Quality control of the samples was done with Genome Studio. A total number of 16 samples were removed: seven had a sample call rate below 99 %; five had incomplete bisulfite conversion and four had gender swaps. Quality control of the probes was done based on the detection p-value calculated with Genome Studio. Probes with a detection p-value of more than 0.01 in more than 1 % of the samples were excluded. This resulted in a total set of 474,528 probes which were normalized using the Dasen option of the WateRmelon R-package [24].
