Simultaneous molecular karyotyping and mapping of viral DNA integration sites by 25-color COBRA-FISH

Genes Chromosomes Cancer. 2000 May;28(1):92-7. doi: 10.1002/(sici)1098-2264(200005)28:1<92::aid-gcc11>;2-2.


Combined binary ratio labeling (COBRA) fluorescence in situ hybridization (FISH) allows 24-color FISH karyotyping of human metaphase chromosomes utilizing only four fluorochromes, instead of the five required for combinatorial labeling procedures. Here we show that by introduction of a fifth fluorochrome, COBRA-FISH permits molecular cytogenetic mapping of viral integration sites in complex karyotypes in the context of a 24-color hybridization. We were able to detect a single copy of the human papillomavirus 16 in the SiHa cell line and to confirm the site of integration at 13q21-31. We also demonstrate the gene mapping possibility of 25-color hybridization by detecting a MYC cosmid on normal metaphase chromosomes. The possibility of mapping single-copy probes in the background of 24-color hybridization expands the tools for cytogenetic mapping of DNA sequences and will contribute to the understanding of the role of viral integration and chromosome rearrangement in virus-mediated carcinogenesis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Human / genetics
  • DNA, Viral / genetics*
  • Female
  • Humans
  • Image Enhancement / methods
  • In Situ Hybridization, Fluorescence / methods*
  • Karyotyping / methods
  • Microscopy, Fluorescence
  • Papillomaviridae / genetics
  • Papillomavirus Infections
  • Tumor Cells, Cultured
  • Tumor Virus Infections
  • Uterine Cervical Neoplasms
  • Virus Integration / genetics*


  • DNA, Viral