Fig. 6: Characterisation of BCLM PDOs.

a Genomic comparison of CSF cfDNA and matched BCLM PDO (early passage) by WES. Top panel, correlation plots of copy number Z-score (one data point per gene) with regression line plotted (purple) and Pearson’s r-value plus two-sided significance values are shown. Lower panel, Venn diagrams of somatic mutations (excluding synonymous) present in CSF cfDNA and matched BCLM PDO, values shown are mutation count. b Comparison of Pearson r-values from Fig. 6a and Supplementary Fig. 17 by Mann-Whitney, two-tailed test showing a higher level of correlation in CNA status between PDO (n = 5) and CSF cfDNA (n = 5) than between PDO and primary tumour DNA (n = 5) (left panel) and higher fraction of shared variants between CSF cfDNA and PDO than primary tumour and PDO (right panel), source data are provided as a Source Data file. c RNAseq of PDOs (fresh early passage) and matched primary tumours (FFPE). Expression levels of adherens junction components are shown as Z-scores of log2-TPM values (transcripts per million). d RTqPCR analysis of CDH1 expression in PDOs as compared with cell line controls. n = 1 biological replicate, n = 3 technical replicates, source data are provided as a Source Data file. e BCLM PDOs and cell line control (DU4475) were cultured in the presence of methotrexate in 0.2% DMSO or 0.2% DMSO alone (vehicle alone). Cell viability was measured by CellTiter-Glo after 14 days. Data represents mean of n = 4 wells per datapoint ± SD, normalised to vehicle alone treatment, source data are provided as a Source Data file.