Site Analysis

As pioneers in integration site analysis (ISA), GeneWerk is forging the path for safer gene therapies. Leveraging our 20+ years of experience in integration site analysis for lentiviral and AAV gene therapies, we support clients across the globe at every stage of the vector safety assessment process.

Leading the way in genome-wide integration site analysis

As novel gene therapies enter development pipelines, regulatory bodies adapt their guidelines to ensure their continued safety. Actively and passively integrating (viral) vectors may trigger adverse effects by undirected or unintended integration into the genome of the target cell.

Integration site analysis (ISA) is the key tool to assess the biosafety of gene therapy vectors and the clonal tracking fate of genetically modified cells in vivo. According to FDA and EMA guidance for viral-vector-based therapies, once the vector integration is confirmed, integration site analysis should be undertaken to monitor integration frequency and site identification.

At GeneWerk, we have developed a comprehensive set of tools for regulatory-compliant, genome-wide integration site analysis. Combining streamlined PCR- and sequencing-based approaches with proprietary bioinformatics pipelines, we can determine the integration site position and frequency of your viral vector with unmatched precision and sensitivity.


Shearing Extension Primer Tag Selection Ligation-Mediated PCR (S-EPTS/LM PCR) is the world’s first validated approach for genome-wide integration site analysis. Having been successfully employed in multiple clinical trials and regulatory filings, S-EPTS/LM PCR is GeneWerk’s most recommended assay for ISA.

  • Superior assay performance in a wide range of viral vectors
  • Validated according to FDA, EMA and ICH guidelines
  • Fast turnaround time, particularly beneficial for CAR-T drug products
Read more about S-EPTS/LM PCR


Target enrichment sequencing (TES) is our most comprehensive assay to simultaneously detect vector integration sites, vector integrity, and vector copy number in a single reaction.

  • NGS-based assay – eliminates PCR artifacts
  • Qualitative and quantitative vector genome analysis
  • Multiple analysis using the same patient sample
Read more about TES


Linear amplification-mediated PCR (LAM-PCR), developed by GeneWerk’s founders, has been the gold standard for ISA for over 20 years. (nr)LAM-PCR – its non-restrictive (nr) variation – is best suited for the detection of rare integration sites.

  • High sensitive analysis of rare vector integration sites
  • Over 100 peer-reviewed scientific publications
  • Automated data mining using customized bioinformatics
Read more about (nr)-LAM-PCR

Want to get in touch?

Consult with our experts about solutions to your biosafety challenges.

Contact us

Latest news

Read our latest press releases and announcements below.

A Sad Message From Our Team. Loss…

We mourn the loss of our dear friend, mentor, eminent scientist, co-founder and CEO...

Read More

Protagen Protein Services merges with GeneWerk

Protagen Protein Services (PPS) today announced that it will merge with GeneWerk, an Ampersand...

Read More

GeneWerk Announces Growth Equity Investment from Ampersand…

GeneWerk will expand capabilities to meet rapidly growing demand for cell and gene therapy...

Read More

Insight into Spatial and Temporal Trends of…

Genewerk GmbH in collaboration with University Heidelberg Germany provided an insight into spatial and...

Read More
I agree to the Privacy Policy and Terms of Service.