Microenvironment, mutations, translocations, and copy number landscape of stage I vs stage III/IV FL. (A) Percentage of positive nucleated cells for CD3, CD4, CD8, FOXP3, and PD1 depicted as boxplots. For CD163 and CD68, the percentage of positive area of the total cell area was computer-assisted scored are plotted in the boxplots (stage I in red [n = 73] and stage in blue III/IV [n = 120]). Significant differences are seen for CD8, PD1, CD163, and CD68 with a P value adjusted for multiple testing: *P = .02, **P = .002, ***P < .001. (B) Comparison plots for CNAs between stage I as filled areas (n = 82) and stage III/IV as lines (n = 139) are percentages of the number of cases with gains (positive value, blue) and losses (negative value, red), sorted for chromosome position (x-axis). (C) Frequency plots with P values (blue) calculated with a 2-sided rank-sum test with 10 000 permutations and FDR (striped segments) of the difference in CNAs; the horizontal dotted lines show the significance threshold P values <.05 in blue, and the FDR <0.1 in red. If the difference in CNA level crosses the P value, and the FDR level is <0.1, the difference is considered significant, which is indicated by * 6q23.3 and 9p21-22 (*P < .05). (D) Frequency of BLC2 and BLC6 translocations and top 20 mutated genes according to stage I in red (n = 82) and stage III/IV in blue (n = 139); significant differences are indicated by ^†q < 0.05 (Fisher’s exact test and a FDR using Benjamini-Hochberg method).