Infinium humanmethylation450 450k array

DNA methylation was analyzed by the Illumina Infinium HumanMethylation450 (450k) array assessing 482,421 CpG sites (Illumina, San Diego, USA), according to the manufacturer’s instructions at the NYU molecular laboratory. DNA methylation data were normalized by performing background correction and dye bias correction (shifting of negative control probe mean intensity to zero and scaling of normalization control probe mean intensity to 10,000, respectively). Filtering of probes was performed as described previously^{4 (link),28 (link)} (removal of probes targeting sex chromosomes, containing single nucleotide polymorphism and not uniquely matched). To enable future comparability, we also removed probes not represented on the novel Illumina Infinium HumanMethylation EPIC array. In total, 428,799 probes were kept for analysis. For unsupervised hierarchical clustering, we selected 5000 probes that showed the highest standard deviation across the beta values. Samples were hierarchically clustered using 1-Pearson correlation as a distance measure and average linkage as agglomeration method. The unscaled methylation levels were shown in a heat map from unmethylated state (blue color) to methylated state (red color). Copy-number profiles were generated using the “conumee” R package in Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/conumee.html), and assessed manually.

The Illumina Infinium HumanMethylation450 (450 k) array was used to assess the DNA methylation status of 482,421 CpG sites (Illumina, San Diego, USA), according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) Heidelberg. DNA methylation data were normalized by performing background correction and dye bias correction (shifting of negative control probe mean intensity to zero and scaling of normalization control probe mean intensity to 10,000, respectively). Probes targeting sex chromosomes, probes containing multiple single nucleotide polymorphism and those that could not be uniquely mapped were removed. In total, 438,370 probes were kept for analysis.