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Scientists have sequenced the whole genome of a cancer cell for the first time. By comparing the DNA sequence of cancerous cells taken from a patient, who died of leukemia in her fifties, with the DNA collected from her healthy tissue, the scientists identified 10 mutations found only in the cancer cells. The mutations appear to affect cancer cell growth, as well as response to chemotherapy drugs.

The experiment, which involved sequencing two complete human genomes, would have been unfeasible just a year ago due to the expense of genome sequencing. But cheap new sequencing technologies are changing the paradigm of genomics research. The project cost about $1 million, compared with the $300 million of the Human Genome Project.

The new study is different than other recent genomics studies of cancer, which focused on candidate genes rather than searching the entire 20,000 genes of the human genome. (See “Cancer Redefined.”) It is also the first female genome to be sequenced.

According to an article in the New York Times,

“This is the first of many of these whole cancer genomes to be sequenced,” said Richard K. Wilson, director of Washington University’s Genome Sequencing Center and the senior author of the study. “They’ll give us a whole bunch of clues about what’s going on in the DNA when cancer starts to bloom.”

Dr. Wilson said he hoped that in 5 to 20 years, DNA sequencing for cancer patients would consist of dropping a spot of blood onto a chip that slides into a desktop computer and getting back a report that suggests which drugs will work best for each person.

… Indeed, 8 of the 10 mutations his group found in the leukemia patient had never been linked to the disease before and would not have been found with the more traditional, “usual suspects” approach.

Some of the patient’s mutated genes appeared to promote cancer growth. One probably made the cancer drug-resistant by enabling the tumor cells to pump chemotherapy drugs right out of the cell before they could do their work. The other mutated genes seemed to be tumor suppressors, the body’s natural defense against dangerous genetic mistakes.

“Their job is surveillance,” Dr. Wilson said. “If cells start to do something out of control, these genes are there to shut it down. When we find three or four suppressors inactivated, it’s almost like tumor has systematically started to knock out that surveillance mechanism. That makes it tougher to kill. It gets a little freaky. This is unscientific, but we say, gee, it looks like the tumor has a mind of its own, it knows what genes it has to take out to be successful. It’s amazing.”

It will take more research to determine exactly what the mutations do. Researchers would also like to know the order in which they occurred, and whether there was one that finally tipped the balance towards cancer.

“When this patient came to the cancer center and had a bone marrow biopsy, she already had 10 mutations,” Dr. Wilson said. “You’d love to know, if you had taken a bone marrow sample a year before, what would you have seen?”

Tests of 187 other patients with acute myelogenous leukemia found that none had the eight new mutations found in the first patient.

That finding suggests that many genetic detours can lead to the same awful destination, and that many more genomes must be studied, but it does not mean that every patient will need his or her own individual drug, Dr. Wilson said.

“Ultimately, one signal tells the cell to grow, grow, grow,” he said. “There has to be something in common. It’s that commonality we’ll find that will tell us what treatment will be the most powerful.”

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Tagged: Biomedicine, cancer, genomics

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