Figure 2.

Independent molecular analysis of stage Ta tumors

(A) CN clusters. Columns, samples; rows, genomic position; yellow, CN gain; blue, CN loss. Left: chromosome number. Top: genomic and expression subtype.

(B) Frequencies of mutations identified by targeted sequencing.

(C) Mutations in chromatin modifier genes that affect enhancer activation status. Blue, mutant; gray, wild type.

(D) TMB as SNVs per megabase according to FGFR3 and KMT2D mutation. Mann-Whitney test.

(E) Recurrence-free survival (RFS) according to PIK3CA mutation status. M, mutant; WT, wild type.

(F) Top: distribution of GS and selected mutations according to expression subtype. Blue, GS1; yellow, GS2; red, mutation present. Lower heatmaps show regulon activity (dES values). Blocks are color coded (left) according to regulon clusters in Figure S4F.

(G) RFS according to expression subtype.

(H) ESTIMATE immune score (left) and expression levels of CD274 (PD-L1) (right) according to expression subtype. Kruskal-Wallis test with Dunn’s multiple comparison correction.

(D and H) Mean, 25th, and 75th percentiles, minimum and maximum values are shown.

(I) RFS according to high (top 25th percentile) and low (lowest 25th percentile) immune score.

(E, G, and I) Log-rank analysis.

∗∗∗∗p < 0.0001, ∗∗∗p < 0.001, ∗∗p < 0.01. See also Figures S3 and S4.