HER2 testing in breast cancer by quantitative PCR: Technical and clinical considerations

[[abstract]]Background: HER2 gene is amplified and/or overexpressed in approximate 15% to 20% of primary breast cancers. Knowing the HER2 status is therefore essential for making right decision. Quantitative PCR is originally designed for analyzing gene expression, and now is gaining wide use in molecular diagnostics. We made some key changes to the steps and streamlined the whole process to provide a convenient method for determining the HER2expression level in breast cancer patients. Methods: A total of 80 freshly-frozen or FFPE breast tumor samples, with a minimal of 30% tumor cell content, were collected from three different locations. Total RNA was extracted by a dual process and was adjusted to a concentration of 25 ng/ml. The same amount of RNA from each sample was analyzed by RT-PCR. Result was reported automatically as delta Ct (ΔCt) respect to a cutoff reference point (CRP), which was derived from a tumor HER2 mRNA population study and monitored in each assay with a traceable material, synthetic oligo. The ΔCtvalue then was used for determination of HER2 expression level. Results: We simplified quantitative PCR steps and optimized assay process by incorporating a self quality control mechanism. Our studies demonstrated that the improved method had a linear range up to 7-order magnitude with less than 8% intra- and inter-assay variance. We established criteria for using total RNA as assay normalizer; therefore, eliminated the needs for choosing a particular reference gene. We introduced a new scoring system based on a CRP, which produced consistent/comparable scoring results on different PCR machines and in different laboratories. A comparison study with FISH revealed an overall 90% agreement. Our method was also suitable for HER2 testing in blood samples, making it feasible to track patient HER2level after clinical intervention. Conclusions: HER2 testing by quantitative PCR method is accurate, consistent, and cost-effective. The whole process can be accomplished in less than 3 hours. The improved method also circumvents many drawbacks associated with testing by IHC and FISH. It is beyond doubt that adoption of quantitative PCR represents a new trend in HER2 testing and would improve clinical outcomes