Oncogenic dependencies and their impact on survival. (A) The associations between acquired mutations, cytogenetic subgroups, CNAs, and copy number (CN) clusters. Positive (red) and negative (blue) associations and their odds ratios are shown, where the size of the circle represents the significance of the P value defined by the 2-sided Fisher’s exact test. Both gain- and loss-of-function mutations were associated with translocations. The t(4;14) group was associated with mutations of FGFR3, DIS3, and PRKD2, gain of 1q, and deletion of 13q, 14q, 4p16.3 (FGFR3), 1p22.1 (RPL5), 11q22.1 (BIRC3), and 12p13.1 (CDKN1B). The t(11;14) group was associated with mutations in IRF4 and CCND1, but not with gain of 1q or 6p or deletion of 13q, 14q, 8p, or 1p22.1 (RPL5). The t(14;16) group was associated with mutations in BRAF, DIS3, and TRAF2, del13q, gain of 1q, and the APOBEC signature. The t(14;20) group was associated with the APOBEC signature. Hyperdiploidy was associated with gain of 6p and translocations involving MYC, but not with mutations in MAX, DIS3, IRF4, or CCND1 or del13q or del14q. The most significant associations were between CN changes on the same chromosomes (del CDKN2C, RPL5, and FAM46C; del TRAF3 and ABCD4; del WWOX and CYLD), as well as CN cluster 2 with HRD, CN cluster 7 with gain of 1q, and CN cluster 6 with del16q. (B) Significant enrichment/depletion of mutated genes within translocation and hyperdiploid CN clusters. The percentage of samples with the gene mutated within the subgroup is shown. Significance is indicated by hatched lines. MAX mutations are significantly underrepresented in the CN-2 group. (C) The distribution of codon usage within KRAS, NRAS, and BRAF by molecular subgroup. Proportion of codon usage is indicated by the distance from the center. KRAS mutations are split between codons G12, G13, and Q61, whereas NRAS is predominantly mutated at codon Q61 (P < 2.2 × 10⁻¹⁶). BRAF mutations mostly affect codon V600, except in the t(14;16) group, where codon D594 is mutated (P = .003).