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Updated: Feb 4, 2026
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DNA Methylation: Bisulphite Modification and Analysis
Published on: October 21, 2011
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Do changes in DNA methylation mediate or interact with SNP variation? A pharmacoepigenetic analysis.
Virginia A Fisher1, Lan Wang2, Xuan Deng2
1Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Ave. 3rd floor, Boston, MA, 02118, USA. vafisher@bu.edu.
BMC Genetics
|September 27, 2018
Summary
This study explored how DNA methylation mediates genotype effects on triglyceride changes after fenofibrate treatment. Results indicate interaction effects between genotype and methylation are more prominent than mediation effects in this biological causality.
Area of Science:
- Genetics and Epigenetics
- Pharmacogenomics
- Systems Biology
Background:
- Multi-omics data, including DNA genotype and methylation, offer insights into biological causality.
- The GAW20 dataset provides longitudinal data on genotype, methylation, and triglyceride levels before and after fenofibrate treatment.
- Investigating interdependent mechanisms requires advanced analytical approaches.
Purpose of the Study:
- To perform mediation analysis incorporating DNA methylation to understand its role in genotype's effect on triglyceride changes.
- To simultaneously test mediation and interaction hypotheses regarding genotype, methylation, and triglyceride levels.
- To analyze SNP-CpG site pairs selected based on proximity and GWAS/EWAS significance.
Main Methods:
- Mediation analysis was applied to the GAW20 dataset.
- 322 single-nucleotide polymorphism-cytosine-phosphate-guanine (SNP-CpG) site pairs were selected for analysis.
- Analysis considered genotype, methylation, and change in triglyceride levels as outcome.
Main Results:
- Three SNP-CpG site pairs exhibited significant interaction effects (Bonferroni-corrected p < 1.55E-4).
- No significant mediation effects were detected for any analyzed sites.
- Power analysis indicated a sample size of at least 19,500 is required to detect significant indirect effects.
Conclusions:
- Evidence suggests interaction between genotype and methylation is more significant than methylation mediating genotype effects on triglyceride changes.
- The findings highlight the complex interplay between genetic and epigenetic factors in drug response.
- Further studies with larger sample sizes are needed to confirm mediation effects.
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