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Directional Genomic Hybridization (dGH) for Detection of Intrachromosomal Rearrangements

  • Erin Robinson
  • Miles J. McKenna
  • Joel S. Bedford
  • Edwin H. Goodwin
  • Michael N. Cornforth
  • Susan M. BaileyEmail author
  • F. Andrew Ray
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1984)

Abstract

Fluorescence in situ Hybridization (FISH) techniques, including whole chromosome painting (WCP), spectral karyotyping (SKY), and multicolor FISH (mFISH), are used extensively to characterize and enumerate inter-chromosomal rearrangements (e.g., translocations). Directional genomic hybridization (dGH) is a relatively new cytogenomics-based methodology that combines the strand-specific strategy of Chromosome Orientation-FISH (CO-FISH) with bioinformatics-driven design of single-stranded DNA probe sets that are unique and of like orientation. Such a strategy produces directional probe sets that hybridize to one—and only one—chromatid of prepared (single-stranded) metaphase chromosomes, thereby facilitating high-resolution visualization of intra-chromosomal rearrangements, specifically inversions, and greatly improving our ability to detect such otherwise cryptic structural variants within the genome. In addition to its usefulness in the study of various disease states, including cancer, relevant applications of dGH include monitoring cytogenetic damage caused by exposure to clastogenic agents (e.g., ionizing radiation). dGH can be applied as a discovery tool to globally assess the integrity of the genome, but it can also be used in a more targeted fashion to interrogate fine structural changes at the kilobase level. Consequently, dGH is capable of providing significant mechanistic insight and information not easily obtainable by other approaches.

Key words

Directional genomic hybridization (dGH) Chromosome orientation-specific fluorescence in situ hybridization (CO-FISH) Chromosomal inversions Biodosimetry 

Notes

Acknowledgments

The authors gratefully acknowledge support from the Colorado State University College Research Council, NASA (NNX09CE42P, NNX10CB05C, NNX12AM92G), and NIH (RO1AI080486-02).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Erin Robinson
    • 1
  • Miles J. McKenna
    • 2
  • Joel S. Bedford
    • 2
  • Edwin H. Goodwin
    • 1
  • Michael N. Cornforth
    • 3
  • Susan M. Bailey
    • 2
    Email author
  • F. Andrew Ray
    • 2
  1. 1.KromaTiD Inc.Fort CollinsUSA
  2. 2.Department of Environmental and Radiological Health SciencesColorado State UniversityFort CollinsUSA
  3. 3.Department of Radiation OncologyUniversity of Texas Medical BranchGalvestonUSA

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