Fig. 1

Choice of cellular model systems. a Effect of cellular ploidy on the proportion of NGS reads representing variant alleles and on variant allele fraction (VAF) distribution. Blue and yellow lines joined by a dotted line represent forward and reverse reads, respectively (only parts of pair-end reads are shown). Horizontal red lines represent the position of a variant on the sequencing reads. b Genome plots and 96-bar plots representing mutational profiles of different cell lines. Shown from the outermost rings (genome plots) moving inwards are (i) the karyotypic ideogram; (ii) base substitutions, plotted as rainfall plots (log₁₀ (intermutation distance) on the radial axis; dot colour: blue, C>A; black, C>G; red, C>T; grey, T>A; green, T>C; pink, T>G); (iii) insertions shown as short green lines; (iv) deletions shown as short red lines; (v) major (green blocks, gain) and minor (red blocks, loss) copy number alleles; and (vi) rearrangements shown as central lines (green, tandem duplications; red, deletions). Mutation burdens in the genome plots are non-representative here as different cell lines have had different lengths of time in culture. CML, chronic myelogenous leukaemia; hiPSC, human induced pluripotent stem cell ; HPV, human papillomavirus; NSCLC, non-small cell lung carcinoma