FDA Clears Test that Helps Identify Type of Cancer in Tumor Sample

The U.S. Food and Drug Administration has cleared for marketing a test that can help health care professionals determine what type of cancer cells are present in a malignant tumor.

The Pathwork Tissue of Origin test compares the genetic material of a patient’s tumor with genetic information on malignant tumor types stored in a database.

It uses a microarray technology to analyze thousands of pieces of genetic material at one time. The test considers 15 common malignant tumor types, including bladder, breast, and colorectal tumors.

"The clearance of the Pathwork test is another step in the continued integration of molecular-based medicine into standard practice," said Daniel Schultz, M.D., director of the FDA's Center for Devices and Radiological Health, which oversees medical diagnostics. "In the past, scientists have classified different types of cancers based on the organs in which the tumors develop. With the help of microarray technology, they will be able to classify these types of cancers in a standardized non-reader dependent manner based on the patterns of gene activity in the tumor cells."

The Pathwork Tissue of Origin test is the second in vitro diagnostic multivariate index assay (IVDMIA) device to be cleared by the FDA. In July 2007, the FDA issued a draft guidance document to address premarket pathways and postmarket requirements for IVDMIAs. IVDMIA tests combine the values of multiple variables to yield a single, patient-specific result.

Nearly every cell of the body contains a full set of chromosomes and identical genes but only a fraction of these genes are turned on or expressed in any given cell. Gene expression occurs when certain molecular information contained within DNA is transcribed to create molecules known as RNA. These molecules in turn make the proteins that perform most of the critical functions of cells.

Microarray technology can simultaneously measure gene expression levels of large numbers of genes. Small DNA fragments are placed or arrayed on a slide and then RNA, which has been extracted from the tumor tissue and labeled with a fluorescent marker, is spread over this "microarray."

Since RNA binds to its complementary DNA strand, how much binding occurs indicates how active the gene being evaluated is. This can be determined by putting the array under a scanning microscope and measuring the intensity of the fluorescent light at each point on the array.

Pathwork’s proprietary software converts the scanned image data to gene expression measurements. The gene expression patterns are compared with known gene expression patterns in the database that correspond to different tumor types.

The Pathwork Tissue of Origin test has been found to provide patterns that confirm existing tissue of origin of the 15 common tumor types using standard clinical and pathological information. This accuracy of this test is similar to that achieved by expert pathologists using current standards of practice.

PathChip, the gene expression array used in the Pathwork Tissue of Origin test, is custom-designed for Pathwork Diagnostics of Sunnyvale, Calif., by Affymetrix Inc., of Santa Clara, Calif. PathChip is the first custom Affymetrix gene expression array to be cleared for diagnostic use.