Sequence-Based High Resolution Chromosomal Comparative Genomic Hybridization (CGH)

  • Agata Kowalska
  • Eva Bozsaky
  • Peter F. AmbrosEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 659)


We aimed to devise an appropriate method to directly link the fluorescence profile of chromosomal copy number alterations detected by chromosomal comparative genomic hybridization (cCGH) or any other hybridization or staining information with the genome sequence data. Our goal was to establish an internal anchoring system that could facilitate profile alignment and thus increase the resolution of cCGH. We were able to achieve the alignment of chromosomes with gene mapping data by superimposition of (a) the fluorescence intensity pattern of a sequence-specific fluorochrome (GGCC binding specificity), (b) the cCGH fluorescence intensity profile of individual chromosomes, and (c) the GGCC motif density profile extracted from a genome sequence database. The adjustment of these three pieces of information allowed us to precisely localize, in cytobands and mega base pairs (Mb), regions of genomic alterations such as gene amplifications, gains, or losses. The combined visualization of sequence information and cCGH data together with application of the Warp tool, presented here, considerably improves the cCGH accuracy by increasing its resolution from 10 to 20 Mb to less than 2 Mb.

Key words

Chromosome CGH Chromomycin A3 Sequence banding Warp tool 



We thank Bettina Brunner for excellent technical assistance, Cornelia Stock for valuable suggestions and overall enormous help, and Marion Zavadil for proofreading. We also gratefully acknowledge Thomas Lörch (MetaSystems, Germany) as well as Zlatko Trajanoski, Dietmar Rieder, Gabriela Bindea, and Thomas Ramsauer (Institute for Genomics and Bioinformatics, Graz University of Technology) for the very helpful collaboration. This work was supported by St. Anna Kinderkrebsforschung.


  1. 1.
    Kallioniemi, A., Kallioniemi, O. P., Piper, J., Tanner, M., Stokke, T., Chen, L., Smith, H. S., Pinkel, D., Gray, J. W., and Waldman, F. M. (1994) Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization, Proc Natl Acad Sci U S A 91, 2156–2160.PubMedCrossRefGoogle Scholar
  2. 2.
    Lichter, P., Bentz, M., and Joos, S. (1995) Detection of chromosomal aberrations by means of molecular cytogenetics: painting of chromosomes and chromosomal subregions and comparative genomic hybridization, Methods Enzymol 254, 334–359.PubMedCrossRefGoogle Scholar
  3. 3.
    Lichter, P., Joos, S., Bentz, M., and Lampel, S. (2000) Comparative genomic hybridization: uses and limitations, Semin Hematol 37, 348–357.PubMedCrossRefGoogle Scholar
  4. 4.
    Stock, C., Kager, L., Fink, F. M., Gadner, H., and Ambros, P. F. (2000) Chromosomal regions involved in the pathogenesis of osteosarcomas, Genes Chromosomes Cancer 28, 329–336.PubMedCrossRefGoogle Scholar
  5. 5.
    Wang, N. (2002) Methodologies in cancer cytogenetics and molecular cytogenetics, Am J Med Genet 115, 118–124.PubMedCrossRefGoogle Scholar
  6. 6.
    Garnis, C., Buys, T. P., and Lam, W. L. (2004) Genetic alteration and gene expression modulation during cancer progression, Mol Cancer 3, 9.PubMedCrossRefGoogle Scholar
  7. 7.
    Kallioniemi, A., Kallioniemi, O. P., Sudar, D., Rutovitz, D., Gray, J. W., Waldman, F., and Pinkel, D. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors, Science 258, 818–821.PubMedCrossRefGoogle Scholar
  8. 8.
    Kallioniemi, O. P., Kallioniemi, A., Piper, J., Isola, J., Waldman, F. M., Gray, J. W., and Pinkel, D. (1994) Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors, Genes Chromosomes Cancer 10, 231–243.PubMedCrossRefGoogle Scholar
  9. 9.
    Bentz, M., Plesch, A., Stilgenbauer, S., Dohner, H., and Lichter, P. (1998) Minimal sizes of deletions detected by comparative genomic hybridization, Genes Chromosomes Cancer 21, 172–175.PubMedCrossRefGoogle Scholar
  10. 10.
    Pinkel, D., Segraves, R., Sudar, D., Clark, S., Poole, I., Kowbel, D., Collins, C., Kuo, W. L., Chen, C., Zhai, Y., Dairkee, S. H., Ljung, B. M., Gray, J. W., and Albertson, D. G. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays, Nat Genet 20, 207–211.PubMedCrossRefGoogle Scholar
  11. 11.
    Schweizer, D. (1976) Reverse fluorescent chromosome banding with chromomycin and DAPI, Chromosoma 58, 307–324.PubMedCrossRefGoogle Scholar
  12. 12.
    Schweizer, D., and Ambros, P. F. (1994) Chromosome banding. Stain combinations for specific regions, Methods Mol Biol 29, 97–112.PubMedGoogle Scholar
  13. 13.
    Hou, M. H., Robinson, H., Gao, Y. G., and Wang, A. H. (2004) Crystal structure of the [Mg2+-(chromomycin A3)2]-d(TTGGCCAA)2 complex reveals GGCC binding specificity of the drug dimer chelated by a metal ion, Nucleic Acids Res 32, 2214–2222.PubMedCrossRefGoogle Scholar
  14. 14.
    Ambros, P. F., and Sumner, A. T. (1987) Correlation of pachytene chromomeres and metaphase bands of human chromosomes, and distinctive properties of telomeric regions, Cytogenet Cell Genet 44, 223–228.PubMedCrossRefGoogle Scholar
  15. 15.
    Kowalska, A., Bozsaky, E., Ramsauer, T., Rieder, D., Bindea, G., Lorch, T., Trajanoski, Z., and Ambros, P. F. (2007) A new platform linking chromosomal and sequence information, Chromosome Res 15, 327–339.PubMedGoogle Scholar
  16. 16.
    Kowalska, A., Brunner, B., Bozsaky, E., Chen, Q. R., Stock, C., Lorch, T., Khan, J., and Ambros, P. F. (2008) Sequence based high resolution chromosomal CGH, Cytogenet Genome Res 121, 1–6.PubMedCrossRefGoogle Scholar
  17. 17.
    Schweizer, D. (1981) Counterstain-enhanced chromosome banding, Hum Genet 57, 1–14.PubMedGoogle Scholar
  18. 18.
    Aviv, A., Levy, D., and Mangel, M. (2003) Growth, telomere dynamics and successful and unsuccessful human aging, Mech Ageing Dev 124, 829–837.PubMedCrossRefGoogle Scholar
  19. 19.
    Riethman, H., Ambrosini, A., and Paul, S. (2005) Human subtelomere structure and variation, Chromosome Res 13, 505–515.PubMedCrossRefGoogle Scholar
  20. 20.
    Ambrosini, A., Paul, S., Hu, S., and Riethman, H. (2007) Human subtelomeric duplicon structure and organization, Genome Biol 8, R151.PubMedCrossRefGoogle Scholar
  21. 21.
    Saitoh, Y., and Laemmli, U. K. (1994) Metaphase chromosome structure: bands arise from a differential folding path of the highly AT-rich scaffold, Cell 76, 609–622.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  1. 1.St. Anna KinderkrebsforschungCCRI, Children’s Cancer Research InstituteViennaAustria

Personalised recommendations