Fig. 4: The neoantigen quality fitness model identifies edited clones to predict the clonal composition of recurrent tumours.
From: Neoantigen quality predicts immunoediting in survivors of pancreatic cancer
a, Recurrent tumour clone composition prediction based on the primary tumour composition and the fitness model. b, Model fitted \({\hat{X}}_{{\rm{rec}}}^{\alpha }/{X}_{{\rm{prim}}}^{\alpha }\) and observed \({X}_{{\rm{rec}}}^{\alpha }/{X}_{{\rm{rec}}}^{\alpha }\) clone frequency changes for the STS (left) and LTS (right) cohorts. Frequency ratios below the sampling threshold were evaluated with pseudocounts. c–e, The immune fitness cost \({\bar{F}}_{I}\) of recurrent tumours (c), new clones (e), and the percentage of new neoantigens in recurrent tumours (d). f, TCR dissimilarity index and immune fitness cost \({\bar{F}}_{I}\) in tumours. n indicates the number of tumours. The green line is a linear regression fit. The horizontal bars show the median values. P values were determined using two-tailed Spearman correlation (b), two-tailed Pearson correlation (f) and two-tailed Mann–Whitney U-tests (c–e).
