Genome-wide gene expression profiling to predict resistance to anthracyclines in breast cancer patients.
Validated biomarkers predictive of response/resistance to anthracyclines in breast cancer are currently lacking. The neoadjuvant Trial of Principle (TOP) study, in which patients with estrogen receptor (ER)-negative tumors were treated with anthracycline (epirubicin) monotherapy, was specifically designed to evaluate the predictive value of topoisomerase II-alpha (TOP2A) and develop a gene expression signature to identify those patients who do not benefit from anthracyclines. Here we describe in details the contents and quality controls for the gene expression and clinical data associated with the study published by Desmedt and colleagues in the Journal of Clinical Oncology in 2011 (Desmedt et al., 2011). We also provide R code to easily access the data and perform the quality controls and basic analyses relevant to this dataset.
Institut Jules Bordet, Brussels, Belgium ; Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium ; Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
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Haibe-Kains
Institut Jules Bordet, Brussels, Belgium.
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Desmedt
Hospital of Prato, Prato, Italy.
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Di Leo
Institut Jules Bordet, Brussels, Belgium.
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Azambuja
Institut Jules Bordet, Brussels, Belgium.
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Larsimont
Institut Jules Bordet, Brussels, Belgium.
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Selleslags
Institut Gustave Roussy, Villejuif, France.
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Delaloge
Centre Hospitalier du Luxembourg, Luxembourg.
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Duhem
HIS-Site Etterbeek-Ixelles, Brussels, Belgium.
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Kains
Hopital Saint-Pierre, Brussels, Belgium.
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Carly
Clinique Saint-Pierre, Ottignies, Belgium.
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Maerevoet
Clinique Ste Elisabeth, Namur, Belgium.
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Vindevoghel
Institut Jules Bordet, Brussels, Belgium.
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Rouas
Institut Jules Bordet, Brussels, Belgium.
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Lallemand
Institut Jules Bordet, Brussels, Belgium.
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Durbecq
Institut Jules Bordet, Brussels, Belgium.
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Cardoso
Institut Jules Bordet, Brussels, Belgium.
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Salgado
Institut Jules Bordet, Brussels, Belgium.
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Rovere
Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium.
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Bontempi
Institut Jules Bordet, Brussels, Belgium.
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Michiels
IDDI, Louvain-La-Neuve, Belgium.
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Buyse
Institut Jules Bordet, Brussels, Belgium.
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Nogaret
Institut Jules Bordet, Brussels, Belgium.
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Qi
The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA.
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Symmans
Yale Cancer Center, Yale University, New Haven, CT, USA.
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Pusztai
Institut Jules Bordet, Brussels, Belgium.
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D'Hondt
Institut Jules Bordet, Brussels, Belgium.
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Piccart-Gebhart
Institut Jules Bordet, Brussels, Belgium.
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Sotiriou
Anthracycline; Bioinformatics; Breast cancer; Gene expression; Microarray