Human1m duo genotyping beadchip

To represent the characteristics of a typical GWAS panel, markers from the Affymetrix Genome-Wide Human SNP Array 6.0, the Illumina Human1M–Duo Genotyping BeadChip, and the Illumina HumanOmni1-Quad BeadChip were downloaded from the UCSC genome browser, using the table browser tool [24] . The union of these three arrays consisted of 1,936,864 unique SNPs from the 22 autosomes. Because of its unique LD and genic properties, the MHC region (chr6: 29624809–33160245 on build 37) was excluded from downstream analyses.
LD proxies or “tagging” SNPs (r²> = 0.8) for the GWAS panel SNPs were identified using VCFtools [25] (link) based on data from the (N = 379) Europeans (Phase I, version 3, March 14, 2012) in the 1000 Genomes Project [26] (link).
GWAS “non-hits” were defined as all those SNPs in our union GWAS set which were neither a GWAS “hit” (see below), nor in high LD (r²> = 0.8) with a GWAS hit.

We explored the utility of each of the three algorithms with each of the three functional annotation sets in order to attribute performance differences to the algorithm and/or annotations. A total of nine model types were created.
In the primary analysis, the set of risk variants used for training all the models were based on whether or not a genetic variant is a hit or a non-hit from a genome-wide association study (GWAS). Hits were defined as those variants present in the NHGRI GWAS Catalogue (www.genome.gov/gwastudies, downloaded on August 7, 2014)13 with a p-value of equal to or less than 5 × 10⁻⁸. There were 3,618 unique genetic variants that met these criteria. (Note that at the time of download the novel hits from the second phase of the schizophrenia GWAS from the Psychiatric Genomics Consortium (PGC2)2 (link) had not yet been included.) A subset of non-hits was selected from common GWAS arrays (Affymetrix Genome-Wide Human SNP Array 6.0, the Illumina Human1M-Duo Genotyping BeadChip, and the Illumina HumanOmni1-Quad BeadChip). Those non-hits in high linkage disequilibrium (r² > 0.8) with hits were removed from the analyses.