β values reported by the Illumina platform were used as the measurement of methylation level for each CpG probe tagged on the chip. We imputed those missing β values using a k-nearest neighbor algorithm for k=100. The primary data analysis includes adjustment of age, sex, and experiment batch variable. We estimated the proportion of NeuN+ cells (primarily neurons) in each brain sample using DNA methylation data36, but we did not find it had significant associations with a pathologic diagnosis of AD (P=0.08). Overall, we have methylation profiles for 740 subjects.
