Extended Data Fig. 4: Targeted sequencing of 10 days and 1 year tumors.
From: Mutant clones in normal epithelium outcompete and eliminate emerging tumours
(a) Protocol: wild-type mice were treated with DEN for two months and the esophageal tumors collected 10-days or 1-year later. Tumors were then sequenced with a targeted approach (192 gene panel). (b) Area of 10-day and 1-year post-DEN tumors (n = 89 and 64 tumors from 2 and 9 mice, respectively). Lines show mean ± s.e.m. (c) Mutational spectrum of 10-day and 1-year tumors. The bar plots illustrate the number of mutations in each of the 96 possible trinucleotides. The mutational spectrum of individual tumors is shown in (d). (e–f) Percentage of silent, missense, nonsense and splice mutations and indels identified in 10-day or 1-year tumors. Graphs show the values for individual tumors (e, each column is a tumor), or the average for all tumors at each time point (f). (g) Maximum VAF for mutations identified in each tumor at 10 days or 1 year post-DEN (n = 80 and 63 tumors, respectively). Colored shadow illustrates VAF > 0.35, as an estimation for clonality. (h) Number of positively selected mutant genes in tumors at 10 days or 1 year post-DEN treatment (n = 80 and 63 tumors, respectively). Lines show mean±s.e.m (two-tailed Mann-Whitney test). (i) Number and type of mutations in the positively selected genes identified by dN/dS analysis from 10-day or 1-year tumors. (j) Proportion of 10-day and 1-year tumors carrying nonsynonymous mutations in the indicated genes.
