Fig. 5.

Haplotype-resolved DNA copy number and rearrangement analysis of post-crisis RPE-1 cells from Ref. [41]. Schematic diagrams of alterations to each homolog and their clonal fractions are shown below the copy-number plots. Non-telomeric chromosomal fragments involved in complex rearrangements are outlined. a Haplotype-specific DNA copy number and rearrangement (black arcs) of Chr.8 in the X-33 sample. Both rearrangements and copy-number alterations are restricted to the red homolog; the non-integer copy-number states indicate that the altered Chr.8 is present in a subclonal population (∼45%). b Haplotype-specific DNA copy number and rearrangement of Chr.4 (black arcs: intrachromosomal; magenta vertical lines: interchromosomal to Chr.13) in the X-25 sample. Rearrangements and copy-number alterations affect both homologs: Segmental changes of both homologs (blue: gain, red: loss) appear to be subclonal (∼90%). c Haplotype-specific copy number of Chr.6 in the X-36 sample. The blue homolog shows non-constant copy number (1-1.3) near the q-terminus that contrasts with constant copy number of the red homolog (∼1) or the rest of the blue homolog (∼0.7). We interpret this pattern as reflecting extensive copy-number heterogeneity in the population