in acute lymphoblastic leukemia of childhood

Abstract Deletion of chromosome 9p21 is a crucial event for the development of several cancers including acute lymphoblastic leukemia (ALL). Double strand breaks (DSBs) triggering 9p21 deletions in ALL have been reported to occur at a few deWned sites by illegiti-mate action of the V(D)J recombination activating protein complex. We have cloned 23 breakpoint junctions for a total of 46 breakpoints in 17 childhood ALL (9 B- and 8 T-lineages) showing diVerent size deletions at one or both homologous chromosomes 9 to investigate which particular sequences make the region susceptible to interstitial deletion. We found that half of 9p21 deletion breakpoints were mediated by ectopic V(D)J recombination mechanisms whereas the remaining half were associated to repeated sequences, including some with potential for non-B DNA structure formation. Other mechanisms, such as microho-mology-mediated repair, that are common in other can-cers, play only a very minor role in ALL. Nucleotide insertions at breakpoint junctions and microinversions Xanking the breakpoints have been detected at 20/23 and 2/23 breakpoint junctions, respectively, both in the presence of recombination signal sequence (RSS)-like sequences and of other unspeciWc sequences. The majority of breakpoints were unique except for two cases, both T-ALL, showing identical deletions. Four of the 46 breakpoints coincide with those reported in other cases, thus conWrming the presence of recurrent deletion hot-spots. Among the six cases with heterozygous 9p dele-tions, we found that the remaining CDKN2A and CDKN2B alleles were hypermethylated at CpG islands