Examples of clusters of rearrangements in primary and metastatic tumor genomes. (a) A cluster of rearrangements involving chromosomes 3 and 6 specific for the primary tumor of patient 4. (b) A cluster of rearrangements on chromosome 13, which could be found in both the primary tumor and the liver metastasis of patient 1. (c) A metastasis-specific cluster of rearrangements involving chromosomes 17 and 21 of patient 4. Orientations of fusions are colored as in Figure 1. Red copy number plots and B allele frequencies correspond to the liver metastasis and blue plots correspond to the primary tumor. Copy number variation and B allele frequencies for matching normal colon and liver tissue are plotted in black. (d) Breakpoints and copy number changes involving a cluster of rearrangements on chromosomes 15 and 20 in the primary tumor genome of patient 3. The upper panel shows a nucleotide-resolution map of fusion points for this cluster. Lines indicate fusions between chromosomal fragments. Genomic coordinates indicate positions of breakpoints. Chromosomal fragments with both head and tail side connected to other fragments are retained, while fragments that lack any link (fusion) are supposed to be deleted. This expected pattern of retained and deleted fragments is reflected by the copy number profile for chromosome 15 (lower panel). BAF, B allele frequency.