Ensuring Genomic Integrity in Allogeneic Cell Therapy Development

Ensuring Genomic Integrity in Allogeneic Cell Therapy Development

The promise of allogeneic cell therapies is enormous — scalable, off-the-shelf treatments that can transform how we fight cancer and other diseases. But delivering safe and effective therapies requires more than just efficient editing tools. It demands a deep understanding of genomic integrity across the entire development pipeline.

At KROMATID, we’re helping partners integrate next-generation cytogenetics into their workflows to reduce risk, guide decision-making, and support regulatory readiness. Here are some of the key insights from our recent discussion with Erin Cross (VP of Platform, KROMATID) and Daniel O’Connell (consultant):

The Challenge: Safe Editing Without Hidden Risks

Cutting-edge approaches like CRISPR-directed integrases and reverse transcriptase-based editing hold immense promise for precise DNA cargo delivery. Yet, even these tools can introduce unintended outcomes:

  • Off-target insertions
  • Structural rearrangements
  • Large-scale DNA variants (>100 bp)

These changes may not always be obvious, but they can impact safety, efficacy, and regulatory approval. As one recent study showed, treated samples often had low on-target but high off-target integration rates, underscoring the need for careful evaluation.

A Genomic Integrity Roadmap for iPSC-Based Therapies

Induced pluripotent stem cells (iPSCs) are a foundation for many allogeneic platforms, CAR-T and CAR-NK therapies, iPSC-derived T cell and NK cell products, and other off-the-shelf immune cell therapies. But to move safely from donor to drug product, teams must evaluate risk at every step:

  1. Donor Evaluation – Compare germline DNA with iPSC genomes to identify pre-existing variants.
  2. Cell Line Engineering – Characterize editing outcomes with whole genome sequencing (WGS), karyotyping, and KROMASURE analysis.
  3. Expansion & Differentiation – Detect emerging subclonal risks and structural variants at high sensitivity.
  4. Final Product Testing – Apply orthogonal approaches to ensure genomic stability before clinical release.

This roadmap not only protects patients but also helps developers make data-driven decisions about which donors, editing strategies, and workflows to advance.

Why Karyotyping is an Integral Part of a Comprehensive Testing Package

No single method captures the full picture of genome stability:

  • Whole Genome Sequencing (WGS): Excellent for base-pair resolution (SNPs, indels, junctions) but limited in detecting large, complex events.
  • KROMASURE G-banded karyotyping: Ideal for identifying structural variants, translocations, and subclonal changes at single-cell resolution.
  • Integrated analysis: Combining orthogonal tools builds confidence and provides the evidence regulators increasingly expect.

By integrating these methods, companies can prioritize variants for further study, evaluate potential oncogenic risk, and ensure IND-readiness.

Partnering for Safer Therapies

Regulators, including the FDA, have made it clear: assessing genomic integrity is essential for cell and gene therapy development. KROMATID’s cytogenetic platform fills a critical gap by enabling detection of rare and complex events at high resolution — insights that traditional methods often miss.

By incorporating genomic integrity testing early in the discovery and research phase, developers can:

  • Validate workflows
  • Support major business decisions
  • Accelerate safe translation to the clinic

Final Thoughts

The path to safe, scalable allogeneic therapies requires more than efficient editing — it requires confidence in genomic integrity. With orthogonal testing strategies like KROMASURE InSite, developers can de-risk their programs, build stronger regulatory packages, and ultimately deliver safer therapies to patients.

 

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KROMATID Marketing