Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia

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Abstract

Chromosomal aberrations are a hallmark of acute lymphoblastic leukaemia (ALL) but alone fail to induce leukaemia. To identify cooperating oncogenic lesions, we performed a genome-wide analysis of leukaemic cells from 242 paediatric ALL patients using high-resolution, single-nucleotide polymorphism arrays and genomic DNA sequencing. Our analyses revealed deletion, amplification, point mutation and structural rearrangement in genes encoding principal regulators of B lymphocyte development and differentiation in 40% of B-progenitor ALL cases. The PAX5 gene was the most frequent target of somatic mutation, being altered in 31.7% of cases. The identified PAX5 mutations resulted in reduced levels of PAX5 protein or the generation of hypomorphic alleles. Deletions were also detected in TCF3 (also known as E2A), EBF1, LEF1, IKZF1 (IKAROS) and IKZF3 (AIOLOS). These findings suggest that direct disruption of pathways controlling B-cell development and differentiation contributes to B-progenitor ALL pathogenesis. Moreover, these data demonstrate the power of high-resolution, genome-wide approaches to identify new molecular lesions in cancer.

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Figure 1: EBF1 deletions in B-progenitor ALL.
Figure 2: PAX5 deletions in ALL.
Figure 3: PAX5 translocations in B-progenitor ALL.
Figure 4: Impaired function of PAX5 mutants.

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Acknowledgements

We thank Z. Cai and L. King for technical assistance; B. Schulman for modelling of PAX5 mutations; M. Roussel, M. Busslinger and J. Hagman for providing reagents; the Tumor Processing Laboratory of SJCRH for providing tumour samples; and C. Li for discussions and modifications of dChipSNP. This work was supported by grants from the National Cancer Institute (to J.R.D. and W.E.E.), the National Institute of General Medical Sciences (to M.V.R.), the National Health and Medical Research Council (Australia) (to C.G.M.), the Royal Australasian College of Physicians (to C.G.M.), the Haematology Society of Australia and New Zealand (to C.G.M), and the American Lebanese and Syrian Associated Charities (ALSAC) of SJCRH.

Author Contributions J.R.D. designed and supervised experiments. C.G.M, S.G., I.R, C.B.M., E.C.-S., J.D.D and K.G. performed experiments. S.A.S. collected and managed clinical samples and data. C.G.M., S.G., J.M., S.B.P. and X.S. analysed data. S.B.P. developed software for DNA copy number analysis. C.-H.P., M.V.R. and W.E.E. provided patient samples. C.G.M. and J.R.D. wrote the manuscript. All authors discussed the results and commented on the manuscript.

The primary SNP microarray data have been deposited in NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE5511. The data are also available at http://www.stjuderesearch.org/data/ALL-SNP1/. Sequences of the PAX5 fusion transcripts have been deposited in GenBank with accessions DQ841178 (PAX5–ETV6), DQ845346 (PAX5–FOXP1) and DQ845345 (PAX5–ZNF521).

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Correspondence to James R. Downing.

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Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, Supplementary Results, Supplementary Tables 1-24, Supplementary Figures 1-33 with Legends and additional references (PDF 5365 kb)

Supplementary S-Plus files

This archive contains two S-Plus files that are the basis for the karyotype-guided SNP array normalization algorithm described in the Supplementary Methods. These can be opened by a text editor, (ZIP 5 kb)

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