Abstract
Targeted quantification of DNA methylation allows for interrogation of the most informative loci across many samples quickly and cost-effectively. Here we report improved bisulfite padlock probes (BSPPs) with a design algorithm to generate efficient padlock probes, a library-free protocol that dramatically reduces sample-preparation cost and time and is compatible with automation, and an efficient bioinformatics pipeline to accurately obtain both methylation levels and genotypes from sequencing of bisulfite-converted DNA.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Deng, J. et al. Nat. Biotechnol. 27, 353–360 (2009).
Liu, G.H. et al. Nature 472, 221–225 (2011).
Liu, G.H. et al. Cell Stem Cell 8, 688–694 (2011).
Xu, Y. et al. Mol. Cell 42, 451–464 (2011).
Hansen, K.D. et al. Nat. Genet. 43, 768–775 (2011).
Gore, A. et al. Nature 471, 63–67 (2011).
Wang, H. et al. Genome Res. 20, 981–988 (2010).
Turner, E.H., Lee, C., Ng, S.B., Nickerson, D.A. & Shendure, J. Nat. Methods 6, 315–316 (2009).
Shoemaker, R., Deng, J., Wang, W. & Zhang, K. Genome Res. 20, 883–889 (2010).
Irizarry, R.A. et al. Nat. Genet. 41, 178–186 (2009).
Doi, A. et al. Nat. Genet. 41, 1350–1353 (2009).
Lister, R. et al. Nature 462, 315–322 (2009).
Figueroa, M.E. et al. Cancer Cell 17, 13–27 (2010).
McLean, C.Y. et al. Nat. Biotechnol. 28, 495–501 (2010).
Lister, R. et al. Nature 471, 68–73 (2011).
Acknowledgements
We thank A. Feinberg and J. Stamatoyannopoulos for providing informative genomic targets, and E. LeProust (Agilent Technology) for long-oligonucleotide synthesis. This work was funded by grants from US National Institutes of Health (R01 DA025779 and R01 GM097253) to K.Z.; A.G. is sponsored by a California Institute of Regenerative Medicine predoctoral fellowship. N.P. is supported by the Royal Thai Government Scholarship.
Author information
Authors and Affiliations
Contributions
K.Z. oversaw the project. D.D. and N.P. performed experiments and bioinformatic analyses. A.G. developed a probe design algorithm. R.S. and A.G. designed probes. H.-L.F. performed sequencing. D.D., N.P., A.G. and K.Z. wrote the manuscript.
Corresponding author
Ethics declarations
Competing interests
K.Z. is a paid consultant for Pathogenica Inc. R.S. is a current employee of Illumina Inc.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–11 and Supplementary Tables 1–4 (PDF 1364 kb)
Rights and permissions
About this article
Cite this article
Diep, D., Plongthongkum, N., Gore, A. et al. Library-free methylation sequencing with bisulfite padlock probes. Nat Methods 9, 270–272 (2012). https://doi.org/10.1038/nmeth.1871
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nmeth.1871
This article is cited by
-
Introduction of a multiplex amplicon sequencing assay to quantify DNA methylation in target cytosine markers underlying four selected epigenetic clocks
Clinical Epigenetics (2023)
-
Laboratory methods to decipher epigenetic signatures: a comparative review
Cellular & Molecular Biology Letters (2021)
-
Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA
Clinical Epigenetics (2021)
-
Epigenetic inactivation of the autophagy–lysosomal system in appendix in Parkinson’s disease
Nature Communications (2021)
-
Target region sequencing and applications in plants
Journal of Crop Science and Biotechnology (2021)