Infinium human610 quad bead chip

We extracted the SNP genotypes of SORL1 from the PLINK format data of Genome-wide association study (GWAS) in ADNI database. The ADNI applied the Illumina Infinium Human610-Quad Bead Chip (Illumina, Inc., San Diego, CA) including 620,901 SNP and CNV markers to conduct genotyping for GWAS data, with ADNI-2/GO participants using Illumina Human Omni Express Bead Chip [52 ]. The quality control (QC) procedures were performed using PLINK version 1.07 (http://pngu.mgh.harvard.edu/~purcell/plink/), including filters for missingness, heterozygosity, and concordance between genotype-determined and reported sex. The inclusion criteria are as follows: minimum call rates > 90%, minimum minor allele frequencies (MAF) > 0.01 and Hardy-Weinberg equilibrium test p > 0.001.

In ADNI-1, genotyping was performed using the Illumina Infinium Human-610-Quad BeadChip. In ADNI-2/GO, genotyping was performed on the Illumina OmniQuad array. Quality control (QC) and statistical analyses were performed using PLINK software (version 1.07; Purcell et al., 2007 (link)). During QC, we excluded Single Nucleotide Polymorphisms (SNPs) with a genotyping efficiency <90%, a minor allele frequency (MAF) < 5%, or deviation from Hardy-Weinberg Equilibrium (p < 1 × 10⁻⁶). This left 515,383 SNPs in ADNI-1 and 605,317 SNPs in ADNI-2/GO. Finally, we merged the two genotyping files for our analyses and again applied a genotyping efficiency <90%. This left a total of 296,267 SNPs for data analysis.