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Series GSE4779 Query DataSets for GSE4779
Status Public on Dec 19, 2008
Title A stroma-related gene signature predicts sensitivity to epirubicin-containing neoadjuvant chemotherapy in breast cancer.
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The goal of the study was to identify a gene expression signature capable of predicting a pathological complete response following neoadjuvant anthracycline-based chemotherapy of breast cancer. The samples were taken from the FEC arm (5-fluorouracil, epirubicin, cyclophosphamide) of the EORTC 10994 trial. EORTC 10994 is a phase III clinical trial comparing FEC with ET (epirubicin, docetaxel) in patients with large operable, locally advanced or inflammatory breast cancer (www.eortc.be). Frozen biopsies were taken at randomisation. RNA was extracted from 100um thickness of 14G core needle biopsies. Adjacent sections were tested by H&E to confirm >20% tumour cell content. 200 ng total RNA per chip was amplified using the Affymetrix small sample protocol (IVT then Enzo). 102 tumours were tested on Affymetrix X3P chips. Single biopsies were tested per tumour. The CEL files were quantile normalised using rma. The clinical response measure was pathological complete response (pCR, disappearance of the tumour after chemotherapy with at most scattered invasive cells detected by histology).
 
Overall design 102 tumors
 
Contributor(s) Farmer P, Bonnefoi H, Iggo R
Citation(s) 19122658
Submission date May 05, 2006
Last update date Jun 06, 2022
Contact name Mauro Delorenzi
E-mail(s) Mauro.Delorenzi@unil.ch
Organization name Swiss Institute of Bioinformatics
Lab BCF
Street address GĂ©nopode Building, Quartier Sorge
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platforms (1)
GPL1352 [U133_X3P] Affymetrix Human X3P Array
Samples (102)
GSM107986 HB01
GSM139539 HB02
GSM139540 HB03
Relations
BioProject PRJNA95553

Clinical Data header descriptions
GSM ids
Name
Label (pCR - pathologic complete response, nPCR - near pCR)
Estrogen Receptor (Ep - ER positive, En - ER negative, E- - unknown)
Progesterone Receptor (Pp - PR positive, Pn - PR negative, P- - unknown)
Size
Node

Data table
GSM ids Name Label (pCR - pathologic complete response, nPCR - near pCR) Estrogen Receptor (Ep - ER positive, En - ER negative, E- - unknown) Progesterone Receptor (Pp - PR positive, Pn - PR negative, P- - unknown) Size Node
GSM107986 HB01 npCR Ep P- T3 N1
GSM139539 HB02 npCR En Pn T2 N0
GSM139540 HB03 npCR Ep Pp T2 N0
GSM139541 HB04 pCR Ep Pp T2 N1
GSM139542 HB05 npCR En Pn T2 N1
GSM139543 HB06 pCR Ep Pp T3 N1
GSM139544 HB07 npCR En Pn T3 N0
GSM139545 HB08 npCR Ep Pn T2 N1
GSM139546 HB09 npCR Ep Pn T2 N0
GSM139547 HB10 npCR En Pp T2 N0
GSM139548 HB11 npCR En Pn T2 N1
GSM139549 HB12 npCR En Pn T2 N1
GSM139550 HB13 pCR En Pn T2 N1
GSM139551 HB14 pCR En Pn T3 N2
GSM139552 HB15 npCR En Pn T3 N0
GSM139553 HB16 npCR Ep Pn T2 N1
GSM139554 HB17 npCR En Pn T2 N1
GSM139555 HB18 npCR Ep Pp T3 N1
GSM139556 HB19 npCR Ep Pp T2 N0
GSM139557 HB20 pCR En Pn T2 N0

Total number of rows: 102

Table truncated, full table size 3 Kbytes.




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
GSE4779_RAW.tar 882.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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