DNA samples derived from whole blood (N=4,381), cell lines (N=68), or saliva (N=8) were genotyped on the Illumina IMv1 (334 families) or Illumina IMv3 Duo Bead-arrays (840 families), which share 1,040,853 probes in common. CNV prediction was performed by PennCNV (PN) (Wang et al., 2007), QuantiSNP (QT) (Colella et al., 2007), and GNOSIS (GN), (www.CNVision.org) (Figure 1). 115 predicted rare (≤50% of the span of the event found at >1% in the database of genomic variation (DGV)) CNVs were evaluated by quantitative polymerase chain reaction (qPCR). A higher positive predictive value was observed for CNVs predicted by PN and QT, with or without GN (PPV=97% with GN, PPV=83% without) than for other combinations of algorithms, irrespective of the number of probes mapping within the structural variation (Table S2, Figure S1); these “high-confidence” criteria were subsequently used to identify all rare transmitted CNVs.
