Abstract PS3-08-26: Comparison of Breast Cancer Index Scores from Core-Needle Biopsies versus Surgical Excisions in Early-Stage Breast Cancer

Abstract Background: Breast cancers are typically diagnosed by core-needle biopsy (CNB) and managed with surgical excision. While CNB collects a small tissue sample for analysis, surgical excision involves removal of a larger amount of tissue, potentially affecting molecular profiling results due to differences in sample size and tissue processing. Breast Cancer Index (BCI) is a validated gene expression assay that provides the risk of overall (0-10 year) and late (5-10 year) distant recurrence and predicts the likelihood of benefit from extended endocrine therapy in hormone receptor positive (HR+) early-stage breast cancer. BCI validation in clinical studies has been performed largely from surgical excisions. This study compares BCI scores and its components, HOXB13/IL17BR ratio (H/I) and Molecular Grade Index (MGI), between CNBs versus surgical excisions submitted for routine BCI testing to evaluate the reliability of BCI results using CNB samples. Methods: Tissue samples were identified using the BCI clinical database, which contains anonymized gene expression data from commercial BCI cases from multiple centers in the U.S. and corresponding clinicopathologic variables. BCI, H/I, and MGI scores were retrieved from the database. The dataset was balanced for nodal status, tumor size, and tumor grade using stratified random sampling, yielding a cohort of CNB cases with a 1:5 matched excision group. Pairwise comparisons by sample type were conducted using BCI scores and delta CT values, which represent normalized gene expression levels adjusted for RNA input and RT-PCR efficiency, analyzed via the Wilcoxon signed-rank test. Results: Of 1,554 patients with HR+ early-stage breast cancer with BCI scores included, 262 (17%) were from CNB and 1292 (83%) samples were from surgical excisions. All patients had HR+ tumors, 92% were post-menopausal and average age was 68 years. Most tumors were T1 (n=1236, 80%) and Grade 2 (n=834, 54%). There were no significant differences in clinicopathologic variables between groups. Among all samples, 63% were classified as (H/I)-Low and 37% as (H/I)-High; 47% were BCI low risk and 53% high risk. In N0 patients (n=1,152), there were no significant differences between CNB and excision groups for BCI, H/I, or MGI scores. Expression of the two H/I genes HOXB13 and IL17BR was also not significantly different between both groups. Individual comparisons for the 5 MGI genes showed no significant differences, with the exception of RRM2 (p=0.0091). Similarly, in N1 patients (n=402) no statistical significance was observed in BCI, H/I and MGI score between the two groups. The comparison of H/I and MGI individual genes also showed no statistical significance between CNB and excision. Conclusion: From this large dataset, BCI, H/I and MGI scores, as well as individual gene expression levels, are comparable between CNB and surgical excision specimens in both N0 and N1 early-stage breast cancer patients, supporting the use of CNB tissue for genomic classification with BCI. Citation Format: N. S. Kapoor, N. K. Siuliukina, Y. Zhang, A. K. Anderson, B. O'Neal, J. Roberts, K. Church-Nguyen, K. Treuner, A. Bardia. Comparison of Breast Cancer Index Scores from Core-Needle Biopsies versus Surgical Excisions in Early-Stage Breast Cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS3-08-26.