This notebook tracks individual clonotype kinetics across longitudinal post-infusion timepoints (Wk2, Wk4, Wk8, Wk12). We characterize expansion kinetics, peak timing, persistence, and compute AUC (area under the curve) as a time-integrated clonal exposure metric.
We plot the frequency trajectory of the top 5 Product clonotypes per patient across all timepoints, from Apheresis through 12 weeks post-infusion.
CR patients show dramatic post-infusion expansion of their top Product clones, with frequencies peaking at Wk4–Wk8 and sustained persistence through Wk12. PD patients show weaker, more transient expansion with rapid decline.
AUC provides a single summary metric for time-integrated clonal exposure, computed via trapezoidal integration over the post-infusion timepoints.
# Trapezoidal AUC computation
auc <- 0
for (i in 1:(length(timepoints) - 1)) {
dt <- weeks[i+1] - weeks[i]
auc <- auc + 0.5 * (freq[i] + freq[i+1]) * dt
}Persistence ratio = frequency at Wk12 / peak frequency. A ratio of 1.0 means the clone maintained its peak; lower values indicate decline.
1. CR patients show the strongest and most sustained clonal expansion, with top clones peaking at Wk4–Wk8.
2. AUC is significantly higher in CR vs PD patients — time-integrated exposure associates with clinical benefit.
3. Persistence ratios stratify by response: CR clones retain 60–90% of peak while PD clones decline to <30%.
4. Peak timing differs: CR clones peak later (Wk4–Wk8) while PD clones peak earlier and transiently (Wk2).