Extended Data Fig. 1: Somatic mutations in FAP and sporadic CRC samples.

a. Oncoplot summarizing the landscape of non-silent exonic single nucleotide variants (SNVs), small insertions/deletions, copy number amplifications (Amp), deletions (Del), and copy neutral loss of heterozygosity (cnLOH) within CRC driver genes based on WES data from the previously published FAP multi-region cohort²⁵ (left) and the sporadic multi-region sequencing cohort²⁶ (right). Only somatic mutations are shown. b-d. Comparison of non-silent exonic mutations across polyp stages between the two FAP cohorts and the CRC cohort (p-values are estimated using two-sided Wilcoxon rank sum tests). In box-and-whisker plots, the box represents the interquartile range (IQR) with the center line representing the median, and the whiskers are the largest and smallest data values within 1.5 times the IQR from the box edges. Each point represents one sequenced normal or polyp sample, with n = 29 mucosal, n = 35 benign, and n = 57 dysplastic samples in the multi-polyp HTAN FAP cohort (b), n = 7 mucosal, n = 13 benign, and n = 22 dysplastic samples in the multi-region FAP cohort (c), and n = 27 adenoma and n = 30 carcinoma samples in the sporadic CRC cohort (d). e. Lollipop plots showing the distribution and classes of mutations in APC across two FAP cohorts and one sporadic CRC cohort.