For many Epstein-Barr virus (EBV)-associated malignancies, it is still a matter of controversy whether infected cells harbor episomal or chromosomally integrated EBV genomes or both. It is well established that the expression of EBV genes per se carries oncogenic potential, but the discrimination between episomal and integrated forms is of great relevance because integration events can contribute to the oncogenic properties of EBV, whereas host cells that exclusively harbor viral episomes may not carry the risks mediated by chromosomal integration. This notion prompted us to establish a reliable technique that not only allows to unequivocally discriminate episomal from integrated EBV DNA, but also provides detailed insights into the genomic organization of the virus. Here, we show that dynamic molecular combing of host cell DNA combined with fluorescence in situ hybridization (FISH) using EBV-specific DNA probes facilitate unambiguous discrimination of episomal from integrated viral DNA. Furthermore, the detection of highly elongated internal repeat 1 (IR1) sequences provides evidence that this method permits detection of major genomic alterations within the EBV genome. Thus, fiber FISH may also provide valuable insights into the genomic organization of viral genomes other than EBV. ' 2005 Wiley-Liss, Inc.Key words: EBV; fiber FISH; episomal; integration Epstein-Barr virus (EBV, human herpes virus 4) is associated with a number of benign and malignant diseases, including infectious mononucleosis, Burkitt's lymphoma, Hodgkin's disease, immunoblastic and transplantation-associated lymphomas. The virus preferentially infects B lymphocytes. 1 Upon infection, the linear viral DNA is covalently closed by its terminal repeat (TR) sequences and circularizes. 2 During latency, EBV DNA persists as an episome in the nuclei of host cells, or can be integrated into the cellular genome via the TR sequences. [3][4][5][6][7] Integration may initiate transformation events by causing chromosomal instability, [8][9][10] or may provide a cis-acting mechanism for altering gene regulation or structure. 11,12 Hence, if integration has an effect on viral or cellular gene expression, 5,13 it could be directly linked to the oncogenic properties of EBV, 14 mediating continuous cell proliferation. It has recently been shown that loss of expression of the putative tumor suppressor gene BACH2 in a Burkitt's lymphoma cell line is attributable to EBV integration within the first intron of the gene. 13 Another Burkitt's lymphoma cell line has been reported to contain integrated EBV DNA between the oncogenes REL and BCL11A associated with an increased expression of REL. 15 The notion that host cells, which exclusively contain episomal viral DNA, are not susceptible to the risks linked to chromosomal integration emphasizes the necessity of having a reliable method permitting distinction between episomal and integrated EBV DNA. We have therefore established a technique based on DNA fiber analysis, facilitating detailed insights into the genomic or...