The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression
Open accessAbstract
Brain cellular heterogeneity may bias cell type specific DNA methylation patterns, influencing findings in psychiatric epigenetic studies. We performed fluorescence activated cell sorting (FACS) of neuronal nuclei and Illumina HM450 DNA methylation profiling in post mortem frontal cortex of 29 major depression and 29 matched controls. We identify genomic features and ontologies enriched for cell type specific epigenetic variation. Using the top cell epigenotype specific (CETS) marks, we generated a publically available R package, "CETS," capable of quantifying neuronal proportions and generating in silico neuronal profiles from DNA methylation data. We demonstrate a significant overlap in major depression DNA methylation associations between FACS separated and CETS model generated neuronal profiles relative to bulk profiles. CETS derived neuronal proportions correlated significantly with age in the frontal cortex and cerebellum and accounted for epigenetic variation between brain regions. CETS based control of cellular heterogeneity will enable more robust hypothesis testing in the brain.
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Cites
DNA methylation arrays as surrogate measures of cell mixture distribution
Houseman, E. A., Accomando, W. P., Koestler, D. C., Christensen, B. C., Marsit, C. J., Nelson, H. H., Wiencke, J. K., & Kelsey, K. T. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-86 · Cited by 3,175
NeuN, a neuronal specific nuclear protein in vertebratesxs
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CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
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Epigenomic Profiling Reveals DNA-Methylation Changes Associated with Major Psychosis
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Self-citationAbundant quantitative trait loci exist for DNA methylation and gene expression in human brain
Gibbs, J. R., van der Brug, M. P., Hernandez, D. G., Traynor, B. J., Nalls, M. A., Lai, S.-L., Arepalli, S., Dillman, A., Rafferty, I. P., Troncoso, J., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000952 · Cited by 769
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DNA methylation signatures in development and aging of the human prefrontal cortex
Numata, S., Ye, T., Hyde, T. M., Guitart-Navarro, X., Tao, R., Wininger, M., Colantuoni, C., Weinberger, D. R., Kleinman, J. E., & Lipska, B. K. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.12.020 · Cited by 364
Differential Control of the Releasable Vesicle Pools by SNAP-25 Splice Variants and SNAP-23
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Cited by
DNA methylation age of human tissues and cell types
Horvath, S. (2013) · Genome Biology · doi:10.1186/gb-2013-14-10-r115 · Cited by 7,075
Accounting for cellular heterogeneity is critical in epigenome-wide association studies
Jaffe, A. E., & Irizarry, R. A. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r31 · Cited by 1,067
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci
De Jager, P. L., Srivastava, G., Lunnon, K., Burgess, J., Schalkwyk, L. C., Yu, L., Eaton, M. L., Keenan, B. T., Ernst, J., McCabe, C., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3786 · Cited by 956
“As discussed in the main text, we used an R package 53 to quantify the proportion of NeuN+ cells (primarily neurons) in each brain sample using DNA methylation data.”
DNA methylation and healthy human aging
Jones, M. J., Goodman, S. J., & Kobor, M. S. (2015) · Aging Cell · doi:10.1111/acel.12349 · Cited by 928
Functional normalization of 450k methylation array data improves replication in large cancer studies
Fortin, J.-P., Labbe, A., Lemire, M., Zanke, B. W., Hudson, T. J., Fertig, E. J., Greenwood, C. M., & Hansen, K. D. (2014) · Genome Biology · doi:10.1186/s13059-014-0503-2 · Cited by 892
Metadata
- Authors
- Guintivano, J., Aryee, M. J., & Kaminsky, Z. A.
- Venue
- Epigenetics
- Publisher
- Informa UK Limited
- Published
- 2013-03
- Volume
- 8
- Issue
- 3
- Pages
- 290-302
- ISSN
- 1559-2294 (ISSN-L)
- 1559-2308
- OpenAlex
- W2109281377
- Cited by
- 368
- References
- 9
- FWCI
- 13.58
- Type
- journal article
- Language
- en
- Open access
- hybrid
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