For linkage analyses, the combined AGRE/NIMH dataset was further merged with Illumina 550K genotype data generated at the Children’s Hospital of Philadelphia (CHOP) and available from AGRE, adding ~300 nuclear families (1,499 samples). We used the extensive overlap of samples between the AGRE/NIMH and the CHOP datasets (2,282 samples) to select an extremely high quality set of SNPs for linkage analysis. Specifically, we required SNPs to be on both the Affymetrix 500K/5.0 and Illumina 550K platforms, with >99.5% concordance across platforms. We further restricted SNPs to MAF > 0.2, < 1% missing data, Hardy Weinberg P> 0.01, and no more than 1 ME. This left ~36,000 SNPs of outstanding quality. For autosomal SNPs, we further pruned using PLINK to remove SNPs with r2 > 0.1, yielding 16,311 SNPs.
