Genomic profiling data of 40 childhood leukemia patients

In this study, we performed an inventory of copy number changes present in childhood acute lymphoblastic leukemias. The cohort contains a total of 40 diagnosis samples, including 7 T-lineage ALLs and 33 precursor B-cell ALLs. High resolution genomic profiling was perfomed using Affymetrix SNP arrays. We detected multiple de novo genetic lesions, including gross aneuploidies and segmental gains and losses, some of which were subtle and affected single genes. Many of these lesions involved recurrent (partially) overlapping deletions and duplications, containing 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 includes microdeletions of 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. The fact that we frequently encountered multiple lesions affecting genes involved in cell cycle regulation and B-cell differentiation, strongly suggests that both these processes need to be targeted independently and simultaneously in order to trigger ALL-development. Keywords: comparative genome hybridization Genomic DNA from 40 bone marrow or periphearal blood was hybridized on Affymetrix Nsp, Xba or Hind SNP-based arrays according to manufacturer's procedures. Copy number detection was performed using CNAG2.0 software, Reference genomes are included in this data set