Detection of 1p and 19q loss in oligodendroglioma by quantitative microsatellite analysis, a real-time quantitative polymerase chain reaction assay

The combined loss of chromosomes 1p and 19q has recently emerged as a genet ic predictor of chemosensitivity in anaplastic oligodendrogliomas, Here, we describe a strategy that uses a novel method of realtime quantitative poly merase chain reaction, quantitative microsatellite analysis (QuMA), for the molecular analysis of 1p and 19q loss in oligodendrogliomas and oligoastro cytomas in archival routinely processed paraffin material. QuMA is performe d on the ABI 7700 and based on amplifications of microsatellite loci that c ontain (CA)n repeats where the repeat itself is the target for hybridizatio n by the fluorescently labeled probe. This single probe can therefore be us ed to determine copy number of miciosatellite loci spread throughout the hu man genome. In genonric DNA prepared from paraffin-embedded brain tumor spe cimens, QuMA detected combined loss of 1p and 19q in 64% (21 of 32) of olig odendrogliomas and 67% (6 of 9) of oligoastrocytomas, We validate the use o f QuMA as a reliable method to detect copy number by showing concordance be tween QuMA and fluorescence in situ hybridization at 37 of 45 chromosomal a rms tested. These results Indicate that QuMA is an accurate, high-throughpu t assay for the detection of copy number at multiple loci; as many as 31 lo ci of an individual tumor can be analyzed on a 96-well plate in a single 2- hour run. In addition, it has advantages over standard allelic imbalance/lo ss of heterozygosity assays in that all loci are potentially informative, p aired normal tissue is not required, and gain can be distinguished from los s. QuMA may therefore be a powerful molecular tool to expedite the genotypi c analysis of human gliomas in a clinical setting for diagnostic/prognostic purposes.