Fig. 2

Wildtype and Rhamm^−/− tumor mutation burden is similar, but Rhamm^−/− tumors uniquely exhibit a strong inter-animal homogeneity in mutation characteristics. A The number of CNV gains and losses detected in primary tumor and metastases from Wildtype and Rhamm^−/− mice (n = 3/group) were compared with two inbred mouse stocks, C57Bl/6J (n = 8) and FVB/NJ (n = 1) and a reference set of inbred mice used for comparison with the inherited CNV burden (n = 114) as described in Methods. CNV gains are shown in red, while losses are shown in blue. Statistically significant differences between genotypes are not detected. Error bars represent standard error. B. Variation in the properties of de novo CNVs and SNVs in Wildtype metastases (WM), Wildtype primary (WP) tumors Rhamm^−/− metastases (RM) and Rhamm^−/− primary tumors (RP), (n = 3/group) is displayed as a principal component analysis (PCA). Results show clustering of these properties in Rhamm^−/− but not Wildtype tumors, indicating that the two genotypes differ in the CNV and SNV properties. C, D Phenograms representing SNV (C) and CNV (D) genetic differences. The numeric values in the sample labels represent the individual mouse identifier number. Scale bars represent genetic differences between samples. WP = Wildtype primary tumor; WM = Wildtype lung metastases; RP = Rhamm^−/− primary tumor; RM = Rhamm^−/− lung metastases. SNV and CNV differences were calculated as described in Methods. SNVs of Rhamm^−/− tumors clearly segregate from Wildtype comparators (C). Clear segregation of CNV differences between genotypes is not observed (C). E Different colors represent different mutation types: C:G > A:T (red), C:G > G:C (blue), C:G > T:A (green), T:A > A:T (purple), T:A > C:G (orange), T:A > G:C (yellow). Rhamm^−/− rainfall plots for both primary and metastatic tumors are similar between all three mice, while Wildtype rainfall plots vary, showing that a strong similarity in the pattern of SNV is acquired with Rhamm-loss. Results predict positive selection of a limited number of Rhamm^−/− tumor clones. F. SNV burden that is unique to Wildtype primary tumors, Wildtype lung metastases, Rhamm^−/− primary tumors and Rhamm^−/− lung metastases. There is a greater number of lung-specific SNVs in Rhamm^−/− metastasis vs. primary tumors, but these are unchanged in Wildtype tumors. Values are the Mean and S.E.M. n = 3 mice/group. **p < 0.01