For the gene expression analyses, we used publicly available, genotyping (performed on the Affymetrix GeneChip Human Mapping 500K Array Set platform) and RNA expression data (performed on the Illumina HumanRefseq-8 Expression BeadChip system) from neuropathologically confirmed 176 late-onset AD cases (mean age = 83.4 years, standard deviation = 6.6) and 188 controls (mean age = 81.2 years, standard deviation = 9.1) from the Gene Expression Omnibus (GEO) data set GSE15222. 16 We additionally evaluated genotype and imaging data obtained from 620 older participants (174 healthy older controls, 311 individuals with mild cognitive impairment (MCI) and 135 individuals with probable AD) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI – see Table 1b and Supplemental Methods). We restricted our analyses to those participants with available genotype and quality-assured baseline and follow-up MRI scans (6 months to 3.5 years, mean of 2.02 years, standard deviation 0.80 years) available as of April 2011. We assessed longitudinal sub-regional change in gray matter volume (atrophy) on serial 2471 T1-weighted MRI scans using a modified version of the FreeSurfer software package (for additional details see Supplemental Methods).
