Schematic illustrations of WGS results from three cases representing the three complex CNVs categories: (1) deletions only, (2) duplications only, and (3) deletions and duplications.

(A) Case P2109_123 with DEL-INV-DEL, (B) Case P4855_512 with DUP-N-DUP, and (C) Case P2109_162 with a complex rearrangement consisting of inversions, deletions and duplications (DEL-INV-DEL-N-DEL-N-DUP). For case P2109_123 the array-CGH analysis only identified a single deletion and the complex rearrangement was only seen by the WGS analysis. For all the array-CGH results are visualized as a plot seen on the left. The individual dots represent specific oligonucleotide probes and are indicated as black (normal copy number), green (copy number gain), and red (copy number loss) compared to a reference sample. Genes are shown as blue arrows below. On right side the WGS result is shown, illustrated as a Circos plots and within the Circos plots as linear plot with copy number status indicated as black (normal copy number), blue (copy number gain), or red (copy number loss) and inverted segments marked with an arrow. Linked reads showing connections between chromosomal BPs are illustrated as dashed lines.