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100+ datasets found
  1. e

    Genome-wide DNA methylation analysis of breast cancer

    • ebi.ac.uk
    Updated Feb 28, 2016
  2. f

    Data from: Integrative analysis identifies potential DNA methylation...

    • tandf.figshare.com
    • commons.datacite.org
    docx
    Updated Feb 16, 2024
  3. n

    MethyCancer

    • neuinfo.org
    • dknet.org
    • +1more
    Updated Oct 14, 2024
  4. e

    Data from: DNA methylation screening identifies driver epigenetic events of...

    • ebi.ac.uk
    Updated Mar 15, 2012
    + more versions
  5. Data from: Partially methylated domains are hypervariable in breast cancer...

    • zenodo.org
    • explore.openaire.eu
    zip
    Updated Jan 24, 2020
    + more versions
  6. e

    Data from: Genome-wide DNA methylation profiles in progression to in situ...

    • ebi.ac.uk
    • omicsdi.org
    Updated Aug 7, 2014
    + more versions
  7. f

    Table_5_Co-occurrence and Mutual Exclusivity Analysis of DNA Methylation...

    • frontiersin.figshare.com
    xlsx
    Updated Jun 10, 2023
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  8. f

    Array-Based DNA Methylation Profiling for Breast Cancer Subtype...

    • figshare.com
    • omicsdi.org
    tiff
    Updated May 31, 2023
  9. f

    Table11_Pan-Cancer DNA Methylation Analysis and Tumor Origin Identification...

    • frontiersin.figshare.com
    xlsx
    Updated May 31, 2023
    + more versions
  10. f

    Identification of Novel High-Frequency DNA Methylation Changes in Breast...

    • plos.figshare.com
    pdf
    Updated Jun 1, 2023
    + more versions
  11. o

    Genome-wide DNA methylation mapping in breast cancer cells (HCC1954) and...

    • omicsdi.org
    Updated Jan 25, 2023
  12. e

    DNA methylation and expression profiling study for prostate cancer

    • ebi.ac.uk
    • omicsdi.org
    Updated Jul 23, 2011
    + more versions
  13. e

    DNA methylation and hormone receptor status in breast cancer, the BCCC study...

    • ebi.ac.uk
    Updated Feb 11, 2016
  14. e

    Breast tumor DNA methylation

    • ebi.ac.uk
    • omicsdi.org
    Updated Jul 27, 2010
    + more versions
  15. o

    DNA methylation profiling in the Carolina Breast Cancer Study

    • omicsdi.org
    xml
    Updated Jan 1, 2017
    + more versions
  16. e

    Integrative Analyses of Gene Expression and DNA Methylation Profiles in a...

    • ebi.ac.uk
    Updated Feb 2, 2014
  17. E

    Data from: DNA methylation database for gynecological cancer detection,...

    • ega-archive.org
  18. o

    DNA methylation in ductal carcinoma in situ related with future development...

    • omicsdi.org
    Updated Mar 31, 2023
  19. MIMESIS Paper Supplementary Dataset

    • zenodo.org
    application/gzip
    Updated Apr 12, 2024
  20. o

    Global Analysis of DNA Methylation by Methyl-Capture Sequencing Reveals...

    • omicsdi.org
    • datamed.org
    Updated Jun 14, 2019
    + more versions
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Markus Ringner; Markus Ringnér; Karolina Holm; Johan Staaf; Göran Jönsson (2016). Genome-wide DNA methylation analysis of breast cancer [Dataset]. https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-75067

Genome-wide DNA methylation analysis of breast cancer

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12 scholarly articles cite this dataset (View in Google Scholar)
Dataset updated
Feb 28, 2016
Authors
Markus Ringner; Markus Ringnér; Karolina Holm; Johan Staaf; Göran Jönsson
Description

Aberrant DNA methylation is frequently observed in breast cancer. However, the relationship between methylation patterns and the heterogeneity of breast cancer has not been comprehensively characterized. Whole-genome DNA methylation analysis using 450K Illumina BeadArrays was performed on 188 human breast tumors. Unsupervised bootstrap consensus clustering was performed to identify DNA methylation epigenetic subgroups (epitypes). The Cancer Genome Atlas data, incluing methylation profiles of 669 human breast tumors, was utilized for validation. The identified epitypes were characterized by integration with publicly available genome-wide data, including gene expression levels, DNA copy numbers, whole-exome sequencing data, and chromatin states. We identified seven breast cancer epitypes. One epitype was distinctly associated with basal-like tumors and with BRCA1 mutations, one epitype contained a subset of ERBB2-amplified tumors characterized by multiple additional amplifications and the most complex genomes, and one epitype displayed a methylation profile similar to normal epithelial cells. Luminal tumors were stratified into the remaining four epitypes, with differences in promoter hypermethylation, global hypomethylation, proliferative rates and genomic instability. We observed two dominant patterns of aberrant methylation in breast cancer. One pattern, constitutively methylated in both basal-like and luminal breast cancer, was linked to genes with promoters in a Polycomb-repressed state in normal epithelial cells and displayed no correlation to gene expression levels. The second pattern correlated with gene expression levels and was associated with methylation in luminal tumors and genes with active promoters in normal epithelial cells. Our results suggest that hypermethylation patterns in basal-like breast cancer may have limited influence on tumor progression and instead reflects the repressed chromatin state of the tissue of origin. On the contrary, hypermethylation patterns specific to luminal breast cancer influence gene expression, may contribute to tumor progression, and may present an actionable epigenetic alteration in some luminal breast cancers. Genome-wide DNA methylation analysis of 188 breast cancers using Illumina Human Methylation 450K Beadchips.

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