Genomic Structural Variants pp 329-341

Part of the Methods in Molecular Biology book series (MIMB, volume 838)

High-Resolution Copy Number Profiling by Array CGH Using DNA Isolated from Formalin-Fixed, Paraffin-Embedded Tissues



We describe protocols to acquire high-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissues for the use in array comparative genome hybridization (CGH). Formalin fixation combined with paraffin embedding is routine procedure for solid malignancies in the diagnostic practice of the pathologist. As a consequence, large archives of FFPE tissues are available in pathology institutes across the globe. This archival material is for many research questions an invaluable resource, with long-term clinical follow-up and survival data available. FFPE is, thus, highly attractive for large genomics studies, including experiments requiring samples for test/learning and validation. Most larger array CGH studies have, therefore, made use of FFPE material and show that CNAs have tumor- and tissue-specific traits (Chin et al. Cancer Cell 10: 529–541, 2006; Fridlyand et al. BMC Cancer 6: 96, 2006; Weiss et al. Oncogene 22: 1872–1879, 2003; Jong et al. Oncogene 26: 1499–1506, 2007). The protocols described are tailored to array CGH of FFPE solid malignancies: from sectioning FFPE blocks to specific cynosures for pathological revisions of sections, DNA isolation, quality testing, and amplification. The protocols are technical in character and elaborate up to the labeling of isolated DNA while further processes and interpretation and data analysis are beyond the scope.

Key words

Formalin fixed, paraffin embedded Chromosomal DNA Microarray Copy number aberrations Archival tissue Sodium thiocyanate Array comparative genome hybridization 


  1. 1.
    Chin, K., DeVries, S., Fridlyand, J., Spellman, P.T., Roydasgupta, R., Kuo, W.L., et al. (2006) Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10, 529–541.PubMedCrossRefGoogle Scholar
  2. 2.
    Fridlyand, J., Snijders, A.M., Ylstra, B., Li, H., Olshen, A., Segraves, R., et al. (2006) Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 6, 96.PubMedCrossRefGoogle Scholar
  3. 3.
    Weiss, M.M., Kuipers, E.J., Postma, C., Snijders, A.M., Siccama, I., Pinkel, D., et al.(2003) Genomic profiling of gastric cancer predicts lymph node status and survival. Oncogene 22, 1872–1879.PubMedCrossRefGoogle Scholar
  4. 4.
    Jong, K., Marchiori, E., van der Vaart, A., Chin, S.F., Carvalho, B., Tijssen, M., et al. (2007) Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors. Oncogene 26, 1499–1506.PubMedCrossRefGoogle Scholar
  5. 5.
    Costa, J.L., Meijer, G., Ylstra, B., Caldas, C. (2008) Array comparative genomic hybridization copy number profiling: a new tool for translational research in solid malignancies. Semin. Radiat. Oncol. 18, 98–104.PubMedCrossRefGoogle Scholar
  6. 6.
    Gallegos Ruiz, M.I., van Cruijsen, H., Smit, E.F., Grünberg, K., Meijer, G.A., Rodriguez, J.A., et al. (2007) Genetic heterogeneity in patients with multiple neoplastic lung lesions: a report of three cases. J. Thorac. Oncol. 2, 12–21.PubMedCrossRefGoogle Scholar
  7. 7.
    Buffart, T.E., Tijssen, M., Krugers, T., Carvalho, B., Smeets, S.J., Brakenhoff, R.H., et al. (2007) DNA quality assessment for array CGH by isothermal whole genome amplification. Cell Oncol. 29, 351–359.PubMedGoogle Scholar
  8. 8.
    Hopman, A.H., van Hooren, E., van de Kaa, C.A., Vooijs, P.G., Ramaekers, F.C. (1991) Detection of numerical chromosome aberrations using in situ hybridization in paraffin sections of routinely processed bladder cancers. Mod. Pathol. 4, 503–513.PubMedGoogle Scholar
  9. 9.
    Johnson, N.A., Hamoudi, R.A., Ichimura, K., Liu, L., Pearson, D.M., Collins, V.P., et al. (2006) Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells. Lab Invest 86, 968–978.PubMedCrossRefGoogle Scholar
  10. 10.
    van de Wiel, M.A., Brosens, R., Eilers, P.H., Kumps, C., Meijer, G.A., Menten, B., et al. (2009) Smoothing waves in array CGH tumor profiles. Bioinformatics 25, 1099–1104.PubMedCrossRefGoogle Scholar
  11. 11.
    Feuk, L., Carson, A.R., Scherer, S.W. (2006) Structural variation in the human genome. Nat. Rev. Genet. 7, 85–97.PubMedCrossRefGoogle Scholar
  12. 12.
    Buffart, T.E., Israeli, D., Tijssen, M., Vosse, S.J., Mrsié, A., Meijer, G.A., et al. (2008) Across array comparative genomic hybridization: a strategy to reduce reference channel hybridizations. Genes Chromosomes. Cancer 47, 994–1004.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.University of Antwerp (UA)AntwerpenBelgium
  2. 2.VU Medical CenterAmsterdamThe Netherlands

Personalised recommendations