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Series GSE10886 Query DataSets for GSE10886
Status Public on Feb 11, 2009
Title A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Purpose: The biological subtypes of breast cancer designated as Luminal A, Luminal B, HER2+/ER-, and Basal-like are clinically important for prognosis and planning treatment strategies. Recognizing that there is a continuum in both the spectrum of breast cancer disease and the risk of survival, we sought to develop a clinical test for the biological subtypes using a supervised risk classier.Methods: Microarray and real-time quantitative RT-PCR (qRT-PCR) data from 189 samples, procured as fresh-frozen and formalin-fixed, paraffin-embedded tissues, were used to statistically select prototypical samples and genes for the biological subtypes of breast cancer. Predictions for biological subtype and risk of recurrence were determined for different stages of disease, treatments, and across analytical platforms. Results: The biological subtype predictions on a large combined microarray test set showed prognostic significance across all patients (1244 subjects; p<0.0001), on node negative patients with no adjuvant systemic therapy (738 subjects; p<0.0001), and on patients treated with endocrine therapy (404 subjects; p=0.001). Analysis of a neoadjuvant chemotherapy study revealed a high pathologic complete response (pCR) rate in HER2+/ER- and Basal-like patients. The subtype and risk predications were also highly significant when using the qRT-PCR assay from archived FFPE breast cancers. Conclusion: Our risk predictor based on distance to biological subtype centroids provides a continuous risk score that applies to all stages of breast cancer given current therapies. The assay can be performed using archived breast tissues and a real-time qRT-PCR assay, thus facilitating application to retrospective cohorts and clinical samples.
Keywords: reference x sample
Overall design Comparison of reference samples against treatment
Contributor(s) Parker JS, Perou CM, Bernard PS
Citation(s) 19204204
Submission date Mar 18, 2008
Last update date Feb 20, 2017
Contact name Charles M. Perou
Organization name University of North Carolina at Chapel Hill
Department Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
Street address 12-044 Lineberger Comprehensive Cancer Center CB# 7295
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7264
Country USA
Platforms (3)
GPL885 Agilent-011521 Human 1A Microarray G4110A (Feature Number version)
GPL887 Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)
GPL1390 Agilent Human 1A Oligo UNC custom Microarrays
Samples (226)
GSM34428 UB44
GSM34430 BR00-0587
GSM34431 UB37
BioProject PRJNA107283

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10886_RAW.tar 6.1 Mb (http)(custom) TAR
Processed data included within Sample table
Raw data included within Sample table

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