Omni 2.5m beadchip array

The ADNI samples were genotyped using with Whole Genome Sequencing and/or the Illumina Omni 2.5M BeadChip array. Quality control checks were performed using PLINK software (www.cog-genomics.org/plink/2.0/). Checks included the exclusion of SNPs with missingness greater than 0.02 and minor allele frequency of less than 0.01. SNPs with Hardy-Weinberg equilibrium p-value less than 1 x 10-6 were also excluded. After such checks 8,990,292 SNPs were left for analysis of which approximately 114,000 were used as part of the polygenic risk scoring algorithm (14 (link)).

The ADNI samples were genotyped using non-CLIA whole-genome sequencing and Illumina Omni 2.5 M BeadChip array and basic QC was performed. Additional QC checks were performed using PLINK (https://www.cog-genomics.org/plink2/) (Marees et al., 2018 (link)). These included exclusion of SNPs with minor allele frequency less than 0.01 and genotype missingness greater than 0.02 and SNPs with Hardy-Weinberg equilibrium p-value ≤ 10⁻⁶. After QC, 7,808,548 SNPs were included in the analyses.
The UKBB contains 35,884,914 imputed SNPs. These imputed data were QCed by removing rare SNPs with minor allele frequency <0.01, SNPs imputed with poor accuracy (INFO ≤0.4), SNPs with posterior probability ≤0.4, SNPs with missing data proportion >0.05, and SNPs which violate Hardy-Weinberg equilibrium with p < 10⁻⁶. After these QC steps, 7,654,308 SNPs remained for the analysis.