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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 Nielsen14*, Brett Wallden2, Carl Schaper3, Sean Ferree2, Shuzhen Liu1, Dongxia Gao1, Garrett Barry1, Naeem Dowidar2, Malini Maysuria2 and James Storhoff2

Author Affiliations

1 British Columbia Cancer Agency, 3427 - 600 W 10TH Avenue, V5Z 4E6 Vancouver, BC, Canada

2 NanoString Technologies, Inc., 530 Fairview Avenue North, Suite 2000, Seattle, WA, USA

3 Myraqa, 3 Lagoon Drive, Redwood Shores, CA, USA

4 Anatomical Pathology JPN 1401, Vancouver Hospital, 855 W. 12th Ave, V5Z 1 M9 Vancouver, BC, Canada

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BMC Cancer 2014, 14:177  doi:10.1186/1471-2407-14-177

Published: 13 March 2014



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.


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.


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).


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

PAM50; Analytical validation; ROR; Subtype; Breast cancer; Prosigna; NanoString; nCounter; Reproducibility; FFPE; Gene expression