Fig. 4. Genomic comparison of primary tumor region-early passage PDX model pairs.

A Schematic representation of engraftment patterns. B Overview of engraftment patterns (monoclonal, green; polyclonal, blue) for each unique P0 PDX sample (for which WES data were available) stacked by tumor. C Mutational distance between regions within each primary tumor in the lung TRACERx421 cohort (n = 1426 regions), P0 PDX models and other regions of their primary tumor (n = 42 regions), and P0 PDX models and their respective region of origin (n = 36 regions). D Examples of phylogenetic trees (left) and clonal composition (right) of P0 PDX models and their regions of origin. Highlighted branches of the phylogenetic trees are those found only in the PDX models (orange), only in the region of origin (primary; green) or both (shared; blue). Clonal composition is shown as clone maps (left: stacked, right: individual clones) where each octagon corresponds to a clone from the phylogenetic tree that is present within the sample. The regions with lowest (upper: CRUK0606 R2) and greatest (lower: CRUK0995 R3) mutational distances between the region of origin and matched PDX model are shown. E Copy number distance between regions within each primary tumor in the lung TRACERx421 cohort (n = 1424 regions), P0 PDX models and other regions of their primary tumor (n = 42 regions), and P0 PDX models and their respective region of origin (n = 36 regions). F Clone proportions of engrafting (n = 34) and non-engrafting (n = 94) clones, excluding ancestral clones that were not detected, within 36 primary tumor regions of origin for which data were available. Dots are colored by the overall engraftment pattern of the P0 PDX models. C, E, F The box plots represent the upper and lower quartiles (box limits), the median (center line) and the whiskers span 1.5*IQR. Two-sided Wilcoxon rank sum test, p values as indicated. LUAD—lung adenocarcinoma; LUSC—lung squamous cell carcinoma.