populations presents a challenge to such analysis, both cytological 10 and genomic data 11 have supported this assumption, as have reports of similar SCNA profiles obtained from paired primary and metastatic lesions Homologue-specific copy ratios (HSCRs; copy-ratio estimates of both homologous chromosomes), are preferred for analysis with ABSOLUTE, and were used for all analyses in this study Although ABSOLUTE can be run on total copy-ratio data (e.g. from array CGH or low-pass sequencing data), we do not present such results here. The use of HSCRs reduces the ambiguity of copy profiles. For example, the total copy-ratio profile of a sample without SCNAs would be equivalent for ploidy values of 1,2,3, etc., however the HSCR profile would rule out odd ploidy values, since these would not be consistent with equal homologous copy-numbers. In addition, since subclonal SCNAs will generally affect only one of the two HSCR values in a given genomic segment, the ratio of clonal to subclonal SCNAs genome-wide is generally higher when considering HSCRs rather than only total copy-numbers.
