A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

Abstract

Motivation: The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different DNA methylation distributions and dynamic range, which may bias downstream analyses. A key statistical issue is therefore how best to adjust for the two different probe designs.Results: Here we propose a novel model-based intra-array normalization strategy for 450 k data, called BMIQ (Beta MIxture Quantile dilation), to adjust the beta-values of type2 design probes into a statistical distribution characteristic of type1 probes. The strategy involves application of a three-state beta-mixture model to assign probes to methylation states, subsequent transformation of probabilities into quantiles and finally a methylation-dependent dilation transformation to preserve the monotonicity and continuity of the data. We validate our method on cell-line data, fresh frozen and paraffin-embedded tumour tissue samples and demonstrate that BMIQ compares favourably with two competing methods. Specifically, we show that BMIQ improves the robustness of the normalization procedure, reduces the technical variation and bias of type2 probe values and successfully eliminates the type1 enrichment bias caused by the lower dynamic range of type2 probes. BMIQ will be useful as a preprocessing step for any study using the Illumina Infinium 450 k platform.Availability: BMIQ is freely available from http://code.google.com/p/bmiq/.Contact: a.teschendorff@ucl.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online

Obesity accelerates epigenetic aging of human liver

“…11. Many authors have described methods for dealing with the two types of probes found on the Illumina 450K array (37)(38)(39). This is not a concern for the epigenetic clock because it only involves type II probes.…”

“…This is not a concern for the epigenetic clock because it only involves type II probes. However, our software implements a data normalization step that repurposes the BMIQ normalization method from Teschendorff et al (38) so that it automatically references each sample to a gold standard based on type II probes (details can be found in supplemental file 2 in ref. 11).…”

Progranulin levels in blood in Alzheimer's disease and mild cognitive impairment

“…Preprocessing was run with the RnBeads package33, using the default options for quality control. Background correction was performed with the normal exponential convolution, using out‐of‐band probes (noob) method,34 and arrays were normalized using beta mixture quantile dilation (BMIQ) 35. The normalized data was corrected for batch effect using the parametric empirical Bayes method from ComBat 26.…”

Inuteroarsenic exposure and epigenome-wide associations in placenta, umbilical artery, and human umbilical vein endothelial cells

“…Finally, a b-mixture quantile intra sample normalization procedure (BMIQ) was further applied to the data to reduce the potential bias that can arise from type 2 probes as previously described. 56 Strip plots and signal intensities of control probes were visually examined for bisulfite conversion, probe hybridization, and single base extension. Density plots for the b-values were examined for all samples at each normalization step described above.…”