Estimation of a significance threshold for epigenome-wide association studies.

Ayden Saffari,Loredana Moi,Patrizia Zavattari,Amedeo Columbano,Frank Dudbridge,Emma L Meaburn,Matt J Silver

doi:10.1002/gepi.22086

Abstract

ABSTRACTEpigenome‐wide association studies (EWAS) are designed to characterise population‐level epigenetic differences across the genome and link them to disease. Most commonly, they assess DNA‐methylation status at cytosine‐guanine dinucleotide (CpG) sites, using platforms such as the Illumina 450k array that profile a subset of CpGs genome wide. An important challenge in the context of EWAS is determining a significance threshold for declaring a CpG site as differentially methylated, taking multiple testing into account. We used a permutation method to estimate a significance threshold specifically for the 450k array and a simulation extrapolation approach to estimate a genome‐wide threshold. These methods were applied to five different EWAS datasets derived from a variety of populations and tissue types. We obtained an estimate of α=2.4×10−7 for the 450k array, and a genome‐wide estimate of α=3.6×10−8. We further demonstrate the importance of these results by showing that previously recommended sample sizes for EWAS should be adjusted upwards, requiring samples between ∼10% and ∼20% larger in order to maintain type‐1 errors at the desired level.

Highlights

Epigenetic marks are mitotically heritable chemical modifications to DNA and histone proteins, which act in concert to regulate gene expression across developmental stages and tissues (Bird, 2002)
The most widely studied of these marks is DNA methylation, describing the addition of a methyl group to the five carbon of cytosine bases to form 5-methylcytosine (5mC), occurring predominantly in the context of CpG dinucleotides
These observations in particular have led to the popularisation of epigenome-wide association studies (EWAS), which profile methylomic variation genome wide in the context of normal development and in disease (Rakyan, Down, Balding, & Beck, 2011)

Summary

Introduction

Epigenetic marks are mitotically heritable chemical modifications to DNA and histone proteins, which act in concert to regulate gene expression across developmental stages and tissues (Bird, 2002). The most widely studied of these marks is DNA methylation, describing the addition of a methyl group to the five carbon of cytosine bases to form 5-methylcytosine (5mC), occurring predominantly in the context of CpG dinucleotides. Aberrant methylation patterns have been associated with a number of diseases (Robertson, 2005), and variation in methylation between individuals could potentially explain a proportion of phenotypic variance (Rakyan & Beck, 2006). These observations in particular have led to the popularisation of epigenome-wide association studies (EWAS), which profile methylomic variation genome wide in the context of normal development and in disease (Rakyan, Down, Balding, & Beck, 2011).

Methods

Results

Conclusion