Detection of Genomic Lesions in Childhood Precursor-B Cell ALL in Diagnosis and Relapse Samples Using High Resolution Genomic Profiling.

Due to advances in therapeutic regimens developed during the last two decades, the majority of children with acute lymphoblastic leukemia (ALL) respond well to therapy. However, in approximately 25% of the patients relapses occur. Chomosome aneuploidies and recurrent chromosomal translocations are of considerable prognostic importance, and are routinely used in the course of clinical decision making. Current technological developments in molecular cytogenetic techniques have revealed that genetic lesions driving tumorigenesis frequently occur at the submicroscopic level and, consequently, escape standard cytogenetic observations. Therefore, we have previously performed high resolution genomic profiling of precursor-B-cell ALL samples obtained at diagnosis, using 250k NspI SNP-based oligoarrays from Affymetrix (Kuiper et al., 2007). By doing so, we detected multiple de novo genetic lesions, some of which were subtle and affected single genes. Many of these lesions involved recurrent (partially) overlapping deletions and duplications, encompassing various established leukemia-associated genes, such as ETV6, RUNX1, and MLL. Importantly, the most frequently affected genes were those controlling G1/S cell cycle progression (e.g. CDKN2A, CDKN1B, and RB1), followed by genes associated with B-cell development. The latter group included the B-lineage transcription factors PAX5, EBF, E2-2, and IKZF1 (Ikaros), as well as genes with other established roles in B-cell development, i.e., RAG1 and RAG2, FYN, PBEF1, or CBP/PAG. Here we have selected 34 additional precursor-B cell ALL cases that suffered from relapses 6 months to 9 years after diagnosis. Lesions affecting genes involved in G1/S cell cycle progression and B-cell development were observed with similar frequencies in the diagnosis and relapse samples as compared to our previous cohort of patients with unknown therapy response. However, additional (secondary) lesions were observed in the relapse samples in nearly all patients analyzed, indicating that these relapse samples are genomically distinct. In addition, several cases were encountered in which the diagnosis and relapse samples carried alternative lesions affecting the same gene(s), including CDKN2A and PAX5, suggesting that inactivation of these genes were secondary but essential events required to develop a full blown leukemia.