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Open Access Highly Accessed Technical advance

Decentral gene expression analysis: analytical validation of the Endopredict genomic multianalyte breast cancer prognosis test

Ralf Kronenwett1*, Kerstin Bohmann1, Judith Prinzler2, Bruno V Sinn2, Franziska Haufe1, Claudia Roth1, Manuela Averdick1, Tanja Ropers1, Claudia Windbergs1, Jan C Brase1, Karsten E Weber1, Karin Fisch1, Berit M Müller2, Marcus Schmidt3, Martin Filipits4, Peter Dubsky5, Christoph Petry1, Manfred Dietel2 and Carsten Denkert2

Author Affiliations

1 Sividon Diagnostics GmbH, Nattermannallee 1, 50829, Cologne, Germany

2 Institute of Pathology, Charité Hospital, Campus Mitte, Berlin, Germany

3 Department of Gynecology and Obstetrics, University of Mainz, Mainz, Germany

4 Department of Medicine I, Medical University of Vienna, Vienna, Austria

5 Department of Surgery, Medical University of Vienna, Vienna, Austria

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BMC Cancer 2012, 12:456  doi:10.1186/1471-2407-12-456

Published: 5 October 2012

Abstract

Background

EndoPredict (EP) is a clinically validated multianalyte gene expression test to predict distant metastasis in ER-positive, HER2-negative breast cancer treated with endocrine therapy alone. The test is based on the combined analysis of 12 genes in formalin-fixed, paraffin-embedded (FFPE) tissue by reverse transcription-quantitative real-time PCR (RT-qPCR). Recently, it was shown that EP is feasible for reliable decentralized assessment of gene expression. The aim of this study was the analytical validation of the performance characteristics of the assay and its verification in a molecular-pathological routine laboratory.

Methods

Gene expression values to calculate the EP score were assayed by one-step RT-qPCR using RNA from FFPE tumor tissue. Limit of blank, limit of detection, linear range, and PCR efficiency were assessed for each of the 12 PCR assays using serial samples dilutions. Different breast cancer samples were used to evaluate RNA input range, precision and inter-laboratory variability.

Results

PCR assays were linear up to Cq values between 35.1 and 37.2. Amplification efficiencies ranged from 75% to 101%. The RNA input range without considerable change of the EP score was between 0.16 and 18.5 ng/μl. Analysis of precision (variation of day, day time, instrument, operator, reagent lots) resulted in a total noise (standard deviation) of 0.16 EP score units on a scale from 0 to 15. The major part of the total noise (SD 0.14) was caused by the replicate-to-replicate noise of the PCR assays (repeatability) and was not associated with different operating conditions (reproducibility). Performance characteristics established in the manufacturer’s laboratory were verified in a routine molecular pathology laboratory. Comparison of 10 tumor samples analyzed in two different laboratories showed a Pearson coefficient of 0.995 and a mean deviation of 0.15 score units.

Conclusions

The EP test showed reproducible performance characteristics with good precision and negligible laboratory-to-laboratory variation. This study provides further evidence that the EP test is suitable for decentralized testing in specialized molecular pathological laboratories instead of a reference laboratory. This is a unique feature and a technical advance in comparison with existing RNA-based prognostic multigene expression tests.

Keywords:
Breast cancer; Prognostic multigene expression test; Analytical validation; PCR; Pathology