Fig. 2: IMPC genomic CNVs in 17 freshly frozen IMPC tumor-normal tissue pairs.

a Copy-number-based hierarchical clustering based on the Control-FREEC region results. Heatmap with log2 copy-number ratios across the genome; 0 indicates no change, a positive value indicates a gain, and a negative indicates a loss (all values range from −2 to 2). The CNV burden is shown on the top of the heatmap. Patient ID with IMPC and lymph node metastasis (LNM) stages are presented on the right, and the chromosomal locus is presented on the left. Two groups are clustered: one contains more CNVs and is called the CNV high group, while the other contains fewer CNVs and is called the CNV low group. b Frequency of copy-number aberrations across the 17 bulk samples. Chromosomes 1–22 are positioned along the x-axis, while the y-axis shows the frequency of copy-number gains (salmon) and losses (light blue). c Arm-level frequency of copy-number aberrations across the 17 bulk samples determined using the GISTIC2.0 method. A significant loss in chromosome 19p and 19q was observed in all 17 samples and between the two CNV groups (Supplementary Data 4). A single asterisk (*) represents both P value (joint hypotheses test) and GISTIC q value (multiple hypothesis testing using the BH FDR method) < 0.05, while double asterisks (**) represents P value < 0.05 and GISTIC q value < 0.01; the exact value is present in sheet 1 of Supplementary Data 4. d Identification of focal recurrent copy-number losses (left panel) and gains (right panel) using the GISTIC2.0 method. e Box plots of the CNV burden (with the box plot center, box, whiskers, and points corresponding to the median, interquartile range, 1.5× interquartile range, and outliers, respectively). Student’s t test for total CNV length burden between the CNV high and CNV low groups; the two groups were significantly different (P = 0.0034). f Relationship between heterogeneity and the lymph node metastasis number in patients with IMPC. Heterogeneity was evaluated using Pyclone with SNVs and CNVs. A gradient threshold was set for SNVs (N = 1–8). Each number represents the correlation of its corresponding horizontal and vertical coordinate conditions, including heterogeneity among SNVs, CNVs, and the lymph node metastasis number. The metastatic potential was evaluated by lymph node metastasis number; a higher lymph node metastasis number indicates the involvement of more lymph nodes and the higher metastatic potential of IMPC.