Journal Article
. 2014 Mar; 14:177.
doi: 10.1186/1471-2407-14-177.

Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens

Torsten Nielsen 1 Brett Wallden  Carl Schaper  Sean Ferree  Shuzhen Liu  Dongxia Gao  Garrett Barry  Naeem Dowidar  Malini Maysuria  James Storhoff  
Affiliations
  • PMID: 24625003
  •     36 References
  •     102 citations

Abstract

Background: NanoString's Prosigna™ Breast Cancer Prognostic Gene Signature Assay is based on the PAM50 gene expression signature. The test outputs a risk of recurrence (ROR) score, risk category, and intrinsic subtype (Luminal A/B, HER2-enriched, Basal-like). The studies described here were designed to validate the analytical performance of the test on the nCounter Analysis System across multiple laboratories.

Methods: Analytical precision was measured by testing five breast tumor RNA samples across 3 sites. Reproducibility was measured by testing replicate tissue sections from 43 FFPE breast tumor blocks across 3 sites following independent pathology review at each site. The RNA input range was validated by comparing assay results at the extremes of the specified range to the nominal RNA input level. Interference was evaluated by including non-tumor tissue into the test.

Results: The measured standard deviation (SD) was less than 1 ROR unit within the analytical precision study and the measured total SD was 2.9 ROR units within the reproducibility study. The ROR scores for RNA inputs at the extremes of the range were the same as those at the nominal input level. Assay results were stable in the presence of moderate amounts of surrounding non-tumor tissue (<70% by area).

Conclusions: The analytical performance of NanoString's Prosigna assay has been validated using FFPE breast tumor specimens across multiple clinical testing laboratories.

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Loki Natarajan, Minya Pu, +10 authors, Karen Messer.
Cancer Epidemiol Biomarkers Prev, 2019 Jun 13; 28(9). PMID: 31186261    Free PMC article.
Indications for prognostic gene expression profiling in early breast cancer.
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Curr Treat Options Oncol, 2015 May 02; 16(5). PMID: 25929335
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The Prosigna 50-gene profile and responsiveness to adjuvant anthracycline-based chemotherapy in high-risk breast cancer patients.
Maj-Britt Jensen, Anne-Vibeke Lænkholm, +9 authors, Bent Ejlertsen.
NPJ Breast Cancer, 2020 Mar 07; 6. PMID: 32140564    Free PMC article.
A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer.
Rachel L Stewart, Katherine L Updike, +4 authors, Katherine E Varley.
Cancer Res, 2019 May 03; 79(13). PMID: 31048497    Free PMC article.
Highly robust model of transcription regulator activity predicts breast cancer overall survival.
Chuanpeng Dong, Jiannan Liu, +6 authors, Yunlong Liu.
BMC Med Genomics, 2020 Apr 04; 13(Suppl 5). PMID: 32241272    Free PMC article.
Fatigue following radiotherapy of low-risk early breast cancer - a randomized controlled trial of intraoperative electron radiotherapy versus standard hypofractionated whole-breast radiotherapy: the COSMOPOLITAN trial (NCT03838419).
Tobias Forster, Cornelia Jäkel, +15 authors, Juliane Hörner-Rieber.
Radiat Oncol, 2020 Jun 04; 15(1). PMID: 32487184    Free PMC article.
A Novel 4-Gene Score to Predict Survival, Distant Metastasis and Response to Neoadjuvant Therapy in Breast Cancer.
Masanori Oshi, Eriko Katsuta, +5 authors, Kazuaki Takabe.
Cancers (Basel), 2020 May 07; 12(5). PMID: 32370309    Free PMC article.
Unraveling the Genomic-Epigenomic Interaction Landscape in Triple Negative and Non-Triple Negative Breast Cancer.
Jiande Wu, Tarun Karthik Kumar Mamidi, Lu Zhang, Chindo Hicks.
Cancers (Basel), 2020 Jun 18; 12(6). PMID: 32545594    Free PMC article.
Delineation of the Germline and Somatic Mutation Interaction Landscape in Triple-Negative and Non-Triple-Negative Breast Cancer.
Jiande Wu, Tarun K K Mamidi, Lu Zhang, Chindo Hicks.
Int J Genomics, 2020 Jul 30; 2020. PMID: 32724790    Free PMC article.
Ribonucleotide reductase small subunit M2 is a master driver of aggressive prostate cancer.
Ying Z Mazzu, Joshua Armenia, +8 authors, Philip W Kantoff.
Mol Oncol, 2020 May 10; 14(8). PMID: 32385899    Free PMC article.
Improving clinical management of colon cancer through CONNECTION, a nation-wide colon cancer registry and stratification effort (CONNECTION II trial): rationale and protocol of a single arm intervention study.
I van den Berg, S van de Weerd, +15 authors, CONNECTION-study group.
BMC Cancer, 2020 Aug 20; 20(1). PMID: 32811457    Free PMC article.
Machine learning for RNA sequencing-based intrinsic subtyping of breast cancer.
Silvia Cascianelli, Ivan Molineris, +2 authors, Enzo Medico.
Sci Rep, 2020 Aug 23; 10(1). PMID: 32826944    Free PMC article.
The Potential Use of Tumour-Based Prognostic and Predictive Tools in Older Women with Primary Breast Cancer: A Narrative Review.
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Oncol Ther, 2020 Jul 24; 8(2). PMID: 32700048    Free PMC article.
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Quadruple Negative Breast Cancers (QNBC) Demonstrate Subtype Consistency among Primary and Recurrent or Metastatic Breast Cancer.
Anusha Angajala, Essynce Mothershed, +5 authors, Clayton Yates.
Transl Oncol, 2018 Dec 30; 12(3). PMID: 30594038    Free PMC article.
Banff 2019 Meeting Report: Molecular diagnostics in solid organ transplantation-Consensus for the Banff Human Organ Transplant (B-HOT) gene panel and open source multicenter validation.
Michael Mengel, Alexandre Loupy, +17 authors, Robert B Colvin.
Am J Transplant, 2020 May 20; 20(9). PMID: 32428337    Free PMC article.
Genomic Signatures in Luminal Breast Cancer.
Julian Puppe, Tabea Seifert, +3 authors, Wolfram Malter.
Breast Care (Basel), 2020 Sep 29; 15(4). PMID: 32982645    Free PMC article.
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Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE).
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Clin Cancer Res, 2020 Jun 20; 26(20). PMID: 32554541    Free PMC article.
Seven-Year Follow-Up Analysis of Adjuvant Paclitaxel and Trastuzumab Trial for Node-Negative, Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer.
Sara M Tolaney, Hao Guo, +23 authors, Eric P Winer.
J Clin Oncol, 2019 Apr 03; 37(22). PMID: 30939096    Free PMC article.
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PIWI-Like 1 and PIWI-Like 2 Expression in Breast Cancer.
Ramona Erber, Julia Meyer, +11 authors, Matthias Ruebner.
Cancers (Basel), 2020 Sep 30; 12(10). PMID: 32987715    Free PMC article.
Artificial Intelligence Applied to in vitro Gene Expression Testing (IVIGET) to Predict Trivalent Inactivated Influenza Vaccine Immunogenicity in HIV Infected Children.
Nicola Cotugno, Veronica Santilli, +14 authors, Paolo Palma.
Front Immunol, 2020 Oct 31; 11. PMID: 33123133    Free PMC article.
Resistance to endocrine therapy in breast cancer: molecular mechanisms and future goals.
Małgorzata Szostakowska, Alicja Trębińska-Stryjewska, Ewa Anna Grzybowska, Anna Fabisiewicz.
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Analytical validation of CanAssist-Breast: an immunohistochemistry based prognostic test for hormone receptor positive breast cancer patients.
Arun Kumar Attuluri, Chandra Prakash V Serkad, +9 authors, Manjiri M Bakre.
BMC Cancer, 2019 Mar 22; 19(1). PMID: 30894144    Free PMC article.
An Improved, Assay Platform Agnostic, Absolute Single Sample Breast Cancer Subtype Classifier.
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Cancers (Basel), 2020 Dec 02; 12(12). PMID: 33255759    Free PMC article.
Scalable Signature-Based Molecular Diagnostics Through On-chip Biomarker Profiling Coupled with Machine Learning.
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HER2-Enriched Subtype and ERBB2 Expression in HER2-Positive Breast Cancer Treated with Dual HER2 Blockade.
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J Natl Cancer Inst, 2019 May 01; 112(1). PMID: 31037288    Free PMC article.
Survival outcomes are associated with genomic instability in luminal breast cancers.
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PLoS One, 2021 Feb 04; 16(2). PMID: 33534788    Free PMC article.
Advanced Approaches to Breast Cancer Classification and Diagnosis.
M Zubair, S Wang, N Ali.
Front Pharmacol, 2021 Mar 16; 11. PMID: 33716731    Free PMC article.
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Creation and validation of models to predict response to primary treatment in serous ovarian cancer.
Jesus Gonzalez Bosquet, Eric J Devor, +7 authors, Kimberly K Leslie.
Sci Rep, 2021 Mar 18; 11(1). PMID: 33727600    Free PMC article.
The immune profile of small HER2-positive breast cancers: a secondary analysis from the APT trial.
R Barroso-Sousa, W T Barry, +14 authors, S M Tolaney.
Ann Oncol, 2019 Feb 13; 30(4). PMID: 30753274    Free PMC article.
In silico screening using bulk and single-cell RNA-seq data identifies RIMS2 as a prognostic marker in basal-like breast cancer: A retrospective study.
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Immune response drives outcomes in prostate cancer: implications for immunotherapy.
Jialin Meng, Yujie Zhou, +7 authors, Chaozhao Liang.
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Independent Validation of the PAM50-Based Chemo-Endocrine Score (CES) in Hormone Receptor-Positive HER2-Positive Breast Cancer Treated with Neoadjuvant Anti-HER2-Based Therapy.
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