Client Challenge
A biopharmaceutical company developing a lipid nanoparticle (LNP)-formulated gene-editing drug product needed a cell based potency assay to measure on-target editing activity, but had not yet established which cell-based model or analytical readout would give the most reliable, reproducible signal. The company needed a documented development path comparing candidate cell substrates and readout platforms before committing to a method for future testing.
Avance Biosciences’ Solution
Avance Biosciences developed and compared cell-based potency assay formats for the LNP drug product. The approach:
- Screened multiple candidate cell lines, for their responsiveness to the drug product across a range of doses
- Built a synthetic quality-control panel spanning a defined series of target editing percentages to confirm each candidate readout method’s ability to recover a known result
- Developed two orthogonal readout methods — targeted next-generation sequencing (NGS) and droplet digital PCR (ddPCR) — to quantify the percentage of edited alleles at the intended target site
- Ran dose-response studies in the candidate cell lines to identify the cell line and working dose range producing the most consistent, highest-magnitude signal
- Directly compared the NGS and ddPCR platforms against one another across the dose range in the selected cell line to evaluate concordance and select a primary readout method
Development Findings
- Cell Line Selection: Which cell background gives the clearest signal? One candidate cell line consistently produced the highest and most reproducible editing response across the tested dose range and was selected as the assay’s cell substrate.
- Dose Response: How does dose editing change with the dose? Editing activity increased with drug product concentration through a defined window before leveling off; at the highest doses tested, the response became less consistent, alongside qualitative signs consistent with reduced cell health at those extremes.
- Accuracy of the known editing levels: Does each readout recover a known, pre-set result? Quality control samples spanning a defined range of target editing levels were recovered in close agreement by both readout platforms.
- Reproducibility: Does the result hold up across independent runs? Repeat runs in the selected cell line produced consistent results, confirming the dose-response pattern was reproducible.
- Platform Comparison: How do the two methods compare to each other? NGS and ddPCR produced closely correlated results across the dose range, with ddPCR showing somewhat greater sensitivity; ddPCR was selected as the primary readout method going forward.
Customer Outcome
- An established, dose-responsive potency assay for its LNP-formulated gene-editing drug product, built on a selected lead cell line.
- Two orthogonal, readout methods, with ddPCR adopted as the primary platform and NGS available as an orthogonal check.
- A defined, optimal dose window to support future assay standardization
Client Impact
The client now has a documented, cross-validated potency method and a selected cell-based model ready to carry into formal assay qualification.
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