Detailed gene dose analysis reveals recurrent focal gene deletions in pediatric B-cell precursor acute lymphoblastic leukemia

References

• Schmiegelow K, Forestier E, Hellebostad M, et al. Long-term results of NOPHO ALL-92 and ALL-2000 studies of childhood acute lymphoblastic leukemia. Leukemia. 2010;24:345–354.
   PubMed Web of Science ®Google Scholar
• Harrison CJ, Haas O, Harbott J, et al. Detection of prognostically relevant genetic abnormalities in childhood B-cell precursor acute lymphoblastic leukaemia: recommendations from the Biology and Diagnosis Committee of the International Berlin-Frankfurt-Munster study group. Br J Haematol. 2010;151:132–142.
   PubMed Web of Science ®Google Scholar
• Moorman AV, Ensor HM, Richards SM, et al. Prognostic effect of chromosomal abnormalities in childhood B-cell precursor acute lymphoblastic leukaemia: results from the UK Medical Research Council ALL97/99 randomised trial. Lancet Oncol. 2010;11:429–438.
   PubMed Web of Science ®Google Scholar
• Schultz KR, Pullen DJ, Sather HN, et al. Risk- and response-based classification of childhood B-precursor acute lymphoblastic leukemia: a combined analysis of prognostic markers from the Pediatric Oncology Group (POG) and Children's Cancer Group (CCG). Blood. 2007;109:926–935.
   PubMed Web of Science ®Google Scholar
• Pui CH, Mullighan CG, Evans WE, et al. Pediatric acute lymphoblastic leukemia: where are we going and how do we get there? Blood. 2012;120:1165–1174.
   PubMed Web of Science ®Google Scholar
• Bhojwani D, Pui CH. Relapsed childhood acute lymphoblastic leukaemia. Lancet Oncol. 2013;14:e205–e217.
   PubMed Web of Science ®Google Scholar
• Malinowska-Ozdowy K, Frech C, Schonegger A, et al. KRAS and CREBBP mutations: a relapse-linked malicious liaison in childhood high hyperdiploid acute lymphoblastic leukemia. Leukemia. 2015;29:1656–1667.
   PubMed Web of Science ®Google Scholar
• Kuiper RP, Schoenmakers EF, van Reijmersdal SV, et al. High-resolution genomic profiling of childhood ALL reveals novel recurrent genetic lesions affecting pathways involved in lymphocyte differentiation and cell cycle progression. Leukemia. 2007;21:1258552.
   Google Scholar
• Mullighan CG, Goorha S, Radtke I, et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature. 2007;446:758–764.
   PubMed Web of Science ®Google Scholar
• Kawamata N, Ogawa S, Zimmermann M, et al. Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray. Blood. 2008;111:776–784.
   PubMed Web of Science ®Google Scholar
• Strefford JC, Worley H, Barber K, et al. Genome complexity in acute lymphoblastic leukemia is revealed by array-based comparative genomic hybridization. Oncogene. 2007;26:4306–4318.
   PubMed Web of Science ®Google Scholar
• Kuchinskaya E, Heyman M, Nordgren A, et al. Array-CGH reveals hidden gene dose changes in children with acute lymphoblastic leukaemia and a normal or failed karyotype by G-banding. Br J Haematol. 2008;140:572–577.
   PubMed Web of Science ®Google Scholar
• Bungaro S, Dell'Orto MC, Zangrando A, et al. Integration of genomic and gene expression data of childhood ALL without known aberrations identifies subgroups with specific genetic hallmarks. Genes Chromosomes Cancer. 2009;48:22–38.
   PubMed Web of Science ®Google Scholar
• Mullighan CG, Su X, Zhang J, et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med. 2009;360:470–480.
   PubMed Web of Science ®Google Scholar
• Kuiper RP, Waanders E, van der Velden VH, et al. IKZF1 deletions predict relapse in uniformly treated pediatric precursor B-ALL. Leukemia. 2010;24:1258–1264.
   PubMed Web of Science ®Google Scholar
• Ofverholm I, Tran AN, Heyman M, et al. Impact of IKZF1 deletions and PAX5 amplifications in pediatric B-cell precursor ALL treated according to NOPHO protocols. Leukemia. 2013;27:1936–1939.
   PubMed Web of Science ®Google Scholar
• Olsson L, Castor A, Behrendtz M, et al. Deletions of IKZF1 and SPRED1 are associated with poor prognosis in a population-based series of pediatric B-cell precursor acute lymphoblastic leukemia diagnosed between 1992 and 2011. Leukemia. 2014;28:302–310.
   PubMed Web of Science ®Google Scholar
• Mullighan CG, Zhang J, Kasper LH, et al. CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature. 2011;471:235–239.
   PubMed Web of Science ®Google Scholar
• Mangum DS, Downie J, Mason CC, et al. VPREB1 deletions occur independent of lambda light chain rearrangement in childhood acute lymphoblastic leukemia. Leukemia. 2014;28:216–220.
   PubMed Web of Science ®Google Scholar
• Clappier E, Auclerc MF, Rapion J, et al. An intragenic ERG deletion is a marker of an oncogenic subtype of B-cell precursor acute lymphoblastic leukemia with a favorable outcome despite frequent IKZF1 deletions. Leukemia. 2014;28:70–77.
   PubMed Web of Science ®Google Scholar
• Zaliova M, Zimmermannova O, Dorge P, et al. ERG deletion is associated with CD2 and attenuates the negative impact of IKZF1 deletion in childhood acute lymphoblastic leukemia. Leukemia. 2014;28:182–185.
   PubMed Web of Science ®Google Scholar
• Olsson L, Ivanov Ofverholm I, Noren-Nystrom U, et al. The clinical impact of IKZF1 deletions in paediatric B-cell precursor acute lymphoblastic leukaemia is independent of minimal residual disease stratification in Nordic Society for Paediatric Haematology and Oncology treatment protocols used between 1992 and 2013. Br J Haematol. 2015;170:847–858.
   PubMed Web of Science ®Google Scholar
• Toft N, Birgens H, Abrahamsson J, et al. Risk group assignment differs for children and adults 1-45 yr with acute lymphoblastic leukemia treated by the NOPHO ALL-2008 protocol. Eur J Haematol. 2013;90:404–412.
   PubMed Web of Science ®Google Scholar
• Olshen AB, Venkatraman ES, Lucito R, et al. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004;5:557–572.
   PubMed Web of Science ®Google Scholar
• Holmfeldt L, Wei L, Diaz-Flores E, et al. The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet. 2013;45:242–252.
   PubMed Web of Science ®Google Scholar
• Perez-Llamas C, Lopez-Bigas N. Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS One. 2011;6:e19541.
   PubMed Web of Science ®Google Scholar
• Dobbins SE, Sherborne AL, Ma YP, et al. The silent mutational landscape of infant MLL-AF4 pro-B acute lymphoblastic leukemia. Genes Chromosomes Cancer. 2013;52:954–960.
   PubMed Web of Science ®Google Scholar
• Othman MA, Melo JB, Carreira IM, et al. High rates of submicroscopic aberrations in karyotypically normal acute lymphoblastic leukemia. Mol Cytogenet. 2015;8:45.
   PubMed Web of Science ®Google Scholar
• Tong W, Zhang J, Lodish HF. Lnk inhibits erythropoiesis and Epo-dependent JAK2 activation and downstream signaling pathways. Blood. 2005;105:4604–4612.
   PubMed Web of Science ®Google Scholar
• Roberts KG, Morin RD, Zhang J, et al. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell. 2012;22:153–166.
   PubMed Web of Science ®Google Scholar
• Mullighan CG, Phillips LA, Su X, et al. Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science. 2008;322:1377–1380.
   PubMed Web of Science ®Google Scholar
• Lundin C, Hjorth L, Behrendtz M, et al. High frequency of BTG1 deletions in acute lymphoblastic leukemia in children with Down syndrome. Genes Chromosomes Cancer. 2012;51:196–206.
   PubMed Web of Science ®Google Scholar
• Willman CL, Sever CE, Pallavicini MG, et al. Deletion of IRF-1, mapping to chromosome 5q31.1, in human leukemia and preleukemic myelodysplasia. Science. 1993;259:968–971.
   PubMed Web of Science ®Google Scholar
• Harrison CJ, Moorman AV, Schwab C, et al. An international study of intrachromosomal amplification of chromosome 21 (iAMP21): cytogenetic characterization and outcome. Leukemia. 2014;28:1015–1021.
   PubMed Web of Science ®Google Scholar
• van Galen JC, Kuiper RP, van Emst L, et al. BTG1 regulates glucocorticoid receptor autoinduction in acute lymphoblastic leukemia. Blood. 2010;115:4810–4819.
   PubMed Web of Science ®Google Scholar
• Huang J, Gong Z, Ghosal G, et al. SOSS complexes participate in the maintenance of genomic stability. Mol Cell. 2009;35:384–393.
   PubMed Web of Science ®Google Scholar
• Li Y, Bolderson E, Kumar R, et al. HSSB1 and hSSB2 form similar multiprotein complexes that participate in DNA damage response. J Biol Chem. 2009;284:23525–23531.
   PubMed Web of Science ®Google Scholar
• Jones CL, Bhatla T, Blum R, et al. Loss of TBL1XR1 disrupts glucocorticoid receptor recruitment to chromatin and results in glucocorticoid resistance in a B-lymphoblastic leukemia model. J Biol Chem. 2014;289:20502–20515.
   PubMed Web of Science ®Google Scholar
• Parker H, An Q, Barber K, et al. The complex genomic profile of ETV6-RUNX1 positive acute lymphoblastic leukemia highlights a recurrent deletion of TBL1XR1. Genes Chromosomes Cancer. 2008;47:1118–1125.
   PubMed Web of Science ®Google Scholar
• Zhang J, Mullighan CG, Harvey RC, et al. Key pathways are frequently mutated in high-risk childhood acute lymphoblastic leukemia: a report from the Children's Oncology Group. Blood. 2011;118:3080–3087.
   PubMed Web of Science ®Google Scholar
• Ma X, Edmonson M, Yergeau D, et al. Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia. Nat Commun. 2015;6:6604.
   PubMed Web of Science ®Google Scholar
• Ogawa R, Streiff MB, Bugayenko A, et al. Inhibition of PDE4 phosphodiesterase activity induces growth suppression, apoptosis, glucocorticoid sensitivity, p53, and p21(WAF1/CIP1) proteins in human acute lymphoblastic leukemia cells. Blood. 2002;99:3390–3397.
   PubMed Web of Science ®Google Scholar
• Yang JJ, Cheng C, Devidas M, et al. Genome-wide association study identifies germline polymorphisms associated with relapse of childhood acute lymphoblastic leukemia. Blood. 2012;120:4197–4204.
   PubMed Web of Science ®Google Scholar
• van Zutven LJ, van Drunen E, de Bont JM, et al. CDKN2 deletions have no prognostic value in childhood precursor-B acute lymphoblastic leukaemia. Leukemia. 2005;19:1281–1284.
   PubMed Web of Science ®Google Scholar
• Mirebeau D, Acquaviva C, Suciu S, et al. The prognostic significance of CDKN2A, CDKN2B and MTAP inactivation in B-lineage acute lymphoblastic leukemia of childhood. Results of the EORTC studies 58881 and 58951. Haematologica. 2006;91:881–885.
   PubMed Web of Science ®Google Scholar
• Russell LJ, Capasso M, Vater I, et al. Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in B-cell precursor acute lymphoblastic leukemia. Blood. 2009;114:2688–2698.
   PubMed Web of Science ®Google Scholar
• Iacobucci I, Storlazzi CT, Cilloni D, et al. Identification and molecular characterization of recurrent genomic deletions on 7p12 in the IKZF1 gene in a large cohort of BCR-ABL1-positive acute lymphoblastic leukemia patients: on behalf of Gruppo Italiano Malattie Ematologiche dell'Adulto Acute Leukemia Working Party (GIMEMA AL WP). Blood. 2009;114:2159–2167.
   PubMed Web of Science ®Google Scholar
• Den Boer ML, van Slegtenhorst M, De Menezes RX, et al. A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study. Lancet Oncol. 2009;10:125–134.
   PubMed Web of Science ®Google Scholar