Cancer Letters
Volume 228, Issue 1 , Pages 71-81 , 18 October 2005

High-resolution cDNA microarray-based comparative genomic hybridization analysis in neuroblastoma

  • Qing-Rong Chen

      Affiliations

    • Qing-Rong Chen and Sven Bilke: Equal contributor.
    • ,
  • Sven Bilke

      Affiliations

    • Qing-Rong Chen and Sven Bilke: Equal contributor.
    • ,
  • Javed Khan

      Affiliations

    • Corresponding Author InformationCorresponding author. Tel.: +1 301 435 2937; fax: +1 301 480 0314/402 3134.

Received 24 November 2004 ,Accepted 14 December 2004.

References 

  1. Brodeur GM. Neuroblastoma: biological insights into a clinical enigma. Nat. Rev. Cancer. 2003;3:203–216
  2. Brodeur GM, Azar C, Brother M, Hiemstra J, Kaufman B, Marshall H, et al. Neuroblastoma. Effect of genetic factors on prognosis and treatment. Cancer. 1992;70:1685–1694
  3. Brinkschmidt C, Christiansen H, Terpe HJ, Simon R, Boecker W, Lampert F, et al. Comparative genomic hybridization (CGH) analysis of neuroblastomas—an important methodological approach in paediatric tumour pathology. J. Pathol. 1997;181:394–400
  4. Plantaz D, Vandesompele J, Van Roy N, Lastowska M, Bown N, Combaret V, et al. Comparative genomic hybridization (CGH) analysis of stage 4 neuroblastoma reveals high frequency of 11q deletion in tumors lacking MYCN amplification. Int. J. Cancer. 2001;91:680–686
  5. Cohen N, Betts DR, Trakhtenbrot L, Niggli FK, Amariglio N, Brok-Simoni F, et al. Detection of unidentified chromosome abnormalities in human neuroblastoma by spectral karyotyping (SKY). Genes Chromosomes Cancer. 2001;31:201–208
  6. Schleiermacher G, Janoueix-Lerosey I, Combaret V, Derre J, Couturier J, Aurias A, et al. Combined 24-color karyotyping and comparative genomic hybridization analysis indicates predominant rearrangements of early replicating chromosome regions in neuroblastoma. Cancer Genet. Cytogenet. 2003;141:32–42
  7. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992;258:818–821
  8. Lastowska M, Nacheva E, McGuckin A, Curtis A, Grace C, Pearson A, et al. Comparative genomic hybridization study of primary neuroblastoma tumors. United Kingdom Children's Cancer Study Group. Genes Chromosomes Cancer. 1997;18:162–169
  9. Vandesompele J, Van Roy N, Van Gele M, Laureys G, Ambros P, Heimann P, et al. Genetic heterogeneity of neuroblastoma studied by comparative genomic hybridisation. Genes Chromosomes Cancer. 1998;23:141–152
  10. Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer. 1997;20:399–407
  11. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 1998;20:207–211
  12. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet. 2001;29:263–264
  13. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, et al. Genomewide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 1999;23:41–46
  14. Chen QR, Bilke S, Wei JS, Whiteford CC, Cenacchi N, Krasnoselsky AL, et al. cDNA array-CGH profiling identifies genomic alterations specific to stage and MYCN-amplification in neuroblastoma. BioMed Cent Genomics. 2004;5:70
  15. Bilke S, Chen QR, Whiteford CC, Khan J. Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays. Bioinformatics. 2005;21:1138–1145
  16. Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet. 2004;36:299–303
  17. Albertson DG. Profiling breast cancer by array CGH. Breast Cancer Res. Treat. 2003;78:289–298
  18. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc. Natl Acad. Sci. USA. 2002;99:12963–12968
  19. Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E, et al. Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res. 2002;62:6240–6245
  20. Brennan C, Zhang Y, Leo C, Feng B, Cauwels C, Aguirre AJ, et al. High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res. 2004;64:4744–4748
  21. Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B. High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J. Clin. Pathol. 2004;57:644–646
  22. Bignell GR, Huang J, Greshock J, Watt A, Butler A, West S, et al. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res. 2004;14:287–295
  23. Beheshti B, Braude I, Marrano P, Thorner P, Zielenska M, Squire JA. Chromosomal localization of DNA amplifications in neuroblastoma tumors using cDNA microarray comparative genomic hybridisation. Neoplasia. 2003;5:53–62
  24. De Preter K, Pattyn F, Berx G, Strumane K, Menten B, Van Roy F, et al. Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons. BioMed Cent Genomics. 2004;5:11
  25. Tonin PN, Yeger H, Stallings RL, Srinivasan PR, Lewis WH. Amplification of N-myc and ornithine decarboxylase genes in human neuroblastoma and hydroxyurea-resistant hamster cell lines. Oncogene. 1989;4:1117
  26. De Preter K, Speleman F, Combaret V, Lunec J, Laureys G, Eussen BH, et al. Quantification of MYCN, DDX1, and NAG gene copy number in neuroblastoma using a real-time quantitative PCR assay. Mod. Pathol. 2002;15:159–166
  27. Kuroda H, White PS, Sulman EP, Manohar CF, Reiter JL, Cohn SL, et al. Physical mapping of the DDX1 gene to 340kb 5′ of MYCN. Oncogene. 1996;13:1561–1565
  28. Jones TA, Flomen RH, Senger G, Nizetic D, Sheer D. The homeobox gene MEIS1 is amplified in IMR-32 and highly expressed in other neuroblastoma cell lines. Eur. J. Cancer. 2000;36:2368–2374
  29. Armstrong BC, Krystal GW. Isolation and characterization of complementary DNA for N-cym, a gene encoded by the DNA strand opposite to N-myc. Cell Growth Differ. 1992;3:385–390
  30. Wimmer K, Zhu XX, Lamb BJ, Kuick R, Ambros PF, Kovar H, et al. Coamplification of a novel gene, NAG, with the N-myc gene in neuroblastoma. Oncogene. 1999;18:233–238
  31. Miyake I, Hakomori Y, Shinohara A, Gamou T, Saito M, Iwamatsu A, et al. Activation of anaplastic lymphoma kinase is responsible for hyperphosphorylation of ShcC in neuroblastoma cell lines. Oncogene. 2002;21:5823
  32. Corvi R, Savelyeva L, Breit S, Wenzel A, Handgretinger R, Barak J, et al. Non-syntenic amplification of MDM2 and MYCN in human neuroblastoma. Oncogene. 1995;10:1081–1086
  33. Hupe P, Stransky N, Thiery JP, Radvanyi F, Barillot E. Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics. 2004;20:3413–3422
  34. Jong K, Marchiori E, Meijer G, Van Der Vaart A, Ylstra B. Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics. 2004;20:3636–3637
  35. Cheng NC, Van Roy N, Chan A, Beitsma M, Westerveld A, Speleman F, et al. Deletion mapping in neuroblastoma cell lines suggests two distinct tumor suppressor genes in the 1p35-36 region, only one of which is associated with N-myc amplification. Oncogene. 1995;10:291–297
  36. White PS, Maris JM, Beltinger C, Sulman E, Marshall HN, Fujimori M, et al. A region of consistent deletion in neuroblastoma maps within human chromosome 1p36.2–36.3. Proc. Natl Acad. Sci. USA. 1995;92:5520–5524
  37. Morowitz M, Shusterman S, Mosse Y, Hii G, Winter CL, Khazi D, et al. Detection of single-copy chromosome 17q gain in human neuroblastomas using real-time quantitative polymerase chain reaction. Mod. Pathol. 2003;16:1248–1256
  38. Tonini GP, Romani M. Genetic and epigenetic alterations in neuroblastoma. Cancer Lett. 2003;197:69–73
  39. Vandesompele J, Speleman F, Van Roy N, Laureys G, Brinskchmidt C, Christiansen H, et al. Multicentre analysis of patterns of DNA gains and losses in 204 neuroblastoma tumors: how many genetic subgroups are there?. Med. Pediatr. Oncol. 2001;36:5–10
  40. von Heydebreck A, Gunawan B, Fuzesi L. Maximum likelihood estimation of oncogenetic tree models. Biostatistics. 2004;5:545–556
  41. Radmacher MD, Simon R, Desper R, Taetle R, Schaffer AA, Nelson MA. Graph models of oncogenesis with an application to melanoma. J. Theor. Biol. 2001;212:535–548
  42. Smith TF. Occam's razor. Nature. 1980;285:620
  43. Fearon ER, Vogelstein B. A genetic model for colorectal tumorigenesis. Cell. 1990;61:759–767
  44. Westermann F, Schwab M. Genetic parameters of neuroblastomas. Cancer Lett. 2002;184:127–147
  45. Beckwith J, Perrin E. In situ neuroblastomas: a contribution to the natural history of neural crest tumors. Am. J. Pathol. 1963;43:1089–1104
  46. Fong CT, Dracopoli NC, White PS, Merrill PT, Griffith RC, Housman DE, et al. Loss of heterozygosity for the short arm of chromosome 1 in human neuroblastomas: correlation with N-myc amplification. Proc. Natl Acad. Sci. USA. 1989;86:3753–3757
  47. Hackett CS, Hodgson JG, Law ME, Fridlyand J, Osoegawa K, De Jong PJ, et al. Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors. Cancer Res. 2003;63:5266–5273
  48. Brodeur GM, Maris JM, Yamashiro DJ, Hogarty MD, White PS. Biology and genetics of human neuroblastomas. J. Pediatr. Hematol. Oncol. 1997;19:93–101
  49. Maris J, Matthay KK. Molecular biology of neuroblastoma. J. Clin. Oncol. 1999;17:2264–2279
  50. Ambros IM, Brodeur GM. Concept of tumorigenesis and regression. In:  Brodeur GM,  Sawada T,  Tsuchida Y,  Voute PA editor. Neuroblastoma. Amsterdam: Elsevier Science B.V.; 2000;p. 21–32

PII: S0304-3835(05)00322-8

doi: 10.1016/j.canlet.2004.12.056

Cancer Letters
Volume 228, Issue 1 , Pages 71-81 , 18 October 2005

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