We first conducted WES of 325 TIC Genetics trios. Dietrich et al. (2015) have previously described ascertainment and phenotyping of this cohort (Dietrich et al., 2015). We utilized the SeqCap EZ Human Exome v.2.0 library kit (Roche NimbleGen) to capture exomes from whole-blood-derived DNA and then sequenced with Illumina HiSeq 2000 technology. In all analyses, we compared TD trios passing quality control to control trios from the Simons Simplex Collection (SSC) (Fischbach and Lord, 2010a). The SSC consists of simplex families: two unaffected parents with a single child affected with autism spectrum disorder (ASD). Approximately 80% of these families also include one or more unaffected siblings. Therefore, our control trios consist of two unaffected parents and an unaffected sibling. We randomly selected 625 control trios from among the 96.9% (n = 2,438 of 2,517) of SSC families that had been captured with the same library used for the TIC Genetics cohort and sequenced using Illumina technology. 311 TD trios (311/325, 95.7%) and 602 SSC trios (602/625, 96.3%) passed quality control (Table 1; Table S1). We summarize sequencing metrics in Table
