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Many of today’s tools for screening and diagnosing cancer are crude at best. So researchers are working to find more-sensitive tests based on specific molecules –  called “biomarkers”  –  that are early signs of tumors and whose concentration could, ideally, be measured in bodily fluids like blood.

While much of that research has focused on protein biomarkers, some of the first molecular tests to arrive on the market may be ones that look instead at a phenomenon called DNA methylation. A few small biotech companies, some partnered with major pharmaceutical companies like Johnson and Johnson and Roche, say their first DNA methylation-based tests for prostate cancer could be available next year.

DNA methylation occurs when methyl groups – carbon atoms surrounded by three hydrogen atoms each – attach to a gene without changing its actual sequence. Methylation can alter a gene’s behavior by, for instance, turning it off, and aberrant patterns of methylation are involved in almost all types of cancer. What’s more, abnormal methylation happens early on in the disease process, which makes it “a highly promising biomarker for cancer,” says Stephen Baylin, an oncology professor at the Johns Hopkins School of Medicine. Researchers have so far identified some 40 to 50 genes whose methylation patterns play a role in the development of cancer.

One of the leading companies in the development of methylation-based cancer tests is OncoMethylome Sciences of Liege, Belgium. It is collaborating with Johnson and Johnson to develop a prostate cancer diagnosis test, which it is currently testing on a few hundred patients in six U.S. medical centers. The test, which OncoMethylome expects to commercialize by next year, would detect methylation in biopsied prostate tissue. The current method of diagnosis – examination of the tissue under a microscope – misses up to 30 percent of cancers, so the new test would be used to confirm that cancer really was absent in biopsies that appeared normal.

OncoMethylome is developing another set of tests to screen patients for cancer before they reach the stage where a biopsy is called for. These screening tests would look at patterns of methylation in two to five genes from DNA in blood, urine, or saliva. The tests, which won’t be available for at least another two years, are designed to detect early signs of cancers of the ovary, bladder, prostate, and lung. Competing company Epigenomics of Berlin, Germany, has partnered with Roche to develop similar blood tests for prostate, breast, and colon cancer, and it expects them to reach market by 2009.

Like most other screening tools, these bodily-fluid tests will likely not offer definitive results; positive tests would still need to be confirmed. However, DNA-methylation screening is designed to be highly accurate in identifying the people who really don’t have cancer so that they won’t needlessly undergo more invasive and expensive testing such as colonoscopy. Still, the tests will first need to be fast and cheap enough for routine use in hospitals and diagnostic labs.

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