To examine whether greater phenotypic homogeneity within ASD could help identify common risk variants, we performed a number of exploratory analyses examining specific sub-groups of the ASD sample. In this study, we report in detail two categorical variables: verbal status and IQ; see Methods for description of exploratory categories. We also evaluated parental origin effects through parental transmission. Sample sizes are given in Table 1; results are given in Supplementary Material, Table S4. None of our exploratory analyses detected association below the threshold of 5 × 10−8 in the AGP discovery sample alone. We do observe signals that are close to the threshold (P < 1 × 10−7, chosen strictly for heuristic purposes) in the discovery sample in PLD5, POU6F2 and an intergenic region on 8p21.3. Moreover, in a combined analysis of the AGP and AGRE data, we observe three associations that cross the P-value threshold: for verbal individuals, for SNPs rs3784730 (in ST8SIA2) and rs2196826 (in PLD5); and, for maternal parent of origin, rs9532931 (in a gene for an uncharacterized predicted protein KIAA0564). Importantly, these findings would not be
