Fig. 4. TmS is associated with known prognostic characteristics and refines prognostication in addition to stage.
a–f, Clinicopathologic annotations for TCGA head and neck (a); TCGA renal papillary (b); TCGA bladder urothelial (c); TCGA prostate (d); TCGA breast (e); and METABRIC breast (f) cancers. Receptor status is indicated as follows: ER, estrogen; PR, progesterone; TNBC, triple-negative. Tumor samples are ordered by TmS from low to high. Benjamini–Hochberg-adjusted P values for Kruskal–Wallis tests comparing TmS across clinicopathologic subgroups are indicated by asterisks. For MYC/PVT1 copy number status, ‘Gain’ indicates either MYC or PVT1 amplification, and ‘Neutral’ indicates that no copy number alterations were detected. g, Kaplan–Meier curves of PFI for TCGA samples. Gray lines denote summary Kaplan–Meier curves of patients with high versus low TmS across all cancer types. Kaplan–Meier curves are further grouped into four groups by TmS and pathologic stage. P values of log-rank tests between high- versus low-TmS groups are indicated by asterisks. h, Forest plot of HRs (center points) and 95% CIs (error bars) of multivariate Cox proportional hazard models for OS or PFI in TCGA. Models are adjusted for age, TmS (high versus low), stage (advanced versus early) as well as an interaction term of TmS × stage, where applicable (see details in Supplementary Table 5). i, Forest plot of HRs (center points) and 95% CIs (error bars) of multivariate Cox proportional hazard models with age, TmS (high versus low), chemotherapy (yes versus no), Oncotype Dx risk classification (high versus intermediate versus low) as predictors for DFS in METABRIC (see details in Supplementary Table 7). For h and i, P values of two-sided Wald tests for the covariates are indicated by asterisks. Kaplan–Meier curves of DFS grouped by TmS (high versus low) for METABRIC TNBC (j) and ER+HER2− (k) patients treated with chemotherapy. P values of log-rank tests between high- versus low-TmS groups are indicated by asterisks. For all P values, significance levels are denoted as follows: *P < 0.05, **P < 0.01 and ***P < 0.001. HPV, human papillomavirus.