To confirm whether any of these top results might indicate true susceptibility loci, we attempted to replicate these signals, as well as others with P < 10−4 in the initial TDT that met stringent genotyping quality criteria (Supplementary Table 3). We used several data sources to replicate the association results. First, we utilized additional autism family samples (318 trios collected by investigators of the Autism Consortium and in Montreal) with genome-wide Affymetrix 5.0/500K array data also genotyped at the Genetic Analysis Platform of the Broad Institute using the same conditions, QC, and analysis pipelines (Methods).
