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Because the basal phenotype is characterised by the lack of expression of ERα, PR and HER2, it is sometimes referred to as triple-negative.
However, because the basal phenotype determined by IHC was strongly correlated with negative ER status (only one of the 50 ER-positive tumors stained positive for CK5/14), and because ER status has been shown to have a strong influence on the gene expression signature of breast tumors [ 2, 4, 6], we performed an analysis in the subset of ER-negative tumors (n = 50) separately.
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As shown in Figure 5A, each drug showed activity to those cells that exhibited the basal phenotype with a discrimination in relation to the luminal phenotype.
BluePrint almost always reconfirms the basal phenotype of TN patients.
All of these characteristics are associated with the basal phenotype.
These properties suggest that unfavorable-phenotype tumors take on not only the "HER2" phenotype [ 7] but also the "basal" phenotype.
The basal phenotype classification by Sorlie's intrinsic gene set correlated strongly with basal cytokeratin IHC (concordance 76%, p = 0.0011).
To this end, we made the assumption that the basal phenotype is equivalent with the hyperrepressed phenotype.
Here, we assumed that the basal phenotype is equivalent to the hyperrepressed phenotype, see Additional file 1 for details.
We have therefore decided to not include the basal phenotype in the main analysis.
Before banding these animals, however, we have undertaken a characterization of the basal phenotype.
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