Novel Focal Gene Deletions in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia Detected By Array Comparative Genomic Hybridization

Cure rates for pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL) are now exceeding 80%, however, genetic markers that signal high risk are infrequent and relapses occur across all genetic risk groups. Moreover, a substantial proportion of patients diagnosed with ALL lack risk-associated genetic aberration in their leukemic cells at diagnosis, indicating that additional prognostic markers are needed. Our aim was to better understand the mechanisms underlying leukemic transformation and to identify new genetic markers in ALL; for that purpose we investigated the gene dose landscape in leukemic bone marrow cells from 50 pediatric BCP ALL cases treated according to Nordic Society of Pediatric Hematology and Oncology (NOPHO) protocols.

Array comparative genomic hybridization (array-CGH) was performed on DNA isolated from diagnostic bone marrow samples; 30 samples harbored known cytogenetic markers and 20 samples lacked risk-associated cytogenetic markers at diagnosis. The samples were run either on the CytoSure ISCA 4x180K UPD array-CGH platform (Oxford Gene Technology, UK), or an in-house 4x180K custom design array-CGH platform with even genome coverage.

In a majority of cases without previously known risk-associated genetic markers we detected copy number alterations (CNAs) recently associated with leukemia development and adverse prognosis, including deletions of the lymphoid development genes IKZF1 and VPREB1. Interestingly, while deletions of IKZF1 consistently occurred together with other CNAs, deletion of VPREB1 was the only somatic imbalance detected in two cases. Deletions of VPREB1 were also present in 55% (5/9) of cases with t(12;21) and associated with a higher white blood cell count in this subtype. Furthermore, deletions of a recently annotated DNA-repair gene, INIP, were recurrent in t(12;21) cases and significantly associated with this subtype (P=0.004). This gene has not previously been described in leukemia. Deletions of the cell-cycle gene RB1 and the hematopoietic signaling gene SH2B3 were present in all cases with intrachromosomal amplification of chromosome 21 (iAMP21, n=3) and both were significantly associated with this subtype (P=0.001 and P<0.001 respectively). The SH2B3 deletion was unique to iAMP21 and has not previously been described as characteristic of this subtype; we are currently investigating this particular subgroup further using high-throughput sequencing technologies and updated results will be presented at the congress. Samples with gain of chromosome 21q (iAMP21 or polysomy 21) showed similarities in the copy number profile, including deletions of the lymphoid development genes BCL11A and BTLA. When we considered the functions of the genes affected by CNAs in the cohort, we found that the majority of samples had concurrent alterations in lymphoid and genome integrity pathways; however, alterations in epigenetic regulators and DNA-repair genes were mutually exclusive in our study.

In summary, we detected leukemia-associated as well as novel recurrent deletions and our results indicate that a majority of the cases without risk-associated cytogenetic markers could be assigned to distinct genetic subtypes, and highlights the additional value of array-CGH in the diagnostics of ALL.