Fig. 1

Identification of the 13q amplicon and establishment as a late event in CRC. a Recurrent focal events from our patient cohort with a frequency higher than 5%. Potential driver genes were identified according to a machine learning-based method for driver gene prediction [46]. The difference in these 3 recurrent focal events between our cohort and the TCGA cohort was analyzed using the chi-squared test. b The TCGA cohort was separated into 2 groups, i.e., balanced and aberrant (including gain and amplification cases). Bar charts illustrate 4 clinical features, i.e., tumor stage, distant metastasis, lymph node metastasis, and tumor location, which showed significant differences between these 2 groups. p values were calculated using the chi-squared test. c, d Plots illustrating the log2 ratio changes on chromosome 13. In C240, C118, and C79, focal amplification of chr13q12.2 was not identified in the primary tumor (PT) but found in the plasma (ctDNA) at a later stage. In C216, chr13q12.2 amplification was detected when the patient status was categorized as progressive disease. Copy number gains are shown in red and balanced regions in green. Tumor fraction (TF) of every sample was calculated using ichorCNA [43]. (SD, stable disease; PD, progressive disease)