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Series GSE23720 Query DataSets for GSE23720
Status Public on Mar 01, 2011
Title High-resolution comparative genomic hybridization of inflammatory breast cancer and identification of candidate genes
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by array
Summary Inflammatory breast cancer (IBC) is an aggressive form of BC poorly defined at the molecular level. We compared the molecular portraits of 63 IBC and 134 non-IBC (nIBC) clinical samples. Genomic imbalances of 49 IBCs and 124 nIBCs were determined using high-resolution array-comparative genomic hybridization, and mRNA expression profiles of 197 samples using whole-genome microarrays. Genomic profiles of IBCs were as heterogeneous as those of nIBCs, and globally relatively close. However, IBCs showed more frequent “complex” patterns and a higher percentage of genes with CNAs per sample. The number of altered regions was similar in both types, although some regions were altered more frequently and/or with higher amplitude in IBCs. Many genes were similarly altered in both types; however, more genes displayed recurrent amplifications in IBCs.
Overall design Pre-treatment tumor tissues were collected from 197 patients with invasive adenocarcinomas. Patients underwent surgical biopsies or initial surgery at the Institut Paoli-Calmettes (IPC, Marseille, France) between 1987 and 2007. Each patient gave written informed consent and the study was approved by the IPC “Comité d’Orientation Stratégique”. Tumor samples were macrodissected and frozen in liquid nitrogen within 30 minutes of removal. Before RNA extraction, tumor sections were reviewed by two pathologists and contained more than 60% of tumor cells. Gene expression data of the 197 BCs were quantified using whole-genome DNA microarrays (HG-U133 Plus 2.0, Affymetrix).
Contributor(s) Bekhouche I, Finetti P, Adelaïde J, Ferrar A, Tarpin C, Charafe-Jauffret E, Charpin C, Houvenaeghel G, Jacquemier J, Bidaut G, Birnbaum D, Viens P, Chaffanet M, Bertucci F
Citation(s) 21339811, 22110708, 22666420
Submission date Aug 19, 2010
Last update date Oct 31, 2019
Contact name Pascal FINETTI
Phone (33)+4 91 22 33 04
Organization name Institut Paoli-Calmettes
Department Centre de cancérologie de Marseille
Lab Molecular Oncology
Street address 232 Bd Ste Marguerite
City Marseille
State/province BdR
ZIP/Postal code 13009
Country France
Platforms (2)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL9128 Agilent-014693 Human Genome CGH Microarray 244A (Probe name version)
Samples (370)
GSM585300 T1
GSM585301 T2
GSM585302 T3
BioProject PRJNA130683

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
GSE23720_RAW.tar 5.1 Gb (http)(custom) TAR (of CEL, TXT)
Processed data included within Sample table

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