Fig. 4

Copy number alterations (CNA) in chromosome 20 are compounded in high-grade adenoma. a CNA was analyzed using high-depth panel sequencing data. CNAs in paired samples were labeled public if the same copy number change (either loss or gain) was found in both the adenoma and the carcinoma isolated from the same sample (gray), or only in adenoma or carcinoma from one sample (orange and red, respectively). Gain and loss in DNA copy number on each chromosome across all samples are depicted in purple and blue, respectively. CNAs from samples grouped by carcinoma stage and b adenoma grade at the time of isolation. Note, samples without CNA data from panel sequencing are not shown (namely, AC4, 27, 34, 35, 36). c A closer look at chromosomes 20 and 18 using WES data reveals the extent of amplification. Samples AC27 and AC31 were low-grade adenomas while AC33 and AC34 were high-grade adenomas. d Quantification of FISH from 16 samples using, where possible, up to 40 cells randomly selected within neoplasia-marked regions. Copy number of EDEM2 gene and centromere 20 (cen20) mean and standard deviation are shown. Unpaired test with Welch’s correction ****p < 0.0001. e Representative images from fluorescent in situ hybridization (FISH) analyses for EDEM2 (orange) and chromosome 20 centromere (green) on 4 samples with either low- or high-grade adenoma