Extended Data Fig. 3. Copy-number profiles of hopeful monster karyotypes.

a, Reciprocal copy-number profiles of two PDTO-19b cells with hopeful monster karyotypes are shown (Fig. 1c, III). Since the ancestor karyotype of these two cells is unclear, reciprocity between hopeful monster karyotypes refers to the observation that all chromosomal segments add up to an even number. Grey dots indicate bin ratios (Bin size: 1 Mbp). Integer copy-number states are indicated with black (no deviation of a tetraploid state), blue (loss) and orange (gain) lines. Below: The copy-number profile of the merged sequencing data of the two hopeful monsters mimics a duplicated core karyotype of the sequenced PDTO-19b organoid. Orange boxes indicate CNAs in the merged profile that deviate from a duplication of the core karyotype, indicating that these CNAs were present in the ancestor cell. b, Reciprocal copy-number profiles of three PDTO-9 cells with hopeful monster karyotypes are shown (Fig. 4a). Grey dots indicate bin ratios (Bin size: 1 Mbp). Integer copy-number states are indicated with black (no deviation of a tetraploid state), blue (loss) and orange (gain) lines. Adding up the copy-number state of chromosome segments across all three hopeful monster karyotypes results in a twice replicated genome (‘ploidy 8’, not shown). Below: The copy-number profile of the merged sequencing data mimics the core karyotype carrying a de novo loss of 1pter-p34.2 (orange box).