E-GEOD-41656 - Gene expression analysis of a series of HER2+ of breast tumors

Status
Released on 22 October 2013, last updated on 2 June 2014
Organism
Homo sapiens
Samples (60)
Array (1)
Protocols (5)
Description
Abstract Motivation Breast cancer is a heterogeneous disease with distinct subtypes. Even within these subtypes differences at the molecular level are present which are reflected in variable responses to chemotherapy. We set out to identify genes associated with chemotherapy resistance by analyzing a set of HER2-positive breast cancers. Methods We collected, gene expression profiled and analyzed 60 HER2-positive breast tumor biopsies, obtained from patients scheduled to undergo neoadjuvant therapy. In addition to conventional supervised approaches for the detection of reporters of resistance, we report on a novel approach specifically tailored to the detection of small groups of resistant samples that show aberrant gene expression patterns. Results We propose a novel analytical approach that takes heterogeneity in response into account. We show that this approach is more powerful than classical approaches for detecting small subgroups of samples showing aberrant expression in a controlled setting. We applied this approach to our 60 breast cancer samples prior to neoadjuvant chemotherapy, and generated candidate response reporter lists for each subtype. Discussion Using a novel analytical approach we report on the mRNA gene expression analysis of a cohort of breast cancers prior to neoadjuvant chemotherapy. An important characteristic of this approach is that it takes heterogeneity in neoadjuvant treatment response into account. Such approaches are needed to identify biomarkers for predicting treatment response. We collected, gene expression profiled and analyzed 60 breast tumor biopsies, obtained from patients scheduled to undergo neoadjuvant therapy.
Experiment type
transcription profiling by array 
Contacts
Jelle Johannes ten Hoeve <j.t.hoeve@nki.nl>, Andrew Vincent, Esther Lips, Gabe Sonke, Guillem Rigaill, Jelle Wesseling, Jorma J de Ronde, Lennart Mulder, Lodewyk F Wessels, Marie-Jeanne Vrancken Peeters, Marja Nieuwland, Ron Kerkhoven, Sjoerd Rodenhuis
Citation
Identifying subgroup markers in heterogeneous populations. de Ronde JJ, Rigaill G, Rottenberg S, Rodenhuis S, Wessels LF. , Europe PMC 24062158
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-41656.idf.txt
Sample and data relationshipE-GEOD-41656.sdrf.txt
Processed data (1)E-GEOD-41656.processed.1.zip
Array designA-MEXP-1173.adf.txt
Links