Supplementary Figures from Dynamics of Genome Alterations in Crohn's Disease–Associated Colorectal Carcinogenesis

Supplementary Figure S1. Overview of tissue samples analyzed for each patient. Supplementary Figure S2. Topology and histomorphology of Crohn''s disease associated colorectal carcinomas (CD-CRCs; n = 32) from our cohort. Supplementary Figure S3. Representative histology images of Crohn''s disease associated colorectal carcinomas. Supplementary Figure S4. Analysis of microsatellite instability. Supplementary Figure S5. Association of microsatellite instability with carcinoma site and histomorphology in Crohn''s disease associated colorectal carcinomas (CD-CRCs; n = 32) from our cohort. Supplementary Figure S6. Frequency plots of copy number profiles reconstructed from the TCGA CRC dataset (Affymetrix SNP 6 data). Supplementary Figure S7. Frequency plot of copy number profiles reconstructed from targeted sequencing data. Supplementary Figure S8. Comparison of variant calling by MuTect and Strelka algorithms. Supplementary Figure S9. Number of genome alterations and base substitution patterns in Crohn''s disease associated CRCs compared to sporadic mucinous CRCs. Supplementary Figure S10. Graphical summary of TP53 mutations from Crohn''s disease associated CRCs (n = 29) and sporadic mucinous CRCs (n = 24). Supplementary Figure S11. Graphical summary of KRAS mutations from Crohn''s disease associated CRCs (n = 29) and sporadic mucinous CRCs (n = 24). Supplementary Figure S12. Graphical summary of APC mutations from Crohn''s disease associated CRCs (n = 29) and sporadic mucinous CRCs (n = 24). Supplementary Figure S13. Genomic alteration patterns in selected pathways in Crohn''s disease associated CRCs (n = 29). Supplementary Figure S14. Genomic alteration patterns in selected pathways in sporadic mucinous CRCs (n = 24). Supplementary Figure S15. Genome alterations during tumor progression in Crohn''s disease. Supplementary Figure S16. Overview of all detected mutations in patients with multiple synchronous lesions. Supplementary Figure S17. Patient C12 Supplementary Figure S18. Patient C26. Supplementary Figure S19. Patient C18. Supplementary Figure S20. Patient C05. Supplementary Figure S21. Patient C02. Supplementary Figure S22. Patient C11. Supplementary Figure S23. Patient C07 Supplementary Figure S24. Patient C06. Supplementary Figure S25. Mutant allele fractions by gene. Supplementary Figure S26-S29. Representative images of histology (H&E, left) and TP53 immunohistochemistry (right) in TP53-mutated and TP53 wild-type tissues comprising non-dysplastic (normal, inflamed) colonic mucosa and dysplasia.