Genomic analysis of acute leukemia

International Journal of Laboratory Hematology

Volumn 31, Issue 4, 2009, Pages 384-397

  Mullighan, C G ^a  

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

Author keywords

Acute lymphoblastic leukemia; IKZF1; Mutation; PAX5; Relapse; SNP microarray

Indexed keywords

APOPTOSIS REGULATORY PROTEIN; ATM PROTEIN; BCR ABL PROTEIN; CD200 ANTIGEN; CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2B; FRAGILE HISTIDINE TRIAD PROTEIN; IKAROS TRANSCRIPTION FACTOR; LYMPHOID ENHANCER FACTOR 1; MYOCYTE ENHANCER FACTOR 2; ONCOPROTEIN; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PROTEIN TYROSINE KINASE INHIBITOR; RAG1 PROTEIN; RAG2 PROTEIN; STEROID RECEPTOR; TRANSCRIPTION FACTOR ERG; TRANSCRIPTION FACTOR ETV6; TRANSCRIPTION FACTOR IKZF1; TRANSCRIPTION FACTOR IKZF2; TRANSCRIPTION FACTOR IKZF3; TRANSCRIPTION FACTOR PAX5; TRANSCRIPTION FACTOR PBX1; TRANSCRIPTION FACTOR RUNX1; TRANSCRIPTION FACTOR TAL1; TUMOR PROTEIN; UNCLASSIFIED DRUG;

ACUTE GRANULOCYTIC LEUKEMIA; ACUTE LYMPHOBLASTIC LEUKEMIA; CANCER RELAPSE; CANCER RESISTANCE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; EPIGENETICS; GENE DELETION; GENE EXPRESSION PROFILING; GENE MUTATION; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; LEUKEMOGENESIS; NONHUMAN; ONCOGENE MYB; PHILADELPHIA 1 CHROMOSOME; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR SUPPRESSOR GENE;

GENE DOSAGE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LEUKEMIA, MYELOID, ACUTE; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA;

EID: 67651108658     PISSN: 17515521     EISSN: 1751553X     Source Type: Journal    
DOI: 10.1111/j.1751-553X.2009.01167.x     Document Type: Review

References (112)

1. Akagi T., Ogawa S., Dugas M., Kawamata N., Yamamoto G., Nannya Y., Sanada M., Miller C.W., Yung A., Schnittger S., Haferlach T., Haferlach C. Koeffler H.P. (2009) Frequent genomic abnormalities in acute myeloid leukemia/ myelodysplastic syndrome with normal karyotype. Haematologica 94, 213 223.
2. An Q., Wright S.L., Konn Z.J., Matheson E., Minto L., Moorman A.V., Parker H., Griffiths M., Ross F.M., Davies T., Hall A.G., Harrison C.J., Irving J.A. Strefford J.C. (2008) Variable breakpoints target PAX5 in patients with dicentric chromosomes: a model for the basis of unbalanced translocations in cancer. Proceedings of the National Academy of Sciences of the United States of America 105, 17050 17054.
3. Andreasson P., Schwaller J., Anastasiadou E., Aster J. Gilliland D.G. (2001) The expression of ETV6/CBFA2 (TEL/AML1) is not sufficient for the transformation of hematopoietic cell lines in vitro or the induction of hematologic disease in vivo. Cancer Genetics and Cytogenetics 130, 93 104.
4. Bousquet M., Broccardo C., Quelen C., Meggetto F., Kuhlein E., Delsol G., Dastugue N. Brousset P. (2007) A novel PAX5-ELN fusion protein identified in B-cell acute lymphoblastic leukemia acts as a dominant negative on wild-type PAX5. Blood 109, 3417 3423.
5. Bungaro S., Dell'orto M.C., Zangrando A., Basso D., Gorletta T., Lo Nigro L., Leszl A., Young B.D., Basso G., Bicciato S., Biondi A., Te Kronnie G. Cazzaniga G. (2009) Integration of genomic and gene expression data of childhood ALL without known aberrations identifies subgroups with specific genetic hallmarks. Genes, Chromosomes and Cancer 48, 22 38.
6. Busslinger M. (2004) Transcriptional control of early B cell development. Annual Review of Immunology 22, 55 79.
7. Campbell P.J., Stephens P.J., Pleasance E.D., O'Meara S., Li H., Santarius T., Stebbings L.A., Leroy C., Edkins S., Hardy C., Teague J.W., Menzies A., Goodhead I., Turner D.J., Clee C.M., Quail M.A., Cox A., Brown C., Durbin R., Hurles M.E., Edwards P.A., Bignell G.R., Stratton M.R. Futreal P.A. (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genetics 40, 722 729.
8. Cazzaniga G., Daniotti M., Tosi S., Giudici G., Aloisi A., Pogliani E., Kearney L. Biondi A. (2001) The paired box domain gene PAX5 is fused to ETV6/TEL in an acute lymphoblastic leukemia case. Cancer Research 61, 4666 4670.
9. Clappier E., Cuccuini W., Kalota A., Crinquette A., Cayuela J.M., Dik W.A., Langerak A.W., Montpellier B., Nadel B., Walrafen P., Delattre O., Aurias A., Leblanc T., Dombret H., Gewirtz A.M., Baruchel A., Sigaux F. Soulier J. (2007) The C-MYB locus is involved in chromosomal translocation and genomic duplications in human T-cell acute leukemia (T-ALL), the translocation defining a new T-ALL subtype in very young children. Blood 110, 1251 1261.
10. Coustan-Smith E., Mullighan C.G., Onciu M., Behm F.G., Raimondi S.C., Pei D., Cheng C., Su X., Rubnitz J.E., Basso G., Biondi A., Pui C.H., Downing J.R. Campana D. (2009) Early T-cell precursor leukaemia: a subtype of very high-risk acute lymphoblastic leukaemia. Lancet Oncol 10, 147 156.
11. Dang J., Mullighan C.G., Phillips L.A., Mehta P. Downing J.R. (2008) Retroviral and chemical mutagenesis identifies Pax5 as a tumor suppressor in B-progenitor acute lymphoblastic leukemia. Blood 112. Abstract 1798).
12. Davidsson J., Andersson A., Paulsson K., Heidenblad M., Isaksson M., Borg A., Heldrup J., Behrendtz M., Panagopoulos I., Fioretos T. Johansson B. (2007) Tiling resolution array comparative genomic hybridization, expression and methylation analyses of dup(1q) in Burkitt lymphomas and pediatric high hyperdiploid acute lymphoblastic leukemias reveal clustered near-centromeric breakpoints and overexpression of genes in 1q22-32.3. Human Molecular Genetics 16, 2215 2225.
13. Davies J.J., Wilson I.M. Lam W.L. (2005) Array CGH technologies and their applications to cancer genomes. Chromosome Research 13, 237 248.
14. Einsiedel H.G., Von Stackelberg A., Hartmann R., Fengler R., Schrappe M., Janka-Schaub G., Mann G., Hahlen K., Gobel U., Klingebiel T., Ludwig W.D. Henze G. (2005) Long-term outcome in children with relapsed ALL by risk-stratified salvage therapy: results of trial acute lymphoblastic leukemia-relapse study of the Berlin-Frankfurt-Munster Group 87. Journal of Clinical Oncology 23, 7942 7950.
15. Fielding A.K., Richards S.M., Chopra R., Lazarus H.M., Litzow M.R., Buck G., Durrant I.J., Luger S.M., Marks D.I., Franklin I.M., Mcmillan A.K., Tallman M.S., Rowe J.M. Goldstone A.H. (2007) Outcome of 609 adults after relapse of acute lymphoblastic leukemia (ALL); an MRC UKALL12/ECOG 2993 study. Blood 109, 944 950.
16. Fitzgibbon J., Smith L.L., Raghavan M., Smith M.L., Debernardi S., Skoulakis S., Lillington D., Lister T.A. Young B.D. (2005) Association between acquired uniparental disomy and homozygous gene mutation in acute myeloid leukemias. Cancer Research 65, 9152 9154.
17. French D., Yang W., Cheng C., Raimondi S.C., Mullighan C.G., Downing J.R., Evans W.E., Pui C.H. Relling M.V. (2008) Acquired variation outweighs inherited variation in whole genome analysis of methotrexate polyglutamate accumulation in leukemia. Blood, December 2008. doi :.
18. Gleissner B., Gokbuget N., Bartram C.R., Janssen B., Rieder H., Janssen J.W., Fonatsch C., Heyll A., Voliotis D., Beck J., Lipp T., Munzert G., Maurer J., Hoelzer D. Thiel E. (2002) Leading prognostic relevance of the BCR-ABL translocation in adult acute B-lineage lymphoblastic leukemia: a prospective study of the German Multicenter Trial Group and confirmed polymerase chain reaction analysis. Blood 99, 1536 1543.
19. Goldman J.M. Melo J.V. (2003) Chronic myeloid leukemia - advances in biology and new approaches to treatment. The New England Journal of Medicine 349, 1451 1464.
20. Gorletta T.A., Gasparini P., D'elios M.M., Trubia M., Pelicci P.G. Di Fiore P.P. (2005) Frequent loss of heterozygosity without loss of genetic material in acute myeloid leukemia with a normal karyotype. Genes, Chromosomes and Cancer 44, 334 337.
21. Graux C., Cools J., Melotte C., Quentmeier H., Ferrando A., Levine R., Vermeesch J.R., Stul M., Dutta B., Boeckx N., Bosly A., Heimann P., Uyttebroeck A., Mentens N., Somers R., Macleod R.A., Drexler H.G., Look A.T., Gilliland D.G., Michaux L., Vandenberghe P., Wlodarska I., Marynen P. Hagemeijer A. (2004) Fusion of NUP214 to ABL1 on amplified episomes in T-cell acute lymphoblastic leukemia. Nature Genetics 36, 1084 1089.
22. Graux C., Cools J., Michaux L., Vandenberghe P. Hagemeijer A. (2006) Cytogenetics and molecular genetics of T-cell acute lymphoblastic leukemia: from thymocyte to lymphoblast. Leukemia 20, 1496 1510.
23. Haferlach T., Bacher U., Kohlmann A. Haferlach C. (2009) Discussion of the applicability of microarrays: profiling of leukemias. Methods in Molecular Biology 509, 15 33.
24. Harrison C.J. (2009) Cytogenetics of paediatric and adolescent acute lymphoblastic leukaemia. British Journal Haematology 144, 147 156.
25. Harrison C.J. Foroni L. (2002) Cytogenetics and molecular genetics of acute lymphoblastic leukemia. Reviews in Clinical and Experimental Hematology 6, 91 113.
26. Hebert J., Cayuela J.M., Berkeley J. Sigaux F. (1994) Candidate tumor-suppressor genes MTS1 (p16INK4A) and MTS2 (p15INK4B) display frequent homozygous deletions in primary cells from T- but not from B-cell lineage acute lymphoblastic leukemias. Blood 84, 4038 4044.
27. Hehir-Kwa J.Y., Egmont-Petersen M., Janssen I.M., Smeets D., Van Kessel A.G. Veltman J.A. (2007) Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis. DNA Research 14, 1 11.
28. Huhta T., Vettenranta K., Heinonen K., Kanerva J., Larramendy M.L., Mahlamaki E., Saarinen-Pihkala U.M. Knuutila S. (1999) Comparative genomic hybridization and conventional cytogenetic analyses in childhood acute myeloid leukemia. Leukaemia & Lymphoma 35, 311 315.
29. Huntly B.J., Shigematsu H., Deguchi K., Lee B.H., Mizuno S., Duclos N., Rowan R., Amaral S., Curley D., Williams I.R., Akashi K. Gilliland D.G. (2004) MOZ-TIF2, but not BCR-ABL, confers properties of leukemic stem cells to committed murine hematopoietic progenitors. Cancer Cell 6, 587 596.
30. Irving J.A., Bloodworth L., Bown N.P., Case M.C., Hogarth L.A. Hall A.G. (2005) Loss of heterozygosity in childhood acute lymphoblastic leukemia detected by genome-wide microarray single nucleotide polymorphism analysis. Cancer Research 65, 3053 3058.
31. Jalali G.R., An Q., Konn Z.J., Worley H., Wright S.L., Harrison C.J., Strefford J.C. Martineau M. (2008) Disruption of ETV6 in intron 2 results in upregulatory and insertional events in childhood acute lymphoblastic leukaemia. Leukemia 22, 114 123.
32. Kawamata N., Ogawa S., Zimmermann M., Kato M., Sanada M., Hemminki K., Yamatomo G., Nannya Y., Koehler R., Flohr T., Miller C.W., Harbott J., Ludwig W.D., Stanulla M., Schrappe M., Bartram C.R. Koeffler H.P. (2008a) Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray. Blood 111, 776 784.
33. Kawamata N., Ogawa S., Zimmermann M., Niebuhr B., Stocking C., Sanada M., Hemminki K., Yamatomo G., Nannya Y., Koehler R., Flohr T., Miller C.W., Harbott J., Ludwig W.D., Stanulla M., Schrappe M., Bartram C.R. Koeffler H.P. (2008b) Cloning of genes involved in chromosomal translocations by high-resolution single nucleotide polymorphism genomic microarray. Proceedings of the National Academy of Sciences of the United States of America 105, 11921 11926.
34. Klein F., Feldhahn N., Herzog S., Sprangers M., Mooster J.L., Jumaa H. Muschen M. (2006) BCR-ABL1 induces aberrant splicing of IKAROS and lineage infidelity in pre-B lymphoblastic leukemia cells. Oncogene 25, 1118 1124.
35. Kuchinskaya E., Nordgren A., Heyman M., Schoumans J., Corcoran M., Staaf J., Borg A., Soderhall S., Grander D., Nordenskjold M. Blennow E. (2007) Tiling-resolution array-CGH reveals the pattern of DNA copy number alterations in acute lymphoblastic leukemia with 21q amplification: the result of telomere dysfunction and breakage/fusion/breakage cycles? Leukemia 21, 1327 1330.
36. Kuchinskaya E., Heyman M., Nordgren A., Schoumans J., Staaf J., Borg A., Soderhall S., Grander D., Nordenskjold M. Blennow E. (2008) Array-CGH reveals hidden gene dose changes in children with acute lymphoblastic leukaemia and a normal or failed karyotype by G-banding. British Journal Haematology 140, 572 577.
37. Kuiper R.P., Schoenmakers E.F., Van Reijmersdal S.V., Hehir-Kwa J.Y., Van Kessel A.G., Van Leeuwen F.N. 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.
38. Lahortiga I., De Keersmaecker K., Van Vlierberghe P., Graux C., Cauwelier B., Lambert F., Mentens N., Beverloo H.B., Pieters R., Speleman F., Odero M.D., Bauters M., Froyen G., Marynen P., Vandenberghe P., Wlodarska I., Meijerink J.P. Cools J. (2007) Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia. Nature Genetics 39, 593 595.
39. Larramendy M.L., Huhta T., Heinonen K., Vettenranta K., Mahlamaki E., Riikonen P., Saarinen-Pihkala U.M. Knuutila S. (1998a) DNA copy number changes in childhood acute lymphoblastic leukemia. Haematologica 83, 890 895. (Pubitemid 28538442)
40. Larramendy M.L., Huhta T., Vettenranta K., El-Rifai W., Lundin J., Pakkala S., Saarinen-Pihkala U.M. Knuutila S. (1998b) Comparative genomic hybridization in childhood acute lymphoblastic leukemia. Leukemia 12, 1638 1644. (Pubitemid 28470451)
41. Lilljebjorn H., Heidenblad M., Nilsson B., Lassen C., Horvat A., Heldrup J., Behrendtz M., Johansson B., Andersson A. 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.
42. Lo K.C., Bailey D., Burkhardt T., Gardina P., Turpaz Y. Cowell J.K. (2008) Comprehensive analysis of loss of heterozygosity events in glioblastoma using the 100K SNP mapping arrays and comparison with copy number abnormalities defined by BAC array comparative genomic hybridization. Genes, Chromosomes and Cancer 47, 221 237.
43. Lundin C., Heidenblad M., Strombeck B., Borg A., Hovland R., Heim S. Johansson B. (2007) Tiling resolution array CGH of dic(7;9)(p11 approximately 13;p11 approximately 13) in B-cell precursor acute lymphoblastic leukemia reveals clustered breakpoints at 7p11.2 approximately 12.1 and 9p13.1. Cytogenetic Genome Research 118, 13 18.
44. Maciejewski J.P. Mufti G.J. (2008) Whole genome scanning as a cytogenetic tool in hematologic malignancies. Blood 112, 965 974.
45. Maser R.S., Choudhury B., Campbell P.J., Feng B., Wong K.K., Protopopov A., O'neil J., Gutierrez A., Ivanova E., Perna I., Lin E., Mani V., Jiang S., Mcnamara K., Zaghlul S., Edkins S., Stevens C., Brennan C., Martin E.S., Wiedemeyer R., Kabbarah O., Nogueira C., Histen G., Aster J., Mansour M., Duke V., Foroni L., Fielding A.K., Goldstone A.H., Rowe J.M., Wang Y.A., Look A.T., Stratton M.R., Chin L., Futreal P.A. Depinho R.A. (2007) Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers. Nature 447, 966 971.
46. Matsuzaki H., Dong S., Loi H., Di X., Liu G., Hubbell E., Law J., Berntsen T., Chadha M., Hui H., Yang G., Webster T.A., Cawley S., Jones K.W., Fodor S.P.A. Mei R. (2004) Genotyping over 100,000 SNPs on a pair of oligonucleotide∼arrays. Nature Methods 1, 109 111.
47. Melo J.V. (1996) The diversity of BCR-ABL fusion proteins and their relationship to leukemia phenotype. Blood 88, 2375 2384.
48. Miller C.B., Mullighan C.G., Su X., Ma J., Wang M., Zhang J., Williams R.T. Downing J.R. (2008) Pax5 haploinsufficiency cooperates with BCR-ABL1 to induce acute lymphoblastic leukemia. Blood 112. Abstract 293.
49. Molnar A. Georgopoulos K. (1994) The Ikaros gene encodes a family of functionally diverse zinc finger DNA-binding proteins. Molecular and Cellular Biology 14, 8292 8303.
50. Mortazavi A., Williams B.A., Mccue K., Schaeffer L. Wold B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621 628.
51. Mullighan C.G. Downing J.R. (2009) Genome-wide profiling of genetic alterations in acute lymphoblastic leukemia: recent insights and future directions. Leukemia, 26 February 2009. doi :.
52. 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., Su X., Pui C.H., Relling M.V., Evans W.E., Shurtleff S.A. Downing J.R. (2007) Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446, 758 764.
53. Mullighan C.G., Miller C.B., Phillips L.A., Dalton J.D., Ma J., Radtke I., White D., Hughes T.P., Le Beau M.M., Pui C.H., Shurtleff S.A. Downing J.R. (2008a) BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature 453, 110 114.
54. Mullighan C.G., Phillips L.A., Kiedrowski L.A., Ma J., Williams R.T., Shurtleff S.A., Sherr C.J. Downing J.R. (2008b) Ultra-high resolution genomic analysis of genomic alterations in high-risk acute lymphoblastic leukemia. Blood 112. Abstract 2053.
55. Mullighan C.G., Phillips L.A., Su X., Ma J., Miller C.B., Shurtleff S.A. Downing J.R. (2008c) Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science 322, 1377 1380.
56. Mullighan C.G., Radtke I., Zhang J., Phillips L.A., Su X., Ma J., Cai Z., Hughes T.P., White D.L., Roberts A.W., Campbell L.J., Shurtleff S. Downing J.R. (2008d) Genome-wide analysis of genetic alterations in chronic myeloid leukemia. Blood 112. Abstract 1089.
57. Mullighan C.G., Su X., Zhang J., Radtke I., Phillips L.A., Miller C.B., Ma J., Liu W., Cheng C., Schulman B.A., Harvey R.C., Chen I.M., Clifford R.J., Carroll W.L., Reaman G., Bowman W.P., Devidas M., Gerhard D.S., Yang W., Relling M.V., Shurtleff S.A., Campana D., Borowitz M.J., Pui C.H., Smith M., Hunger S.P., Willman C.L. Downing J.R. (2009) Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. The New England Journal of Medicine 360, 470 480.
58. Nakase K., Ishimaru F., Avitahl N., Dansako H., Matsuo K., Fujii K., Sezaki N., Nakayama H., Yano T., Fukuda S., Imajoh K., Takeuchi M., Miyata A., Hara M., Yasukawa M., Takahashi I., Taguchi H., Matsue K., Nakao S., Niho Y., Takenaka K., Shinagawa K., Ikeda K., Niiya K. Harada M. (2000) Dominant negative isoform of the Ikaros gene in patients with adult B-cell acute lymphoblastic leukemia. Cancer Research 60, 4062 4065.
59. Nebral K., Konig M., Harder L., Siebert R., Haas O.A. Strehl S. (2007) Identification of PML as novel PAX5 fusion partner in childhood acute lymphoblastic leukaemia. British Journal Haematology 139, 269 274.
60. Nebral K., Denk D., Attarbaschi A., Konig M., Mann G., Haas O.A. Strehl S. (2008) Incidence and diversity of PAX5 fusion genes in childhood acute lymphoblastic leukemia. Leukemia 23, 134 143. doi :.
61. Nishii K., Kita K., Miwa H., Shikami M., Taniguchi M., Usui E., Katayama N. Shiku H. (2000) Expression of B cell-associated transcription factors in B-cell precursor acute lymphoblastic leukemia cells: association with PU.1 expression, phenotype, and immunogenotype. International Journal of Hematology 71, 372 378.
62. Nutt S.L. Kee B.L. (2007) The transcriptional regulation of B cell lineage commitment. Immunity 26, 715 725.
63. Nutt S.L., Heavey B., Rolink A.G. Busslinger M. (1999) Commitment to the B-lymphoid lineage depends on the transcription factor Pax5. Nature 401, 556 562.
64. Nutt S.L., Eberhard D., Horcher M., Rolink A.G. Busslinger M. (2001) Pax5 determines the identity of B cells from the beginning to the end of B-lymphopoiesis. International Reviews of Immunology 20, 65 82.
65. O'neil J., Grim J., Strack P., Rao S., Tibbitts D., Winter C., Hardwick J., Welcker M., Meijerink J.P., Pieters R., Draetta G., Sears R., Clurman B.E. Look A.T. (2007) FBW7 mutations in leukemic cells mediate NOTCH pathway activation and resistance to gamma-secretase inhibitors. Journal of Experimental Medicine 204, 1813 1824.
66. Ogawa S., Hangaishi A., Miyawaki S., Hirosawa S., Miura Y., Takeyama K., Kamada N., Ohtake S., Uike N. Shimazaki C. (1995) Loss of the cyclin-dependent kinase 4-inhibitor (p16; MTS1) gene is frequent in and highly specific to lymphoid tumors in primary human hematopoietic malignancies. Blood 86, 1548 1556.
67. Okuda T., Shurtleff S.A., Valentine M.B., Raimondi S.C., Head D.R., Behm F., Curcio-Brint A.M., Liu Q., Pui C.H. Sherr C.J. (1995) Frequent deletion of p16INK4a/MTS1 and p15INK4b/MTS2 in pediatric acute lymphoblastic leukemia. Blood 85, 2321 2330.
68. Olivero S., Maroc C., Beillard E., Gabert J., Nietfeld W., Chabannon C. Tonnelle C. (2000) Detection of different Ikaros isoforms in human leukaemias using real-time quantitative polymerase chain reaction. British Journal Haematology 110, 826 830.
69. Olshen A.B., Venkatraman E.S., Lucito R. Wigler M. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557 572.
70. Palomero T., Sulis M.L., Cortina M., Real P.J., Barnes K., Ciofani M., Caparros E., Buteau J., Brown K., Perkins S.L., Bhagat G., Agarwal A.M., Basso G., Castillo M., Nagase S., Cordon-Cardo C., Parsons R., Zuniga-Pflucker J.C., Dominguez M. Ferrando A.A. (2007) Mutational loss of PTEN induces resistance to NOTCH1 inhibition in T-cell leukemia. Nature Medicine 13, 1203 1210.
71. Peiffer D.A., Le J.M., Steemers F.J., Chang W., Jenniges T., Garcia F., Haden K., Li J., Shaw C.A., Belmont J., Cheung S.W., Shen R.M., Barker D.L. Gunderson K.L. (2006) High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Research 16, 1136 1148.
72. Pinkel D. Albertson D.G. (2005) Comparative genomic hybridization. Annual Review of Genomics and Human Genetics 6, 331 354.
73. Pounds S., Cheng C., Mullighan C., Raimondi S.C., Shurtleff S. Downing J.R. (2009) Reference alignment of SNP microarray signals for copy number analysis of tumors. Bioinformatics 25, 315 321.
74. Pui C.H., Relling M.V. Downing J.R. (2004a) Acute lymphoblastic leukemia. The New England Journal of Medicine 350, 1535 1548.
75. Pui C.H., Robison L.L. Look A.T. (2008) Acute lymphoblastic leukaemia. Lancet 371, 1030 1043.
76. Pui C.H., Sandlund J.T., Pei D., Campana D., Rivera G.K., Ribeiro R.C., Rubnitz J.E., Razzouk B.I., Howard S.C., Hudson M.M., Cheng C., Kun L.E., Raimondi S.C., Behm F.G., Downing J.R., Relling M.V. Evans W.E. (2004b) Improved outcome for children with acute lymphoblastic leukemia: results of Total Therapy Study XIIIB at St Jude Children's Research Hospital. Blood 104, 2690 2696.
77. Rabin K.R., Man T.K., Yu A., Folsom M.R., Zhao Y.J., Rao P.H., Plon S.E. Naeem R.C. (2008) Clinical utility of array comparative genomic hybridization for detection of chromosomal abnormalities in pediatric acute lymphoblastic leukemia. Pediatric Blood Cancer 51, 171 177.
78. Radtke I., Mullighan C.G., Ishii M., Ma J., Su X., Goorha S., Ganti R., Cai Z., Phillips L.A., Pounds S.B., Dalton J., Raimondi S.C., Rubnitz J.E., Ribeiro R.C., Shurtleff S.A. Downing J.R. (2007) High-resolution genome-wide profiling of DNA copy number abnormalities and gene resequencing in pediatric acute myeloid leukemia (AML). ASH Annual Meeting Abstracts 110, 103.
79. Raghavan M., Smith L.L., Lillington D.M., Chaplin T., Kakkas I., Molloy G., Chelala C., Cazier J.B., Cavenagh J.D., Fitzgibbon J., Lister T.A. Young B.D. (2008) Segmental uniparental disomy is a commonly acquired genetic event in relapsed acute myeloid leukemia. Blood 112, 814 821.
80. Raimondi S.C. (2006) Cytogenetics of acute leukemias. In : Childhood Leukemias ed. C.H. Pui 2nd edn, pp. 235 271. Cambridge University Press, Cambridge.
81. Raimondi S.C., Pui C.H., Head D.R., Rivera G.K. Behm F.G. (1993) Cytogenetically different leukemic clones at relapse of childhood acute lymphoblastic leukemia. Blood 82, 576 580.
82. Renneville A., Roumier C., Biggio V., Nibourel O., Boissel N., Fenaux P. Preudhomme C. (2008) Cooperating gene mutations in acute myeloid leukemia: a review of the literature. Leukemia 22, 915 931.
83. Ribeiro R.C., Abromowitch M., Raimondi S.C., Murphy S.B., Behm F. Williams D.L. (1987) Clinical and biologic hallmarks of the Philadelphia chromosome in childhood acute lymphoblastic leukemia. Blood 70, 948 953.
84. Rivera G.K., Zhou Y., Hancock M.L., Gajjar A., Rubnitz J., Ribeiro R.C., Sandlund J.T., Hudson M., Relling M., Evans W.E. Pui C.H. (2005) Bone marrow recurrence after initial intensive treatment for childhood acute lymphoblastic leukemia. Cancer 103, 368 376.
85. Ross M.E., Zhou X., Song G., Shurtleff S.A., Girtman K., Williams W.K., Liu H.C., Mahfouz R., Raimondi S.C., Lenny N., Patel A. Downing J.R. (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood 102, 2951 2959. (Pubitemid 37248870)
86. Ross M.E., Mahfouz R., Onciu M., Liu H.C., Zhou X., Song G., Shurtleff S.A., Pounds S., Cheng C., Ma J., Ribeiro R.C., Rubnitz J.E., Girtman K., Williams W.K., Raimondi S.C., Liang D.C., Shih L.Y., Pui C.H. Downing J.R. (2004) Gene expression profiling of pediatric acute myelogenous leukemia. Blood 104, 3679 3687.
87. Rowe J.M., Buck G., Burnett A.K., Chopra R., Wiernik P.H., Richards S.M., Lazarus H.M., Franklin I.M., Litzow M.R., Ciobanu N., Prentice H.G., Durrant J., Tallman M.S. Goldstone A.H. (2005) Induction therapy for adults with acute lymphoblastic leukemia: results of more than 1500 patients from the international ALL trial: MRC UKALL XII/ECOG E2993. Blood 106, 3760 3767.
88. Rowley J.D. (2008) Chromosomal translocations: revisited yet again. Blood 112, 2183 2189.
89. Savona M. Talpaz M. (2008) Getting to the stem of chronic myeloid leukaemia. Nature Reviews. Cancer 8, 341 350.
90. Schoumans J., Johansson B., Corcoran M., Kuchinskaya E., Golovleva I., Grander D., Forestier E., Staaf J., Borg A., Gustafsson B., Blennow E. Nordgren A. (2006) Characterisation of dic(9;20)(p11-13;q11) in childhood B-cell precursor acute lymphoblastic leukaemia by tiling resolution array-based comparative genomic hybridisation reveals clustered breakpoints at 9p13.2 and 20q11.2. British Journal Haematology 135, 492 499.
91. Shendure J. (2008) The beginning of the end for microarrays? Nature Methods 5, 585 587.
92. Steinemann D., Cario G., Stanulla M., Karawajew L., Tauscher M., Weigmann A., Gohring G., Ludwig W.D., Harbott J., Radlwimmer B., Bartram C., Lichter P., Schrappe M. Schlegelberger B. (2008) Copy number alterations in childhood acute lymphoblastic leukemia and their association with minimal residual disease. Genes, Chromosomes and Cancer 47, 471 480.
93. Strefford J.C. Parker H. (2009) Array-based comparative genomic hybridization as a tool for analyzing the leukemia genome. Methods in Molecular Biology 538, 1 27.
94. Strefford J.C., Van Delft F.W., Robinson H.M., Worley H., Yiannikouris O., Selzer R., Richmond T., Hann I., Bellotti T., Raghavan M., Young B.D., Saha V. Harrison C.J. (2006) Complex genomic alterations and gene expression in acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Proceedings of the National Academy of Sciences of the United States of America 103, 8167 8172.
95. Strefford J.C., Worley H., Barber K., Wright S., Stewart A.R., Robinson H.M., Bettney G., Van Delft F.W., Atherton M.G., Davies T., Griffiths M., Hing S., Ross F.M., Talley P., Saha V., Moorman A.V. Harrison C.J. (2007) Genome complexity in acute lymphoblastic leukemia is revealed by array-based comparative genomic hybridization. Oncogene 26, 4306 4318.
96. Strehl S., Konig M., Dworzak M.N., Kalwak K. Haas O.A. (2003) PAX5/ETV6 fusion defines cytogenetic entity dic(9;12)(p13;p13). Leukemia 17, 1121 1123.
97. Sun L., Crotty M.L., Sensel M., Sather H., Navara C., Nachman J., Steinherz P.G., Gaynon P.S., Seibel N., Mao C., Vassilev A., Reaman G.H. Uckun F.M. (1999a) Expression of dominant-negative Ikaros isoforms in T-cell acute lymphoblastic leukemia. Clinical Cancer Research 5, 2112 2120.
98. Sun L., Goodman P.A., Wood C.M., Crotty M.L., Sensel M., Sather H., Navara C., Nachman J., Steinherz P.G., Gaynon P.S., Seibel N., Vassilev A., Juran B.D., Reaman G.H. Uckun F.M. (1999b) Expression of aberrantly spliced oncogenic ikaros isoforms in childhood acute lymphoblastic leukemia. Journal of Clinical Oncology 17, 3753 3766.
99. Sun L., Heerema N., Crotty L., Wu X., Navara C., Vassilev A., Sensel M., Reaman G.H. Uckun F.M. (1999c) Expression of dominant-negative and mutant isoforms of the antileukemic transcription factor Ikaros in infant acute lymphoblastic leukemia. Proceedings of the National Academy of Sciences of the United States of America 96, 680 685.
100. Takanashi M., Yagi T., Imamura T., Tabata Y., Morimoto A., Hibi S., Ishii E. Imashuku S. (2002) Expression of the Ikaros gene family in childhood acute lymphoblastic leukaemia. British Journal Haematology 117, 525 530.
101. Tuna M., Knuutila S. Mills G.B. (2009) Uniparental disomy in cancer. Trends in Molecular Medicine 15, 120 128.
102. Tyybakinoja A., Elonen E., Piippo K., Porkka K. Knuutila S. (2007) Oligonucleotide array-CGH reveals cryptic gene copy number alterations in karyotypically normal acute myeloid leukemia. Leukemia 21, 571 574.
103. Tyybakinoja A., Elonen E., Vauhkonen H., Saarela J. Knuutila S. (2008) Single nucleotide polymorphism microarray analysis of karyotypically normal acute myeloid leukemia reveals frequent copy number neutral loss of heterozygosity. Haematologica 93, 631 632.
104. Van Vlierberghe P., Meijerink J.P., Lee C., Ferrando A.A., Look A.T., Van Wering E.R., Beverloo H.B., Aster J.C. Pieters R. (2006a) A new recurrent 9q34 duplication in pediatric T-cell acute lymphoblastic leukemia. Leukemia 20, 1245 1253.
105. Van Vlierberghe P., Van Grotel M., Beverloo H.B., Lee C., Helgason T., Buijs-Gladdines J., Passier M., Van Wering E.R., Veerman A.J., Kamps W.A., Meijerink J.P. Pieters R. (2006b) The cryptic chromosomal deletion del(11)(p12p13) as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemia. Blood 108, 3520 3529.
106. Van Vlierberghe P., Van Grotel M., Tchinda J., Lee C., Beverloo H.B., Van Spek Der P.J., Stubbs A., Cools J., Nagata K., Fornerod M., Buijs-Gladdines J., Horstmann M., Van Wering E.R., Soulier J., Pieters R. Meijerink J.P. (2008) The recurrent SET-NUP214 fusion as a new HOXA activation mechanism in pediatric T-cell acute lymphoblastic leukemia. Blood 111, 4668 4680.
107. Weng A.P., Ferrando A.A., Lee W., Morris J.P.T., Silverman L.B., Sanchez-Irizarry C., Blacklow S.C., Look A.T. Aster J.C. (2004) Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia. Science 306, 269 271.
108. Williams R.T., Roussel M.F. Sherr C.J. (2006) Arf gene loss enhances oncogenicity and limits imatinib response in mouse models of Bcr-Abl-induced acute lymphoblastic leukemia. Proceedings of the National Academy of Sciences of the United States of America 103, 6688 6693.
109. Wouters B.J., Lowenberg B. Delwel R. (2009) A decade of genome-wide gene expression profiling in acute myeloid leukemia: flashback and prospects. Blood 113, 291 298.
110. Xavier R.J. Rioux J.D. (2008) Genome-wide association studies: a new window into immune-mediated diseases. Nature Reviews. Immunology 8, 631 643.
111. Yang J.J., Cheng C., Yang W., Pei D., Cao X., Fan Y., Pounds S.B., Neale G., Trevino L.R., French D., Campana D., Downing J.R., Evans W.E., Pui C.H., Devidas M., Bowman W.P., Camitta B.M., Willman C.L., Davies S.M., Borowitz M.J., Carroll W.L., Hunger S.P. Relling M.V. (2009) Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia. JAMA 301, 393 403.
112. Yeoh E.J., Ross M.E., Shurtleff S.A., Williams W.K., Patel D., Mahfouz R., Behm F.G., Raimondi S.C., Relling M.V., Patel A., Cheng C., Campana D., Wilkins D., Zhou X., Li J., Liu H., Pui C.H., Evans W.E., Naeve C., Wong L. Downing J.R. (2002) Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 1, 133 143.