Fig. 8
From: Forward and reverse mutations in stages of cancer development
Serial orders of copy number (CN) changes in B-N-P-T tetra samples. a Frequencies of three classes of sequential orders of CN changes. Total numbers of CNV windows conformed to each serial order of changes are plotted out for all 26 possible orders. The CN status of 500 kb windows of N-, P-, or T-stage was determined relative to B-stage for 12 B-N-P-T tetra samples as described in the “Methods” section. The total numbers of windows that conformed to the different possible serial orders of CN changes (Additional file 15: Table S11) provided the basis for their partition into three frequency classes (separated by two vertical dashed lines). U stands for CN-unaltered, G for CN-gain, and L for CN-loss. b Circos diagram showing the chromosomal distribution of different CNV serial orders. The 26 different orders are arranged from the rim, showing chromosome banding, inward in accordance to their left-to-right arrangement in part a, viz. ULU (blue) in the outermost ring followed by LUU (red), UGU (blue), etc., where orders with a CN-status of U at N-stage are colored blue, and orders with a CN-status of G or L at N-stage are colored red. Classes I–III are separated by dashed circles in black. c GUG/GUL and LUL/LUG frequency ratios determined using different window sizes. Without lineage effects, these ratios would be expected to yield Q = 1 (as represented by the red dashed line). In contrast, all the Q values of GUG/GUL (blue) and LUL/LUG (red) observed in sequence windows varying from 50 to 500 kb significantly exceeded unity (*p < 10−16) (see Fig. 1 for abbreviations)