In summary, although we could confirm the presence of CNAs in each subgroup according to the integrated AID/RAG2 signature profile, we report that the abundance of RAG2 alone correlated rather with higher CNA levels and IKZF1 deletions, particularly in the BCR::ABL1pos context (p = 0.001), while a lower CNA mutation number or CNAneg was more frequently accompanied by AIDhigh/RAG2low, particularly in NEG ALL context, suggesting involvement of secondary mutations other than CNA, e.g., SNV (see Table S2 for details). Here, IKZF1 is linked to acute lymphoblastic leukemia.