Extended Data Fig. 2: Dynamics of the growing population compared to a constant size population model.

Tumours simulated using our tumour growth model (growing population, (a)–(c)) and a death-birth Moran process (constant size population, (d)–(f)) at different selection strength and mutation rate regimes, as indicated in each row and detailed in the main text. Simulations were run for a final population of 10,000 cells in the growing population model and for 50,000 steps in the constant size model. (a)&(d) The mean antigenicity of the tumour for 6 individual simulations. Tumours that reached detectable size are shown in blue, eradicated tumours (cell count reaches 0) are in red, the constant size tumours are invariably in grey. (b)&(e) Distribution of CCF values of the most common neoantigen computed from 20 tumours. For the growing population, only tumours that did not go extinct are shown, and consequently no graph is included for the last two rows. (c)&(f) Cumulative VAF distribution of all mutations (grey) and neoantigens (red). The thick line shows the mean of 20 simulated cumulative distributions, the shaded regions represent ±1 standard deviation around this mean. Note that in the first row, there are no neoantigens in the studied frequency range (no red line), while in the last row the grey and red curves overlap.