Seminars in Radiation Oncology
Volume 18, Issue 2 , Pages 98-104 , April 2008

Array Comparative Genomic Hybridization Copy Number Profiling: A New Tool for Translational Research in Solid Malignancies

  • José Luis Costa, PhD

      Affiliations

    • Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal.
    • Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
  • ,
  • Gerrit Meijer, MD, PhD

      Affiliations

    • Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
  • ,
  • Bauke Ylstra, PhD

      Affiliations

    • Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
  • ,
  • Carlos Caldas, MD

      Affiliations

    • Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Cambridge, United Kingdom.
    • Corresponding Author InformationAddress reprint requests to Carlos Caldas, Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

References 

  1. Albertson DG, Collins C, McCormick F. Chromosome aberrations in solid tumors. Nat Genet. 2003;34:369–376
  2. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell. 2000;100:57–70
  3. Albertson DG, Ylstra B, Segraves R. Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet. 2000;25:144–146
  4. Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet. 2005;37:S11–S17
  5. Pollack JR, Sorlie T, Perou CM. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A. 2002;99:12963–12968
  6. Alitalo K, Schwab M, Lin CC. Homogeneously staining chromosomal regions contain amplified copies of an abundantly expressed cellular oncogene (c-myc) in malignant neuroendocrine cells from a human colon carcinoma. Proc Natl Acad Sci U S A. 1983;80:1707–1711
  7. Slamon DJ, Godolphin W, Jones LA. Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer. Science. 1989;244:707–712
  8. Hermsen MA, Meijer GA, Baak JP. Comparative genomic hybridization: A new tool in cancer pathology. Hum Pathol. 1996;27:342–349
  9. Oostlander AE, Meijer GA, Ylstra B. Microarray-based comparative genomic hybridization and its applications in human genetics. Clin Genet. 2004;66:488–495
  10. Kallioniemi A, Kallioniemi OP, Sudar D. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992;258:818–821
  11. Forozan F, Karhu R, Kononen J. Genome screening by comparative genomic hybridization. Trends Genet. 1997;13:405–409
  12. Weiss MM, Hermsen MA, Meijer GA. Comparative genomic hybridisation. Mol Pathol. 1999;52:243–251
  13. van den Ijssel P, Tijssen M, Chin SF. Human and mouse oligonucleotide-based array CGH. Nucleic Acids Res. 2005;33:e192
  14. Coe BP, Ylstra B, Carvalho B. Resolving the resolution of array CGH. Genomics. 2007;89:647–653
  15. van de Wiel MA, Costa JL, Smid K. Expression microarray analysis and oligo array comparative genomic hybridization of acquired gemcitabine resistance in mouse colon reveals selection for chromosomal aberrations. Cancer Res. 2005;65:10208–10213
  16. Chin K, DeVries S, Fridlyand J. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006;10:529–541
  17. Fridlyand J, Snijders AM, Ylstra B. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer. 2006;6:96
  18. Weiss MM, Kuipers EJ, Postma C. Genomic profiling of gastric cancer predicts lymph node status and survival. Oncogene. 2003;22:1872–1879
  19. Mitelman F, Johansson B, Mertens F. Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet. 2004;36:331–334
  20. Jong K, Marchiori E, van der Vaart A. Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors. Oncogene. 2007;26:1499–1506
  21. Jonsson G, Naylor TL, Vallon-Christersson J. Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization. Cancer Res. 2005;65:7612–7621
  22. van Beers EH, van Welsem T, Wessels LFA. Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations. Cancer Res. 2005;65:822–827
  23. Wilting S, Snijders P, Meijer G. Increased gene copy numbers at chromosome 20q are frequent in both squamous cell carcinomas and adenocarcinomas of the cervix. J Pathol. 2006;209:220–230
  24. Smeets SJ, Braakhuis BJM, Abbas S. Genome-wide DNA copy number alterations in head and neck squamous cell carcinomas with or without oncogene-expressing human papillomavirus. Oncogene. 2006;25:2558–2564
  25. Bergamaschi A, Kim YH, Wang P. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer. 2006;45:1033–1040
  26. Chin SF, Wang Y, Thorne NP. Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers. Oncogene. 2007;26:1959–1970
  27. Callagy G, Pharoah P, Chin SF. Identification and validation of prognostic markers in breast cancer with the complementary use of array-CGH and tissue microarrays. J Pathol. 2005;205:388–396
  28. Garcia MJ, Pole JCM, Chin SF. A 1Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene. 2005;24:5235–5245
  29. Ruiz MIG, van Cruijsen H, Smit EF. Genetic heterogeneity in patients with multiple neoplastic lung lesions: A report of three cases. J Thorac Oncol. 2007;2:12–21
  30. Pollack JR, Perou CM, Alizadeh AA. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet. 1999;23:41–46
  31. Ylstra B, van den Ijssel P, Carvalho B. BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 2006;34:445–450
  32. Kitsiou-Tzeli S, Sismani C, Ioannides M. Array-CGH analysis and clinical description of 2q37.3 de novo subtelomeric deletion. Eur J Med Genet. 2007;50:73–78
  33. Algar EM, St Heaps L, Darmanian A. Paternally inherited submicroscopic duplication at 11p15.5 implicates insulin-like growth factor II in overgrowth and Wilms’ tumorigenesis. Cancer Res. 2007;67:2360–2365
  34. Snijders AM, Nowak N, Segraves R. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 2001;29:263–264
  35. Ishkanian AS, Malloff CA, Watson SK. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet. 2004;36:299–303
  36. Lips EH, Dierssen JW, van Eijk R. Reliable high-throughput genotyping and loss-of-heterozygosity detection in formalin-fixed, paraffin-embedded tumors using single nucleotide polymorphism arrays (Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting). Cancer Res. 2005;65:10188–10191
  37. Andersen CL, Wiuf C, Kruhoffer M. Frequent occurrence of uniparental disomy in colorectal cancer. Carcinogenesis. 2007;28:38–48
  38. Barrett MT, Scheffer A, Ben-Dor A. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A. 2004;101:17765–17770
  39. Dupuy A, Simon RM. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst. 2007;99:147–157
  40. Willenbrock H, Fridlyand J. A comparison study: Applying segmentation to array CGH data for downstream analyses. Bioinformatics. 2005;21:4084–4091
  41. Venkatraman ES, Olshen AB. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics. 2007;23:657–663
  42. Chen W, Houldsworth J, Olshen AB. Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas. Blood. 2006;107:2477–2485
  43. Engler DA, Mohapatra G, Louis DN. A pseudolikelihood approach for simultaneous analysis of array comparative genomic hybridizations. Biostatistics. 2006;7:399–421
  44. van de Wiel MA, Kim KI, Vosse SJ. CGHcall: Calling aberrations for array CGH tumor profiles. Bioinformatics. 2007;23:892–894
  45. Wang P, Kim Y, Pollack J. A method for calling gains and losses in array CGH data. Biostatistics. 2005;6:45–58
  46. van de Wiel MA, van Wieringen WN. CGHregions: Dimension reduction for array CGH data with minimal information loss. Cancer Inform. 2007;2:55–63
  47. Neve RM, Chin K, Fridlyand J. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 2006;10:515–527
  48. Jong K, Marchiori E, Meijer G. Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics. 2004;20:3636–3637
  49. Ichimura K, Mungall AJ, Fiegler H. Small regions of overlapping deletions on 6q26 in human astrocytic tumours identified using chromosome 6 tile path array-CGH. Oncogene. 2006;25:1261–1271
  50. Veltman JA, Fridlyand J, Pejavar S. Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res. 2003;63:2872–2880
  51. Blaveri E, Brewer JL, Roydasgupta R. Bladder cancer stage and outcome by array-based comparative genomic hybridization. Clin Cancer Res. 2005;11:7012–7022
  52. Mastracci TL, Shadeo A, Colby SM. Genomic alterations in lobular neoplasia: a microarray comparative genomic hybridization signature for early neoplastic proliferationin the breast. Genes Chromosomes Cancer. 2006;45:1007–1017
  53. Han W, Han MR, Kang JJ. Genomic alterations identified by array comparative genomic hybridization as prognostic markers in tamoxifen-treated estrogen receptor-positive breast cancer. BMC Cancer. 2006;6:92
  54. Yao J, Weremowicz S, Feng B. Combined cDNA array comparative genomic hybridization and serial analysis of gene expression analysis of breast tumor progression. Cancer Res. 2006;66:4065–4078
  55. Nessling M, Richter K, Schwaenen C. Candidate genes in breast cancer revealed by microarray-based comparative genomic hybridization of archived tissue. Cancer Res. 2005;65:439–447
  56. Naylor TL, Greshock J, Wang Y. High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization. Breast Cancer Res. 2005;7:R1186–R1198
  57. Chin SF, Teschendorff AE, Marioni JC. High-resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol. 2007;8:R215
  58. Morrison C, Radmacher M, Mohammed N. MYC amplification and polysomy 8 in chondrosarcoma: array comparative genomic hybridization, fluorescent in situ hybridization, and association with outcome. J Clin Oncol. 2005;23:9369–9376
  59. Swede H, Bartos JD, Chen N. Genomic profiles of colorectal cancers differ based on patient smoking status. Cancer Genet Cytogenet. 2006;168:98–104
  60. Kim MY, Yim SH, Kwon MS. Recurrent genomic alterations with impact on survival in colorectal cancer identified by genome-wide array comparative genomic hybridization. Gastroenterology. 2006;131:1913–1924
  61. Nakao K, Mehta KR, Fridlyand J. High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis. 2004;25:1345–1357
  62. Ishizuka T, Tanabe C, Sakamoto H. Gene amplification profiling of esophageal squamous cell carcinomas by DNA array CGH. Biochem Biophys Res Commun. 2002;296:152–155
  63. Weiss MM, Kuipers EJ, Postma C. Genomic alterations in primary gastric adenocarcinomas correlate with clinicopathological characteristics and survival. Cell Oncol. 2004;26:307–317
  64. Buffart TE, Carvalho B, Hopmans E. Gastric cancers in young and elderly patients show different genomic profiles. J Pathol. 2007;211:45–51
  65. Korshunov A, Sycheva R, Golanov A. Genetically distinct and clinically relevant subtypes of glioblastoma defined by array-based comparative genomic hybridization (array-CGH). Acta Neuropathol (Berl). 2006;111:465–474
  66. Jonkers YM, Claessen SM, Feuth T. Novel candidate tumour suppressor gene loci on chromosomes 11q23-24 and 22q13 involved in human insulinoma tumourigenesis. J Pathol. 2006;210:450–458
  67. Wilhelm M, Veltman JA, Olshen AB. Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res. 2002;62:957–960
  68. Steinemann D, Skawran B, Becker T. Assessment of differentiation and progression of hepatic tumors using array-based comparative genomic hybridization. Clin Gastroenterol Hepatol. 2006;4:1283–1291
  69. Patil MA, Gutgemann I, Zhang J. Array-based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for 8q gain in hepatocellular carcinoma. Carcinogenesis. 2005;26:2050–2057
  70. McCabe MG, Ichimura K, Liu L. High-resolution array-based comparative genomic hybridization of medulloblastomas and supratentorial primitive neuroectodermal tumors. J Neuropathol Exp Neurol. 2006;65:549–561
  71. Man TK, Lu XY, Jaeweon K. Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma. BMC Cancer. 2004;4:45
  72. Mayr D, Kanitz V, Anderegg B. Analysis of gene amplification and prognostic markers in ovarian cancer using comparative genomic hybridization for microarrays and immunohistochemical analysis for tissue microarrays. Am J Clin Pathol. 2006;126:101–109
  73. Natrajan R, Little SE, Sodha N. Analysis by array CGH of genomic changes associated with the progression or relapse of Wilms’ tumour. J Pathol. 2007;211:52–59
  74. Natrajan R, Williams RD, Hing SN. Array CGH profiling of favourable histology Wilms tumours reveals novel gains and losses associated with relapse. J Pathol. 2006;210:49–58

 Supported by the EU-sixth framework project DISMAL (contract no. LSHC-CT-2005 to 018911). JL Costa was financially supported by a grant from “Fundação para a Ciência e Tecnologia” (SFRH/ BPD/ 20,370/ 2004).

PII: S1053-4296(07)00096-3

doi: 10.1016/j.semradonc.2007.10.005

Seminars in Radiation Oncology
Volume 18, Issue 2 , Pages 98-104 , April 2008