Figure 5

Concordance assessment of methods (a) and platforms (b) for de novo CNVs in the DiGeorge critical region on chromosome 22. (a) The physical position of de novo deletions and amplifications for 25 trios are indicated by orange and blue boxes, respectively, for MinimumDistance (left panel) and PennCNV (right panel). Boxed numbers indicate the number of Illumina markers. Blue y-axis labels indicate trios validated by qPCR. (b) Each point is the minimum distance of the CopyCaller^TM copy number estimates (y-axis) from the qPCR platform and the minimum distance of the spanning CBS segment from the Illumina platform (x-axis) for one trio. A total of eight trios and three TaqMan probes were used in the validation experiment, generating 24 points on the scatterplot. The inter-platform concordance is high as indicated by the clusters at the bottom left and top right of the display. The four trios at the bottom left have a putative de novo CNV called by MinimumDistance and PennCNV at the 19.60 Mb locus. TaqMan probes flanking the de novo deletion (16.04 and 20.64 Mb) for these trios have minimum distance estimates that cluster near zero (top right). The top right cluster also contains four trios for whom the putative copy numbers were inferred to be diploid by MinimumDistance and PennCNV at the 19.60 Mb locus.