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

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

Abstract

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 

Notes

Acknowledgements

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.

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

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

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