The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias

Human Molecular Genetics

Volumn 19, Issue 16, 2010, Pages 3150-3158

  Lilljebjörn, Henrik ^a   Soneson, Charlotte ^a   Andersson, Anna ^a,b   Heldrup, Jesper ^a   Behrendtz, Mikael ^c   Kawamata, Norihiko ^d   Ogawa, Seishi ^e   Koeffler, H Phillip ^d,f   Mitelman, Felix ^a   Johansson, Bertil ^a   Fontes, Magnus ^a   Fioretos, Thoas ^a  

^a LUND UNIVERSITY HOSPITAL   (Sweden)

^b ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^c LINKÖPING UNIVERSITY HOSPITAL   (Sweden)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF TOKYO   (Japan)

^f NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B; TRANSCRIPTION FACTOR ETV6; TRANSCRIPTION FACTOR PAX5; TRANSCRIPTION FACTOR RUNX1;

ACUTE LYMPHOBLASTIC LEUKEMIA; ADOLESCENT; ARTICLE; B LYMPHOCYTE; CHILD; CHILDHOOD CANCER; CLINICAL ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; FEMALE; FUSION GENE; GENE DELETION; GENE IDENTIFICATION; GENE MUTATION; GENE TARGETING; GENETIC CORRELATION; HUMAN; MALE; ONCOGENE; PRESCHOOL CHILD; PRIORITY JOURNAL; SCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM;

ADOLESCENT; CELL LINE, TUMOR; CHILD; CHILD, PRESCHOOL; CLUSTER ANALYSIS; FEMALE; GENE DOSAGE; GENETIC HETEROGENEITY; GENOMICS; HUMANS; MALE; ONCOGENE PROTEINS, FUSION; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; RECURRENCE; SIGNAL TRANSDUCTION;

EID: 77955061229     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddq224     Document Type: Article

References (30)

1. Shurtleff, S., Buijs, A., Behm, F., Rubnitz, J., Raimondi, S., Hancock, M., Chan, G., Pui, C., Grosveld, G. and Downing, J. (1995) TEL/AML1 fusion resulting from a cryptic t(12;21) is the most common genetic lesion in pediatric ALL and defines a subgroup of patients with an excellent prognosis. Leukemia, 9, 1985-1989.
2. Forestier, E., Heyman, M., Andersen, M.K., Autio, K., Blennow, E., Borgström, G., Golovleva, I., Heim, S., Heinonen, K., Hovland, R. et al. (2008) Outcome of ETV6/RUNX1-positive childhood acute lymphoblastic leukaemia in the NOPHO-ALL-1992 protocol: frequent late relapses but good overall survival. Br. J. Haematol., 140, 665-672.
3. Wiemels, J., Cazzaniga, G., Daniotti, M., Eden, O., Addison, G., Masera, G., Saha, V., Biondi, A. and Greaves, M. (1999) Prenatal origin of acute lymphoblastic leukaemia in children. Lancet, 354, 1499-1503. 3158 Human Molecular Genetics, 2010, Vol. 19, No. 16
4. Horsley, S.W., Colman, S., McKinley, M., Bateman, C.M., Jenney, M., Chaplin, T., Young, B.D., Greaves, M. and Kearney, L. (2008) Genetic lesions in a preleukemic aplasia phase in a child with acute lymphoblastic leukemia. Genes Chromosomes Cancer, 47, 333-340.
5. Hong, D., Gupta, R., Ancliff, P., Atzberger, A., Brown, J., Soneji, S., Green, J., Colman, S., Piacibello, W., Buckle, V. et al. (2008) Initiating and cancer-propagating cells in TEL-AML1-associated childhood leukemia. Science, 319, 336-339.
6. Mullighan, C.G., Goorha, S., Radtke, I., Miller, C.B., Coustan-Smith, E., Dalton, J.D., Girtman, K., Mathew, S., Ma, J., Pounds, S.B. et al. (2007) Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature, 446, 758-764.
7. Kawamata, N., Ogawa, S., Zimmermann, M., Kato, M., Sanada, M., Hemminki, K., Yamatomo, G., Nannya, Y., Koehler, R., Flohr, T. et al. (2008) Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray. Blood, 111, 776-784.
8. Lilljebjörn, H., Heidenblad, M., Nilsson, B., Lassen, C., Horvat, A., Heldrup, J., Behrendtz, M., Johansson, B., Andersson, A. and Fioretos, T. (2007) Combined high-resolution array-based comparative genomic hybridization and expression profiling of ETV6/RUNX1-positive acute lymphoblastic leukemias reveal a high incidence of cryptic Xq duplications and identify several putative target genes within the commonly gained region. Leukemia, 21, 2137-2144.
9. Kuiper, R.P., Schoenmakers, E.F.P.M., van Reijmersdal, S.V., Hehir-Kwa, J.Y., van Kessel, A.G., van Leeuwen, F.N. and Hoogerbrugge, P.M. (2007) High-resolution genomic profiling of childhood ALL reveals novel recurrent genetic lesions affecting pathways involved in lymphocyte differentiation and cell cycle progression. Leukemia, 21, 1258-1266.
10. Parker, H., An, Q., Barber, K., Case, M., Davies, T., Konn, Z., Stewart, A., Wright, S., Griffiths, M., Ross, F.M. et al. (2008) The complex genomic profile of ETV6-RUNX1 positive acute lymphoblastic leukemia highlights a recurrent deletion of TBL1XR1. Genes Chromosomes Cancer, 47, 1118-1125.
11. Mullighan, C.G., Miller, C.B., Radtke, I., Phillips, L.A., Dalton, J., Ma, J., White, D., Hughes, T.P., Le Beau, M.M., Pui, C. et al. (2008) BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature, 453, 110-114.
12. Tsuzuki, S., Karnan, S., Horibe, K., Matsumoto, K., Kato, K., Inukai, T., Goi, K., Sugita, K., Nakazawa, S., Kasugai, Y. et al. (2007) Genetic abnormalities involved in t(12;21) TEL-AML1 acute lymphoblastic leukemia: analysis by means of array-based comparative genomic hybridization. Cancer Sci., 98, 698-706.
13. Jiang, F., Desper, R., Papadimitriou, C.H., Schäffer, A.A., Kallioniemi, O.P., Richter, J., Schraml, P., Sauter, G., Mihatsch, M.J. and Moch, H. (2000) Construction of evolutionary tree models for renal cell carcinoma from comparative genomic hybridization data. Cancer Res., 60, 6503-6509.
14. Sweeney, C., Boucher, K.M., Samowitz, W.S., Wolff, R.K., Albertsen, H., Curtin, K., Caan, B.J. and Slattery, M.L. (2009) Oncogenetic tree model of somatic mutations and DNA methylation in colon tumors. Genes Chromosomes Cancer, 48,1-9.
15. Pathare, S., Schäffer, A.A., Beerenwinkel, N. and Mahimkar, M. (2009) Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression. Int. J. Cancer, 124, 2864-2871.
16. Desper, R., Jiang, F., Kallioniemi, O.P., Moch, H., Papadimitriou, C.H. and Schäffer, A.A. (1999) Inferring tree models for oncogenesis from comparative genome hybridization data. J. Comput. Biol., 6, 37-51.
17. Desper, R., Jiang, F., Kallioniemi, O.P., Moch, H., Papadimitriou, C.H. and Schäffer, A.A. (2000) Distance-based reconstruction of tree models for oncogenesis. J. Comput. Biol., 7, 789-803.
18. Nutt, S.L., Heavey, B., Rolink, A.G. and Busslinger, M. (1999) Commitment to the B-lymphoid lineage depends on the transcription factor Pax5. Nature, 401, 556-562.
19. Lin, H. and Grosschedl, R. (1995) Failure of B-cell differentiation in mice lacking the transcription factor EBF. Nature, 376, 263-267.
20. Zhuang, Y., Cheng, P. and Weintraub, H. (1996) B-lymphocyte development is regulated by the combined dosage of three basic helix-loop-helix genes, E2A, E2-2, and HEB. Mol. Cell. Biol., 16, 2898-2905.
21. Yoon, H., Choi, Y., Cole, P.A. and Wong, J. (2005) Reading and function of a histone code involved in targeting corepressor complexes for repression. Mol. Cell. Biol., 25, 324-335.
22. Paulsson, K. and Johansson, B. (2009) High hyperdiploid childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer, 48, 637-660.
23. McLean, T., Ringold, S., Neuberg, D., Stegmaier, K., Tantravahi, R., Ritz, J., Koeffler, H., Takeuchi, S., Janssen, J., Seriu, T. et al. (1996) TEL/ AML-1 dimerizes and is associated with a favorable outcome in childhood acute lymphoblastic leukemia. Blood, 88, 4252-4258.
24. Mullighan, C.G. and Downing, J.R. (2009) Genome-wide profiling of genetic alterations in acute lymphoblastic leukemia: recent insights and future directions. Leukemia, 23, 1209-1218.
25. Novara, F., Beri, S., Bernardo, M.E., Bellazzi, R., Malovini, A., Ciccone, R., Cometa, A.M., Locatelli, F., Giorda, R. and Zuffardi, O. (2009) Different molecular mechanisms causing 9p21 deletions in acute lymphoblastic leukemia of childhood. Hum. Genet., 126, 511-520.
26. Edgar, R., Domrachev, M. and Lash, A.E. (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
27. Lin, M., Wei, L., Sellers, W.R., Lieberfarb, M., Wong, W.H. and Li, C. (2004) dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics, 20, 1233-1240.
28. Venkatraman, E.S. and Olshen, A.B. (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 23, 657-663.
29. Brodeur, G.M., Tsiatis, A.A., Williams, D.L., Luthardt, F.W. and Green, A.A. (1982) Statistical analysis of cytogenetic abnormalities in human cancer cells. Cancer Genet. Cytogenet., 7, 137-152.
30. Storey, J.D. (2002) A direct approach to false discovery rates. J. R. Stat. Soc. Ser. B Stat. Methodol., 64, 479-498.