Cell & Gene Therapy

Cell and Gene Therapy

Cell and gene therapies are important novel approaches to activate immune response, repair pathogenic mutations, and repair or replace damaged tissue or cells. Ensuring correct genetic modification of these products is key in ensuring safe and effective therapies, and is important to demonstrate unambiguously during the regulatory approval process.

Cergentis' TLA technology contributes to upstream and downstream stages of cell and gene therapy product development and production.

Quality control in the upstream process

TLA analyses support:

  • Optimization and validation of new cell line generation technologies
  • Clone selection
  • Cell line characterization
  • Clonality assessment
  • Genetic stability analyses





Quality control in the downstream process

In downstream processing of gene and cell therapy products, TLA can map viral integration sites and quality control the results of targeted gene editing.

TLA-based targeted sequencing has been used to:

  • Quantify the number of correct and incorrect integration and/or gene editing events at an intended location
  • Assess the targeting of a CAR to the TRAC locus
  • Completely sequence the HIV genome and determine integration sites in a patient's blood sample
  • Evaluate transfected/transduced immune cell samples (e.g. T- and B-cells). For example, towards the development of CAR-T cell therapies



Cergentis supports all leading pharmaceutical companies in their cell line development and quality control of genetically engineered cells.

Our team of PhD-level scientists has extensive experience characterizing plasmid and viral integrations in, for example, viral-producing cell lines and CAR-T products.

Through this, Cergentis has established its position as a trusted partner and leader in the genetic analysis of genome-engineered therapeutic cell lines.

A genome map of HIV integration sites identified in a patient’s sample on the basis of HIV – human genome breakpoint sequences.
Example of an NGS coverage profile across a transgene. A large part of the transgene has been sequenced with > 1000x coverage (i.e. with at least 1000 NGS reads). Y-axis shows NGS coverage, cut-off at 1000x. X-axis shows the position within the transgene sequence.
Example of a table with identified SNVs and indels in a transgene sequence. Region: Indication of annotated region in the transgene sequence. Pos: Position of the mutation in the specified transgene sequence. Ref: Reference nucleotide present within the transgene sequence. Mut: Identified mutation compared to the reference sequence. Cov: Sequencing coverage at the position of the mutation (for primer set 1 or 2). %: Percentage of reads in which the mutation was identified.
Example of a whole-genome coverage plot of a targeted transgene integration in a heterogeneous human sample. The integration site is identified at the targeted position in chromosome 14. No other peaks are identified, indicating that no abundant off-target integration sites are present in the sample.
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