Quantitative measurement of relative gene expression in human tumors

Quantitative measurement of specific mRNA species is of major importance for approaching many fundamental questions in biology. Until now, quantitation of gene expression has usually been done by Northern blotting, but this procedure is relatively insensitive, requiring microgram amounts of RNA. Furthermore, unless linear ranges of RNA concentration are determined, the procedure is semiquantitative at best. Because of the limitations of Northern blotting, various strategies have been developed for quantitation of cDNA by polymerase chain reaction (PCR)-based methods (1-3), most of them utilizing the principle of competitive PCR in which a synthetic segment is coamplified along the target DNA segment. We were interested in comparing the expression of drug target genes in very small samples of human tumor material, such as would be obtained from biopsies or even paraffin blocks. The competitive PCR was not entirely suitable for this purpose because: (1) the "input" RNA or DNA concentration must be known with precision in order to provide a normalization factor, and (2) our results suggested that the competitor and target were not necessarily amplified with the same efficiency even when the segments to be amplified were the same size (4). To overcome these problems, we developed an alternate method of PCR quantitation with the following key features: