Brief Communication | Published:

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

Nature Methods volume 7, pages 133136 (2010) | Download Citation

Abstract

Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical samples: here we outline how restriction digestion targets bisulfite sequencing to hotspots of epigenetic regulation and describe a statistical method for assessing significance of altered DNA methylation patterns. Thirty nanograms of DNA was sufficient for genome-scale analysis and our protocol worked well on formalin-fixed, paraffin-embedded samples.

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Acknowledgements

We thank K. Halachev (Max Planck Institute for Informatics) for providing genome annotation files and H. Cedar (The Hebrew University of Jerusalem) for providing the human blood DNA samples. C.B. is supported by a Feodor Lynen Fellowship from the Alexander von Humboldt Foundation. A.M. is supported by the Massachusetts Life Science Center and the Pew Charitable Trusts. The described work was in part funded by US National Institutes of Health grants R01HG004401, U54HG03067 and U01ES017155.

Author information

Author notes

    • Hongcang Gu
    •  & Christoph Bock

    These authors contributed equally to this work.

Affiliations

  1. Broad Institute, Cambridge, Massachusetts, USA.

    • Hongcang Gu
    • , Christoph Bock
    • , Tarjei S Mikkelsen
    • , Natalie Jäger
    • , Zachary D Smith
    • , Eleni Tomazou
    • , Andreas Gnirke
    • , Eric S Lander
    •  & Alexander Meissner
  2. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.

    • Christoph Bock
    • , Natalie Jäger
    • , Zachary D Smith
    • , Eleni Tomazou
    •  & Alexander Meissner
  3. Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.

    • Christoph Bock
    • , Natalie Jäger
    • , Zachary D Smith
    • , Eleni Tomazou
    •  & Alexander Meissner
  4. Max Planck Institute for Informatics, Saarbrücken, Germany.

    • Christoph Bock
  5. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Eric S Lander
  6. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.

    • Eric S Lander

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Contributions

H.G., C.B., A.G., E.S.L. and A.M. conceived and designed the experiments; H.G. and E.T. performed the experiments; C.B. analyzed data; T.S.M., N.J. and Z.D.S. contributed materials or analysis tools; and H.G., C.B. and A.M. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Alexander Meissner.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–2 and Supplementary Table 1

Zip files

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    Supplementary Note

    Source code of Epigenome pipeline package with documentation and demonstration data.

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DOI

https://doi.org/10.1038/nmeth.1414

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