Finally, we reasoned that while the overall number of de novo structural variations identified might not differ between cases and controls, specific CNVs might nonetheless be conferring disease risk. Consequently, we focused on large rare de novo exonic variants, given both the trend toward larger and more gene-rich de novo CNVs in cases versus controls in this study and strong evidence from studies in ASD, demonstrating that these CNVs carry significant risks (27, 38, 61). To ensure that we did not overlook such an event due to reliance on the reduced “consensus” probe sets, we re-analyzed cases for de novo CNVs using predictions derived from the full array probe sets. Our results were identical. We detected four de novo CNVs which were subsequently all confirmed using qPCR. The largest of these is a heterozygous duplication that spans 51.8Mb and 447 RefSeq genes (Figure 3A) on chromosome 5q (chr5: 127,500,000-179,295,570). Three other de novo variants were detected: a 316 kb duplication at 6p25.3 (chr6: 744,618-1,060,897; 1 RefSeq gene), a 1.2 Mb deletion at 20p13 (chr20: 2,758,098-3,942,609; 27 RefSeq genes) (Figure 3B),
