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Separating Microbial Wheat From Human Chaff

Researchers have long suspected that some kinds of cancer and autoimmune disease might be caused by bacteria and viruses that slide their genetic material into our DNA, but tracking down the interloping DNA was an overwhelming task. A new genetic technique, described online in Nature Genetics, may help researchers pick out the microbial fifth column in the genes of sick people.

Some of the best evidence that contagious diseases can lead to cancer comes from studies of cervical cancer. The human papillomavirus (HPV) causes genital warts and has been found in more than 90% of cervical tumors. The researchers, led by pathologist Matthew Meyerson and his colleagues at Harvard Medical School in Boston, used this disease as a test case for detecting foreign genes.

The team compared a computer library of 7073 active gene sequences collected from human cervical cancer cells with the sequenced genome from the Human Genome Project, as well as other human and mouse sequence databases--all of which were taken from presumably healthy individuals. Twenty-two didn't match sequences in these libraries. Of these, the researchers eliminated another 20. The two remaining sequences are dead ringers for DNA from the virus HPV-18, an infectious agent previously linked to cervical cancer.

David Relman, a microbiologist at Stanford University, says the method has promise. But he says "the challenge will come when you stumble across a transcript that doesn't have such a well-known story" as HPV and cervical cancer. He suspects our DNA may accumulate quite a bit of harmless microbial detritus, making it difficult to separate the traces of pathogens from the background noise of innocuous cohabitors.

Related sites
Matthew Meyerson's home page
More about cervical cancer and HPV from the National Cancer Institute
The Human Genome Project