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.

“ 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 Paolo Fortina, at Jefferson Medical College of Thomas Jefferson University in Philadelphia.

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 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 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.

Source: Children's Hospital of Philadelphia and Thomas Jefferson University, 2005


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