The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
A DNA methylation fingerprint of 1628 human samples
Open accessAbstract
Most of the studies characterizing DNA methylation patterns have been restricted to particular genomic loci in a limited number of human samples and pathological conditions. Herein, we present a compromise between an extremely comprehensive study of a human sample population with an intermediate level of resolution of CpGs at the genomic level. We obtained a DNA methylation fingerprint of 1628 human samples in which we interrogated 1505 CpG sites. The DNA methylation patterns revealed show this epigenetic mark to be critical in tissue-type definition and stemness, particularly around transcription start sites that are not within a CpG island. For disease, the generated DNA methylation fingerprints show that, during tumorigenesis, human cancer cells underwent a progressive gain of promoter CpG-island hypermethylation and a loss of CpG methylation in non-CpG-island promoters. Although transformed cells are those in which DNA methylation disruption is more obvious, we observed that other common human diseases, such as neurological and autoimmune disorders, had their own distinct DNA methylation profiles. Most importantly, we provide proof of principle that the DNA methylation fingerprints obtained might be useful for translational purposes by showing that we are able to identify the tumor type origin of cancers of unknown primary origin (CUPs). Thus, the DNA methylation patterns identified across the largest spectrum of samples, tissues, and diseases reported to date constitute a baseline for developing higher-resolution DNA methylation maps and provide important clues concerning the contribution of CpG methylation to tissue identity and its changes in the most prevalent human diseases.
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Cites
Human DNA methylomes at base resolution show widespread epigenomic differences
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Epigenetic differences arise during the lifetime of monozygotic twins
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Self-citationGenome-scale DNA methylation maps of pluripotent and differentiated cells
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Whole-Genome Analysis of Histone H3 Lysine 4 and Lysine 27 Methylation in Human Embryonic Stem Cells
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Epigenetic mechanisms that underpin metabolic and cardiovascular diseases
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Cited by
A decade of exploring the cancer epigenome—biological and translational implications
Baylin, S. B., & Jones, P. A. (2011) · Nature Reviews Cancer · doi:10.1038/nrc3130 · Cited by 2,871
DNA methylation aging clocks: challenges and recommendations
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Distinct DNA methylomes of newborns and centenarians
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Self-citationDNA methylation profiling in the clinic: applications and challenges
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Self-citationThe emerging role of cell-free DNA as a molecular marker for cancer management
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Metadata
- Authors
- Fernandez, A. F., Assenov, Y., Martin-Subero, J. I., Balint, B., Siebert, R., Taniguchi, H., Yamamoto, H., Hidalgo, M., Tan, A.-C., Galm, O., Ferrer, I., Sanchez-Cespedes, M., Villanueva, A., Carmona, J., Sanchez-Mut, J. V., Berdasco, M., Moreno, V., Capella, G., Monk, D., Ballestar, E., Ropero, S., Martinez, R., Sanchez-Carbayo, M., Prosper, F., Agirre, X., Fraga, M. F., Graña, O., Perez-Jurado, L., Mora, J., Puig, S., Prat, J., Badimon, L., Puca, A. A., Meltzer, S. J., Lengauer, T., Bridgewater, J., Bock, C., & Esteller, M.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-05-25
- Volume
- 22
- Issue
- 2
- Pages
- 407-419
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2165541556
- Cited by
- 411
- References
- 11
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Fernandez, A. F., Assenov, Y., Martin-Subero, J. I., Balint, B., Siebert, R., Taniguchi, H., Yamamoto, H., Hidalgo, M., Tan, A.-C., Galm, O., Ferrer, I., Sanchez-Cespedes, M., Villanueva, A., Carmona, J., Sanchez-Mut, J. V., Berdasco, M., Moreno, V., Capella, G., Monk, D., . . . Esteller, M. (2012). A DNA methylation fingerprint of 1628 human samples. Genome Research. https://doi.org/10.1101/gr.119867.110
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