Next, haplotype patterns from the 1000 Genomes Project reference panel were used to impute genotypes for markers not directly assayed. Prior to imputation, the orientation of all genotyped markers in relation to the plus strand alignment of the reference panel genome (NCBI build 37 coordinates) was verified and monomorphic variants from the reference panel were excluded. Minimac16 was used to impute samples within groups based on the genotyping platform employed (Illumina 610-Quad or OmniExpress). Following imputation, SNPs with r2 < 0.5 between imputed and assayed genotypes were removed.17 The remaining array SNPs demonstrated > 99.9% concordance between imputed and assayed genotypes. The independently-imputed data sets were then merged to generate a common set of more than 10 million SNPs for the full ADNI sample. Following quality control (SNP call rate < 95%, Hardy-Weinberg p < 1 × 10−6) and frequency filtering (MAF < 5%), 6,108,668 SNPs were included in the GWAS. Of the 602 participants with Aβ PET data, 559 individuals were included in the resulting genetic data set. Among these individuals, four pairs exhibited significant relatedness (PLINK identity by
