Fig. 1.

Copy number alterations involve chromosome breaks. As aneuploidy strictly refers to numerical changes of whole chromosomes, segmental gains and losses require that part of a chromosome has obtained a different copy number from the remainder of the same chromosome. The example shows chromosome 11 from Figure 3. Segmental gains and losses create a growth advantage by uncoupling the copy number of oncogenes (e.g. cycD1) and tumor suppressor genes (e.g. chk1) from general gene dosage. Frequently, the gains and losses over a single chromosome are complementary, as segments without gains are not copy number neutral but normally show losses. Intrachromosomal segment borders that delineate copy number alterations correspond to unprotected (reactive) ends that are functionally equivalent to breaks.