Extended Data Fig. 5: T cell subsets and clonal expansion behaviour.

a, Tissue expansion patterns of clonotypes by T cell cluster. Bar plot shows the distribution of tissue-associated clones—having at least one cell in tumour or NAT—and a primary T cell cluster assigned, grouped by primary cluster. Clones in each primary cluster are further divided by their tissue residency pattern. b, Tissue expansion patterns of cells by T cell cluster. Bar plots show distributions of T cells in NAT and tumour compartments, grouped by their assigned cluster. The counts in each row, corresponding to a cluster in a, comprise all tissue-resident cells—from tumour or NAT—assigned to that cluster. Cell counts are further distinguished by the tissue expansion pattern of their parent clone, with dual expansion shown on the right pair of bar plots, and singletons and multiplets shown on the left. P value is from a chi-square test on counts of tissue-resident T cells. Asterisks indicate statistically significant over-representation of the given T cell cluster and tissue expansion pattern, with a one-sided P value from a post hoc Fisher exact test on the same counts of tissue-resident T cells as the chi-square test, shown when a Bonferroni-adjusted P < 0.01. c, Clonal expansion patterns for T cell clusters. Scatter plot for each T cell cluster shows tissue-associated clones with the corresponding primary cluster, integrated from all 14 patients in this study and plotted by their clone sizes in NAT and tumour on logarithmic scales. Dots are coloured by their tissue expansion pattern, as per the two-dimensional palette, except that blood singleton and multiplet clones were not plotted because only four patients had blood samples. d, e, Analysis of external datasets. The same methodology of c was applied to datasets from Guo et al.³ on 14 patients with non-small cell lung carcinoma (c) and Zhang et al.⁴ on 12 patients with colorectal adenocarcinoma (d). Clones were grouped according to their primary cluster from the original analyses, and coloured by the two-dimensional palette for tissue expansion pattern at the bottom right of e. Blood clone sizes are indicated by dot size, as in e.