Defining chromosome copy number and allele ratios is fundamental to understanding the structure and history of the cancer genome. Current genomic characterization techniques measure somatic alterations in a cancer sample in units of genomes (DNA mass). The meaning of such measurements is dependent on the tumor's purity and its overall ploidy; they are hence complicated to interpret and compare across samples. Ideally, copy-number should be measured in copies-per-cancer-cell. Such measurements are straightforward to interpret and, for alterations that are fixed in the cancer cell population, are simple integer values. This is considerably more challenging than measuring relative copy-number in units of diploid DNA mass in a tumor-derived sample.
