In contrast with the Ph(+) ALL results, we found that the loss of IKZF1 always precedes the deletions of CDKN2A and that losses of RNF38 were always accompanied by loss of the 9p13-p23.1 region that houses, among others, CDKN2A, IFNA, RNF38, PAX5 and MLLT3. In addition, we demonstrated by FISH the presence of clonal evolution leading to the concomitant 7p/9p loss as seen in less than half of patients (5/12 samples) (see typical aCGH profiles in Additional file 10: Figure S7). Here, MLLT3 is linked to acute lymphoblastic leukemia.