Transcriptomics

Dataset Information

7

A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies


ABSTRACT: We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by correlation between individual methylation markers and present methods to restore statistical independence. Bisulfite-converted DNA for 2,664 human samples and 36 technical replicates were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2.

ORGANISM(S): Homo sapiens  

SUBMITTER: Uzma Afzal   Marie Loh  Weihua Zhang  John C Chambers  Mark I McCarthy  Jaspal S Kooner  Paul Elliott  Marjo R Jarvelin  William R Scott  James Scott  Sian T Tan  Benjamin Lehne  Alexander Drong 

PROVIDER: E-GEOD-55763 | ArrayExpress | 2015-01-22

SECONDARY ACCESSION(S): GSE55763PRJNA240908

REPOSITORIES: GEO, ArrayExpress

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