Fig. 3. Patient-derived organoids (PDOs) retain key genomic features of parental tumors (PT).

a Tumor purity in PT and matched PDOs of non-muscle invasive bladder cancer (NMIBC, left) and muscle invasive bladder cancer (MIBC, right) samples (n = 15 biological samples; mean estimate ± SE). Two-sided paired Wilcoxon test between PDOs and PT, p-value = 0.31. b Allele-specific copy-number (CN) similarity in randomly paired samples and matched paired ones (n = 312 randomly matched, n = 13 matched PDOs with corresponding PT). Boxplots indicate median (middle line), 25th, 75th percentile (box) and 5th and 95th percentile (whiskers). Two-sided Wilcoxon test, p-value = 4.2e⁻⁰⁹. c Proportion of shared and private deleterious single nucleotide variants (SNVs) between PDOs and PTs. For each sample, proportions were compared using two-sided Chi-squared test, p-value <0.05. d Distributions of the tumor content and ploidy corrected allelic fraction (AF) of all the shared and private SNVs in PDOs and PTs in two representative samples (NMIBC BLCa112 left, n = 266 shared tumor SNVs, n = 263 shared organoids SNVs, n = 141 private tumor SNVs, n = 296 private organoid SNVs; MIBC BLCa86 right, n = 201 shared tumor SNVs, n = 209 shared organoids SNVs, n = 281 private tumor SNVs, n = 1436 private organoid SNVs). Boxplots indicate median (middle line), 25th, 75th percentile (box), and 5th and 95th percentile (whiskers). Two-sided Wilcoxon test, p-value <2.22e⁻¹⁶. e Clonality of shared point mutations of matched PDOs and PTs (BLCa112 and BLCa86). Two-sided correlation test p-value and Pearson’s correlation coefficient (R) are reported within the figure, p-value <2.22e⁻¹⁶. f Copy-number and point mutations profiles between PDOs and PTs for two representative samples (NMIBC BLCa112 left, MIBC BLCa86 right).