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Additional file 1. Supplementary Table 1. Characteristics of patients.

Additional file 3 Supplementary Fig. 2. (A) Spearman’s correlation of variant allele fractions (VAFs) between organoid RNA and organoid DNA. (B) Characteristics of variants detected in organoid DNA and not in tissue RNA; the variants detected in organoids only were associated with low read depth in primary tissue sequences or subclonal events based on organoid sequencing (Wilcoxon rank-sum test). (C) Spearman’s correlation of VAFs between organoid DNA and tissue RNA. (D) Spearman’s correlation of VAF in each gene between organoid DNA and tissue RNA.

Additional file 6 Supplementary Fig. 5. (A) Ki-67 immunohistochemistry in the primary tumor tissues and its interpretation by a pathologist and by image analysis. (B) Significant correlation of the Ki-67 proliferation index between the pathologist’s result and image analysis. (C) No correlations in Ki-67 mRNA expression between bulk primary tissues including tumor microenvironment and cancer cells and CCOs. (D) Comparison of our molecular subgrouping and CMS classification in CCOs (Chi-squared test). CCO, colorectal cancer organoid.

Additional file 2 Supplementary Fig. 1. (A) Histology and immunohistochemistry of the established CCOs and the corresponding primary tumors. (B) Distribution of variant allele fraction (VAF) of detected variants in the MSI-high group and the MSI-low/MSS group. CCO, colorectal cancer organoid; MSI, microsatellite instability; MSS, microsatellite stable; H&E, hematoxylin and eosin.

Additional file 5 Supplementary Fig. 4. (A) Spearman’s correlation coefficient matrix of CCOs versus primary tumor tissues. (B) Total immune score and stromal score of CCOs versus primary tumor tissues. (C) Genes that are differentially expressed between CCOs and primary tumor tissues. (D) Spearman correlation of the expression of differentiation or stem cell markers in CCOs versus primary tumor tissues. CCO, colorectal cancer organoid; TIM, tumor immune microenvironment.

Additional file 4 Supplementary Fig. 3. (A) Profiles of copy number variations with microsatellite instability (MSI) information in the 87 CCOs. (B) Circos plot of the detected fusions in the 87 CCOs. (C) HLA class I molecular typing and its frequency in 87 CCOs. (D) Frequency of the HLA supertype in 87 CCOs. CCO, colorectal cancer organoid.

Additional file 8 Supplementary Fig. 7. (A) Prognostic impact of gene expression in HLA class II in CCOs. (B) Patient survival based on HLA class II expression level using immunohistochemistry (IHC) in cancer cells from primary tissue (log-rank test).