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67 Genes That Count in Cancer

By Kate Ruder

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Cancer
Microarrays

Microarrays like this one are used to monitor the activity of thousands of genes.
Using a new online cancer database, scientists have sifted through genetic information about some 3,000 tumors and identified a group of genes that are altered in most if not all cancers.

The 67 genes are either more or less active in cancer cells than they are in healthy cells. For scientists, the genes are a resource for developing diagnostic tests and therapies that target these genes.

In addition, the researchers identified 69 genes that are altered in aggressive cancers, including some genes from the original group.

“We were intrigued to find a core set of genes that are activated in aggressive cancer regardless of the cancer type,” says Daniel Rhodes of the University of Michigan, Ann Arbor, who worked on the study.

This is the first substantial report from a group of scientists at the University of Michigan who founded Oncomine, a searchable online database for cancer researchers everywhere.

For cancer researchers, Oncomine is a little like Google. It can be searched for results and data from 65 cancer studies that involve DNA microarray technology. Users can get information about how a gene behaves in a variety of cancers in many patients.

“I don’t know of any other place that you can so easily go and ask questions about what your gene of interest is doing in other human tumor samples,” says Mark Rubin of Brigham and Women's Hospital and Harvard Medical School in Boston.

Rubin adds that he uses Oncomine “all the time” and knows plenty of researchers that do too. The database has more than 1,000 registered users from 20 different countries.

A year and a half ago, Arul Chinnaiyan of the University of Michigan and his colleagues began collecting data for Oncomine. There have been more than 200 studies using DNA microarrays, also known as gene chips, to study genes involved in cancer.

Now the Michigan researchers have shown just how useful the database can be, reporting their findings in Proceedings of the National Academy of Sciences. Some of the genes have previously shown promise as targets for new drugs and clinical trials on these drugs are underway.

This isn’t the first time that researchers have found common patterns of gene activity in cancers, and it surely won’t be the last. For example, Sridhar Ramaswamy of Dana-Farber Cancer Institute in Boston and his colleagues have found genes that are altered in cancers that are most likely to metastasize or spread.

“In cancer, you’re looking at complex phenomenon,” says Ramaswamy. “It is clear that they have found statistically meaningful results, but the jury is still out on whether these markers will be broadly informative to disease.”

One of the strengths of the research, says Ramaswamy, is that they looked at twelve types of cancer and many studies. “They went and grabbed every high-quality data set they could find to see what trends they could see in genes,” he adds.

Rhodes says traffic on the site has shot up since the paper was published and their lab has been “barraged with emails” about Oncomine, including from pharmaceutical companies interested in using the data to develop new drugs.

Oncomine is available free of charge to academic scientists and researchers from private companies can purchase licensing rights.

Rhodes, D.R. et al. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of the National Academy of Sciences (Published online June 7, 2004).
Ramaswamy, S. et al. A molecular signature of metastasis in primary solid tumors. Nat Genet 33, 49-54 (January 2003).

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