Extended Data Fig. 2: Adaptive immune and tumour co-evolution.

a) Scatter plots showing relationship between shared TCRα and TCRβ VDJ sequences across sampled metastatic sites (inter-sample comparisons: patient 308 n = 36. patient 315: n = 28). TCR sequences down sampled. P value and R² obtained from linear regression analysis. b) Correlation plot showing relationship between tumour immune microenvironment components deconvoluted from the bulk RNA-Seq data using MCPcounter. Inset: scatter plot showing relationship between T and B cell enrichment. P value and R² obtained from linear regression. c) Top: heatmap showing Pearson’s correlations between tumour immune microenvironment composition (obtained using Danaher gene sets) and activity. Enrichment scores obtained using bulk RNA-Seq data. ****P < 0.0001, ***P < 0.001, **P < 0.01, *P < 0.05. Bottom: scatter plot showing correlation between B cell activation and cytolytic activity (CYT). P value and R² obtained from linear regression analysis. d) Scatter plots showing relationship between B and T cell enrichment and expression of a tertiary lymphoid structure gene set. P value and R² obtained from linear regression analysis. e) Relationship between B cell, T cell and tertiary lymphoid structure (TLS) hallmark signature in the TCGA breast cancer cohort (n = 1083 tumours). P value and R² obtained from linear regression analysis. f) Spatio-migratory map of B cell clonal migration between metastatic sites. Edge width proportional to relative number of shared BCR clones between sites. g) Heatmaps showing relative number of shared BCR clones between sites. h) Scatter plots showing relationship between shared TCRα VDJ sequences and predicted MHC class I and II neoantigens across pairwise metastatic sites. i) Scatter plots showing relationship between shared TCRβ VDJ sequences and predicted MHC class I and II neoantigens across pairwise metastatic sites. b–d) Data from all sites (n = 27) from all patients used. a–d, h, i) The shaded area, in grey, represents the 95% confidence interval. a, f-i) Data from two patients with more than four metastatic sites sampled used (308, 315). h, i) TCR sequences were downsampled. P value and R² obtained from linear regression analysis. Inter-sample comparisons: patient 308 n = 36; patient 315: n = 28.