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

Loughman, Tony ; Barron, Stephen ; Wang, Chan-Ju Angel ; Dynoodt, Peter ; Fender, Bozena ; Lopez-Ruiz, Cesar ; Stapleton, Sharon ; Fabre, Aurelie ; Quinn, Cecily and Nodin, Björn LU , et al. (2022) In Clinical Chemistry 68(6). p.837-847
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... (More)
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. (Less)
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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
RT-qPCR, breast cancer, gene expression, prognostic biomarker
in
Clinical Chemistry
volume
68
issue
6
pages
837 - 847
publisher
American Association for Clinical Chemistry
external identifiers
  • pmid:35312747
  • scopus:85131223550
ISSN
0009-9147
DOI
10.1093/clinchem/hvac028
language
English
LU publication?
yes
id
c80064a3-205c-4e8d-9df9-6ca0a54ba164
date added to LUP
2022-07-16 08:37:53
date last changed
2024-01-29 02:55:16
@article{c80064a3-205c-4e8d-9df9-6ca0a54ba164,
  abstract     = {{Background<br/>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.<br/>Methods<br/>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.<br/>Results<br/>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 &gt; 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.<br/>Conclusion<br/>The OncoMasTR prognostic test displays robust analytical performance that is suitable for deployment by local pathology laboratories for decentralized use.}},
  author       = {{Loughman, Tony and Barron, Stephen and Wang, Chan-Ju Angel and Dynoodt, Peter and Fender, Bozena and Lopez-Ruiz, Cesar and Stapleton, Sharon and Fabre, Aurelie and Quinn, Cecily and Nodin, Björn and Jirström, Karin and Razmara, Fatemeh and O’Grady, Anthony and Baird, Anne-Marie and Gray, Steven G. and Freixo, Ana and Moelans, Cathy B. and van Diest, Paul J. and Duffy, Michael J. and O’Leary, Desmond and Crown, John and Bracken, Adrian P. and Gallagher, William M.}},
  issn         = {{0009-9147}},
  keywords     = {{RT-qPCR; breast cancer; gene expression; prognostic biomarker}},
  language     = {{eng}},
  month        = {{06}},
  number       = {{6}},
  pages        = {{837--847}},
  publisher    = {{American Association for Clinical Chemistry}},
  series       = {{Clinical Chemistry}},
  title        = {{Analytical Validation of a Novel 6-Gene Signature for Prediction of Distant Recurrence in Estrogen Receptor-Positive, HER2-Negative, Early-Stage Breast Cancer}},
  url          = {{http://dx.doi.org/10.1093/clinchem/hvac028}},
  doi          = {{10.1093/clinchem/hvac028}},
  volume       = {{68}},
  year         = {{2022}},
}