To identify common genetic risk factors for ASDs, we carried out a genome-wide association study on 943 ASDs families (4,444 subjects) from the Autism Genetic Resource Exchange (AGRE cohort, Table 1)19. The subjects with ASDs in the AGRE cohort were diagnosed using both the Autism Diagnostic Interview-Revised (ADI-R)20 and Autism Diagnostic Observation Schedule (ADOS)21 diagnostic tools, which are the gold standard diagnostic tools for individuals with ASDs. All subjects were genotyped using the Illumina HumanHap550 BeadChip with over 550,000 single nucleotide polymorphism (SNP) markers. We applied stringent quality control criteria (Supplementary Methods), including call rates, Mendelian inconsistencies and genetically inferred ancestry, to identify a set of 3,101 subjects of European ancestry in 780 AGRE families for association tests. We performed analysis with the Pedigree Disequilibrium Test (PDT)22 for autosomes, and with X-APL23 for the X chromosome, using genotypes from 486,864 markers. The complete sets of SNP genotype data and signal intensity data were released to the academic research community in April 2008 (http://www.agre.org).
