Extended Data Fig. 1: Top ranked T cells in LTS tumours have more similar CDR3β sequences.
From: Neoantigen quality predicts immunoediting in survivors of pancreatic cancer
(a) T cell receptor (TCR) CDR3β sequence dissimilarity (TCR dissimilarity index) in STS and LTS primary and recurrent PDACs. TCR dissimilarity index calculated using the Restricted Boltzmann Machine model18. n = individual tumours. Horizontal bars = median. (b) Trend of P value of TCR dissimilarity index between STS and LTS PDACs (as in left panel) with number of clones in the sample. n = 17 tumours. Blue line indicates a P value of 0.05; circle = mean P value; error bars = standard error of the mean. (c) TCR dissimilarity index based on T cell clone size (Supplementary Methods) and immune fitness cost \({\bar{F}}_{I}\). Green line = linear regression fit. P value by two-tailed Mann-Whitney U-test (a) and two-tailed Pearson correlation (c).
