Why Use OGM + Karyotyping Together in Genome-Edited Cell Analysis

1. Complementary Strengths
   • Karyotyping excels at detecting large-scale structural changes, including whole-arm translocations, aneuploidies, and centromeric rearrangements—especially at the chromosome level.
   • OGM provides much higher resolution- (it provides breakpoints at the basepair level), detecting balanced and unbalanced SVs as small as ~30 kbp that karyotyping would miss, including insertions, deletions, inversions, and complex rearrangements.
2. Improved Sensitivity for Low-Prevalence Events
   • Low-level mosaicism (i.e., SVs present in a small fraction of cells) can be hard to detect by either method alone.
   • OGM can detect some low-level events (>5% cell frequency), especially when the SV alters optical maps, but struggles with complex events and heterogeneity.
   • Karyotyping can also spot low-frequency changes if the event is visible in the metaphase spreads—but typically only with enough cells analyzed (we are breaking through this ceiling).
   • Together, they increase the chance of identifying rare but important off-target events in genome-edited populations.
3. Cross-Validation of Results
   • Structural variants identified by one method can be confirmed by the other, increasing confidence in the findings and reducing false positives or misinterpretations.  
4. Detection of Centromeric and Telomeric Events
   • Karyotyping is superior in visualizing rearrangements involving centromeres and subtelomeric regions, which OGM may not fully resolve.
   • These regions are often involved in whole-arm translocations or chromosomal instability—important considerations in genome-edited cells.
5. Broader Spectrum of Detectable Events
   • Some SVs (e.g., Robertsonian translocations, polyploidies, or balanced whole-arm rearrangements) may be completely invisible to OGM.
   • Conversely, cryptic or complex SVs—especially those below karyotyping’s 5–10 Mbp resolution—are often only detectable with OGM.
6. Contextual Structural Insight
   • OGM can often localize breakpoints and disrupted genes, helping to predict functional consequences.
   • Karyotyping provides a whole-chromosome context, which is valuable when evaluating global genomic stability.
7. High Relevance for Therapeutic Cell Lines
   • In genome-edited therapeutics, regulatory guidelines increasingly demand single-cell level characterization of genomic integrity.
   • Using both methods provides a more robust and defensible dataset for clinical translation or regulatory submission.

Karyotyping + OGM = Wide lens + fine focus.
Together, they provide the resolution, sensitivity, and coverage needed to detect both subtle and large-scale structural variants, especially when present in low-prevalence subpopulations—a critical need when evaluating genome-edited cell lines for safety and stability.