Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity

Benjamin Planterose Jiménez¹, Fan Liu^{1, 2, 3}, Amke Caliebe^{4, 5}, Diego Montiel González¹, Jordana T. Bell⁶, Manfred Kayser¹, Athina Vidaki¹

¹ Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.

² Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, P.R. China.

³ University of Chinese Academy of Sciences, Beijing, P.R. China.

⁴ Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany.

⁵ University Medical Centre Schleswig-Holstein, Kiel, Germany.

⁶ Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom.

Requirements

Operating system: tested on Ubuntu 16.04LTS
R: tested on R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
RAM requirements: Especially for data preprocessing, do not attempt to run without at least 50 GB of RAM.

Structure

Under the folder /Scripts/ you may find all R-scripts employed in the data analysis of our Genome Biology paper. These are separated into the 7 sections, corresponding to those of the paper:

1. Data preparation: all scripts employed in the preprocessing of 450K data whose raw IDAT data were available: E-risk (GSE105018), Danish Twin Cohort (GSE61496), TwinsUK, NSPHS (GSE87571), Chinese Children (GSE104812), ENID-Gambia (GSE99863) and Longitudinal adipose tissue (GSE103768).

2. evCpG discovery: all scripts employed in the identification of evCpGs in the E-risk cohort.

3. evCpG annotation: all scripts employed in the functional annotation of evCpGs.

4. evCpG technical and longitudinal variation assessment: all scripts employed in the assessment of technical and longitudinal stability of evCpGs.

5. evCpGs' relationship with aging: all scripts employed in the assessment of the effects of aging on evCpGs.

6. evCpGs' variation across tissues: all scripts employed in the exploration of evCpGs' behaviour in post-mortem tissues, the replication of evCpGs and there longitudinal stability in adipose tissue.

7. evCpGs validation across technologies: all scripts employed in the validation of evCpGs in whole-genome bisulfite sequencing data of monozygotic twins in blood and in adipose tissue.

Please contact me at b.planterosejimenez@erasmusmc.nl for any questions or issues concerning the scripts.

References and Supporting Information

B. Planterose et al (2020). Equivalent DNA methylation variation between monozygotic co-twins and unrelated individuals reveals universal epigenetic inter-individual dissimilarity. Genome Biology