Illumina 450K Methylation Data of Alzheimer's Disease: Middle Temporal Gyrus and Cerebellum

Methylation analysis of 404 samples (Alzheimer's disease = 225; controls = 179) from two brain regions, the middle temporal gyrus (MTG) and the cerebellum (CBL), using the Illumina 450K methylation array. Banner Sun Health Research Institute Brain and Tissue Bank provided 404 samples from the middle temporal gyrus (area 21) consisting of 225 cases with Alzheimer’s disease (AD) and 179 non-demented (ND) cases. The tissue was collected within hours of death (average postmortem delay = 2.6 hours) and stored at -80ºC after autopsy. The cognitive ability of all cases was assessed prior to death by a board-certified neurologist using NIH AD Center criteria for Alzheimer’s disease. The diagnosis of clinical Alzheimer’s disease was confirmed postmortem via neuropathological assessment. DNA was extracted from each sample and hybridized to one of nine randomly assigned Illumina 450K methylation arrays. Data was normalized using the R packages minfi (version 1.23.4) and SVA (version 3.26.0). NOOB and functional normalization were performed through the minfi package, followed by SVA and ComBat correction of confounding variables and batch effects. Differentially methylated positions (DMPs) and regions (DMRs) related to Alzheimer’s were identified using the minfi dmpfinder and bumphunter algorithms, respectively. All results were filtered at an adjusted FDR of 0.05.