Second, independent Autism Genome Project (AGP) families, along with a set of Finnish families and a set of Iranian trios were used for replication of our top findings (n=1,755 trios). Two Sequenom replication pools were designed, attempting to include as many of the regions associated at P < 10−4 as possible. The full set of SNPs considered and those successfully genotyped are shown in Supplementary Table 3, with linkage disequilibrium (r2) noted for SNPs selected as proxies for Affymetrix markers. One of the eight SNPs with P < 10−5 (rs10513025) that failed in this Sequenom assay was subsequently replaced in a subset of AGP samples with a TaqMan assay. This assay showed 99.89% concordance with Affymetrix genotypes in the overlapping AGRE-NIMH samples (2,797/2,800 concordant genotypes), with manual review of the Affymetrix genotype calls also confirming the marker to be of extremely high quality (Supplementary Figure 4). In the independent replication effort, only rs10513025 was associated with P < 0.01 (Table 1).
