We used the transmission disequilibrium test (TDT) across all SNPs passing quality control in the complete family dataset for association analyses since the TDT is not biased by population stratification. We estimated a threshold for genome-wide significance using both permutation (P < 2.5 × 10−7) and estimating the effective number of tests (P < 3.4 × 10−7) and use the more conservative, here (see Methods). No SNP met criteria for genome-wide significance at P < 2.5 × 10−7. However, we observed an excess of independent regions associated at P < 10−5 (6 observed vs. 1 expected) and P < 10−4 (30 observed vs. 15 expected) despite the lack of overall statistical inflation (λ = 1.03, Supplementary Figure 1), suggesting that common variants in autism exist, but that our initial scan did not have sufficient statistical power to identify them definitively (Supplementary Figure 2, Table 1).
