Genome-wide DNA-mapping of CD34+ cells from patients with myelodysplastic syndrome using 500K SNP arrays identifies significant regions of deletion and uniparental disomy

Experimental Hematology

Volumn 37, Issue 2, 2009, Pages

  Nowak, Daniel ^a   Nolte, Florian ^a   Mossner, Maximilian ^a   Nowak, Verena ^a   Baldus, Claudia D ^a   Hopfer, Olaf ^a   Noll, Stefanie ^a   Thiel, Eckhard ^a   Wagner, Florian ^b   Hofmann, Wolf Karsten ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b German Genome Resource Center RZPD   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ARTICLE; BONE MARROW CELL; CD34 SELECTION; CHROMOSOME 13; CHROMOSOME 16; CHROMOSOME 17; CHROMOSOME 2; CHROMOSOME 20; CHROMOSOME 9; CHROMOSOME DELETION; CLINICAL ARTICLE; CONTROLLED STUDY; DOWN REGULATION; FEMALE; GENE DELETION; GENE EXPRESSION; GENE MAPPING; GENOMICS; HETEROZYGOSITY; HUMAN; HUMAN CELL; MALE; MYELODYSPLASTIC SYNDROME; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; TANDEM REPEAT; UNIPARENTAL DISOMY;

EID: 58149194736     PISSN: 0301472X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.exphem.2008.10.012     Document Type: Article

References (41)

1. Corey S.J., Minden M.D., Barber D.L., Kantarjian H., Wang J.C., and Schimmer A.D. Myelodysplastic syndromes: the complexity of stem-cell diseases. Nat Rev Cancer 7 (2007) 118-129
2. Bernasconi P., Boni M., Cavigliano P.M., et al. Clinical relevance of cytogenetics in myelodysplastic syndromes. Ann N Y Acad Sci 1089 (2006) 395-410
3. Hofmann W.K., and Koeffler H.P. Myelodysplastic syndrome. Annu Rev Med 56 (2005) 1-16
4. Tiu R., Gondek L., O'Keefe C., and Maciejewski J.P. Clonality of the stem cell compartment during evolution of myelodysplastic syndromes and other bone marrow failure syndromes. Leukemia 21 (2007) 1648-1657
5. Komura D., Shen F., Ishikawa S., et al. Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res 16 (2006) 1575-1584
6. Robinson W.P. Mechanisms leading to uniparental disomy and their clinical consequences. Bioessays 22 (2000) 452-459
7. Gondek L.P., Tiu R., Haddad A.S., et al. Single nucleotide polymorphism arrays complement metaphase cytogenetics in detection of new chromosomal lesions in MDS. Leukemia 21 (2007) 2058-2061
8. O'Keefe C.L., Tiu R., Gondek L.P., et al. High-resolution genomic arrays facilitate detection of novel cryptic chromosomal lesions in myelodysplastic syndromes. Exp Hematol 35 (2007) 240-251
9. Gondek L.P., Dunbar A.J., Szpurka H., McDevitt M.A., and Maciejewski J.P. SNP array karyotyping allows for the detection of uniparental disomy and cryptic chromosomal abnormalities in MDS/MPD-U and MPD. PLoS One 2 (2007) e1225
10. Gondek L.P., Tiu R., O'Keefe C.L., Sekeres M.A., Theil K.S., and Maciejewski J.P. Chromosomal lesions and uniparental disomy detected by SNP arrays in MDS, MDS/MPD, and MDS-derived AML. Blood 111 (2008) 1534-1542
11. Mohamedali A., Gaken J., Twine N.A., et al. Prevalence and prognostic significance of allelic imbalance by single-nucleotide polymorphism analysis in low-risk myelodysplastic syndromes. Blood 110 (2007) 3365-3373
12. Wang L., Fidler C., Nadig N., et al. Genome-wide analysis of copy number changes and loss of heterozygosity in myelodysplastic syndrome with del(5q) using high-density single nucleotide polymorphism arrays. Haematologica 93 (2008) 994-1000 Epub 2008 May 1027
13. Mullighan C.G., Goorha S., Radtke I., et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446 (2007) 758-764
14. Garraway L.A., Widlund H.R., Rubin M.A., et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436 (2005) 117-122
15. Walker B.A., Leone P.E., Jenner M.W., et al. Integration of global SNP-based mapping and expression arrays reveals key regions, mechanisms, and genes important in the pathogenesis of multiple myeloma. Blood 108 (2006) 1733-1743
16. Takeyama K., Monti S., Manis J.P., et al. Integrative analysis reveals 53BP1 copy loss and decreased expression in a subset of human diffuse large B-cell lymphomas. Oncogene 27 (2007) 318-322
17. Hofmann W.K., de Vos S., Komor M., Hoelzer D., Wachsman W., and Koeffler H.P. Characterization of gene expression of CD34+ cells from normal and myelodysplastic bone marrow. Blood 100 (2002) 3553-3560
18. Komor M., Guller S., Baldus C.D., et al. Transcriptional profiling of human hematopoiesis during in vitro lineage-specific differentiation. Stem Cells 23 (2005) 1154-1169
19. Carvalho B., Bengtsson H., Speed T.P., and Irizarry R.A. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 8 (2007) 485-499
20. Downey T. Analysis of a multifactor microarray study using Partek genomics solution. Methods Enzymol 411 (2006) 256-270
21. Huang J., Wei W., Zhang J., et al. Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 1 (2004) 287-299
22. Dutt A., and Beroukhim R. Single nucleotide polymorphism array analysis of cancer. Curr Opin Oncol 19 (2007) 43-49
23. 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 65 (2005) 6071-6079
24. 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-nucleotide-polymorphism genotyping microarrays. Am J Hum Genet 81 (2007) 114-126
25. Beroukhim R., Lin M., Park Y., et al. Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol 2 (2006) e41
26. Livak K.J., and Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25 (2001) 402-408
27. Weksberg R., Hughes S., Moldovan L., Bassett A.S., Chow E.W., and Squire J.A. A method for accurate detection of genomic microdeletions using real-time quantitative PCR. BMC Genomics 6 (2005) 180
28. Xie D., Hofmann W.K., Mori N., Miller C.W., Hoelzer D., and Koeffler H.P. Allelotype analysis of the myelodysplastic syndrome. Leukemia 14 (2000) 805-810
29. Hofmann W.K., Takeuchi S., Xie D., Miller C.W., Hoelzer D., and Koeffler H.P. Frequent loss of heterozygosity in the region of D1S450 at 1p36.2 in myelodysplastic syndromes. Leuk Res 25 (2001) 855-858
30. Sadlon T.J., Dell'Oso T., Surinya K.H., and May B.K. Regulation of erythroid 5-aminolevulinate synthase expression during erythropoiesis. Int J Biochem Cell Biol 31 (1999) 1153-1167
31. Gu T.L., Mercher T., Tyner J.W., et al. A novel fusion of RBM6 to CSF1R in acute megakaryoblastic leukemia. Blood 110 (2007) 323-333
32. Samani N.J., Erdmann J., Hall A.S., et al. Genomewide association analysis of coronary artery disease. N Engl J Med 357 (2007) 443-453
33. Nilsson L., Astrand-Grundstrom I., Anderson K., et al. Involvement and functional impairment of the CD34(+)CD38(-)Thy-1(+) hematopoietic stem cell pool in myelodysplastic syndromes with trisomy 8. Blood 100 (2002) 259-267
34. Nilsson L., Eden P., Olsson E., et al. The molecular signature of MDS stem cells supports a stem-cell origin of 5q myelodysplastic syndromes. Blood 110 (2007) 3005-3014 Epub 2007 Jul 3006
35. Ogata K., Nakamura K., Yokose N., et al. Clinical significance of phenotypic features of blasts in patients with myelodysplastic syndrome. Blood 100 (2002) 3887-3896 Epub 2002 Jul 3818
36. Ogata K., Kishikawa Y., Satoh C., Tamura H., Dan K., and Hayashi A. Diagnostic application of flow cytometric characteristics of CD34+ cells in low-grade myelodysplastic syndromes. Blood 108 (2006) 1037-1044 Epub 2006 Mar 1030
37. Kanter-Lewensohn L., Hellstrom-Lindberg E., Kock Y., and Elmhorn-Rosenborg A. Ost A Analysis of CD34-positive cells in bone marrow from patients with myelodysplastic syndromes and acute myeloid leukemia and in normal individuals: a comparison between FACS analysis and immunohistochemistry. Eur J Haematol 56 (1996) 124-129
38. Starczynowski D.T., 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 28 (2008) 28
39. Feuk L., Carson A.R., and Scherer S.W. Structural variation in the human genome. Nat Rev Genet 7 (2006) 85-97
40. Gibson J., Morton N.E., and Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet 15 (2006) 789-795 Epub 2006 Jan 2025
41. Baxter E.J., Scott L.M., Campbell P.J., et al. Acquired mutation of the tyrosine kinase JAK2 in human myeloproliferative disorders. Lancet 365 (2005) 1054-1061