Research article

Comparison of gene expression profiles in core biopsies and corresponding surgical breast cancer samples

Rosanna Zanetti-Dällenbach¹ , Vincent Vuaroqueaux^2,3 , Edward Wight¹ , Martin Labuhn³ , Gad Singer⁴ , Patrick Urban² , Urs Eppenberger² , Wolfgang Holzgreve¹ and Serenella Eppenberger-Castori²

¹  Women's University Hospital Basel, Switzerland

²  Stiftung Tumorbank Basel, Switzerland

³  OncoScore AG, Riehen, Switzerland

⁴  Department of Pathology, University Hospital Basel, Switzerland

author email corresponding author email

Breast Cancer Research 2006, 8:R51doi:10.1186/bcr1542

Published:	18 August 2006

Abstract

Introduction

Gene expression profiling has been successfully used to classify breast cancer into clinically distinct subtypes, and to predict the risk of recurrence and treatment response. The aim of this study was to investigate whether the gene expression profile (GEP) detected in a core biopsy (CB) is representative for the entire tumor, since CB is an important tool in breast cancer diagnosis. Moreover, we investigated whether performing CBs prior to the surgical excision could influence the GEP of the respective tumor.

Methods

We quantified the RNA expression of 60 relevant genes by quantitative real-time PCR in paired CBs and surgical specimens from 22 untreated primary breast cancer patients. Subsequently, expression data were compared with independent GEPs obtained from tumors of 317 patients without preceding CB.

Results

In 82% of the cases the GEP detected in the CB correlated very well with the corresponding profile in the surgical sample (r_s ≥ 0.95, p < 0.001). Gene-by-gene analysis revealed four genes significantly elevated in the surgical sample compared to the CB; these comprised genes mainly involved in inflammation and the wound repair process as well as in tumor invasion and metastasis.

Conclusion

A GEP detected in a CB are representative for the entire tumor and is, therefore, of clinical relevance. The observed alterations of individual genes after performance of CB deserve attention since they might impact the clinical interpretation with respect to prognosis and therapy prediction of the GEP as detected in the surgical specimen following CB performance.