Genome-wide analysis of Myelodysplastic syndromes

Current Pharmaceutical Design

Volumn 18, Issue 22, 2012, Pages 3163-3169

  Sanada, Masashi ^a   Ogawa, Seishi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Cnn loh; High throughput parallel sequencing; Microarray; Snp array; Somatic mutation

Indexed keywords

CBL PROTEIN; ISOCITRATE DEHYDROGENASE 1; ISOCITRATE DEHYDROGENASE 2; K RAS PROTEIN; RIBOSOME PROTEIN; TRANSCRIPTION FACTOR EZH2;

COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; CYTOGENETICS; EXOME; GENE DOSAGE; GENE FREQUENCY; GENE MUTATION; GENE TRANSLOCATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; HIGH THROUGHPUT SCREENING; HUMAN; KARYOTYPING; MUTATIONAL ANALYSIS; MYELODYSPLASTIC SYNDROME; ONCOGENE N RAS; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; UNIPARENTAL DISOMY;

EID: 84862568008     PISSN: 13816128     EISSN: 18734286     Source Type: Journal    
DOI: 10.2174/1381612811209023163     Document Type: Review

References (103)

1. Tefferi A, Vardiman JW. Myelodysplastic syndromes. N Engl J Med 2009; 361(19): 1872-85.
2. Bejar R, Levine R, Ebert BL. Unraveling the molecular pathophysiology of myelodysplastic syndromes. J Clin Oncol 2011 Feb 10; 29(5): 504-15.
3. Greenberg P, Cox C, LeBeau MM, et al. International scoring system for evaluating prognosis in myelodysplastic syndromes. Blood 1997; 89(6): 2079-88.
4. Haase D, Germing U, Schanz J, et al. New insights into the prognostic impact of the karyotype in MDS and correlation with subtypes: evidence from a core dataset of 2124 patients. Blood 2007; 110(13): 4385-95.
5. Garcia-Manero G. Prognosis of myelodysplastic syndromes. Hematology Am Soc Hematol Educ Program 2010; 2010: 330-7.
6. Schoch C, Haferlach T. Cytogenetics in acute myeloid leukemia. Curr Oncol Rep 2002; 4(5): 390-7.
7. Swerdlow S, Campo E, Harris N, et al. World Health Organization Classification of Tumours: Pathology and Genetics of Tumours of Haematopoietic and Lymphoid Tissues. Lyon: IARC; 2008.
8. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet 2005; 37 Suppl: S11-7.
9. Rauch A, Ruschendorf F, Huang J, et al. Molecular karyotyping using an SNP array for genomewide genotyping. J Med Genet 2004; 41(12): 916-22.
10. Mullighan CG, Goorha S, Radtke I, et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 2007; 446(7137): 758-64.
11. 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(2): 776-84.
12. Chen Y, Takita J, Choi YL, et al. Oncogenic mutations of ALK kinase in neuroblastoma. Nature 2008; 455(7215): 971-4.
13. Kato M, Sanada M, Kato I, et al. Frequent inactivation of A20 in B-cell lymphomas. Nature 2009; 459(7247): 712-6.
14. Sanada M, Suzuki T, Shih LY, et al. Gain-of-function of mutated C-CBL tumour suppressor in myeloid neoplasms. Nature 2009; 460(7257): 904-8.
15. Delhommeau F, Dupont S, Della Valle V, et al. Mutation in TET2 in myeloid cancers. N Engl J Med 2009; 360(22): 2289-301.
16. Langemeijer SM, Kuiper RP, Berends M, et al. Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat Genet 2009; 41(7): 838-42.
17. Ernst T, Chase AJ, Score J, et al. Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders. Nat Genet 2010; 42(8): 722-6.
18. Nikoloski G, Langemeijer SM, Kuiper RP, et al. Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat Genet 2010; 42(8): 665-7.
19. Silverman LR, Demakos EP, Peterson BL, et al. Randomized controlled trial of azacitidine in patients with the myelodysplastic syndrome: a study of the cancer and leukemia group B. J Clin Oncol 2002; 20(10): 2429-40.
20. Silverman LR, McKenzie DR, Peterson BL, et al. Further analysis of trials with azacitidine in patients with myelodysplastic syndrome: studies 8421, 8921, and 9221 by the Cancer and Leukemia Group B. J Clin Oncol 2006; 24(24): 3895-903.
21. Kantarjian H, Oki Y, Garcia-Manero G, et al. Results of a randomized study of 3 schedules of low-dose decitabine in higherrisk myelodysplastic syndrome and chronic myelomonocytic leukemia. Blood 2007; 109(1): 52-7.
22. Malcovati L, Germing U, Kuendgen A, et al. Time-dependent prognostic scoring system for predicting survival and leukemic evolution in myelodysplastic syndromes. J Clin Oncol 2007; 25(23): 3503-10.
23. Sole F, Espinet B, Sanz GF, et al. Incidence, characterization and prognostic significance of chromosomal abnormalities in 640 patients with primary myelodysplastic syndromes. Grupo Cooperativo Espanol de Citogenetica Hematologica. Br J Haematol 2000; 108(2): 346-56.
24. Sole F, Luno E, Sanzo C, et al. Identification of novel cytogenetic markers with prognostic significance in a series of 968 patients with primary myelodysplastic syndromes. Haematologica 2005; 90(9): 1168-78.
25. Bernasconi P, Klersy C, Boni M, et al. World Health Organization classification in combination with cytogenetic markers improves the prognostic stratification of patients with de novo primary myelodysplastic syndromes. Br J Haematol 2007; 137(3): 193-205.
26. Rigolin GM, Bigoni R, Milani R, et al. Clinical importance of interphase cytogenetics detecting occult chromosome lesions in myelodysplastic syndromes with normal karyotype. Leukemia 2001; 15(12): 1841-7.
27. Barrett MT, Scheffer A, Ben-Dor A, et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci USA 2004; 101(51): 17765-70.
28. Coe BP, Ylstra B, Carvalho B, Meijer GA, Macaulay C, Lam WL. Resolving the resolution of array CGH. Genomics 2007; 89(5): 647-53.
29. Paulsson K, Heidenblad M, Strombeck B, et al. High-resolution genome-wide array-based comparative genome hybridization reveals cryptic chromosome changes in AML and MDS cases with trisomy 8 as the sole cytogenetic aberration. Leukemia 2006; 20(5): 840-6.
30. O'Keefe CL, Tiu R, Gondek LP, et al. High-resolution genomic arrays facilitate detection of novel cryptic chromosomal lesions in myelodysplastic syndromes. Exp Hematol 2007; 35(2): 240-51.
31. Starczynowski DT, Vercauteren S, Telenius A, et al. High- resolution whole genome tiling path array CGH analysis of CD34+ cells from patients with low-risk myelodysplastic syndromes reveals cryptic copy number alterations and predicts overall and leukemia-free survival. Blood 2008; 112(8): 3412-24.
32. Thiel A, Beier M, Ingenhag D, et al. Comprehensive array CGH of normal karyotype myelodysplastic syndromes reveals hidden recurrent and individual genomic copy number alterations with prognostic relevance. Leukemia 2011; 25(3): 387-99.
33. Matsuzaki H, Dong S, Loi H, et al. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 2004; 1(2): 109-11.
34. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007; 447(7145): 661-78.
35. Zhao X, Li C, Paez JG, et al. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 2004; 64(9): 3060-71.
36. Nannya Y, Sanada M, Nakazaki K, et al. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 2005; 65(14): 6071-9.
37. Van Loo P, Nordgard SH, Lingjaerde OC, et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA 2010; 107(39): 16910-5.
38. Thoennissen NH, Krug UO, Lee DH, et al. Prevalence and prognostic impact of allelic imbalances associated with leukemic transformation of Philadelphia chromosome-negative myeloproliferative neoplasms. Blood 2010; 115(14): 2882-90.
39. Greenway SC, Pereira AC, Lin JC, et al. De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot. Nat Genet 2009; 41(8): 931-5.
40. Murray SS, Oliphant A, Shen R, et al. A highly informative SNP linkage panel for human genetic studies. Nat Methods 2004; 1(2): 113-7.
41. Beroukhim R, Lin M, Park Y, et al. Inferring loss-of-heterozy- gosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol 2006; 2(5): e41.
42. Laframboise T, Harrington D, Weir BA. PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data. Biostatistics 2007; 8(2): 323-36.
43. Yamamoto G, Nannya Y, Kato M, et al. Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of affymetrix single-nucleotidepolymorphism genotyping microarrays. Am J Hum Genet 2007; 81(1): 114-26.
44. Kralovics R, Passamonti F, Buser AS, et al. A gain-of-function mutation of JAK2 in myeloproliferative disorders. N Engl J Med 2005; 352(17): 1779-90.
45. Gondek LP, Tiu R, O'Keefe CL, Sekeres MA, Theil KS, Maciejewski JP. Chromosomal lesions and uniparental disomy detected by SNP arrays in MDS, MDS/MPD, and MDS-derived AML. Blood 2008; 111(3): 1534-42.
46. Heinrichs S, Kulkarni RV, Bueso-Ramos CE, et al. Accurate detection of uniparental disomy and microdeletions by SNP array analysis in myelodysplastic syndromes with normal cytogenetics. Leukemia 2009; 23(9): 1605-13.
47. Raghavan M, Smith LL, Lillington DM, et al. Segmental uniparental disomy is a commonly acquired genetic event in relapsed acute myeloid leukemia. Blood 2008; 112(3): 814-21.
48. Akagi T, Shih LY, Kato M, et al. Hidden abnormalities and novel classification of t(15; 17) acute promyelocytic leukemia (APL) based on genomic alterations. Blood 2009; 113(8): 1741-8.
49. Akagi T, Shih LY, Ogawa S, et al. Single nucleotide polymorphism genomic arrays analysis of t(8; 21) acute myeloid leukemia cells. Haematologica 2009; 94(9): 1301-6.
50. Walter MJ, Payton JE, Ries RE, et al. Acquired copy number alterations in adult acute myeloid leukemia genomes. Proc Natl Acad Sci USA 2009; 106(31): 12950-5.
51. Tiu RV, Gondek LP, O'Keefe CL, et al. New lesions detected by single nucleotide polymorphism array-based chromosomal analysis have important clinical impact in acute myeloid leukemia. J Clin Oncol 2009; 27(31): 5219-26.
52. Bullinger L, Kronke J, Schon C, et al. Identification of acquired copy number alterations and uniparental disomies in cytogenetically normal acute myeloid leukemia using high-resolution single-nucleotide polymorphism analysis. Leukemia 2010; 24(2): 438-49.
53. Dunbar AJ, Gondek LP, O'Keefe CL, et al. 250K single nucleotide polymorphism array karyotyping identifies acquired uniparental disomy and homozygous mutations, including novel missense substitutions of c-Cbl, in myeloid malignancies. Cancer Res 2008; 68(24): 10349-57.
54. Fitzgibbon J, Smith LL, Raghavan M, et al. Association between acquired uniparental disomy and homozygous gene mutation in acute myeloid leukemias. Cancer Res 2005; 65(20): 9152-4.
55. Bejar R, Stevenson K, Abdel-Wahab O, et al. Clinical effect of point mutations in myelodysplastic syndromes. N Engl J Med 2011; 364(26): 2496-506.
56. Kosmider O, Gelsi-Boyer V, Ciudad M, et al. TET2 gene mutation is a frequent and adverse event in chronic myelomonocytic leukemia. Haematologica 2009; 94(12): 1676-81.
57. Abdel-Wahab O, Mullally A, Hedvat C, et al. Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies. Blood 2009; 114(1): 144-7.
58. Metzeler KH, Maharry K, Radmacher MD, et al. TET2 mutations improve the new European LeukemiaNet risk classification of acute myeloid leukemia: a Cancer and Leukemia Group B study. J Clin Oncol 2011; 29(10): 1373-81.
59. Smith AE, Mohamedali AM, Kulasekararaj A, et al. Next- generation sequencing of the TET2 gene in 355 MDS and CMML patients reveals low-abundance mutant clones with early origins, but indicates no definite prognostic value. Blood 2010; 116(19): 3923-32.
60. Tahiliani M, Koh KP, Shen Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009; 324(5929): 930-5.
61. Ito S, D'Alessio AC, Taranova OV, et al. Hong K, Sowers LC, Zhang Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 2010; 466(7310): 1129-33.
62. Wu H, D'Alessio AC, Ito S, et al. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 2011; 473(7347): 389-93.
63. Pastor WA, Pape UJ, Huang Y, et al. Genome-wide mapping of 5- hydroxymethylcytosine in embryonic stem cells. Nature 2011; 473(7347): 394-7.
64. Guo JU, Su Y, Zhong C, et al. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 2011; 145(3): 423-34.
65. Williams K, Christensen J, Pedersen MT, et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011; 473(7347): 343-8.
66. Quivoron C, Couronne L, Della Valle V, et al. TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis. Cancer Cell 2011; 20(1): 25-38.
67. Parsons DW, Jones S, Zhang X, et al. An integrated genomic analysis of human glioblastoma multiforme. Science 2008; 321(5897): 1807-12.
68. Mardis ER, Ding L, Dooling DJ, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 2009; 361(11): 1058-66.
69. Marcucci G, Maharry K, Wu YZ, et al. IDH1 and IDH2 gene mutations identify novel molecular subsets within de novo cytogenetically normal acute myeloid leukemia: a Cancer and Leukemia Group B study. J Clin Oncol 2010; 28(14): 2348-55.
70. Paschka P, Schlenk RF, Gaidzik VI, et al. IDH1 and IDH2 mutations are frequent genetic alterations in acute myeloid leukemia and confer adverse prognosis in cytogenetically normal acute myeloid leukemia with NPM1 mutation without FLT3 internal tandem duplication. J Clin Oncol 2010; 28(22): 3636-43.
71. Yoshida K, Sanada M, Kato M, et al. A nonsense mutation of IDH1 in myelodysplastic syndromes and related disorders. Leukemia 2011; 25(1): 184-6.
72. Tefferi A, Lasho TL, Abdel-Wahab O, et al. IDH1 and IDH2 mutation studies in 1473 patients with chronic-, fibroticor blastphase essential thrombocythemia, polycythemia vera or myelofibrosis. Leukemia 2010; 24(7): 1302-9.
73. Pardanani A, Lasho TL, Finke CM, et al. IDH1 and IDH2 mutation analysis in chronicand blast-phase myeloproliferative neoplasms. Leukemia 2010; 24(6): 1146-51.
74. Figueroa ME, Abdel-Wahab O, Lu C, et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 2010; 18(6): 553-67.
75. Grand FH, Hidalgo-Curtis CE, Ernst T, et al. Frequent CBL mutations associated with 11q acquired uniparental disomy in myeloproliferative neoplasms. Blood 2009; 113(24): 6182-92.
76. Loh ML, Sakai DS, Flotho C, et al. Mutations in CBL occur frequently in juvenile myelomonocytic leukemia. Blood 2009; 114(9): 1859-63.
77. Thien CB, Langdon WY. Cbl: many adaptations to regulate protein tyrosine kinases. Nat Rev Mol Cell Biol 2001; 2(4): 294-307.
78. Perez B, Kosmider O, Cassinat B, et al. Genetic typing of CBL, ASXL1, RUNX1, TET2 and JAK2 in juvenile myelomonocytic leukaemia reveals a genetic profile distinct from chronic myelomonocytic leukaemia. Br J Haematol 2010; 151(5): 460-8.
79. Kohlmann A, Grossmann V, Klein HU, et al. Next-generation sequencing technology reveals a characteristic pattern of molecular mutations in 72.8% of chronic myelomonocytic leukemia by detecting frequent alterations in TET2, CBL, RAS, and RUNX1. J Clin Oncol 2010; 28(24): 3858-65.
80. Niemeyer CM, Kang MW, Shin DH, et al. Germline CBL mutations cause developmental abnormalities and predispose to juvenile myelomonocytic leukemia. Nat Genet 2010; 42(9): 794-800.
81. Martinelli S, De Luca A, Stellacci E, et al. Heterozygous germline mutations in the CBL tumor-suppressor gene cause a Noonan syndrome-like phenotype. Am J Hum Genet 2010; 87(2): 250-7.
82. Ogawa S, Sanada M, Shih LY, et al. Gain-of-function c-CBL mutations associated with uniparental disomy of 11q in myeloid neoplasms. Cell Cycle 2010; 9(6): 1051-6.
83. Sargin B, Choudhary C, Crosetto N, et al. Flt3-dependent transformation by inactivating c-Cbl mutations in AML. Blood 2007; 110(3): 1004-12.
84. Rathinam C, Thien CB, Flavell RA, Langdon WY. Myeloid leukemia development in c-Cbl RING finger mutant mice is dependent on FLT3 signaling. Cancer Cell 2010; 18(4): 341-52.
85. Valk-Lingbeek ME, Bruggeman SW, van Lohuizen M. Stem cells and cancer; the polycomb connection. Cell 2004; 118(4): 409-18.
86. Majewski IJ, Ritchie ME, Phipson B, et al. Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells. Blood 2010; 116(5): 731-9.
87. Le Beau MM, Espinosa R, 3rd, Davis EM, et al. Eisenbart JD, Larson RA, Green ED. Cytogenetic and molecular delineation of a region of chromosome 7 commonly deleted in malignant myeloid diseases. Blood 1996; 88(6): 1930-5.
88. Dohner K, Brown J, Hehmann U, et al. Molecular cytogenetic characterization of a critical region in bands 7q35-q36 commonly deleted in malignant myeloid disorders. Blood 1998; 92(11): 4031-5.
89. Wong JC, Zhang Y, Lieuw KH, et al. Use of chromosome engineering to model a segmental deletion of chromosome band 7q22 found in myeloid malignancies. Blood 2010; 115(22): 4524-32.
90. List A, Dewald G, Bennett J, et al. Lenalidomide in the myelodysplastic syndrome with chromosome 5q deletion. N Engl J Med 2006; 355(14): 1456-65.
91. Nimer SD. Clinical management of myelodysplastic syndromes with interstitial deletion of chromosome 5q. J Clin Oncol 2006; 24(16): 2576-82.
92. Le Beau MM, Espinosa R, 3rd, Neuman WL, et al. Cytogenetic and molecular delineation of the smallest commonly deleted region of chromosome 5 in malignant myeloid diseases. Proc Natl Acad Sci USA 1993; 90(12): 5484-8.
93. Boultwood J, Fidler C, Strickson AJ, et al. Narrowing and genomic annotation of the commonly deleted region of the 5q-syndrome. Blood 2002; 99(12): 4638-41.
94. Ebert BL, Pretz J, Bosco J, et al. Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Nature 2008; 451(7176): 335-9.
95. Barlow JL, Drynan LF, Hewett DR, et al. A p53-dependent mechanism underlies macrocytic anemia in a mouse model of human 5q-syndrome. Nat Med 2010; 16(1): 59-66.
96. Draptchinskaia N, Gustavsson P, Andersson B, et al. The gene encoding ribosomal protein S19 is mutated in Diamond-Blackfan anaemia. Nat Genet 1999; 21(2): 169-75.
97. Boria I, Garelli E, Gazda HT, et al. The ribosomal basis of Diamond-Blackfan Anemia: mutation and database update. Hum Mutat 2010; 31(12): 1269-79.
98. Van den Berghe H, Cassiman JJ, David G, et al. Fryns JP, Michaux JL, Sokal G. Distinct haematological disorder with deletion of long arm of no. 5 chromosome. Nature 1974; 251(5474): 437-8.
99. Tinegate H, Gaunt L, Hamilton PJ. The 5q-syndrome: an underdiagnosed form of macrocytic anaemia. Br J Haematol 1983; 54(1): 103-10.
100. Starczynowski DT, Kuchenbauer F, Argiropoulos B, et al. Identification of miR-145 and miR-146a as mediators of the 5q-syndrome phenotype. Nat Med 2010; 16(1): 49-58.
101. Tiu RV, Gondek LP, O'Keefe CL, et al. Prognostic impact of SNP array karyotyping in myelodysplastic syndromes and related myeloid malignancies. Blood 2011; 117(17): 4552-60.
102. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008; 26(10): 1135-45.
103. Yoshida K, Sanada M, Shiraishi Y, et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 2011; 478(7367):64-9.