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:
- Donor Evaluation – Compare germline DNA with iPSC genomes to identify pre-existing variants.
- Cell Line Engineering – Characterize editing outcomes with whole genome sequencing (WGS), karyotyping, and KROMASURE analysis.
- Expansion & Differentiation – Detect emerging subclonal risks and structural variants at high sensitivity.
- 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.