20009 Background: The risk of distant recurrence in patients with invasive breast carcinoma (BrCa) is predicted imperfectly by currently used factors (e.g. nuclear grade, hormone receptor status), complicating adjuvant therapy decisions. In an effort to discover biomarkers for recurrence, we retrospectively analyzed BrCa recurrence and tumor gene amplification. Multi-gene marker sets were evaluated for predictive significance and accuracy. Because studies of HER2 as a suitable biomarker report positive and negative results, we compared our marker sets with HER2. Methods: 229 of 723 BrCa patients met inclusion criteria: invasive ductal carcinoma, no isolated local recurrence, minimum 4 years follow-up, and archived specimens adequate for fluorescent in situ hybridization (FISH) assay. Study endpoint was recurrence, or non-recurrence throughout follow-up. FISH was performed on formalin-fixed paraffin sections with probes for previously identified genomic regions. Signals were counted with a Metasystems workstation, and used in a “Prognostic Index” (PI) to categorize recurrence risk. One-sided Fisher’s exact test was used to assess increased incidence of distant recurrence in relation to PI and HER2, and increased incidence of HER2 amplification in relation to PI. Results: Two separate 3-gene marker sets were obtained that predict clinical outcome for hormone receptor + (HR+) and hormone receptor − (HR−) tumors. In HR+ samples a PI based upon regions surrounding CYP24, PDCP6IP, and BIRC5 was the best predictor of recurrence, while for HR- specimens the PI was based on the NR1D1, SMARCE1, and BIRC5 regions. The PIs are significantly associated with recurrence of HR+ and HR− tumors (OR = 9.52, 95% CI > 2.12, p = 0.0024; and OR = 12.3, 95% CI > 1.45, p = 0.0188, respectively). However, tumor HER2 amplification was not prognostic for recurrence (OR = 1.76, 95% CI > 0.77, p = 0.1395). Furthermore, there was no significant association of PI with HER2 status (OR = 1.56, CI > 0.57, p = 0.862). Conclusions: Prognostic Indices based on copy numbers of two 3-gene marker sets significantly predict clinical outcome of stage I-III invasive ductal carcinoma. HER2 amplification, included in our previous whole genome survey but not present in our final marker sets, had no prognostic value. [Table: see text]
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