Extended Data Fig. 3: Landscape of somatic copy-number alterations in FAP lesions and sporadic colorectal tumors.

a-c. Fraction of samples with copy-number gains (red, positive y-axis) or losses (blue, negative y-axis) in the HTAN FAP multi-polyp cohort (a), FAP multi-region cohort²⁵ (b), and sporadic CRC multi-region cohort²⁶ (c). Centromeres are shown as light yellow vertical regions. Only samples without whole-genome doubling (WGD) inferred by FACETS are shown, and the HTAN AdCas were not shown since only one sample was in this group. d-f. Comparison of the fraction genome altered (FGA) across disease stages for the HTAN FAP cohort (d), multi-region FAP cohort (e), and the sporadic CRC cohort (f). In e-f, the points of the same color and at the same x-axis position within each disease stage indicate multiple regions sequenced from the same lesion. WGD samples were included in these plots. In total there were n = 29 mucosal, n = 35 benign, and n = 57 dysplastic samples in the multi-polyp HTAN FAP cohort (d), n = 7 mucosal, n = 13 benign, n = 22 dysplastic, and n = 17 AdCa samples in the multi-region FAP cohort (e), and n = 27 adenoma and n = 30 carcinoma samples in the sporadic CRC cohort (f). P-values were computed using two-sided Wilcoxon tests. In box-and-whisker plots, the box represents the 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.