Competitive-differential polymerase chain reaction for gene dosage estimation of erbB-1 (egfr), erbB-2, and erbB-3 oncogenes

Increases in the average gene copy number (AGCN) of the erbB oncogenes, especially the erbB-2 gene, have been found in a variety of human cancers. Such information is useful with respect to prognosis of the disease. Poor reproducibility and DNA damage complicate quantitative polymerase chain reaction (PCR)-based methods. Therefore, we describe a quantitative PCR method for the estimation of AGCN in the oncogenes erbB-1 (egfr), erbB-2, and erbB-3. The method comprises a competitive and differential PCR in a one-tube reaction (competitive-differential PCR, or cdPCR), Genomic sequences of the oncogene and the human beta-globin (HBB) reference gene and two competitors for the oncogene and reference gene were amplified with two primer pairs simultaneously. The competitors were chosen to be amplified with the same efficiency as the genomic sequences. Using this method, we confirmed egfr and erbB-2 amplification in cancer cell lines and tumor tissue, and we also detected erbB-3 amplifications, Furthermore, gene dosage decreases were detectable, e.g., an erbB-2 hemizygosity in MCF-7 cells. Thus, cdPCR facilitates the detection of both increases and decreases in AGCN with high reproducibility, sensitivity, and accuracy. This method is therefore suitable for clinical studies on erbB oncogene dosage deviations.