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Modeling dependency structures in 450k DNA methylation data
- Source :
- Bioinformatics
- Publication Year :
- 2021
- Publisher :
- Oxford University Press (OUP), 2021.
-
Abstract
- Motivation DNA methylation has been shown to be spatially dependent across chromosomes. Previous studies have focused on the influence of genomic context on the dependency structure, while not considering differences in dependency structure between individuals. Results We modeled spatial dependency with a flexible framework to quantify the dependency structure, focusing on inter-individual differences by exploring the association between dependency parameters and technical and biological variables. The model was applied to a subset of the Finnish Twin Cohort study (N = 1611 individuals). The estimates of the dependency parameters varied considerably across individuals, but were generally consistent across chromosomes within individuals. The variation in dependency parameters was associated with bisulfite conversion plate, zygosity, sex and age. The age differences presumably reflect accumulated environmental exposures and/or accumulated small methylation differences caused by stochastic mitotic events, establishing recognizable, individual patterns more strongly seen in older individuals. Availability and implementation The twin dataset used in the current study are located in the Biobank of the National Institute for Health and Welfare, Finland. All the biobanked data are publicly available for use by qualified researchers following a standardized application procedure (https://thl.fi/en/web/thl-biobank/for-researchers). A R-script for fitting the dependency structure to publicly available DNA methylation data with the software used in this article is provided in supplementary data. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Dependency (UML)
AcademicSubjects/SCI01060
Context (language use)
Biology
01 natural sciences
Biochemistry
010104 statistics & probability
03 medical and health sciences
Spatial Dependency
0101 mathematics
GENETIC-CONTROL
Molecular Biology
030304 developmental biology
0303 health sciences
Age differences
1184 Genetics, developmental biology, physiology
Genome Analysis
Original Papers
BEADCHIP
Dependency structure
Zygosity
Computer Science Applications
GENOME
3141 Health care science
Computational Mathematics
Computational Theory and Mathematics
Evolutionary biology
DNA methylation
Subjects
Details
- ISSN :
- 13674811 and 13674803
- Volume :
- 38
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....83390e836c7a33f7b8b542a8bdd40ed6