Extended Data Fig. 9: Further analysis of TCR clusters.

a, The clustering algorithm was run on all patients, and the number of distinct clusters containing expanded ubiquitous and regional TCRs are shown. The number is normalized for the number of expanded TCRs of each type. The Mann–Whitney P value is shown; n = 46. b, A full alignment of the cluster shown in Fig. 3b,c. c, The GLIPH (https://github.com/immunoengineer/gliph) clustering algorithm was run on all patients. The panels show the number of distinct GLIPH clusters containing expanded ubiquitous, expanded regional and randomly selected CDR3 β-chain sequences. The number is normalized for the number of TCRs of each type. The ubiquitous TCRs show greater clustering than randomly selected TCRs (left), with the Mann–Whitney P value shown; n = 46. There was no significant difference between GLIPH clustering of normalized ubiquitous and regional expanded TCRs (right), with the Mann–Whitney P value shown; n = 46. d, The cluster Shannon diversity (see Methods) for all clusters containing ubiquitous or regional expanded TCRs. The Mann–Whitney P value is shown; n = 46. e, As an additional control in the TCR clustering analysis, we took expanded ubiquitous TCRs from patients CRUK0041 and CRUK0322 and mixed them in silico, and we then looked to see whether the resulting clusters were primarily composed of TCRs from individual patients. We analyzed three pairs of patients in whom we observed prominent clustering in this way. One representative example is shown.