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Series GSE22249 Query DataSets for GSE22249
Status Public on Oct 19, 2011
Title Epigenetic portraits of human breast cancers (methylation data 2)
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Breast cancer is a molecularly, biologically and clinically heterogeneous group of disorders. Understanding this diversity is essential to improving diagnosis and optimising treatment. Both genetic and acquired epigenetic abnormalities participate in cancer, but information is scant on the involvement of the epigenome in breast cancer and its contribution to the complexity of the disease. Here we used the Infinium Methylation Platform to profile at single-CpG resolution (over 14,000 genes interrogated) the methylomes of 119 breast tumours. It emerges that many genes whose expression is linked to the ER status are epigenetically controlled (or/ we show that the two major phenotypes of breast cancers determined by ER status are widely involving epigenetic regulatory mechanisms), offering the prospect of a novel approach to treating ER-positive tumours. We have distinguished methylation-profile-based tumour clusters, some coinciding with known “expression subtypes” but also new entities that may provide a meaningful basis for refining breast tumour typology. We show that methylation patterns may reflect the cellular origins of tumours. Having highlighted an unexpectedly strong epigenetic component in the regulation of key immune pathways, we show that a set of immune genes have high prognostic value in specific tumour categories. By laying the ground for better understanding of breast cancer heterogeneity and improved tumour taxonomy, the precise epigenetic portraits drawn here should contribute to better management of breast cancer patients.
 
Overall design 125 gene expression profiling of breast tissues (117 tumors + 8 normal). Study of epigenetic variation (methylation) linked to gene expression. No replicate, no reference sample.
 
Contributor(s) Dedeurwaerder S, Desmedt C, Calonne E, Singhal SK, Haibe-Kains B, Luciani J, Putmans P, Lallemand F, Larsimont D, Toussaint J, Haussy S, Rothé F, Rouas G, Metzger O, Georges M, Sotiriou C, Fuks F
Citation(s) 21910250
Submission date Jun 09, 2010
Last update date Jan 02, 2015
Contact name Benjamin Haibe-Kains
E-mail(s) benjamin.haibe.kains@utoronto.ca
Phone +14165818626
Organization name Princess Margaret Cancer Centre
Department Princess Margaret Research
Lab Bioinformatics and Computational Genomics
Street address 610 University Avenue
City Toronto
State/province Ontario
ZIP/Postal code M5G 2M9
Country Canada
 
Platforms (1)
GPL8490 Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
Samples (125)
GSM553748 Breast tumor from patient P2_104 (methylation data)
GSM553749 Breast tumor from patient P2_103 (methylation data)
GSM553750 Breast tumor from patient P2_105 (methylation data)
This SubSeries is part of SuperSeries:
GSE20713 Epigenetic portraits of human breast cancers
Relations
BioProject PRJNA128645

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
GSE22249_RAW.tar 5.8 Mb (http)(custom) TAR
GSE22249_non_normalized.txt.gz 18.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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