgent projects. During the consultation, we define achievable milestones while maintaining GMP compliance.
Detect mycoplasma contamination in cell cultures using sensitive molecular detection methods.
High-accuracy DNA sequencing for PCR products, plasmids, and targeted genetic regions.
Quantify the residual host cell DNA in your samples using digital PCR technology.
Speak with our experts to discuss your cell line identification project. We will help you determine the appropriate analysis approach and provide reliable sequencing results to support your research and quality control workflows.
