However, given the likely importance of de novo variation, and the relative challenge of accurately detecting these CNVs (Lupski, 2007), we focused on this small subset of predictions and further optimized our detection strategy using the first 585 quartets with complete genotyping data (Figure 1). We predicted putative de novo events from the group of rare high-confidence CNVs based on the combination of within-family intensity and genotypic data and used a blinded qPCR confirmation process (Figure S1). 53% of de novo predictions based on ≥20 probes (N=94) were confirmed compared with 2.6% with <20 probes (N=430). 82% of failures were false-positive predictions in offspring, 18% were false-negatives in parents. The data from this experiment were used to refine de novo prediction thresholds (supplementary materials). In addition, given the large number of predictions of small CNVs, and the low yield of true positives in the pilot data set (Figure S1), we elected to restrict all further statistical analysis to rare de novo events encompassing ≥20 probes that were also confirmed by qPCR in whole-blood DNA (Figure S1).
