A blood draw for genomic DNA extraction was obtained at the screening or baseline visit for all study participants.14 Genotyping on these samples was performed according to manufacturer’s protocol (Illumina, Inc., San Diego, CA) using the Human610-Quad BeadChip (for subjects initially enrolled during ADNI-1) or the Human OmniExpress BeadChip (for subjects initially enrolled in ADNI-GO or ADNI-2). In addition, the two SNPs characterizing APOE ε2/ε3/ε4 status (rs429358 and rs7412) were genotyped separately as previously described14 and merged with the array data sets. All genotype data underwent stringent quality control procedures14 (sample exclusion for call rate < 95% or failed identity or gender check, and SNP exclusion for call rate < 95%, Hardy-Weinberg equilibrium test p < 1 × 10−6, or minor allele frequency (MAF) < 1%) using PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/), version 1.07.15 In addition, to limit possible effects of population stratification, multidimensional clustering analysis was used to select only participants with non-Hispanic Caucasian (CEU or TSI) ancestry based on HapMap3 reference populations. Overall, one individual was excluded due to a failed gender check and 42 individuals were excluded based on ancestry.
