Genomics

Dataset Information

47

Epigenetic signature of breast cancer and its association with gene expression and copy number


ABSTRACT: Recent advances in multiple whole genome technologies provide unprecedented opportunities to profile epigenomic signatures in cancer cells. Previously we used a human gene promoter tiling microarray platform to identify genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. Interestingly, the clustered nature of epigenetic targets that we identified, along with our concurrent karyotype analyses, have now led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy) may be superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes. This SuperSeries is composed of the SubSeries listed below. Overall design: Refer to individual Series. In the present study, we have refined our previous epigenetic profiling study by crossreferencing data sets generated from multiple whole-genome platforms. We undertook simultaneous highresolution, whole-genome analyses using Affymetrix gene expression (U133), promoter (1.0R) and SNP/CNV (SNP 6.0) microarray platforms to correlate epigenetic (DNA methylation), gene expression and combination single nucleotide polymorphism / copy number variant (SNP 6.0) microarrays in an isogenic paired cell line model of breast cancer metastasis.

INSTRUMENT(S): [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

SUBMITTER: Ann Chambers  

PROVIDER: GSE15619 | GEO | 2009-07-03

SECONDARY ACCESSION(S): GSE12122PRJNA116705 GSE11683 GSE14867S-EPMC2801616

REPOSITORIES: GEO

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Publications

Multi-platform whole-genome microarray analyses refine the epigenetic signature of breast cancer metastasis with gene expression and copy number.

Andrews Joseph J   Kennette Wendy W   Pilon Jenna J   Hodgson Alexandra A   Tuck Alan B AB   Chambers Ann F AF   Rodenhiser David I DI  

PloS one 20100113 1


<h4>Background</h4>We have previously identified genome-wide DNA methylation changes in a cell line model of breast cancer metastasis. These complex epigenetic changes that we observed, along with concurrent karyotype analyses, have led us to hypothesize that complex genomic alterations in cancer cells (deletions, translocations and ploidy) are superimposed over promoter-specific methylation events that are responsible for gene-specific expression changes observed in breast cancer metastasis.<h4  ...[more]

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