Figure 2Features of Phylogenies and Driver Genes in Pam01, Pam02, Pam03, and Pam04
a. Time is represented on the vertical axis, divergence is represented on the horizontal axis. Trunks are colored blue, while branches leading to primary tumors are orange and metastases are green. Each tree is rooted at the germline (“g”). Branch and trunk lengths are relative to the number of underlying variants. Driver alterations are labeled where each is inferred to occur during tumor evolution. b. Representative immunolabeling for CDKN2A, TP53, and SMAD4 illustrating the concordance of labeling for each sample analyzed by WGS for Pam01 in the matched available formalin-fixed paraffin embedded tumor tissues for the primary tumor (PT5) and metastases LiM1, LiM2, NoM1 and NoM2. scale bars, 10 μm. c. CIRCOS plots showing statistically significant copy number variants among Pam01 whole genome samples. For each sample ring, the y-axis spans −2 to 2, with 0 representing a normal diploid copy number in unaffected regions, deletions as a −1 or −2, and amplifications as 1 or 2. Copy number variants > 2 are scored as 2. All values were log 2 transformed for visualization. The outermost ring shows the chromosomes in a clock-wise order. Deletions are shown in blue while amplifications are red. Gene names are those described in . From innermost to outermost the samples are PT5, LiM1, LiM2, NoM1 and NoM2.