Customized Gene Chip Provides Rapid Detection of Genetic Changes in Children's Cancer; Microarray Scans DNA Regions in Neuroblastoma Tumors to Forecast Outcomes, Guide Treatments

08/2/2005

PHILADELPHIA, Aug. 2 /PRNewswire/ -- Genetics researchers have developed a
customized gene chip to rapidly scan tumor samples for specific DNA changes
that offer clues to prognosis in cases of neuroblastoma, a common form of
children's cancer. Rather than covering the entire genome, the microarray
focuses on suspect regions of chromosomes for signs of deleted genetic
material known to play a role in the cancer.

The investigators, from The Children's Hospital of Philadelphia and Thomas
Jefferson University, say their technique may be readily adapted for other
types of cancer. The proof-of-principle study appears in the August issue of
"Genome Research."

One advantage of their technique is its flexibility, said co-author John M. Maris, M.D., a pediatric oncologist at The Children's Hospital of Philadelphia. "As future research identifies other genes active in neuroblastoma, we can modify the microarray to include such regions," he added.

"We have customized this tool for neuroblastoma, but the approach might
also be adapted to other types of cancer in which DNA changes are important,"
said co-author Paolo Fortina, M.D., Ph.D., professor of medicine at Jefferson
Medical College of Thomas Jefferson University in Philadelphia and section
chief, Genomics and Diagnostics, in the Jefferson Department of Medicine's
Center for Translational Medicine.

The most common cancer found in infants, neuroblastoma strikes the
peripheral nervous system, often appearing as a solid tumor in a child's chest or abdomen. Some types of neuroblastoma are low risk, resolving after surgeons remove the tumor, while others are much more aggressive. Identifying the correct risk level allows doctors to treat aggressive cancers appropriately, while not subjecting children with low-risk cancer to overtreatment.

Cancer researchers have pinpointed specific genetic abnormalities that
influence the aggressiveness of neuroblastoma. An important abnormality is loss of heterozygosity (LOH), the deletion of one copy of a pair of genes.
When the gene involved is a tumor suppressor gene, LOH removes a brake on uncontrolled cell growth, the growth that is the hallmark of cancer.

Researchers in Dr. Maris' laboratory previously established that LOH in a
region of chromosome 11 allows aggressive neuroblastoma to take hold. The new microarray can detect such gene defects on chromosome 11 and other genetic regions implicated in neuroblastoma.

Microarrays are silicon chips that contain tightly ordered selections of genetic material upon which sample material can be tested. When DNA bases from a sample bind to complementary sequences on the microarray, they cause
fluorescent tags to shine under laser light. This is a signal that a particular gene variation is present in the sample.

"We can test DNA from peripheral blood and from the tumor, and we should see a loss of signal in the cancer," said Dr. Fortina. He noted that the researchers can simultaneously evaluate seven chromosomal regions known to be
involved in neuroblastoma.

Unlike gene expression microarrays, which detect varying levels of RNA to
measure the activity levels of different genes as DNA transfers information to
RNA, the current microarray directly identifies changes in DNA. "These DNA
changes, involving gain or loss of genetic material, are important for neuroblastoma prognosis," said Dr. Maris.

In pinpointing specific regions of chromosomes with loss in DNA, the
technology may help confirm a clinical diagnosis, said Saul Surrey, Ph.D.,professor of medicine and Associate Director of Research at the Cardeza
Foundation for Hematologic Research and the Division of Hematology at Jefferson Medical College. If a clinical diagnosis isn't known, the method might provide some clues.

The microarray described in the paper has only been used in their laboratory study, but the researchers hope that with further study it may become more widely available as a diagnostic tool for oncologists treating patients with neuroblastoma, and possibly for other cancers.

In addition to Drs. Maris, Fortina, and Surrey, other co-authors are George Hii, Peter S. White, Ph.D., and Eric Rappaport, Ph.D., of The Children's Hospital of Philadelphia; and Craig A. Gelfand, Ph.D., and Shobha Varde, M.S., of Orchid Biosciences, Princeton, N.J. Grants from the National Institutes of Health and the Children's Oncology Group supported the work.

About The Children's Hospital of Philadelphia: The Children's Hospital of
Philadelphia was founded in 1855 as the nation's first pediatric hospital. Through its longstanding commitment to providing exceptional patient care, training new generations of pediatric healthcare professionals and pioneering major research initiatives, Children's Hospital has fostered many discoveries that have benefited children worldwide. Its pediatric research program is among the largest in the country, ranking second in National Institutes of Health funding. In addition, its unique family-centered care and public
service programs have brought the 430-bed hospital recognition as a leading
advocate for children and adolescents. For more information, visit http://www.chop.edu.

About Thomas Jefferson University: Thomas Jefferson University is composed
of three schools -- Jefferson Medical College, the Jefferson College of Graduate Studies and the Jefferson College of Health Professions. The three
colleges enroll more than 2,300 future physicians, scientists and health-care
professionals. Thomas Jefferson University Hospital, part of the academic
health center complex, admits more than 40,000 patients a year for advanced
treatment and care. Founded in 1824, Jefferson Medical College is one of the
largest private medical colleges in the nation, with among the largest living
alumni groups. For more information, visit http://www.jefferson.edu.

Contacts:
Rachel Salis-Silverman
The Children's Hospital of Philadelphia
(267) 426-6063
Salis@email.chop.edu

Steve Benowitz
Thomas Jefferson University
(215) 955-6300
steven.benowitz@jefferson.edu