Figure 4. Tumouroids preserve the genetic alterations from the original tumour.

(a) Ploidy analysis of tumouroid cultures expanded for at least 2 months in culture. Results are expressed as % of ploidy per number of metaphases counted (at least 21 total). Healthy-derived organoids were used as control. A minimum of two independent experiments were performed. (b) Representative images of organoid metaphases used for the ploidy analysis. Scale bar, 10µm. (c-e) Whole exome sequencing analysis of patient's tumour tissues and corresponding tumouroid cultures expanded for < 2 months (early passage) or >4 months (late passage) in culture. All variants identified in all samples (21 total; 7 patients with 3 samples each (Tissue/early organoid/late organoid) were used for the global analyses after filtering for quality control as detailed in methods). (c) Correlation heat-map between the variants identified in PLC-tissues (_T) and PLC-tumouroids (_O). (d) Proportions of exonic variants across the samples, the 6 types of SNVs and the Indels are represented. (e) Percentage of the 6 types of SNVs averaged across all samples. Graph represents mean±SD. (f-g) A cancer-related set of variants (f) and variants predicted to impair protein function (SIFT score <0.05 filter) (g) were identified as described in methods. (f) Bar plots indicate the concordance (%) between the cancer-related variants identified in the tumour-of-origin and the corresponding tumouroids expanded for short term in culture. (g) Damaging coding mutations found in genes already described mutated in liver cancer (Full list is found in Supplementary Dataset 4, spread sheet 15 details the references). The type of mutation is indicated in the legend. _T, tissue; _O, organoid.