Open Access Technical advance

Identification of microbial DNA in human cancer

Christopher G Duncan1, Rebecca J Leary2, Jimmy Cheng-Ho Lin2, Jordan Cummins2, Chunhui Di1, Carl F Schaefer3, Tian-Li Wang2, Gregory J Riggins4, Jennifer Edwards4, Darell Bigner1, Levy Kopelovich5, Bert Vogelstein2, Kenneth W Kinzler2, Victor E Velculescu2 and Hai Yan1*

Author Affiliations

1 Preston Robert Tisch Brain Tumor Center, Pediatric Brain Tumor Foundation Institute, Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA

2 The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute, The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland 21231, USA

3 Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, Maryland 20852, USA

4 Department of Neurosurgery, Johns Hopkins University Medical School, Baltimore, MD 21231, USA

5 Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892-7322, USA

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BMC Medical Genomics 2009, 2:22  doi:10.1186/1755-8794-2-22

Published: 8 May 2009



Microorganisms have been associated with many types of human diseases; however, a significant number of clinically important microbial pathogens remain to be discovered.


We have developed a genome-wide approach, called Digital Karyotyping Microbe Identification (DK-MICROBE), to identify genomic DNA of bacteria and viruses in human disease tissues. This method involves the generation of an experimental DNA tag library through Digital Karyotyping (DK) followed by analysis of the tag sequences for the presence of microbial DNA content using a compiled microbial DNA virtual tag library.


To validate this technology and to identify pathogens that may be associated with human cancer pathogenesis, we used DK-MICROBE to determine the presence of microbial DNA in 58 human tumor samples, including brain, ovarian, and colorectal cancers. We detected DNA from Human herpesvirus 6 (HHV-6) in a DK library of a colorectal cancer liver metastasis and in normal tissue from the same patient.


DK-MICROBE can identify previously unknown infectious agents in human tumors, and is now available for further applications for the identification of pathogen DNA in human cancer and other diseases.