Fig. 1: Chromosomal CNAs emerge and propagate during clonal PDTO outgrowth.

a, Schematic of the procedure to perform single-cell whole-genome sequencing of the entire cell population from individual organoids. Clonal PDTO structures are mechanically dissociated into single cells before manual picking of individual cells for prospective genome-wide CNA analysis. b, Karyotype heatmap showing 62 cells derived from a clonal PDTO-9 structure expressing transgenic H2B-Dendra2 and consisting of 67 cells (93% recovery). A total of 18 cells showed de novo CNAs. Reciprocal gains and losses are indicated with solid red boxes. Dashed boxes indicate CNA events where a reciprocal loss or gain is missing. Sub-chromosomal CNAs were counted as events when represented in more than one cell. Parallel emergence of de novo CNAs involving chromosome 1q (lineages I and II) was determined by co-occurrence of a sub-chromosomal CNA in chromosome 18. Scale bar, 10 μm. c, As in b. The sequencing data of 58 PDTO-19b cells are shown (87% recovery). A total of 16 cells showed de novo CNAs. The bottom panel shows a population of polyploid cells with large deviations from the core karyotype. Two cells show reciprocal gains and losses across their genome (lineage III). Scale bar, 10 μm. d, Graph indicating the number of CNA events per dataset (eight datasets). The dataset size is indicated within each circle. Events include reciprocal CNAs, non-reciprocal whole-chromosome gains or losses and non-reciprocal sub-chromosomal CNAs represented in more than one cell. Hopeful monster karyotypes were excluded from this analysis. CNAs that occurred in the same cell division were considered as one event.