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Open Access Highly Accessed Research article

Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue

Janine Antonov1, Vlad Popovici2, Mauro Delorenzi2, Pratyaksha Wirapati2, Anna Baltzer1, Andrea Oberli1, Beat Thürlimann38, Anita Giobbie-Hurder4, Giuseppe Viale5, Hans Jörg Altermatt6, Stefan Aebi178 and Rolf Jaggi1*

Author Affiliations

1 Department of Clinical Research, University of Bern, Bern, Switzerland

2 National Center of Competence in Research (NCCR) Molecular Oncology, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland

3 Senology Center of Eastern Switzerland, Kantonsspital, St. Gallen, Switzerland

4 International Breast Cancer Study Group Statistical Center, Dana-Farber Cancer Institute, Boston, MA, USA

5 Division of Pathology and Laboratory Medicine, European Institute of Oncology, University of Milan, Milan, Italy

6 Pathology Länggasse, Bern, Switzerland

7 Medical Oncology, University Hospital Bern, Bern, Switzerland

8 Swiss Group of Clinical Cancer Research (SAKK), Bern, Switzerland

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BMC Cancer 2010, 10:37  doi:10.1186/1471-2407-10-37

Published: 9 February 2010

Abstract

Background

The purpose of the work reported here is to test reliable molecular profiles using routinely processed formalin-fixed paraffin-embedded (FFPE) tissues from participants of the clinical trial BIG 1-98 with a median follow-up of 60 months.

Methods

RNA from fresh frozen (FF) and FFPE tumor samples of 82 patients were used for quality control, and independent FFPE tissues of 342 postmenopausal participants of BIG 1-98 with ER-positive cancer were analyzed by measuring prospectively selected genes and computing scores representing the functions of the estrogen receptor (eight genes, ER_8), the progesterone receptor (five genes, PGR_5), Her2 (two genes, HER2_2), and proliferation (ten genes, PRO_10) by quantitative reverse transcription PCR (qRT-PCR) on TaqMan Low Density Arrays. Molecular scores were computed for each category and ER_8, PGR_5, HER2_2, and PRO_10 scores were combined into a RISK_25 score.

Results

Pearson correlation coefficients between FF- and FFPE-derived scores were at least 0.94 and high concordance was observed between molecular scores and immunohistochemical data. The HER2_2, PGR_5, PRO_10 and RISK_25 scores were significant predictors of disease free-survival (DFS) in univariate Cox proportional hazard regression. PRO_10 and RISK_25 scores predicted DFS in patients with histological grade II breast cancer and in lymph node positive disease. The PRO_10 and PGR_5 scores were independent predictors of DFS in multivariate Cox regression models incorporating clinical risk indicators; PRO_10 outperformed Ki-67 labeling index in multivariate Cox proportional hazard analyses.

Conclusions

Scores representing the endocrine responsiveness and proliferation status of breast cancers were developed from gene expression analyses based on RNA derived from FFPE tissues. The validation of the molecular scores with tumor samples of participants of the BIG 1-98 trial demonstrates that such scores can serve as independent prognostic factors to estimate disease free survival (DFS) in postmenopausal patients with estrogen receptor positive breast cancer.

Trial Registration

Current Controlled Trials: NCT00004205