Advertisement

DNA Copy Number Analysis on Tissue Microarrays

  • Anne KallioniemiEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 664)

Abstract

Detection of DNA sequence copy number changes is essential in both clinical practice and basic research, especially in cancer research. The combination of fluorescence in situ hybridization (FISH) and tissue microarray (TMA) technology provides high-throughput means for the evaluation of genetic aberrations in a large number of tissue samples. FISH on TMA is technically demanding and several protocols that include a variety of tissue pretreatment steps have been developed to improve the success of this methodology. Despite of the technical difficulties, FISH analysis on TMA has been successfully used not only to uncover genetic alterations in various malignancies but to also rapidly establish the clinical significance of such changes.

Key words

Tissue microarray High-throughput screening Copy number analysis Fluorescence in situ hybridization Molecular cytogenetics Molecular pathology Genetic aberrations 

Notes

Acknowledgments

The author would like to thank Ms. Eeva Laurila and Ms. Kati Rouhento for their assistance in preparing this article.

References

  1. 1.
    Tibiletti, M. G. (2007) Interphase FISH as a new tool in tumor pathology. Cytogenet. Genome Res. 118, 229–236.PubMedCrossRefGoogle Scholar
  2. 2.
    Dave, B. J. and Sanger, W. G. (2007) Role of cytogenetics and molecular cytogenetics in the diagnosis of genetic imbalances. Semin. Pediatr. Neurol. 14, 2–6.PubMedCrossRefGoogle Scholar
  3. 3.
    Ross, J. S., Fletcher, J. A., Linette, G. P., Stec, J., Clark, E., Ayers, M., Symmans, W. F., Pusztai, L., and Bloom, K. J. (2003) The Her-2/neu gene and protein in breast cancer: biomarker and target of therapy. Oncologist 8, 307–325.PubMedCrossRefGoogle Scholar
  4. 4.
    Nunes, R. A. and Harris, L. N. (2002) The HER2 extracellular domain as a prognostic and predictive factor in breast cancer. Clin. Breast Cancer 3, 125–135.PubMedCrossRefGoogle Scholar
  5. 5.
    Kononen, J., Bubendorf, L., Kallioniemi, A., Bärlund, M., Schraml, P., Leighton, S., Torhorst, J., Mihatsch, M. J., Sauter, G., and Kallioniemi, O. P. (1998) Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat. Med. 4, 844–847.PubMedCrossRefGoogle Scholar
  6. 6.
    Bärlund, M., Forozan, F., Kononen, J., Bubendorf, L., Chen, Y., Bittner, M. L., Torhorst, J., Haas, P., Bucher, C., Sauter, G., Kallioniemi, O. P., and Kallioniemi, A. (2000) Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis. J. Natl. Cancer Inst. 92, 1252–1259.PubMedCrossRefGoogle Scholar
  7. 7.
    Al-Kuraya, K., Schraml, P., Torhorst, J., Tapia, C., Zaharieva, B., Novotny, H., Spichtin, H., Maurer, R., Mirlacher, M., Köchli, O., Zuber, M., Dieterich, H., Mross, F., Wilber, K., Simon, R., and Sauter, G. (2004) Prognostic relevance of gene amplifications and coamplifications in breast cancer. Cancer Res. 64, 8534–8540.PubMedCrossRefGoogle Scholar
  8. 8.
    Simon, R. and Sauter, G. (2003) Tissue microarray (TMA) applications: implications for molecular medicine. Expert. Rev. Mol. Med. 5, 1–12.PubMedCrossRefGoogle Scholar
  9. 9.
    Schraml, P., Kononen, J., Bubendorf, L., Moch, H., Bissig, H., Nocito, A., Mihatsch, M. J., Kallioniemi, O. P., and Sauter, G. (1999) Tissue microarrays for gene amplification surveys in many different tumor types. Clin. Cancer Res. 5, 1966–1975.PubMedGoogle Scholar
  10. 10.
    Andersen, C. L., Monni, O., Wagner, U., Kononen, J., Bärlund, M., Bucher, C., Haas, P., Nocito, A., Bissig, H., Sauter, G., and Kallioniemi, A. (2002) High-throughput copy number analysis of 17q23 in 4788 tissue specimens by fluorescence in situ hybridization to tissue microarrays. Am. J. Pathol. 161, 73–79.PubMedCrossRefGoogle Scholar
  11. 11.
    Hughes-Davies, L., Huntsman, D., Ruas, M., Fuks, F., Bye, J., Chin, S. F., Milner, J., Brown, L. A., Hsu, F., Gilks, B., Nielsen, T., Schulzer, M., Chia, S., Ragaz, J., Cahn, A., Linger, L., Ozdag, H., Cattaneo, E., Jordanova, E. S., Schuuring, E., Yu, D. S., Venkitaraman, A., Ponder, B., Doherty, A., Aparicio, S., Bentley, D., Theillet, C., Ponting, C. P., Caldas, C., and Kouzarides, T. (2003) EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer. Cell 115, 523–535.PubMedCrossRefGoogle Scholar
  12. 12.
    Andersen, C. L., Hostetter, G., Sauter, G., and Kallioniemi, A. (2001) Improved procedure for fluorescence in situ hybridization on tissue microarrays. Cytometry. 45, 83–86.PubMedCrossRefGoogle Scholar
  13. 13.
    Chin, S. F., Daigo, Y., Huang, H. E., Iyer, N. G., Callagy, G., Kranjac, T., Gonzalez, M., Sangan, T., Earl, H., and Caldas, C. (2003) A simple and reliable pretreatment protocol facilitates fluorescent in situ hybridisation on tissue microarrays of paraffin wax embedded tumour samples. Mol. Pathol. 56, 275–279.PubMedCrossRefGoogle Scholar
  14. 14.
    Brown, L. A. and Huntsman, D. (2007) Fluorescent in situ hybridization on tissue microarrays: challenges and solutions. J. Mol. Histol. 38, 151–157.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.Institute of Medical TechnologyUniversity of Tampere and Tampere University HospitalTampereFinland

Personalised recommendations