Exome capture and sequencing of blood-derived DNA from 222 affected children and their parents (666 samples total) were performed at the Yale Center for Genomic Analysis (YCGA), using the NimbleGen SeqCap EZExomeV2 (109 trios) or MedExome (113 trios) capture libraries (Roche NimbleGen, Madison, WI, USA) and the Illumina HiSeq 2000 platform (74 bp paired-end reads; Illumina, San Diego, CA). We multiplexed six samples during each capture reaction and sequencing lane, pooling parents and probands when possible. WES data from 855 unaffected parent-child trios (2565 samples total) were obtained from the Simons Simplex Collection (SSC) via the NIH Data Archive (https://ndar.nih.gov/edit_collection.html?id=2042). These control trios are comprised of unaffected siblings of autism probands from the SSC and their parents; these siblings and their parents have no evidence of autism spectrum or other neurodevelopmental disorders (36). Like our OCD samples, control WES was from blood-derived DNA and sequenced on the Illumina HiSeq 2000 sequencing platform after capture with the NimbleGen SeqCap EZExomeV2 library.
