Figure 4
From: Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data
Grid plot and expected VAF levels of simulated tumor sample. (a) Grid plot of simulated, noise- and bias-free array CNs. The scale of the array CNs is unknown. The four colored points suggest the grid pattern drawn for subclone A, but it is unknown whether (1,1) integer copies happen at (g2, g2), (g3, g3) or (g4, g4). (b-d) The three scenarios are illustrated., Each scenario has one colored column for each of the colored genome segments. Two of the segments have mutations on them (red crosses), with VAFs as shown on the y-axes (simulated without noise or bias). The different scalings suggest different integer CNs (c1, c2) of the segments (labels on x-axes), which give different potential expected VAF levels under certain assumptions (horizontal lines). The mutation on the blue segment does not fit any suggested VAF level in (d), suggesting g4 ≠ 1. Assuming that some VAF levels are more plausible than others (thick rather than thin horizontal lines) also rules out (b) in favor of (c): g3 = 1 (see Materials and methods).