Evidence of batch effects masking treatment effect in GAW20 methylation data

Angelo J Canty,Andrew D Paterson

doi:10.1186/s12919-018-0129-6

Angelo J Canty, Andrew D Paterson

Open Access

https://doi.org/10.1186/s12919-018-0129-6

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Journal: BMC Proceedings	Publication Date: Sep 1, 2018
Citations: 3	License type: open-access

Affiliation: Hospital for Sick Children, McMaster University

Abstract

Using the real data set from GAW20, we examined changes in the distribution of DNA methylation before and after treatment. Paired analysis of differences in both mean and variance had grossly inflated type 1 error, suggesting either a very large number of changes across the entire epigenome or major non-biological issues, such as batch effects. Separate analysis of Infinium I and II probes indicated differences in the paired t-test statistics between these two types of probes. Examination of combined principal components showed that the first and fourth principal components discriminate between the before and after treatment measurements, further evidencing the presence of batch effects that make any conclusions about treatment effect suspect.

Highlights

Treatment of CD4+ T cells with fenofibrate results in differences in gene expression and interferon γ protein levels [1], suggesting some of its actions may be mediated by effects on DNA methylation
We examined the differences in methylation, and adjusted for principal components and change in triglyceride levels to examine changes in the distribution of methylation before and after treatment
There seems to be a shoulder in the histogram of the paired t test statistic, suggesting a possible mixture of two distributions

Summary

Introduction

Treatment of CD4+ T cells with fenofibrate results in differences in gene expression and interferon γ protein levels [1], suggesting some of its actions may be mediated by effects on DNA methylation. For the GAW20 data, the Illumina Human Methylation 450 K BeadChip was used to measure methylation in CD4+ T cells before and after 3 weeks of treatment with 160 mg oral fenofibrate. This chip uses two different probe chemistries (Infinium Type I and Infinium Type II) to assess methylation [2]. Methylation measures before and after treatment were normalized

Methods

Results

Conclusion