Fig. 2

Using OncoGEMINI filtering tools to identify variants with specific patterns. Genetic variants corresponding to all samples originating from representative patients, #1 and #3 (further details in “Results” section), are indicated with single gray lines at their respective alternate allele frequencies, where darker grays represent a greater accumulation of variants with similar frequencies. Samples are represented by their sampling time as indicated in the sample manifest file, where a time of 0 indicates a normal tissue sample and values greater than 0 correspond to subsequent tumor samples. Individual variants and their alternate allele frequency changes across multiple tumor time points are highlighted with colored points connected by lines and were isolated from all other variants using the OncoGEMINI filtering tools: bottleneck (red), loh (blue), and truncal (yellow). For each of these variants, the gene in which they occur and their specific mutation are listed next to the point in the final sample for each patient