VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
Fig 2
Estimation of repertoire diversity using multinomial model.
A. Rarefaction analysis of repertoire samples from healthy donors and multiple sclerosis patients. The number of unique clonotypes in a sub-sample plotted against its size (number of T-cell receptor cDNA molecules, TRBM). Solid and dashed lines are diversity estimates computed by interpolating and extrapolating using a multinomial model respectively [29]. Note that generally rarefaction curves for MS samples go below those of control donors. Post-HSCT sample (MS8-HSCT) displays the lowest diversity. B. Comparison of repertoire diversity using normalized Chao1 estimate. Normalization is performed by down-sampling datasets to the size of smallest dataset and computing the estimate for resulting datasets (mean estimate value from n = 3 re-samples is used). MS8-HSCT sample is discarded from calculations. *—P = 0.022, two-tailed T-test; effect size estimated by Cohen’s d is 0.98.