PGP and HABS subjects were genotyped from whole blood DNA using the Illumina Infinium HumanOmniExpressExome BeadChip Kit (San Diego, CA) and the Affymetrix Axiom Biobank Genotyping Array (Santa Clara, CA), respectively. In short, EIGENSTRAT v3.0 was used to identify population outliers, which were discarded. The BEAGLE software (version: 3.3.2) was used to impute the post-QC genotyped markers using reference Haplotype panels from the 1000 Genomes Project Consortium Phase I Integrated Release Version 3 (for PGP) or Version 1 (for HABS). These methods are described in detail elsewhere12 (link).
In ROS-MAP, DNA was extracted from whole blood or frozen post-mortem brain tissue. Genotype data was generated using the Affymetrix Genechip 6.0 platform at the Broad Institute’s Genetic Analysis Platform or the Translational Genomics Research Institute, as previously described24 (link). In short, data underwent quality control analyses using the PLINK toolkit (http://pngu.mgh.harvard.edu/~purcell/ plink/ ) and quality controlled genotypes were pooled. The quality control process included a principal components analysis using default parameters in EIGENSTRAT to identify and remove population outliers. Imputation in ROS-MAP was performed using MACH software (version 1.0.16a) and HapMap release 22 CEU (build 36).
In ROS-MAP, DNA was extracted from whole blood or frozen post-mortem brain tissue. Genotype data was generated using the Affymetrix Genechip 6.0 platform at the Broad Institute’s Genetic Analysis Platform or the Translational Genomics Research Institute, as previously described24 (link). In short, data underwent quality control analyses using the PLINK toolkit (