What once took teams of scientists a decade and billions of dollars to create, Dr. Lesleyann Hawthorn and colleagues can do in 10 days for around $10,000.
Being able to sequence the human genome so quickly and cheaply, thanks to new equipment at Georgia Health Sciences University Cancer Center, allows them to take aim at nasty forms of breast cancer and brain tumors that often have poor outcomes.
The HiSeq 2000 sequencing system is the only one running in a core laboratory in Georgia and is part of a push among geneticists to get to the point where a person's entire genetic makeup could be sequenced for about $1,000, a key to moving toward personalized medicine, said Hawthorn, the director of shared resources for the cancer center.
That would be particularly important in cancer, especially in cancers that don't respond well to therapy, she said.
"That's like the ultimate goal for personalized medicine is to be able to target specific tumors in specific people," Hawthorn said. "Because every tumor is a little bit different."
A current sequencing project is focusing on what it is known as "triple negative" breast cancer, cancers that lack receptors for estrogen, progesterone and human epidermal growth factor 2, or HER-2, which all have therapies that target them specifically.
"Our problem with triple negative is there are no targets right now," she said. "So they're just doing conventional (chemotherapy) therapy, which is nasty."
The cancers actually respond to standard chemotherapy, said Dr. Thomas Samuel, the director of the Multidisciplinary Breast Cancer Program at the cancer center. "The problem is it tends to come back," he said. "They tend to have higher relapse rates. Those patients also tend to have more aggressive outcomes in terms of these tumors don't come back slowly; they come back very quickly and they tend to be very widespread and aggressive."
The cancers show up most often in younger black women and could help explain why black women are less likely to develop breast cancer than whites but tend to have worse results, Samuel said.
"We think this whole idea of being more likely to have a triple-negative (breast cancer) profile is what adds to that poor prognosis," he said.
The sequencing is looking not only at the tumor sample but also at blood samples from the patient in order to study normal tissue for comparison, Hawthorn said. They are sequencing both the DNA and the RNA of those patients to see what is there and what is active. They are finding intriguing things -- some of what is there is active like a gene but does not fit the standard definition of what a gene should look like, Hawthorn said.
"We're finding all of this stuff that we didn't think was there before. Or should be expressed, according to our rules of what a gene is," she said. "It's nice to be able to look at things that way because there may be genes that are being expressed we didn't ever know about and they are playing a huge role in these tumors."
It also uncovers a huge number of gene variations that must be sifted through to determine whether they are a real mutation that could have an impact or are a common blip in the genetic code. The center works with bioinformaticians at the school to help write formulas to analyze it.
"We have these massive amounts of data coming off this, as you can imagine," Hawthorn said. "It's just really drilling down to what do we have here."
Triple-negative breast cancer, in particular, is of high interest to many centers in the U.S. because of the lack of signature markers that could be uncovered by an approach like this, Samuel said.
"It's sort of the Holy Grail of breast cancer oncology right now to find the next marker, particularly a biomarker that is going to be unique to this particular population since we don't have one at the moment," he said.
The cancer center recently sequenced brain cancer tumors called glioblastoma multiforme that tend to be fast and aggressive and have poor outcomes.
The key is getting patients to help with research, Samuel said.
"A big part of this is getting patients to contribute to the tumor repository, signing the consent form to say it is OK to use their specimen in research like this, rather than just sitting on a shelf, gathering dust," he said.
That in turn could lead to more specific and personalized treatment for them down the road, Hawthorn said.
"I think that's the way medicine has to go," she said. "Because thinking everyone is the same and has the same tumor has proven to be not an effective approach -- to cancer treatment, anyway."