Infinium humanmethylation450 beadchip

DNA methylation profiles for ALSPAC children were generated using the Illumina Infinium HumanMethylation450 BeadChip as part of the Accessible Resource for Integrated Epigenomic Studies (ARIES)
^{29 (link)}. DNA was bisulphite-converted using the Zymo EZ DNA Methylation
^TM kit (Zymo, Irvine, CA). Infinium HumanMethylation450 BeadChips (Illumina, Inc.) and used to measure genome-wide DNA methylation levels at over 485,000 CpG sites. The arrays were scanned using an Illumina iScan, with initial quality review using
GenomeStudio (version 2011.1). This assay detects methylation of cytosine at CpG islands using one probe to detect the methylated and one to detect the unmethylated loci. Single-base extension of the probes incorporated a labelled chain-terminating ddNTP, which was then stained with a fluorescence reagent. The ratio of fluorescent signals from the methylated site versus the unmethylated site determines the level of methylation at the locus.
Quality control and normalization of the profiles was performed using the
meffil R package (version 1.1.0) as previously described
^{30 (link)}. The level of methylation is expressed as a percentage (β-value) ranging from 0 (no cytosine methylation) to 1 (complete cytosine methylation). Finally, to reduce influence of outliers in statistical models, normalized β-values were 90%-Winsorized.

Extraction of genomic DNA from blood was performed using the AllPrep DNA/RNA/protein kit (QIAGEN, Hilden, Germany). Sodium bisulphite conversion for Infinium HumanMethylation450 beadchip was performed using the EZ-DNA methylation-gold kit and the EZ-96 DNA methylation kit, respectively, and genome-wide DNA methylation was analyzed using the Infinium HumanMethylation450 beadchip (Illumina, San Diego, CA) following the manufacturer’s instructions. Arrays were scanned by HiScan (Illumina).