Single-nucleotide polymorphism array karyotyping in clinical practice: Where, when, and how?

Seminars in Oncology

Volumn 39, Issue 1, 2012, Pages 13-25

  Sato Otsubo, Aiko ^a   Sanada, Masashi ^a   Ogawa, Seishi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACUTE GRANULOCYTIC LEUKEMIA; ALLELE; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CANCER PATIENT; CHRONIC MYELOID LEUKEMIA; CLINICAL PRACTICE; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; GENE AMPLIFICATION; GENE DOSAGE; GENE MUTATION; GENE TRANSLOCATION; GENETIC ASSOCIATION; GENOME; GENOTYPE; HETEROZYGOSITY; HIDDEN MARKOV MODEL; HUMAN; KARYOTYPING; MICROARRAY ANALYSIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

HUMANS; KARYOTYPING; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYSICIAN'S PRACTICE PATTERNS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84856398561     PISSN: 00937754     EISSN: None     Source Type: Journal    
DOI: 10.1053/j.seminoncol.2011.11.010     Document Type: Article

References (74)

1. P. Nowell, D. Hungerford A minute chromosome in human chronic granulocytic leukemia Science 132 1960 1497
2. Mitelman database of chromosome aberrations and gene fusions in cancer http://cgap.nci.nih.gov/Chromosomes/Mitelman (accessed Dec 17, 2011)
3. S.G. O'Brien, F. Guilhot, R.A. Larson Imatinib compared with interferon and low-dose cytarabine for newly diagnosed chronic-phase chronic myeloid leukemia N Engl J Med 348 2003 994 1004 (Pubitemid 36302244)
4. Z.Y. Wang, Z. Chen Acute promyelocytic leukemia: from highly fatal to highly curable Blood 111 2008 2505 2515
5. D. Grimwade, H. Walker, F. Oliver The importance of diagnostic cytogenetics on outcome in AML: analysis of 1,612 patients entered into the MRC AML 10 trial The Medical Research Council Adult and Children's Leukaemia Working Parties Blood 92 1998 2322 2333 (Pubitemid 28452973)
6. M.L. Slovak, K.J. Kopecky, P.A. Cassileth Karyotypic analysis predicts outcome of preremission and postremission therapy in adult acute myeloid leukemia: a Southwest Oncology Group/Eastern Cooperative Oncology Group Study Blood 96 2000 4075 4083
7. J.C. Byrd, K. Mrozek, R.K. Dodge Pretreatment cytogenetic abnormalities are predictive of induction success, cumulative incidence of relapse, and overall survival in adult patients with de novo acute myeloid leukemia: results from Cancer and Leukemia Group B (CALGB 8461) Blood 100 2002 4325 4336 (Pubitemid 35429670)
8. J.D. Rowley Chromosome studies in the non-Hodgkin's lymphomas: the role of the 14;18 translocation J Clin Oncol 6 1988 919 925
9. M.E. Williams, C.D. Westermann, S.H. Swerdlow Genotypic characterization of centrocytic lymphoma: frequent rearrangement of the chromosome 11 bcl-1 locus Blood 76 1990 1387 1391 (Pubitemid 20342756)
10. M.E. Lieberfarb, M. Lin, M. Lechpammer Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP Cancer Res 63 2003 4781 4785 (Pubitemid 37022605)
11. A. Rauch, F. Ruschendorf, J. Huang Molecular karyotyping using an SNP array for genomewide genotyping J Med Genet 41 2004 916 922 (Pubitemid 40007252)
12. Y. Nannya, M. Sanada, K. Nakazaki A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays Cancer Res 65 2005 6071 6079 (Pubitemid 40994391)
13. H. Matsuzaki, S. Dong, H. Loi Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays Nat Methods 1 2004 109 111
14. S.S. Murray, A. Oliphant, R. Shen A highly informative SNP linkage panel for human genetic studies Nat Methods 1 2004 113 117
15. S. Ogawa, A. Matsubara, M. Onizuka Exploration of the genetic basis of GVHD by genetic association studies Biol Blood Marrow Transplant 15 2009 39 41
16. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
17. T.A. Manolio Genomewide association studies and assessment of the risk of disease N Engl J Med 363 2010 166 176
18. Y. Chen, J. Takita, Y.L. Choi Oncogenic mutations of ALK kinase in neuroblastoma Nature 455 2008 971 974
19. C.S. Walsh, S. Ogawa, H. Karahashi ERCC5 is a novel biomarker of ovarian cancer prognosis J Clin Oncol 26 2008 2952 2958
20. C.G. Mullighan, S. Goorha, I. Radtke Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia Nature 446 2007 758 764 (Pubitemid 46582031)
21. R. Beroukhim, C.H. Mermel, D. Porter The landscape of somatic copy-number alteration across human cancers Nature 463 2010 899 905
22. S. Ogawa, Y. Nannya, G. Yamamoto Genome-wide copy number analysis on GeneChip platform using copy number analyzer for Affymetrix GeneChip 2.0 software Comparative genomics vol. 2 2007 Humana Press Bergman, NH 185 206 (Pubitemid 350190042)
23. D. Pinkel, R. Segraves, D. Sudar High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays Nat Genet 20 1998 207 211 (Pubitemid 28455458)
24. A.S. Ishkanian, C.A. Malloff, S.K. Watson A tiling resolution DNA microarray with complete coverage of the human genome Nat Genet 36 2004 299 303 (Pubitemid 38282757)
25. G. Yamamoto, Y. Nannya, M. Kato 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 (Pubitemid 47001161)
26. E. Przybytkowski, C. Ferrario, M. Basik The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome BMC Med Genomics 4 2011 16
27. N. Kawamata, S. Ogawa, M. Zimmermann Cloning of genes involved in chromosomal translocations by high-resolution single nucleotide polymorphism genomic microarray Proc Natl Acad Sci U S A 105 2008 11921 11926
28. N. Kawamata, S. Ogawa, M. Zimmermann Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray Blood 111 2008 776 784
29. C.G. Mullighan, C.B. Miller, I. Radtke BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros Nature 453 2008 110 114 (Pubitemid 351630327)
30. M. Kato, M. Sanada, I. Kato Frequent inactivation of A20 in B-cell lymphomas Nature 459 2009 712 716
31. A.C. Smith, C. Shuman, D. Chitayat Severe presentation of Beckwith-Wiedemann syndrome associated with high levels of constitutional paternal uniparental disomy for chromosome 11p15 Am J Med Genet A 143A 2007 3010 3015 (Pubitemid 350274815)
32. D.J. Amor, J. Halliday A review of known imprinting syndromes and their association with assisted reproduction technologies Hum Reprod 23 2008 2826 2834
33. R.D. Nicholls, J.L. Knepper Genome organization, function, and imprinting in Prader-Willi and Angelman syndromes Annu Rev Genomics Hum Genet 2 2001 153 175 (Pubitemid 35265004)
34. M. Tuna, S. Knuutila, G.B. Mills Uniparental disomy in cancer Trends Mol Med 15 2009 120 128
35. M. Sanada, T. Suzuki, L.Y. Shih Gain-of-function of mutated C-CBL tumour suppressor in myeloid neoplasms Nature 460 2009 904 908
36. S. Heinrichs, C. Li, A.T. Look SNP array analysis in hematologic malignancies: avoiding false discoveries Blood 115 2010 4157 4161
37. S.A. Hagstrom, T.P. Dryja Mitotic recombination map of 13cen-13q14 derived from an investigation of loss of heterozygosity in retinoblastomas Proc Natl Acad Sci U S A 96 1999 2952 2957 (Pubitemid 29148825)
38. T. Akagi, S. Ogawa, M. Dugas Frequent genomic abnormalities in acute myeloid leukemia/myelodysplastic syndrome with normal karyotype Haematologica 94 2009 213 223
39. T. Akagi, L.Y. Shih, M. Kato Hidden abnormalities and novel classification of t(15;17) acute promyelocytic leukemia (APL) based on genomic alterations Blood 113 2009 1741 1748
40. M. Raghavan, D.M. Lillington, S. Skoulakis Genome-wide single nucleotide polymorphism analysis reveals frequent partial uniparental disomy due to somatic recombination in acute myeloid leukemias Cancer Res 65 2005 375 378
41. R.V. Tiu, L.P. Gondek, C.L. O'Keefe New lesions detected by single nucleotide polymorphism array-based chromosomal analysis have important clinical impact in acute myeloid leukemia J Clin Oncol 27 2009 5219 5226
42. B. Parkin, H. Erba, P. Ouillette Acquired genomic copy number aberrations and survival in adult acute myelogenous leukemia Blood 116 2010 4958 4967
43. L.P. Gondek, R. Tiu, C.L. O'Keefe, M.A. Sekeres, K.S. Theil, J.P. Maciejewski Chromosomal lesions and uniparental disomy detected by SNP arrays in MDS, MDS/MPN, and MDS-derived AML Blood 111 2008 1534 1542 (Pubitemid 351213443)
44. S.M. Langemeijer, R.P. Kuiper, M. Berends Acquired mutations in TET2 are common in myelodysplastic syndromes Nat Genet 41 2009 838 842
45. J. Fitzgibbon, S. Iqbal, A. Davies Genome-wide detection of recurring sites of uniparental disomy in follicular and transformed follicular lymphoma Leukemia 21 2007 1514 1520 (Pubitemid 46965294)
46. R. Kralovics, F. Passamonti, A.S. Buser A gain-of-function mutation of JAK2 in myeloproliferative disorders N Engl J Med 352 2005 1779 1790 (Pubitemid 40570926)
47. C. James, V. Ugo, J.P. Le Couedic A unique clonal JAK2 mutation leading to constitutive signalling causes polycythaemia vera Nature 434 2005 1144 1148 (Pubitemid 40663494)
48. D.P. Steensma, G.W. Dewald, T.L. Lasho The JAK2 V617F activating tyrosine kinase mutation is an infrequent event in both "atypical" myeloproliferative disorders and myelodysplastic syndromes Blood 106 2005 1207 1209 (Pubitemid 41129580)
49. N. Kawamata, S. Ogawa, G. Yamamoto Genetic profiling of myeloproliferative disorders by single-nucleotide polymorphism oligonucleotide microarray Exp Hematol 36 2008 1471 1479
50. A.J. Dunbar, L.P. Gondek, C.L. O'Keefe 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 68 2008 10349 10357
51. J. Fitzgibbon, L.L. Smith, M. Raghavan Association between acquired uniparental disomy and homozygous gene mutation in acute myeloid leukemias Cancer Res 65 2005 9152 9154 (Pubitemid 41507976)
52. J. Fridlyand, A. Snijders, D. Pinkel, D. Albertson, A.N. Jain Hidden Markov models approach to the analysis of array CGH data J Multivariate Analysis 90 2004 132 153 (Pubitemid 41137010)
53. E.S. Venkatraman, A.B. Olshen A faster circular binary segmentation algorithm for the analysis of array CGH data Bioinformatics 23 2007 657 663 (Pubitemid 46554715)
54. J. Staaf, D. Lindgren, J. Vallon-Christersson Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays Genome Biol 9 2008 R136
55. S. Jacobs, E.R. Thompson, Y. Nannya Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays Cancer Res 67 2007 2544 2551 (Pubitemid 46548939)
56. S. Ishikawa, D. Komura, S. Tsuji Allelic dosage analysis with genotyping microarrays Biochem Biophys Res Commun 333 2005 1309 1314 (Pubitemid 40910145)
57. A.J. Iafrate, L. Feuk, M.N. Rivera Detection of large-scale variation in the human genome Nat Genet 36 2004 949 951 (Pubitemid 39167488)
58. J. Sebat, B. Lakshmi, J. Troge Large-scale copy number polymorphism in the human genome Science 305 2004 525 528 (Pubitemid 38971344)
59. R. Redon, S. Ishikawa, K.R. Fitch Global variation in copy number in the human genome Nature 444 2006 444 454 (Pubitemid 44809057)
60. T. Vallespi, M. Imbert, C. Mecucci, C. Preudhomme, P. Fenaux Diagnosis, classification, and cytogenetics of myelodysplastic syndromes Haematologica 83 1998 258 275 (Pubitemid 28209132)
61. D. Haase, U. Germing, J. Schanz New insights into the prognostic impact of the karyotype in MDS and correlation with subtypes: evidence from a core dataset of 2124 patients Blood 110 2007 4385 4395 (Pubitemid 351377805)
62. P. Greenberg, C. Cox, M.M. LeBeau International scoring system for evaluating prognosis in myelodysplastic syndromes Blood 89 1997 2079 2088 (Pubitemid 27132124)
63. L. Malcovati, M.G. Porta, C. Pascutto Prognostic factors and life expectancy in myelodysplastic syndromes classified according to WHO criteria: a basis for clinical decision making J Clin Oncol 23 2005 7594 7603 (Pubitemid 46291823)
64. H. Szpurka, L.P. Gondek, S.R. Mohan, E.D. Hsi, K.S. Theil, J.P. Maciejewski UPD1p indicates the presence of MPL W515L mutation in RARS-T, a mechanism analogous to UPD9p and JAK2 V617F mutation Leukemia 23 2009 610 614
65. T. Ernst, A.J. Chase, J. Score Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders Nat Genet 42 2010 722 726
66. D. O'Shea, C. O'Riain, M. Gupta Regions of acquired uniparental disomy at diagnosis of follicular lymphoma are associated with both overall survival and risk of transformation Blood 113 2009 2298 2301
67. D. Pfeifer, M. Pantic, I. Skatulla Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays Blood 109 2007 1202 1210 (Pubitemid 46220669)
68. S. Lehmann, S. Ogawa, S.D. Raynaud Molecular allelokaryotyping of early-stage, untreated chronic lymphocytic leukemia Cancer 112 2008 1296 1305 (Pubitemid 351429745)
69. P. Ouillette, H. Erba, L. Kujawski, M. Kaminski, K. Shedden, S.N. Malek Integrated genomic profiling of chronic lymphocytic leukemia identifies subtypes of deletion 13q14 Cancer Res 68 2008 1012 1021 (Pubitemid 351272218)
70. B.A. Walker, P.E. Leone, M.W. Jenner 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 (Pubitemid 44316144)
71. L. Agnelli, L. Mosca, S. Fabris A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide gene dosage effect Genes Chromosomes Cancer 48 2009 603 614
72. A.D. Pardanani, R.L. Levine, T. Lasho MPL515 mutations in myeloproliferative and other myeloid disorders: a study of 1182 patients Blood 108 2006 3472 3476
73. M. Jasek, L.P. Gondek, N. Bejanyan TP53 mutations in myeloid malignancies are either homozygous or hemizygous due to copy number-neutral loss of heterozygosity or deletion of 17p Leukemia 24 2010 216 219
74. C. Flotho, D. Steinemann, C.G. Mullighan Genome-wide single-nucleotide polymorphism analysis in juvenile myelomonocytic leukemia identifies uniparental disomy surrounding the NF1 locus in cases associated with neurofibromatosis but not in cases with mutant RAS or PTPN11 Oncogene 26 2007 5816 5821 (Pubitemid 47312813)