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Series GSE41656 Query DataSets for GSE41656
Status Public on Oct 22, 2013
Title Gene expression analysis of a series of HER2+ of breast tumors
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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.
 
Overall design We collected, gene expression profiled and analyzed 60 breast tumor biopsies, obtained from patients scheduled to undergo neoadjuvant therapy.
 
Contributor(s) de Ronde JJ, Lips E, Mulder L, Rigaill G, Vincent A, Wesseling J, Nieuwland M, Kerkhoven R, Vrancken Peeters M, Sonke G, Rodenhuis S, Wessels LF
Citation(s) 24062158
Submission date Oct 17, 2012
Last update date Feb 18, 2019
Contact name Jelle Johannes ten Hoeve
E-mail(s) j.t.hoeve@nki.nl
Organization name Netherlands Cancer Institute
Department Molecular Biology
Lab Bioinformatics and Statistics
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
 
Platforms (1)
GPL6884 Illumina HumanWG-6 v3.0 expression beadchip
Samples (60)
GSM842410 pCR+npCR mamma breast cancer BC_4531933092_F
GSM842411 pCR+npCR mamma breast cancer BC_4531933069_B
GSM842412 pCR+npCR mamma breast cancer BC_4531933069_F
Relations
BioProject PRJNA177841

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
GSE41656_RAW.tar 6.3 Mb (http)(custom) TAR
GSE41656_non-normalized.txt.gz 15.0 Mb (ftp)(http) TXT
Processed data included within Sample table
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