Analytical Validation of a Novel 6-Gene Signature for Prediction of Distant Recurrence in Estrogen Receptor-Positive, HER2-Negative, Early-Stage Breast Cancer

Tony Loughman, Stephen Barron, Chan-Ju Angel Wang, Peter Dynoodt, Bozena Fender, Cesar Lopez-Ruiz, Sharon Stapleton, Aurelie Fabre, Cecily Quinn, Björn Nodin, Karin Jirström, Fatemeh Razmara, Anthony O’Grady, Anne-Marie Baird, Steven G. Gray, Ana Freixo, Cathy B. Moelans, Paul J. van Diest, Michael J. Duffy, Desmond O’LearyJohn Crown, Adrian P. Bracken, William M. Gallagher

Research output: Contribution to journalArticlepeer-review

Abstract

Background
OncoMasTR is a recently developed multigene prognostic test for early-stage breast cancer. The test has been developed in a kit-based format for decentralized deployment in molecular pathology laboratories. The analytical performance characteristics of the OncoMasTR test are described in this study.
Methods
Expression levels of 6 genes were measured by 1-step reverse transcription-quantitative PCR on RNA samples prepared from formalin-fixed, paraffin-embedded (FFPE) breast tumor specimens. Assay precision, reproducibility, input range, and interference were determined using FFPE-derived RNA samples representative of low and high prognostic risk scores. A pooled RNA sample derived from 6 FFPE breast tumor specimens was used to establish the linear range, limit of detection, and amplification efficiency of the individual gene expression assays.
Results
The overall precision of the OncoMasTR test was high with an SD of 0.16, which represents less than 2% of the 10-unit risk score range. Test results were reproducible across 4 testing sites, with correlation coefficients of 0.94 to 0.96 for the continuous risk score and concordance of 86% to 96% in low-/high-risk sample classification. Consistent risk scores were obtained across a > 100-fold RNA input range. Individual gene expression assays were linear up to quantification cycle values of 36.0 to 36.9, with amplification efficiencies of 80% to 102%. Test results were not influenced by agents used during RNA isolation, by low levels of copurified genomic DNA, or by moderate levels of copurified adjacent nontumor tissue.
Conclusion
The OncoMasTR prognostic test displays robust analytical performance that is suitable for deployment by local pathology laboratories for decentralized use.
Original languageEnglish
Pages (from-to)837-847
JournalClinical Chemistry
Volume68
Issue number6
DOIs
Publication statusPublished - 2022 Jun 1

Subject classification (UKÄ)

  • Cancer and Oncology

Free keywords

  • RT-qPCR
  • breast cancer
  • gene expression
  • prognostic biomarker

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