Fig. 2

Timing of genetic alterations and tumor progression history. a Genetic alteration profiles for tumor crc3913. Copy ratio, heterozygous SNP BAF, and somatic SNV MAF profiles are displayed. The numbers on the right side of the copy ratio plot represent predicted integer copy numbers. b MAF profiles and timing estimation for CN-LOH regions. The two plots on the left are allele fraction distributions in two CN-LOH regions, and the plots on the right demonstrate how somatic SNVs accumulate in a CN-LOH chromosome. c–f MAF profiles for copy-neutral, one-copy gain, bi-allelic two-copy gain, and three-copy gain chromosomes. Mutational history is shown for one-copy gain and three-copy gain chromosomes. In one-copy gain chromosomes (panel d), the SNVs in the middle peak of the MAF profile are SNVs present on one out of the three chromosomes and are a mixture of SNVs occurring both before (red SNVs) and after (blue SNVs) the copy gain, since red SNVs on the green chromosome are not duplicated. g Tumor progression map of crc3913. The tumor progresses from left to right. The heights of colored bars on the right represent the proportions of cells. For example, in this tumor, 74% of the cells are tumor cells and 26% of cells are stroma cells. The arrows point out the timing of the events with the 95% of confidence interval shown as a bar above or below the arrows. The time windows when point mutations occur are shown as pink horizontal lines. h Complex aneuploidy history inferred by data integration for chromosomes 2 and 9. The variants’ profiles are shown on the left and the proposed mutational history is on the right. i Tumor progression map of crc2683