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Genome Scans May Reveal Life-Saving Alternatives for Cancer Patients

By Amanda Gardner
HealthDay Reporter

TUESDAY, April 19 (HealthDay News) -- A 39-year-old woman is referred to Washington University's Siteman Cancer Center in St. Louis with suspected acute myeloid leukemia (AML), a cancer that can be treated relatively simply with medication, or not so simply with a high-risk stem cell transplant, depending on the tumor subtype.

But finding out which type of cancer she has proves trickier than expected.

While the pathologist sees a type of leukemia known as M3AML, which generally has a good outcome and can be treated with the drug ATRA, the cytogeneticist sees something entirely different. In his analysis, the woman has a type of leukemia with poor long-term survival that is usually treated with stem cell transplantation -- a risky therapy that sometimes leads to death.

Fortunately, in this case study, documented in the April 20 issue of the Journal of the American Medical Association, the woman's oncologist is aware of a clinical trial and, deferring treatment for six weeks, refers her there so the researchers can do a full scan of her genome -- and come up with an answer.

Full-genome sequencing involves scanning all the thousand of genes on the human genome to try to find a mistake. It's different from the more common gene testing these days, which looks only for specific DNA that might or might not be responsible for a particular problem.

In the St. Louis case, the more in-depth sequencing, done in only seven weeks, uncovered a new genetic "mistake" that showed the woman could be treated with ATRA and not the more-complicated, risky stem cell transplantation.

"A small portion of chromosome 15 had popped into chromosome 17," explained Richard K. Wilson, co-author of two case studies on full-genome sequencing in the journal.

The woman in this case study is now in remission and researchers have actually used the new information to assess other atypical cases of the leukemia, added Wilson, who is director of The Genome Institute at the Washington University School of Medicine in St Louis.

In a second case, also documented in the journal, the outcome was not so good for the patient, who died after battling several different forms of cancer. But it did provide hope for her children, who may have inherited her genes, and for other people with the same syndrome.

This woman, 37 years old when she was first diagnosed with breast cancer, had what's known as "cancer susceptibility syndrome," in which people of a relatively young age without an apparent family history of cancer develop multiple different types of the disease.

While the woman had breast and ovarian cancer first, the last cancer she developed was AML, which this group has been studying.

Although the woman died at the age of 42, a full-genome scan did reveal some useful information.

"We were expecting to find some interesting mutations in the tumor but we actually found the mutations in the germ line -- the normal cell DNA," Wilson explained.

This meant that "this was a mutation that happened very early in her life that presumably resulted in a high susceptibility to these cancers," he said.

The mutation was in the TP53 gene, which is involved in tumor suppression.

"The finding came too late to help her case but, we thought, if we're reading this correctly and if she has passed this gene along to her children, that would be very useful information for the family," Wilson said.

They went back to her physicians with the information who then, assumedly, shared it with the family.

So when are other patients going to have access to this type of sophisticated and sometimes life-saving scan?

Wilson guesses in about five-to-10 years.

One issue is cost, though Wilson is less worried about that one. The scans for the two patients in the journal studies cost about $40,000 to $50,000. They were free to the patients as part of the study, but that's not the case for most Americans.

However, the price tag for genomic scans is falling. Wilson noted that a year and a half ago, the cost was closer to $500,000 or $700,000. "Ask me next year, and it's going to be $10,000," he added.

A bigger challenge is having the skilled labor -- oncology experts, cancer biology experts, geneticists, the patients' own physician -- to do this. But Wilson is optimistic about that, too.

The case studies are also significant for "the speed at which they were able to turn around the information, both on the germ-line mutations [passed down between generations] and the tumor-tissue mutations," noted Dr. Steven K. Libutti, director of the Montefiore Einstein Center for Cancer Care in New York City. "We've known how to sequence for decades. The major barriers were cost and speed. They couldn't really sequence the entire genome in a reasonable amount of time and expense to make it practical. Now they've showed that advances have been made which can be applied to clinical problems."

More information

For more on the latest genetics research and discoveries, head to the Human Genome Project.

SOURCES: Richard K. Wilson, Ph.D., professor of genetics, and director, The Genome Institute, Washington University School of Medicine, St Louis; Steven K. Libutti, M.D., vice chair of surgery, and director, Montefiore Einstein Center for Cancer Care, New York City; April 20, 2011, Journal of the American Medical Association

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