American Association for Cancer Research
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Supplementary Tables S1-S9 from Mutational Heterogeneity in APC and KRAS Arises at the Crypt Level and Leads to Polyclonality in Early Colorectal Tumorigenesis

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posted on 2023-03-31, 20:07 authored by Mireia Gausachs, Ester Borras, Kyle Chang, Sara Gonzalez, Daniel Azuara, Axel Delgado Amador, Adriana Lopez-Doriga, F. Anthony San Lucas, Xavier Sanjuan, Maria J. Paules, Melissa W. Taggart, Gareth E. Davies, Erik A. Ehli, Jerry Fowler, Victor Moreno, Marta Pineda, Y. Nancy You, Patrick M. Lynch, Conxi Lazaro, Nicholas E. Navin, Paul A. Scheet, Ernest T. Hawk, Gabriel Capella, Eduardo Vilar

Table S1. Summary of adenomas with multiple APC and KRAS somatic hits identified by next-generation sequencing. Table S2. Clinical and pathologic characteristics of patients analyzed in this manuscript. Table S3. Analysis of APC, KRAS and 5q loss using AmpliSeq and SNP array TableS4. Number of normal mucosa, adenomas, tumors and crypts analyzed per case. NM; normal mucosa. Table S5. Analytical sensibility of Light Cycler® 480 (Roche) and dynamic array (Fluidigm) to detect KRAS mutations. Table S6. In silico of the APC somatic hits observed by next-generaiton sequencing that were labelled as VUS. B, benign; N, neutral; D, damaging; P, Probably damaging. Table S7. APC analysis of adenomas and carcinomas in bulk biopsies and isolated crypts. The analysis of adjancent normal mucosa was not performed. Table S8. KRAS genotyping results of adenomas and carcinomas by digital and dynamic array (Fluidigm) in bulk biopsies and isolated crypts Table S9. Primers and probes used in this manuscript.




University of Texas MD Anderson Cancer Center

Spanish Ministry of Economy and Competitiveness

Carlos III Health Institute


Scientific Foundation Asociación Española Contra el Cáncerancer, the Government of Catalonia

Scientific Foundation Asociación Española Contra el Cáncer



Purpose: The majority of genomic alterations causing intratumoral heterogeneity (ITH) in colorectal cancer are thought to arise during early stages of carcinogenesis as a burst but only after truncal mutations in APC have expanded a single founder clone. We have investigated if the initial source of ITH is consequent to multiple independent lineages derived from different crypts harboring distinct truncal APC and driver KRAS mutations, thus challenging the prevailing monoclonal monocryptal model.Experimental Design: High-depth next-generation sequencing and SNP arrays were performed in whole-lesion extracts of 37 familial adenomatous polyposis colorectal adenomas. Also, ultrasensitive genotyping of hotspot mutations of APC and KRAS was performed using nanofluidic PCRs in matched bulk biopsies (n = 59) and crypts (n = 591) from 18 adenomas and seven carcinomas and adjacent normal tissues.Results: Multiple co-occurring truncal APC and driver KRAS alterations were uncovered in whole-lesion extracts from adenomas and subsequently confirmed to belong to multiple clones. Ultrasensitive genotyping of bulk biopsies and crypts revealed novel undetected APC mutations that were prominent among carcinomas, whereas abundant wild-type APC crypts were detected in adenomas. KRAS mutational heterogeneity within crypts was evident in both adenomas and carcinomas with a higher degree of concordance between biopsy and crypt genotyping in carcinomas. Nonrandom heterogeneity among crypts was also observed.Conclusions: The striking degree of nonrandom intercrypt heterogeneity in truncal and driver gene mutations observed in adenomas and carcinomas is consistent with a polycryptal model derived from multiple independent initiation linages as the source of early ITH in colorectal carcinogenesis. Clin Cancer Res; 23(19); 5936–47. ©2017 AACR.

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