Extended Data Fig. 2: Derivation of CMV score.
(a) ROC analysis of CMV seropositivity prediction using the first principal component of DEGs between baseline CD8+ samples based on CMV status. Area under the curve (y axis) is plotted against the Benjamini-Hochberg-corrected -log10(adjusted P value) threshold (x axis) used to determine genes to be incorporated in the score with the optimal threshold labelled. (b) CMV score of pre-treatment patient CD8+ T-cell samples according to CMV seropositivity (n = 111 CMV-, n = 95 CMV+, P < 2.2 × 10−16, two-sided Wilcoxon rank sum test); lower and upper box hinges represent the 25th to 75th percentiles, the central line represents the median and the whiskers extend to the highest and lowest values no greater than 1.5 × interquartile range. (c) Correlation of CMV score with number of CD8+ clones stratified by repertoire occupancy post one cycle of immunotherapy (n = 180, Spearman’s Rank Correlation test, rho denotes the Spearman rho, and P value is from two-sided t-test). (d) Cytotoxicity score is not induced following sICB, irrespective of CMV status (n = 43, CMV- P = 0.93, CMV + P = 0.58, two-sided Wilcoxon signed-rank test; boxplot as in (b)).
