Extended Data Fig. 5: Genomic aberrations in pre-invasive lung CIS lesions.
Comparisons of the number of substitutions (a), small insertions and deletions (b), genome rearrangements (c) and copy number changes (d), showing significantly more genomic changes in progressive (n = 29) than regressive (n = 10) lesions. Although there were more clonal substitutions in progressive than regressive lesions (e), the proportion of substitutions that were clonal and the number of clones were similar (f-g). Progressive lesions had more putative driver mutations (h). Telomere lengths (base pairs) were similar between the two groups (i). To confirm an association between CIN gene expression and copy number change we correlated Weighted Genome Integrity Index (wGII) with mean CIN gene expression for the CIS samples in which we have both gene expression and whole-genome sequencing data (n = 11). Pearson correlation coefficient r2 = 0.473 (j). All P values were calculated using likelihood ratio tests of a mixed effects model with outcome (progressive or regressive) included as a fixed effect versus a model that was identical but for the fact that outcome was not included as a fixed effect. Boxplots are generated using the R boxplot function, which displays the first and third quartile as hinges and places whiskers at the most extreme data point that is no more than 1.5 times the length of the box away from the box.
