BaseClear combines GMP-compliant laboratory workflows, advanced genomics technologies, and dedicated scientific support to deliver reliable, regulatory-ready data for biopharmaceutical applications.
Biopharmaceutical products such as vaccines, viral vectors, cell therapies, and biologics require rigorous quality control and validated analytical methods to ensure product safety, consistency, and regulatory compliance. BaseClear’s GMP solutions support clients with both standardized validated services and client-specific method development and validation projects, helping organizations meet regulatory expectations while accelerating development and manufacturing timelines. Our expertise covers areas such as microbial and viral safety testing, mycoplasma detection, sequencing, dPCR, qPCR, identity testing, and characterization of complex biological materials.
What makes BaseClear distinctive is our combination of scientific expertise, regulatory understanding, and flexible customer-focused execution. Rather than offering only fixed testing packages, we work closely with clients to develop tailored validation strategies that fit their product, process, and regulatory requirements. Our GMP-licensed laboratory, ISO 17025 accreditation, ISO 27001 certification, in-house bioinformatics expertise, and dedicated project management ensure reliable execution, transparent communication, and high-quality data throughout every stage of the project.
BaseClear provides flexible Sanger sequencing services ranging from rapid single-run sequencing for routine applications to fully managed GMP-compliant sequencing projects for regulated environments. Using the gold-standard Sanger sequencing methodology, we generate highly accurate DNA sequence data for applications such as plasmid verification, clone confirmation, PCR product validation, sequence verification and regulatory studies. For GMP projects, BaseClear offers validated workflows with full traceability, documentation and quality oversight, including nucleic acid preparation, primer design, sequencing reactions, primer walking and sequence assembly. Clients receive high-quality chromatogram files, sequence data and, where required, GMP-compliant reporting packages that support development, quality control and regulatory submission activities.
BaseClear specializes in rapid microbial identification of bacteria and fungi utilizing molecular techniques like (q)PCR, DNA sequencing, and MALDI-TOF. Our methods surpass traditional phenotypic approaches in speed and are effective for screening challenging samples. Utilizing the MicroSEQ® system, endorsed by major agencies like the FDA and EMA, we can analyze pure colonies, agar plates, and food matrices within a single working day. Our MALDI-TOF method ensures bacterial and yeast identification with a delivery time of 1-3 working days.
BaseClear provides rapid microbial identification services using MALDI-TOF VITEK® MS, a validated mass spectrometry platform for the identification of bacterial and yeast isolates. By generating protein-based molecular fingerprints and comparing them against the validated VITEK® MS reference database, the service delivers fast and cost-effective identification at species, genus, or family level. This approach is particularly suited for routine quality control, environmental monitoring, contamination investigations, and industrial microbiology applications where turnaround time is critical. Clients receive a concise identification report containing the best database match and interpretation of the results, typically within three working days, with fast-track options available within one working day. For regulated environments, GMP-compliant workflows can be provided upon request, supported by enhanced documentation, traceability, and quality assurance procedures.
BaseClear provides highly sensitive mycoplasma detection services for cell therapies, biologics, viral vectors, vaccines, and other advanced biopharmaceutical products. Using validated PCR-based detection workflows aligned with European Pharmacopoeia chapter 2.6.7 and GxP quality requirements, the service enables rapid identification of mycoplasma contamination before it impacts product quality, patient safety, or regulatory compliance. Our workflows support a broad range of sample types, including cell banks, production cell lines, raw materials, in-process samples, and final products, with matrix validation available to confirm assay suitability for specific sample types. Clients receive a comprehensive GMP-compliant report suitable for quality systems, manufacturing release testing, and regulatory submissions, supported by controlled laboratory processes, full traceability, and validated analytical performance.
BaseClear provides ISO & GMP-compliant bacterial whole genome sequencing services for comprehensive characterization of bacterial strains in research, manufacturing, quality control, and regulatory environments. Using validated Illumina sequencing workflows, the service covers the complete process from DNA extraction and library preparation through sequencing, bioinformatics analysis, and quality-controlled reporting. Whole genome sequencing enables high-resolution analysis of bacterial genomes, including strain characterization, SNP and variant detection, antimicrobial resistance gene identification, contamination investigations, and microbial safety assessments. The workflow is performed under controlled laboratory conditions with full sample traceability, validated LIMS support, multiple quality control checkpoints, and regulatory-ready documentation. Clients receive raw sequencing data, bioinformatics outputs, variant calling results against a provided reference genome, and a comprehensive ISO & GMP-compliant report suitable for research, product development, quality assurance, and regulatory submissions.
BaseClear provides highly sensitive residual host cell DNA quantification services using advanced digital PCR (dPCR) technology to support the development, manufacturing, and release testing of biological products. Residual host cell DNA is a critical process-related impurity that must be monitored to ensure product safety, quality, and regulatory compliance. Our platform supports a wide range of producer cell lines, including CHO, HEK293, Vero, Sf9, and E. coli, enabling accurate quantification of residual host DNA across diverse biological matrices and manufacturing stages. By using digital PCR-based absolute quantification rather than standard curve-dependent approaches, the assay delivers high precision, improved robustness against matrix effects, and enhanced sensitivity compared with traditional qPCR methods. Clients receive comprehensive study reports, raw analytical data, and, where required, tailored CMC and regulatory data packages that support phase-appropriate development programs, process monitoring, batch release testing, and regulatory submissions.
BaseClear provides GMP-compliant viral variant detection services using validated Illumina whole genome sequencing and bioinformatics workflows to identify SNPs, insertions, and deletions across viral genomes. The service supports vaccine developers, viral vector manufacturers, cell and gene therapy organizations, biopharmaceutical companies, and research groups that require accurate characterization of viral genetic variation for product development, process monitoring, genomic stability assessment, and quality control. Sequencing data are analyzed using a validated variant-calling pipeline that has been demonstrated for accuracy, precision, sensitivity, repeatability, and reproducibility across multiple viral genomes and sequencing conditions. Clients receive quality-controlled sequencing data, alignment files, detailed variant call reports, and comprehensive GMP-compliant documentation that supports research, manufacturing, regulatory submissions, and long-term viral genome monitoring.
BaseClear provides Adventitious Virus Testing (AVT) using next-generation sequencing (NGS) to detect unexpected viral contaminants in biological products, raw materials, and manufacturing samples. Unlike targeted assays that only identify predefined viruses, our untargeted sequencing approach screens for both known and unknown DNA and RNA viruses, providing a comprehensive assessment of viral safety. The service is ideally suited for gene therapies, viral vectors, vaccines, recombinant proteins, cell banks, and other biologics where viral contamination poses a critical quality and regulatory risk. BaseClear manages the complete workflow from sample preparation and sequencing through bioinformatic analysis and expert interpretation, delivering a clear understanding of any viral signatures detected. For additional confirmation and quantification, digital PCR (dPCR) can be incorporated as an orthogonal method. Clients receive a comprehensive report containing sequencing results, identified viral sequences, scientific interpretation, and all supporting raw and processed data files suitable for internal risk assessments and regulatory submissions.
BaseClear provides GxP-compliant cell line species identification services using mitochondrial cytochrome c oxidase subunit I (COI) sequencing to verify the biological origin of animal-derived cell cultures. Accurate species identification is a critical quality control measure for biotechnology, pharmaceutical, academic, and contract research organizations, helping to prevent cell line misidentification, cross-species contamination, and compromised experimental results. Our sequencing-based DNA barcoding workflow combines PCR amplification of the mitochondrial COI gene with high-quality Sanger sequencing and comparison against curated reference databases to determine the most likely species match. The assay is performed within BaseClear’s quality management system using validated molecular biology workflows that support both research and regulated biopharmaceutical applications. Clients receive a comprehensive GMP-compliant analytical report containing sequencing chromatograms, processed DNA sequences, database comparison results, and expert interpretation suitable for cell bank documentation, quality control programs, and regulatory submissions.
BaseClear develops custom quantitative PCR (qPCR) assays for the sensitive detection and absolute quantification of DNA targets in complex biological and industrial matrices. Our service covers the complete assay development process, including target selection, primer and probe design, optimization of extraction and sample preparation workflows, and experimental evaluation of assay performance under real-world sample conditions. The service is particularly valuable for clients operating in regulated and technically demanding environments such as cell and gene therapy, microbial production, industrial biotechnology, and biopharmaceutical manufacturing, where standard off-the-shelf assays may not provide the required specificity, sensitivity, or matrix compatibility. Using a combination of in silico assay design, experimental optimization, and controlled laboratory workflows, BaseClear develops fit-for-purpose qPCR methods tailored to the target organism, nucleic acid sequence, and sample matrix. Clients receive a fully optimized assay workflow, performance data, development documentation, and, where required, support for method validation and traceable documentation through Electronic Lab Notebook (ELN) integration to support quality, regulatory, and operational requirements.
BaseClear provides GMP-compliant phage genome sequencing services to support the identification, characterization, and quality assessment of bacteriophages used in research, development, and therapeutic applications. Using high-quality next-generation sequencing (NGS) workflows, we generate comprehensive genomic data that enable confirmation of phage identity, assessment of genomic purity, detection of sequence variations, and long-term monitoring of phage products throughout development and manufacturing. The service is particularly relevant for biopharmaceutical companies developing phage-based therapeutics that require sequencing data generated within a controlled, traceable, and audit-ready environment. To support regulated applications, BaseClear combines validated laboratory workflows, LIMS-based sample and data traceability, QA-approved documentation, controlled work instructions, and client-specific bioinformatics pipelines maintained under formal change control. Clients receive quality-controlled sequencing data, genome assemblies, bioinformatics analyses, and comprehensive GMP-compliant reporting packages that support product characterization, process development, quality control, and future regulatory submissions.
BaseClear provides comprehensive cell line and cell bank characterization using whole genome sequencing and advanced bioinformatics analysis to confirm identity, verify genetic modifications, assess genetic stability, and detect off-target genomic changes. Using Oxford Nanopore long-read sequencing, complemented by Illumina sequencing where required, we identify transgene integration sites, copy numbers, structural variants, SNPs, and copy number variations in mammalian cell lines, microbial strains, master cell banks, and working cell banks. Clients receive a detailed characterization package including sequencing data, genome assemblies, integration site mapping, variant analyses, and expert interpretation to support cell line development, biopharmaceutical manufacturing, gene therapy programs, and quality control activities.
BaseClear combines advanced sequencing, dPCR, qPCR, and bioinformatics services within a GMP-compliant environment. Our GMP license, ISO 17025 accreditation, and ISO 27001 certification help clients meet strict regulatory and quality requirements with confidence.
All GMP workflows are supported by LabWare LIMS and integrated ELN systems, ensuring complete sample traceability, secure data handling, audit-ready documentation, and regulatory compliance throughout the entire project lifecycle.
In addition to standardized GMP services, BaseClear develops client-specific validation and testing workflows for vaccines, viral vectors, biologics, and cell-based products. Our scientific experts work closely with clients to create fit-for-purpose solutions aligned with product-specific and regulatory requirements.
Clients benefit from dedicated project management, direct access to scientific experts, and highly automated laboratory workflows that reduce turnaround times and improve consistency. From sample pick-up to final data delivery, BaseClear provides a responsive and personalized customer experience.
GMP
ISO 17025
Audited since 2022
GMP Compliant Projects Executed
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BaseClear supports GMP-regulated testing and validation projects for vaccines, viral vectors, biologics, cell therapies, and other advanced biopharmaceutical products. Our services cover product characterization, microbial and viral safety testing, residual DNA analysis, identity testing, sequencing, qPCR, dPCR, and custom validation projects throughout the development and manufacturing lifecycle.
BaseClear develops and validates customer-specific analytical methods tailored to product, process, and regulatory requirements. In addition to standardized GMP services, our scientific team works closely with clients to design fit-for-purpose testing strategies, validation protocols, and analytical workflows that support regulatory submissions and quality control programs.
BaseClear operates GMP-compliant laboratory workflows supported by a GMP license, ISO 17025 accreditation, and ISO 27001 certification. Projects are managed through LabWare LIMS and integrated Electronic Laboratory Notebook (ELN) systems, ensuring complete traceability, secure data handling, audit-ready documentation, and regulatory compliance.
Sequencing technologies can be successfully applied within GMP-regulated workflows when supported by validated methods, controlled processes, and appropriate documentation.
Working with a single GMP-regulated testing partner improves project efficiency, consistency, and accountability. Because BaseClear combines sequencing, qPCR, dPCR, bioinformatics, validation support, and project management within one organization, clients benefit from streamlined communication, reduced project complexity, faster turnaround times, and a single source of reliable, regulatory-ready data.
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.
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