Overview of the Illumina 450K beadchip data filtering process.

<p>Methylation data (β-values) for the 485,777 CpGs were filtered in five steps. First, probes for which no β-values were obtained for one or more samples were removed, resulting in a complete dataset for 471,956 CpGs. Second, 144,273 differentially methylated CpGs (DMCs) between maternal Blood Cells (MBC) and Chorionic villus samples (CVS) were identified using a False Discovery Rate (FDR) of <0.05 and delta β>0.2.Third, a more stringent definition of DMCs where MBC samples are hypomethylated (mean β<0.25) and CVS samples are hypermethylated (mean β>0.75), or <i>vice versa</i>, dramatically reduced the number of DMCs to 5,956. Fourth, requiring DMCs to overlap a restriction site for a methylation–sensitive restriction enzyme (MSRE), further reduced the number of DMCs to 2,184. Fifth, only DMCs where at least 10 sampleswithin the group pass the hypo- and hyper-methylation thresholds are included, resulting in 958 MSRE-overlapping CpGs with markedly different and highly consistent methylation status between MBC- and CVS-samples.