Results of Chromosomal Microarray Need to Always Be Checked by (Molecular) Cytogenetics—Even If They Seem to Be Simple Deletions

<b>Background/Objectives:</b> Chromosome microarrays (CMAs) tend to be used as the first line test or as a test that does not require confirmation or verification by a second test. However, to understand the implications of a duplication or deletion for a family seeking genetic counseling, it is crucial to know the nature of the underlying chromosomal rearrangement. Here, we present seven cases with apparent isolated copy number loss, five of which showed unexpected complexity. <b>Methods:</b> Seven cases were investigated by CMA due to intellectual disability and/or dysmorphic features. Isolated deletions ranging in size from ~0.6 to ~21 Mb were found and referred for further characterization of the underlying chromosomal rearrangement. To elucidate the cases, fluorescence in situ hybridization was performed using locus-specific, whole and partial chromosome painting and/or multicolor banding. <b>Results:</b> Among the seven selected cases, there were five with unexpected complexity. Isolated deletions were actually evidence of chromoanasynthesis, ring chromosome formation, unbalanced translocation, or unbalanced insertion. <b>Conclusions:</b> These results clearly underscore that it seems reasonable to examine every case with a copy number variant-even if it appears to be "only" a simple partial deletion-using banding and/or molecular cytogenetic testing in order to make a qualified assessment of the situation and, on this basis, ensure sound genetic counseling.