dmrff: identifying differentially methylated regions efficiently with power and control
Open accessAbstract
A differentially methylated region (DMR) is a genomic region in which DNA methylation is consistently positively or negatively associated with a phenotype or exposure. We demonstrate that existing algorithms for identifying DMRs either fail to consistently control false positive rates (comb-p and DMRcate), suffer from low power (bumphunter) or lack modeling flexibility (seqlm). We introduce a new method, dmrff, that overcomes these shortcomings and can additionally be used to meta-analyze multiple datasets. When applied to investigate associations of age in multiple datasets, dmrff identifies novel DMRs near genes previously linked to age. An R implementation is available on Github (http://github.com/perishky/dmrff).
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The comb-p software may have an inflated false-positive rate, so the resulting DMRs need to be interpreted cautiously.
“However, because the comb-p software may have an inflated false-positive rate [95], the resulting DMRs need to be interpreted cautiously.”
From Distinct sex-specific DNA methylation differences in Alzheimer’s disease (2022) · cites this paper as [95]
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Epigenetic and genetic profiling of comorbidity patterns among substance dependence diagnoses
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Examination of newborn DNA methylation among women with polycystic ovary syndrome/hirsutism
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Epigenome-wide association study on ambient PM2.5 exposure in Han Chinese, the NSPT study
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Developmentally dynamic changes in DNA methylation in the human pancreas
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Epigenome-wide association study of pregnancy exposure to green space and placental DNA methylation
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An epigenome-wide association study of child appetitive traits and DNA methylation
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Prenatal black carbon exposure and DNA methylation in umbilical cord blood
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Neuroimaging and epigenetic analysis reveal novel epigenetic loci in major depressive disorder
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ANGPT1 methylation and delayed cerebral ischemia in aneurysmal subarachnoid hemorrhage patients
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Wu, C., Mou, X., & Zhang, H. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05711-y · Cited by 3 · see citing works
Epigenome-wide association study of left-handedness for different tissues and agesPreprint
Odintsova, V. V., Suderman, M. J., Hagenbeek, F. A., Caramaschi, D., Hottenga, J., Pool, R., Dolan, C. V., Ligthart, L., van Beijsterveldt, C., Willemsen, G. A. H. M., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-375556/v1 · Cited by 3 · see citing works
Self-citationAcute stress induces changes in epigenome-wide DNA methylation
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S-adenosylmethionine as an epigenetic treatment of depression in adults with childhood trauma
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Antidepressant Exposure and DNA Methylation: Insights from a Methylome-Wide Association StudyPreprint
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Epigenome-wide association study of psilocybin-induced methylome changes in alcohol use disorder
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Identification of epigenome-wide DNA methylation differences between carriers of APOE ε4 and APOE ε2Preprint
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Developmentally dynamic changes in DNA methylation in the human pancreasPreprint
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Epigenome-wide association study of posttraumatic stress disorder in a South African populationPreprint
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DNA methylation in peripheral tissues and Left-handednessPreprint
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Epigenetic and cognitive signatures of striatal DAT binding among healthy elderly individualsPreprint
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- Authors
- Suderman, M., Staley, J. R., French, R., Arathimos, R., Simpkin, A., & Tilling, K.
- Affiliations
- University of Bristol (GB)
- University Hospital of Wales (GB)
- National University of Ireland (IE)
- Corresponding author
- Suderman, Matthew
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2018-12-31
- OpenAlex
- W2907751907
- Cited by
- 120
- References
- 26
- Citations by year
- 2026: 13 · 2025: 16 · 2024: 29 · 2023: 13 · 2022: 20 · 2021: 17 · 2020: 9 · 2019: 3
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nd
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- Funders
- Medical Research Council (MR/N015428/1, MC_UU_12013_2, MC_UU_12013, MC UU 12013/8, MC_UU_00011/5, MR/M025020/1, ES/N000498/1, MC_UU_12013/9)
- Biotechnology and Biological Sciences Research Council (BB/P028187/1, BB/I025263/1)
- Economic and Social Research Council (ES/N000498/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Keywords
- differentially methylated regions, DNA methylation, false positive rate control, statistical power, meta-analysis, age, epigenetics
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