Extended Data Fig. 2: Intratumoral heterogeneity and interpatient characteristics of NJs across various cancer types.

A. Multi-region RNA-seq data of multiple cancer types were collected across various studies. Multi-region sampling is defined in studies in which multiple biopsies were isolated from the same tumor for downstream sequencing analyses. B. Counts per million (CPM) of non-annotated, protein-coding NJs across multi-region samples in LIHC, PRAD, MESO, GBM, and LGG cases. C. Heatmap illustrating the number of metastases within an SKCM patient (columns) that have a detectable expression of NJs (rows). The intensity of each cell indicates the proportion of regions within the same tumor that have putative expression of each NJ, with the intensity of 1 representing an NJ expressed in all metastases within a corresponding patient. D. Histogram of the number of multi-region sampled glioma cases with the corresponding number of tumor-wide NJs. E. Distribution of glioma-specific NJs (n = 789, columns) based on their ITH across patients. F. Total number of NJs found in n cores per patient (n = 52). G. Slope charts demonstrating patient-matched pairs (n = 52) of the number of NJs found in n cores compared to 10 cores. Paired t-test analysis was performed on all matched values, and the corresponding p-value is displayed above each slope chart iteration. H. Dot-plot with best-fitting curve mapping the p-values of all iterations of paired n core and 10 core comparisons. I-K. Percentage of NJs identified in primary tumors that were conserved in paired metastases (COAD, n = 1; PRAD, n = 1; SKCM, n = 2) (I), recurrence (COAD, n = 1; GBM, n = 3; LGG, n = 12; LIHC, n = 2; LUAD, n = 2) (J), and recurrence following temozolomide treatment with or without hypermutation (HM) (hypermutated, n = 16, non-hypermutated, n = 6) (K). Further statistical details are found in Supplementary Table 3.