Use of DNA microarrays to determine estrogen and HER-2 receptor status in breast cancer

Abstract

546 Purpose: To evaluate whether estrogen receptor (ER) and HER-2 receptor status in breast cancer is accurately determined using gene expression profiles. Patients and Methods: Gene expression profiles were obtained from 82 fine needle aspiration (FNA) samples and 40 frozen tissue samples in 122 patients with newly diagnosed breast cancer. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) were used to define ER and HER-2 status. The cohorts of FNA and tissue samples were evaluated in two laboratories using Affymetrix U133A GeneChip technology and all expression data were normalized using a single digital standard (dCHIP software). Thresholds of gene expression to determine ER and HER-2 status were defined in the cohort of 82 FNAs and then tested in the 40 tissue samples. Results: ER gene expression (probe ESR1 205225) ≥ 500 (arbitrary units) defined ER-positive status (IHC ≥ 10%) in 82 FNAs with 96% overall accuracy (95% CI, 90%–99%), and was validated with 90% overall accuracy (95% CI, 76%–97%) in 40 tissues. Considering ER IHC > 0% as positive, the overall accuracies were 98% (FNA) and 100% (tissue). ER reporter genes (55 probes) were identified by co-expression with ER (ESR1) (Spearman correlation, R ≥ 0.7) in the 82 FNAs, and their mean expression in the 40 tissue samples was correlated with ER (ESR1) expression (R = 0.84) and ER IHC status (p < 0.0001). HER-2 gene expression (probe ERBB2 216836) expression ≥ 1500 defined clinical HER-2-positive status (IHC = 3 and/or FISH ratio ≥ 2) in 82 FNAs with 96% overall accuracy (95% CI, 90%–99%), and was validated with 100% overall accuracy (95% CI, 91%–100%) in 40 tissues. Conclusion: Expression values of ESR1, ERBB2, and a set of ER reporter genes from Affymetrix GeneChips accurately determined ER and HER-2 status, and were comparable in FNA and tissue samples from two independent laboratories. DNA microarrays could be become a single assay to report ER and HER-2 status included with other clinically relevant predictions. No significant financial relationships to disclose.