Nimblegen seqcap ez exome v2 capture library

DNA was collected from all children meeting eligibility criteria and from their parents, using the Oragene OG-500 collection kit and standard extraction protocols (DNA Genotek, Ottowa, Ontario, Canada). Exome capture and sequencing were performed at the Yale Center for Genome Analysis (YCGA), using the NimbleGen SeqCap EZExomeV2 capture library (Roche NimbleGen, Madison, WI, USA) and the Illumina HiSeq 2500 platform (Illumina, San Diego, CA, USA). WES data from 853 unaffected parent-child trios (2,559 samples total) were obtained from the Simons Simplex Collection via the NIH Data Archive (https://ndar.nih.gov/edit_collection.html?id=2042). These children and their parents have no evidence of autism spectrum or other neurodevelopmental disorders [48 (link)]. The same exome capture and sequencing platforms were used for these control samples.

Exome capture, sequencing and variant detection were performed at the Yale Center for Genomic Analysis, as described previously^{11 (link)} and summarized below.
The DNA samples from whole blood were enriched for exonic sequence with the NimbleGen SeqCap EZ Exome v2 capture library (Roche NimbleGen, Madison, WI, USA). The samples were sequenced using the Illumina HiSeq 2000 platform (74 bp paired-end reads; Illumina, San Diego, CA, USA). We multiplexed four samples during each capture reaction and sequencing lane, pooling parents and probands when possible.