For linkage analyses, the common 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 only included SNPs genotyped in both datasets with >99.5% concordance and ≤1 Mendelian error.
