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

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.