Extended Data Fig. 5: Longitudinal whole exome sequencing (WES) analysis of selected clonal populations.

a, Coverage Summary of 27 Whole Exome Sequencing (WES, see Methods) experiments. Total reads obtained per sample (orange) and median on-target coverage per base (blue) are shown. Other stats and WES quality control are available in Supplementary Tables 12,13. b, Fraction of SNPs detected per coverage bin in different cell lines (mutational burden). Calls from all clones were aggregated per cell line. Coverage per base was obtained by DepthOfCoverage module of GATK v3.5. c, Allele frequency (AF) distributions of detected variants in HCT116 clones sampled after 78 days (top) and 168 days (bottom). d, Spatial distribution of SNPs detected in HCT116 clones. e, Comparison of allele frequencies in five HCT116 single-cell derived clones after 78 days (x axis) and 168 days (y axis). If selection was greatly affecting the process, allele frequencies were not expected to remain stable as observed in practice. f, Expression of marker genes in six A549 clones that were selected for exome analysis (colored in brown). g, Similar to Fig. 2c, kinship analysis of A549 clones. Rows above column show normalized expression of KRT18 (red) and SERPINE1 (blue) genes in each clone. h, Selection of seven NCI-H1299 clones (colored in magenta). i, Kinship analysis as in Fig. 2c for NCI-H1299 clones. j, Normalized expression of the SERPINE1 and ID modules in H1299. Single cells represented by small grey dots. Clones profiled by WES are labeled in black and red (as in panel i). Note the concordance between the genetic and transcriptional sub-clonal structure for these cells.