Extended Data Fig. 4: Validation of TCR diversity metrics.

a, Cartoon overview of the use of ImmuneLENS to calculate Shannon diversity values from TRAV segment usage as well as divergence metrics between two samples using the Jensen–Shannon divergence (JSD) from TRAV segment usage. The figure is created with BioRender.com. b, Proportion of TRAV segment usage in samples as measured from either TRACERx TCR-seq data (separated into 4 quartiles) or predicted by ImmuneLENS. c, Correlation of Shannon entropy measurements as measured by either TRAV segments predicted by ImmuneLENS or from MiXCR (RNA-seq). d, Jensen–Shannon divergence of samples either from different or same TRACERx patients, for tumor–tumor or tumor–blood sample comparisons measured by ImmuneLENS or TCR-seq from TRAV segment proportions, with significance assessed using a two-sided Wilcoxon rank-sum test. Boxplots in b and d show the median, lower and upper quartile and with whiskers extending to 1.5× the interquartile range above and below the interquartile range. P values for Spearman’s ρ were derived from a two-tailed t-distribution using the correlation coefficient and sample size.