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Gerber Brings Genechip To VAI
VARI researchers are using the new system to identify the genetic profiles of young patients with various types of childhood cancers.
The hope is that faster identification of genetic patterns in children will help predict whether or not a tumor will metastasize, or spread cancer to other parts of the body.
VARI Senior Scientific Investigator Bin Tean Teh, who is leading the study, said the grant positions VARI at the forefront of modern technology.
“A lot of cancers appear to have molecular or genetic signatures that correlate with a lot of features, such as the behavior of tumors, how aggressive they are and what type of drugs they will respond to,” Teh explained.
“Our purpose of doing this is to try to identify the molecular signatures. The results of this research will form the basis of a patient’s diagnosis and prognosis and will potentially help guide the treatment plan.”
VARI’s Affymetrix Genechip System, which had a price tag of $200,000, allows scientists to view up to 22,000 genes on a single microchip. Each chip costs about $400.
The system is highly prized at VARI because of its superb quality control features and the fact that it is used globally, Teh said.
VARI scientists can now compare their data with the data of other scientists throughout the world that are using the same system, so they have the opportunity to learn from one another on a continual basis.
“I can compare my data with Japan or Australia or we can pool our data together,” Teh said.
Catherine Obits, Gerber Foundation’s program manager, said the VARI grant is the third largest of nine national grants Gerber awarded this year for initiatives designed to enhance the quality of life for infants and children.
The nonprofit also awards some 20 to 30 smaller Heritage Grants each year.
The Gerber grant is boosted by a $100,000 grant from the United Kingdom-based Fischer Family Foundation to support the work of a scientist dedicated solely to analyzing data generated by the system.
VARI is internationally known for its kidney cancer research, Teh said, and because one member of the Fischer family has kidney cancer, the foundation decided to contribute to VARI’s research efforts.
Teh recruited Min-Han Tan, M.D., an internist from Singapore, to operate the new system. Tan moved to town about four months ago to do his postdoctoral research.
“I noticed that he was very, very technical and extremely hard-working,” Teh recalled. “So I said, ‘OK. You go ahead and set up the whole system.’ And he did.”
In addition to reading everything he could about the new technology, Tan spent some time training with a representative of the company that sold the institute the genechip system.
Teh additionally tapped VARI Bioinformatics Scientist Eric Kort, M.S., to do the data analysis. Kort joined VARI’s staff this past summer.
Currently, Tan is the only scientist on VARI’s staff trained to operate the system.
A lot of his job involves gene comparison. The system allows him to superimpose two genes to study their differences and similarities.
The computer automatically sorts out and groups tumors of the same type, which means they clearly have a distinct molecular signature in comparison to other tumors in the study.
The computer uses very complex mathematical algorithms to group like tumors and differentiate between those that are actively spreading and those that are benign or much more controlled, Tan explained.
Studying the genes in look-alike tumors that haven’t spread will give scientists a better understanding of the underlying molecular mechanisms of favorable tumors and, hopefully, a clearer idea of which particular genes could be blocked to help prevent the spread of cancer, he said.
Once scientists identify the major players in the spread of cancer, new drugs can be designed to combat them, Teh said.
“In the future,” he said, “this technology will contribute to what we call personalized treatment of diseases, including cancers. If we can predict which cases are going to be the bad ones, we can give them more drugs or treatment.”
Eventually, both training and usage on the genechip system will be extended to other scientists, as well, Teh said. In fact, scientists outside of VARI that have funding for research projects are welcome to use the system, too, he added.
The genechip system could be put to use in any number of the multiple research projects VARI has going on, but the Gerber and Fischer grants were specifically for the study of pediatric cancer, so that will be the focus for the next year.
For this particular project, VARI scientists are studying tumor tissue samples supplied by DeVos Children’s Hospital. The said they’ve started with the study of pediatric kidney tumors but will expand the study to include many types pediatric cancer, such as brain tumors and leukemia.
The new gene-chip technology will also benefit the DeVos Children’s Hospital pediatric fellowship program. Beginning next July, the hospital will recruit one fellow a year for the three-year training program.
The program teams DeVos Children’s with VARI to train the next generation of pediatric oncologists and hematologists.
During the first 18 months of the program, the fellow physician will focus on patient care at the hospital and then spend the remaining 18 months of training working directly with VARI cancer biologists and geneticists on research.
The collaboration will give young pediatric physicians access and exposure to the new gene-chip technology, in addition to all the other powerful technologies being applied at VARI.
“Research is a major component of the training and this is a perfect collaboration,” Teh remarked.
The technology opens up a whole new range of possibilities for treatment of other types of cancers, said Albert Cornelius, M.D., the hospital’s director of outreach and education, as well as the hospital’s pediatric brain tumor clinic.
“In the future it may help determine which cancers could be treated with a certain drug as opposed to some of the more common therapies,” he said. “The research conducted at VARI will potentially allow our doctors to administer more specific treatment plans for our patients.”