The AGRE samples were genotyped on Affymetrix 5.0 chips at the Genetic Analysis Platform of the Broad Institute, using standard protocols. The 5.0 chip was designed to genotype nearly 500,000 SNPs across the genome in order to enable genome-wide association studies 26,27. The NIMH controls were genotyped at the Broad Institute using the Affymetrix 500K Sty and Nsp chips, using a similar protocol 6. The Autism Consortium and Montreal replication samples were also genotyped at the Broad Institute under the same conditions. The NIMH autism samples were genotyped at the Johns Hopkins Center for Complex Disease on the Affymetrix 500K (Nsp and Sty) and 5.0 platforms using similar standard protocols.
