Characterize transgenic cell lines and cell banks with whole genome sequencing to verify genetic modifications, map integration sites, assess genetic stability, and identify genomic variants using state-of-the-art long-read and short-read sequencing technologies.
Cell Line and Cell Bank Characterization using Whole Genome Sequencing provides a comprehensive genomic assessment of transgenic cell lines, microbial strains, and cell banks to confirm identity, verify intended genetic modifications, determine transgene copy number, assess genetic stability, and detect unintended genomic changes. By analyzing the entire genome, the service provides detailed insight into transgene integration, structural variation, and genomic integrity throughout the development and production lifecycle. This enables organizations to confidently characterize their biological production systems and establish a robust genomic baseline for future monitoring.
This service is designed for biotechnology and biopharmaceutical companies developing recombinant proteins, vaccines, cell and gene therapies, RNA therapeutics, and other advanced biological products. It is equally valuable for organizations managing Master Cell Banks (MCBs), Working Cell Banks (WCBs), End-of-Production Cells (EPCs), and Cells at the Limit (CAL), as well as research groups working in synthetic biology, stem cell biology, and drug discovery. Typical applications include clone selection, cell bank qualification, transgene verification, process development, and long-term genetic stability studies.
BaseClear combines Oxford Nanopore Technologies (ONT) long-read whole genome sequencing with advanced bioinformatics workflows to generate a high-resolution view of the genome. Long-read sequencing enables accurate mapping of transgene integration sites, determination of integration orientation, and detection of structural variants that are often difficult to resolve with short-read technologies alone. Where copy number variation (CNV) analysis and SNP detection are required, Illumina sequencing can be incorporated to provide additional genomic resolution. The downstream analysis includes transgene integration site mapping, copy number determination, CNV analysis, SNP identification, and structural variant detection relative to a reference genome.
Clients receive a comprehensive characterization package that includes quality-controlled sequencing data, assembled genomes, integration site mapping results, structural variant analyses, and detailed bioinformatics outputs. Depending on the project scope, deliverables can also include transgene copy number determination, CNV analyses, SNP reports, and custom scientific reporting tailored to the specific development program. The final report provides a clear overview of the analytical approach, data quality, genomic findings, and interpretation, supporting cell line development, cell bank qualification, manufacturing readiness, and regulatory documentation.
Discuss your cell line, cell bank, genetic modification, and characterization objectives with our experts. Together, we determine the most appropriate sequencing and analysis strategy based on your development, manufacturing, or research goals.
Provide cell pellets, cell bank material, high-molecular-weight DNA, or existing sequencing data together with reference genome information and transgene details. Our team verifies project requirements and confirms the analysis plan before starting the study.
Your samples undergo high-quality whole genome sequencing using Oxford Nanopore long-read technology, with Illumina sequencing added when copy number or SNP analysis is required. This generates the genomic data needed for comprehensive characterization of the modified cell line or strain.
BaseClear analyzes the sequencing data to identify transgene integration sites, determine integration orientation and copy number, assess genetic stability, and detect structural variants, copy number variations, and SNPs where applicable. The analysis is tailored to your specific cell line and modification strategy.
You receive a comprehensive characterization package containing sequencing data, genome assemblies, integration site mapping, variant analyses, and a detailed scientific report. The results provide the genomic evidence needed to support cell line development, cell bank qualification, manufacturing readiness, and research decisions.
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
Long-read whole genome sequencing enables accurate identification of transgene integration sites, integration orientation, and structural context within the host genome. Unlike targeted PCR-based approaches, Oxford Nanopore long reads can span large genomic regions and complex insertion events, making it possible to resolve integration structures that may be difficult to detect with short-read sequencing alone. This provides a more complete understanding of how and where a recombinant construct has integrated into the genome.
Copy number variation analysis should be included when the number of integrated transgene copies or the success of a genetic modification must be quantified. While ONT sequencing is used to identify the location and structure of integrations, CNV analysis requires complementary Illumina sequencing data to accurately determine transgene copy numbers and detect genomic duplications or deletions. This information is particularly important during clone selection, cell bank qualification, and process development.
Accurate characterization requires detailed information about the host organism, expected genome size, reference genome sequence, and the sequence of the inserted genetic construct. Providing this information enables precise mapping of integration sites, variant detection, and comparison against the intended genetic design. The more complete the background information, the more comprehensive and biologically meaningful the final analysis will be.
Whole genome sequencing is a powerful approach for evaluating the genetic stability of Master Cell Banks (MCBs) and Working Cell Banks (WCBs). By comparing genomic data across different stages of development or production, the analysis can confirm retention of recombinant constructs and identify structural variants, SNPs, or other genomic changes that may have occurred during cell expansion, banking, or manufacturing. This helps organizations monitor long-term stability and reduce development risk.
The service delivers both raw sequencing data and actionable genomic insights to support scientific and operational decision-making. Depending on the project scope, deliverables may include quality-filtered sequencing data (FASTQ), assembled genomes, transgene integration site mapping, structural variant analyses, CNV results, SNP reports, and a detailed scientific report describing the analytical approach, findings, and interpretation. These outputs can be used to support cell line development, cell bank qualification, quality control, and regulatory documentation.
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.
