Axiom 815k spanish biobank array

Participants were genotyped using the Axiom 815K Spanish Biobank array (Thermo Fisher). Genotyping was performed in the Spanish National Center for Genotyping (CeGEN, Santiago de Compostela, Spain).
We removed samples with genotype call rates below 97%, excess heterozygosity, duplicates, samples genetically related to other individuals in the cohort or sample mix-up (PIHAT > 0.1875). If a sex discrepancy was detected, the sample was removed unless the discrepancy was safely resolved. To detect population outliers of non-European ancestry (>6 SD from European population mean), principal component analysis (PCA) was conducted using SMARTPCA from EIGENSOFT 6.1.4.
We removed variants with a call rate < 95% or that grossly deviated from Hardy–Weinberg equilibrium in controls (P-value ≤ 1 × 10^–4), markers with a different missing rate between case and control (P-value < 5 × 10^–4 for the difference) or minor allele frequency (MAF) below 0.01. Imputation was carried out using Haplotype reference consortium (HRC) panel in Michigan Imputation servers³. Only common markers (MAF > 0.01) with a high imputation quality (R² > 0.30) were selected to conduct downstream association analyses.

The GR@ACE-DEGESCO cohort comprises AD patients and controls from the Spanish population. Patients with AD were collected from the ACE Alzheimer Center Barcelona and 12 other cohorts included in the Dementia Genetics Spanish Consortium (DEGESCO) (Table S11). Control individuals were provided by the ACE Alzheimer Center (Barcelona, Spain), Valme University Hospital, the Spanish National DNA Bank Carlos III (Salamanca, Spain), and other DEGESCO members. DNA extracted from peripheral blood or saliva (Table S11) was genotyped in the Spanish National Center for Genotyping (CeGen, Santiago de Compostela, Spain) using the Axiom 815K Spanish Biobank Array (Thermo Fisher), as described previously [26 (link),27 (link)].