Fish or Chips

GenoSensor System, showing results of hybridization to biochip (left) and display of data using software (right). Gene amplification and rearrangements have long been known to occur in cancer cells, and the connection between these events and disease outcome is of great interest, especially in light of the relationship between HER-2/neu amplification and a poor breast cancer prognosis. It is with this backdrop that Vysis, a genomic disease management company based in Downer's Grove, Ill., has been developing genetic tools for research and clinical use. Two products in particular, the GenoSensor™ System, a platform for detecting oncogene amplification, and PathVysion™ HER-2 DNA Probe Kit, a FISH assay for detecting amplification of the HER-2/neu gene, address the growing interest in this area. The PathVysion HER-2/neu DNA probe is not the first of its kind to be offered. However, this kit is unique in that it includes the means to normalize the signal with respect to the number of chromosome 17s present in the sample. In a certain percentage of the cancer cells, chromosome 17 is present in greater than two copies, which can make it look like HER-2/neu (which is located on chromosome 17) is amplified when in fact it is not. With a built-in chromosome 17-specific probe, the PathVysion assay provides a clear answer with respect to the amplification status of this critically important locus. Vysis' GenoSensor System, the latest entry in the burgeoning field of microarray technologies, also has features that are unique. Unlike other chip arrays that measure expression levels or check sequence integrity, the Vysis array is designed to measure amplification levels of cancer-related genes. The first Vysis GenoSensor biochip, the AmpliOnc™ I chip contains targets for all loci reported to be amplified in human tumor cells, totaling greater than 50 different loci to date. Among these loci are HER-2/neu, cyclin D1, and myc. Using the GenoSensor System, a company spokesman claims three-fold amplifications or greater can be detected. Being able to acquire the amplification status of multiple targets simultaneously should help to establish the connection between the copy number of specific loci and pathology, and to provide insights into the interactions among these gene products. The AmpliOnc I biochip contains large fragments (80 to 150 kilobase) of genomic DNA isolated from BACs, PACs and P1s, spotted onto chromium-coated glass slides. Genomic DNA, isolated from tissues of interest, presumably tumor cells, is labeled with Vysis' SpectrumGreen™ fluorescent label by nick translation, and hybridized to the chip in the presence of a normal standard genomic DNA labeled with red fluorochrome (provided with the GenoSensor System). Following a standard in situ hybridization protocol, the slides are read with the GenoSensor Reader, a fluorescent imager optimized for the fluors. GenoSensor Software then analyzes the data, performing the necessary background corrections and normalizations, finally providing the ratio of green to red fluorescence for each locus on the chip. Olli Kallioniemi, section head of the Cancer Genetics Branch of the National Human Genetics Research Institute and co-inventor of a related technology, comparative genomic hybridization (CGH), has tested the GenoSensor System. Using an alpha version of the chip in preliminary experiments, Dr. Kallioniemi was able to detect all genes known to be amplified in a breast cancer sample, as well as some not previously reported to be amplified in breast cancer. In these pilot experiments, a five- to ten-fold amplification was required to register a signal. However, he feels that with improvements in sample preparation and labeling, as well as chip preparation, results more in line with company expectations will be possible. Another related and complementary technology developed in Kallioniemi's lab is tissue microarray analysis, with which molecular profiles of multiple tumor samples can be produced simultaneously. These two array technologies used in tandem have the potential of speeding up the identification of important cancer-associated genetic abnormalities. With the GenoSensor, a single sample can quickly be scanned for those specific genes that are amplified, and following that, scanning a tissue microarray can demonstrate how widespread the amplification of a specific gene is in a large population of tumors. The author, Laura DeFrancesco, can be contacted at ldefrancesco@the-scientist.com. For more information, call Vysis at 630-271-7000 or visit the company Web site at www.vysis.com.

Fish or Chips

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